Ruiz-García Et Al 2021 Calbifrons, Potos, Nasua

Chapter 6
Effects of Sample Size in the Determination

of the True Number of Haplogroups
or ESUs Within a Species
with Phylogeographic and Conservation
Purposes: The Case of Cebus albifrons
in Ecuador, and the Kinkajous and Coatis
Throughout Latin America
Manuel Ruiz-García, María Fernanda Jaramillo, Sebastián Sánchez-Castillo,

María Ignacia Castillo, Christian Miguel Pinto, and Joseph Mark Shostell
1 Introduction
The identification and conservation of local differentiated genetic populations is of

great importance because the conservation of many heterogeneous genetic popula-
tions augments the evolutionary potential of a given species, minimizing the risk of
extinction. It is also important to determine the gene flow between these heteroge-
neous populations (Hobbs and Mooney 1998; Hilborn et al. 2003; Luck et al. 2003).
The importance of protecting intraspecific units is of such magnitude that it is
M. Ruiz-García ()
Laboratorio de Genética de Poblaciones Molecular-Biología Evolutiva, Unidad de Genética,
Departamento de Biología, Facultad de Ciencias, Pontificia Universidad Javeriana,
Bogota, Cundinamarca, Colombia
e-mail: mruiz@javeriana.edu.co
Instituto Nacional de Biodiversidad (INABIO), Quito, Ecuador
M. F. Jaramillo · S. Sánchez-Castillo · M. I. Castillo
Laboratorio de Genética de Poblaciones Molecular-Biología Evolutiva, Unidad de Genética,
Departamento de Biología, Facultad de Ciencias, Pontificia Universidad Javeriana,
Bogota, Cundinamarca, Colombia
e-mail: j.sanchezc@javeriana.edu.co
C. M. Pinto
Instituto de Ciencias Biológicas, Escuela Politécnica Nacional, Quito, Pichincha, Ecuador
e-mail: miguel.pinto@epn.edu.ec
J. M. Shostell
Math, Science and Technology Department, University of Minnesota Crookston,
Crookston, MN, USA
© Springer Nature Switzerland AG 2021 101

M. Nardelli, J. I. Túnez (eds.), Molecular Ecology and Conservation Genetics of
Neotropical Mammals, https://doi.org/10.1007/978-3-030-65606-5_6
102 M. Ruiz-García et al.
supported by the Extinction Species Act (ESA) of USA, thus allowing for the full
protection of Different Population Segments (DPS) in various species.
Templeton (1986, 1989) showed that if there are populations with particular features,
or exclusive genetic characteristics, and if these populations are not especially small in
their effective numbers, it is vital then to conserve the distinctive phylogenetic history
and the co-adaptions corresponding to each one of the involved populations. This author
also noted that the loss of specific adaptations to exclusive environments by hybridiza-
tion should be avoided due to the effects of exogamy depression destroying genetic
complexes perfectly co-adapted to the unique features of these relevant environments. In
Latin America, there are some megadiverse countries (such as Brazil, Colombia, Peru,
Mexico, Bolivia, and others), where the level of illegal fauna traffic is high. Therefore,
once this fauna is confiscated, the rehabilitated animals must be released in the geo-
graphical areas of which they were illegally extracted.
Some population genetics studies have employed mitochondrial genes to geo-
graphical assignment of individuals of different mammalian species sized from ille-
gal traffic in Colombia and in other South American countries. Two of these works
were those from Ruiz-García et al. (2010b, 2020a). The first of them, focused on
Colombian primates. Primates are one of more confiscated mammalian taxa of
Colombia. A total of 115 individuals from 5 different primate species were
sequenced at the mitochondrial cytochrome oxidase II gene (COII). These sequences
were compared with those obtained from individuals directly sampled in the field,
with precise geographic origin. Different geographical groups were recovered and
the majority of the confiscated specimens were released into the geographical
regions where they were illegally extracted. In the second work, 172 specimens of
wild mammals seized in the city of Bogotá (Colombia) were sequenced for different
mitochondrial and nuclear genes. These mammals belonged to 5 orders (Primates,
Rodentia, Carnivora, Didelphimorpha, and Xenarthra) and represented 28 different
species. Most of the seized specimens, of which a large sample size was analyzed
and the number of Management Units (MUs), Evolutionarily Significant Units
(ESUs), or subspecies was well known in Colombia, were correctly assigned to
their geographical areas where the animals were illegally removed. In contrast, for
the species with small sample sizes, and where the number of MUs, ESUs, or sub-
species was uncertain, many specimens could not be geographically assigned in a
correct manner. Henceforth, the exact determination of the number and geographi-
cal localization of MUs or ESUs is essential. The same is required for a fine and
correct phylogeographic and evolutionary reconstruction of a species given and for
its correct intraspecific systematics.
Mitogenomes, or individual mitochondrial genes, are interesting for phyloge-
netic and phylogeographic tasks because they include a rapid accumulation of
mutations, rapid coalescence time, lack introns, have a high number of copies per
cell, a negligible recombination rate, and haploid inheritance (Avise et al. 1987).
Despite representing a single linked locus, selection pressures and evolutionary
rates are highly heterogeneous across mitochondrial DNA (mtDNA) (Galtier et al.
2006; Nabholz et al. 2012). For all of these reasons, mitogenomes, or individual
mitochondrial genes, are more precise in reconstructing the divergence history
6 Effects of Sample Size in the Determination of the True Number of Haplogroups… 103
among closely related species, or within species, than other molecular markers
(Moore 1995).
Furthermore, mitochondrial markers are important in determining how many
MUs or ESUs are within the distribution of a given species. MUs are defined by
significant divergence in allele frequencies of neutral markers regardless of the phy-
logeny of the alleles (allele frequencies respond to population isolation more rap-
idly than phylogenetic structure). These divergences are mainly caused by a strong
restriction of the gene flow (Avise 2000). For this reason, mtDNA is especially
useful for detecting boundaries between MUs, because differences between popula-
tions are more readily detected with mtDNA than with nuclear genes. Additionally,
MUs are populations with different demographic characteristics due to different
population growth rates. Then, mtDNA is usually more prone to genetic drift than
nuclear genes. This involves a differential management in the short-term.
ESUs can be defined as a population, or group of them, that merit separate con-
servation management due to evident genetic and ecologic distinctiveness, but these
differences are the result of a long-term process. There are different definitions of
ESU; Ryder (1986) defined it as populations representing significant adaptive varia-
tion demonstrated by different data sets. This thinking was in reference to which
subspecies should be prioritized for conservation actions due to the limitations of
zoos or captive breeding programs. Waples (1991) defined ESUs as populations that
are reproductively isolated from other populations (inferred from molecular data)
and that have different adaptations, which represent an important fraction of the
evolutionary trajectory of a given species. Dizon et al. (1992) defined ESUs as pop-
ulations that are different based on morphology, geographic distribution, population
parameters and some degree of genetic differentiation. Crandall et al. (2000) based
their ESU definition on the lack of ecological (different adaptations or selective
pressures) and genetic (no recent gene flow and correlation between phylogenetic
and geographic discontinuities) exchange. Fraser and Bernatchez (2001) defined
ESU as a lineage with highly restricted gene flow with other lineages inside of a
higher organizational level of the species. Nevertheless, the most practical criteria
for detecting ESUs comes from the definition of Moritz (1994), who defines ESUs
as populations which were reciprocally monophyletic for mtDNA and which yielded
significant divergence for allele frequencies at nuclear loci. This divergence was not
necessarily the result of differential adaptation. This definition of ESU is the most
used for practicality.
In the current work, we want to determine how many MUs or ESUs are present
in three regularly seized Neotropical mammalian taxa in Latin America using differ-
ent genetic datasets (larger sample sizes with few mitochondrial markers and smaller
sample sizes with entire mitogenomes). These three cases were: the white-fronted
capuchins (Cebus albifrons) in Ecuador, the kinkajou (Potos flavus) in Latin
America, and three coati species (Nasua nasua, Nasua narica, and Nasuella oliva-
cea) also in Latin America. Herein, we only studied mtDNA and therefore we can-
not strictly apply the concept of ESUs for the significant groups or clades that we
detected. Nevertheless, at least, these groups should be defined, as a first step, as
MUs for conservation purposes. Future studies with nuclear genes should show that
many of these MUs are really ESUs.
The main characteristics of these three taxa are as follows: (1) the white-fronted
capuchin (Cebus albifrons) is a medium-sized monkey (body mass 2.9 kg for
females and 3.4 kg for males), which has hair on a smooth crown. The crown-cap
extends forward and is rounded in front. The forehead is light. The body pelage
color is a shade of brown, and the hands, feet, and the distal part of the tail are a
lighter color (Groves 2001). Its distribution includes Bolivia, Brazil, Colombia,
Ecuador, Peru, Trinidad Island, and Venezuela. It is omnivorous and lives in a vari-
ety of biomes, including gallery forests and island forests in Colombian Eastern
Llanos, and closed-canopy rainforests in Ecuador and Peru (Groves 2001). Cebus
albifrons has very confusing intraspecific systematics with a large number of frag-
mented and isolated populations throughout its geographical distribution, especially
in Colombia and Ecuador. The first systematics of C. albifrons was completed by
Hershkovitz (1949), who defined 13 subspecies. More recently, Rylands et al.
(2000) proposed ten subspecies, Groves (2001, 2005) proposed five subspecies, and
da Silva (2001) did not propose subspecies within C. albifrons. Here we analyze
how many MUs (or eventually ESUs or subspecies) of this species there are in
Ecuador using one dataset from Ruiz-García et al. (2018) [complete mitogenomes
and 49 individuals, total length 13,662 base pairs (bp)] versus a second dataset ana-
lyzed here (2 mitochondrial genes COI and COII with 65 Ecuadorian C. albifrons;
the previous 49 individuals plus another 16 individuals considered; total length
1377 bp). (2) The kinkajou (Potos flavus) is a Neotropical procyonid that inhabits
tropical forests from southern Mexico through Brazil. Body mass ranges from 1.4
to 4.6 kg, although no published studies provide data by age or sex (Nowak and
Paradiso 1983). Kinkajous have a rounded head, short skull, and a highly arched
braincase; the rostrum is short and broad with the postorbital process well devel-
oped. They have small rounded ears, a prehensile tail, a long and narrow extensible
tongue, and a characteristically woolly pelage. Local people sometimes mistake
them for primates because of their large, forwardly directed eyes, wide and flat
angular process of the mandible, and prehensile tail (Ford and Hoffmann 1988).
Cabrera (1958) and Kortlucke (1973) determined eight subspecies of P. flavus based
on morphology, two in Central America and another six in South America. The first
dataset was studied by Ruiz-García et al. (2019a), which offered a sample size of
129 individuals of P. flavus representing Mexico, Guatemala, Honduras, Colombia,
Ecuador, Peru, and Bolivia, and especially many different regions and biomes
within Colombia, Ecuador, Peru, and Bolivia. In this first dataset, five mitochondrial
genes were sequenced (Cytb, COI, ND4, ND5, and D-loop). This equaled a total of
3899 bp sequenced. In the current work, we analyzed a second dataset with a sam-
ple size of 46 individuals of P. flavus for complete mitogenomes representing the
same seven countries studied for the previous dataset. The total length sequenced
was 16,089 bp. (3) Among coatis, also procyonid carnivores, three extant species
are currently recognized: the white-nosed coati (Nasua narica), the South American
or brown-nosed coati (Nasua nasua), and the western mountain coati (Nasuella
olivacea). N. narica is the only coati species distributed in North, Central and South
America, from Arizona and New Mexico in the United States to northern Colombia
(Gompper 1995). The brown-nosed coati (N. nasua) is distributed in South America,
from Colombia and Venezuela to Uruguay and northern Argentina (Redford and
Eisenberg 1992; Gompper and Decker 1998; Nowak 1999). It is found primarily in
forested habitats, ranging from tropical rainforest and gallery forest to chaco, cer-
rado and dry scrub environments (Emmons 1990; Gompper and Decker 1998).
N. olivacea is found in the Andes of Venezuela, Colombia, and Ecuador in cloud
forest and paramo at altitudes of 1300–4250 m above the sea level. This Andean
species is smaller than the two other coati species. The first dataset was analyzed by
Ruiz-García et al. (2020b) and includes only three mitochondrial genes (ND5,
265 bp; Cyt-b, 407 bp; D-loop, 306 bp; summing up 978 bp), with a total of 345
coatis (222 N. nasua, 51 N. olivacea, and 72 N. narica). The second dataset contains
complete mitogenomes (total sequence length of 16,200 bp) and 205 coatis were
analyzed (108 N. nasua, 40 N. olivacea, and 57 N. narica).
Taking into consideration all of the above comments, the main aims of the cur-
rent work are as follows: (1) To determine if the nucleotide substitution models are
the same for two molecular datasets (one with larger sample sizes and broader geo-
graphical distribution but with few mitochondrial genes and the other with smaller
sample sizes and more restricted geographical distribution but with complete
mitogenomes) in three Neotropical mammalian taxa (white-fronted capuchin, kin-
kajou, and coatis); (2) To determine which of these two molecular datasets detect a
higher number of significant units (they should be MUs, ESUs, or subspecies), and
if these genetic units for both molecular datasets are the same to be considered in
terms of conservation biology (sized or hunted animals) and also for phylogeo-
graphic studies; (3) To determine if the spatial genetic structure found is the same,
or not, for both molecular datasets; and (4) To review the intra-specific systematics
of the three mammalian groups studied in regards to the results of these two molecu-
lar datasets.
2 Materials and Methods
2.1 Sampling Strategy
For the first taxon studied in Ecuador (C. albifrons), a total of 65 specimens were
sampled throughout the country, including the following provinces: Esmeraldas,
Imbabura, Loja, Manabí, Morona-Santiago, Napo, Pastaza, Pichincha, and Zamora-
Chinchipe. This enclosed both the trans and the cis-Andean Ecuador and the two
supposed subspecies of C. albifrons assigned to this country, C. a. aequatorialis for
the trans-Andean Ecuador (Pacific area) and C. a. yuracus for the cis-Andean
Ecuador (Amazonian area) (Table 6.1). Samples consisted of pieces of skin obtained
in museums as well as hairs with bulbs, and teeth directly obtained in the wild.
Table 6.1 (A) Sources of the 65 samples of white-fronted capuchins (Cebus albifrons) sampled in
Ecuador for two mitochondrial genes (COI and COII), NS number of samples. (B) Sources of the
129 samples of Potos flavus collected and analyzed at 5 mitochondrial genes (Cytb, COI, ND4,
ND5, and D-loop) by Ruiz-García et al. (2019b), and at their mitogenomes (46 specimens) in the
current work. Into parenthesis, the number of specimens analyzed for mitogenomes. (C) Sources
of the coatis collected and analyzed at three mitochondrial genes (ND5, Cyt-b, and D-loop)
(222 Nasua nasua, 51 Nasuella olivacea, and 72 Nasua narica) by Ruiz-García et al. (2020b), and
at their mitogenomes (110 Nasua nasua, 38 Nasuella olivacea, and 57 Nasua narica) in the current
work. Into parenthesis, the number of specimens analyzed for mitogenomes.
(A)
Possible subspecies NS Geographical origins
C. a. aequatorialis (a priori) 2 Esmeraldas-Imbabura Province
(Cotacachi-Cayapas) (Ecuador)
C. a. aequatorialis (a priori) 6 Pichincha Province (Ecuador)
C. a. aequatorialis (a priori) 3 Manabí Province (Ecuador)
C. a. yuracus (a priori) 13 Napo Province (Ecuador)
C. a. yuracus (a priori) 26 Pastaza Province (Ecuador)
C. a. yuracus (a priori) 5 Morona-Santiago Province (Ecuador)
C. a. yuracus (a priori) 5 Loja Province (Ecuador)
C. a. yuracus (a priori) 5 Zamora-Chinchipe Province (Ecuador)
Total 65
(B)
Location Number of
samples
Mexico n = 2 (n = 1)
Campeche State 2 (1)
Guatemala n = 5 (n = 4)
Petén Department 3 (2)
Huehuetenango Department 2 (2)
Honduras n = 2 (n = 1)
Roatan Island 2 (1)
Colombia n = 42 (n = 15)
Bogotá 1 (1)
Amazonas Department 14 (3)
Antioquia Department 5 (1)
Caldas Department 1
Caquetá Department 1 (1)
Casanare Department 1
Cauca Department 1 (1)
Cesar Department 1
Chocó Department 1 (2)
Cundinamarca Department 1
Huila Department 2 (2)
Meta Department 2
Nariño Department 1 (1)
(continued)
Table 6.1 (continued)

Norte de Santander Department 1
Risaralda Department 1 (1)
Tolima Department 1
Valle del Cauca Department 1 (1)
Vaupés Department 1
Vichada Department 2 (1)
Ecuador n = 18 (n = 9)
Cotopaxi Province 2
Esmeralda Province 1(1)
Imbabura Province 2
Manabí Province 1 (1)
Morona-Santiago Province 2 (2)
Napo Province 3 (1)
Pastaza Province 3 (3)
Pichincha Province 4 (1)
Peru n = 41 (n = 14)
Cajamarca Department 1 (1)
Huánuco Department 3 (1)
Loreto Department 23 (7)
Pasco Department 5 (1)
San Martín Department 1
Ucayali Department 8 (4)
Bolivia n = 19 (n = 2)
Beni Department 4
Cochabamba Department 12 (2)
Pando Department 2
Santa Cruz Department 1
(C)
Species and Location Number of
samples
Nasua nasua n = 222 (n = 110)
Amazonas Department 10 (5)
Cauca Department 2
Caquetá Department 1 (1)
Cauca Department 2
Cundinamarca Department 1 (1)
Guaviare Department 3 (2)
Huila Department 3
Meta Department 8 (3)
Nariño Department 1
Norte de Santander Department 2 (2)
(continued)

Quindio Department 1
Santander Department 2
Tolima Department 1 (1)
Vichada Department 1 (1)
Esmeraldas Province 3 (2)
Guayas Province 3
Imbabura Province 3 (1)
Manabí Province 3
Napo Province 6 (2)
Orellana Province 3
Pastaza Province 8 (2)
Santo Domingo de Tsáchilas 2
Province
Sucumbios Province 1
Zamora-Chinchipe Province 1
Peru n = 69 (n = 45)
Apurimac Department 5 (4)
Cuzco Department 6 (6)
Huánuco Department 1 (1)
Junín Department 1
Loreto Department 18 (7)
Madre de Dios Department 17 (14)
Pasco Department 1
San Martín Department 6 (4)
Ucayali Department 14 (9)
Bolivia n = 26 (n = 16)
Beni Department 16 (10)
Cochabamba Department 5 (4)
La Paz Department 3 (2)
Santa Cruz Department 2
Brazil n = 23 (n = 7)
Amazonas State 7 (2)
Goias State 1
Paraná State 15 (5)
Paraguay n = 9 (n = 7)
Alto Paraná Department 9 (7)
Uruguay n = 4 (n = 4)
Tucuarembó Department 3 (3)
Artigas Department 1 (1)
(continued)

Chile n = 1 (n = 1)
Robinson Crusoe Island 1 (1)
Nasuella olivacea n = 51 (n = 38)
Antioquia Department 1
Boyacá Department 5 (5)
Caldas Department 4 (1)
Cauca Department 2 (1)
Chocó Department 1 (1)
Cundinamarca Department 14 (13)
Nariño Department 1 (1)
Norte de Santander Department 9 (7)
Tolima Department 1 (1)
Carchi Province 1 (1)
Cotopaxi Province 1 (1)
Morona-Santiago Province 1
Napo Province 1
Peru n = 2 (n = 1)
Apurimac Department (possible 1
N. olivacea)
Cuzco Department 1(1)
Bolivia n = 1 (n = 0)
Cochabamba Department 1
(possible N. olivacea)
Nasua narica n = 72 (n = 57)
Mexico n = 24 (n = 20)
Campeche State 10 (9)
Chiapas State 3 (3)
Quintana Roo State (Cozumel 1 (1)
Island)
Tabasco State 7(4)
Yucatan State 3 (3)
Guatemala n = 24 (n = 16)
Alta Verapaz Department 3 (3)
Alta Verapaz Department 1(1)
Izabal Department 2 (1)
Peten Department 18 (11)
Belize n = 3 (n = 3)
Rio Bravo Conservation Area 3 (3)
(continued)

Honduras n = 7 (n = 7)
Olancho Department 5 (5)
Roatán Island 2 (2)
El Salvador n = 3 (n = 3)
La Libertad Department 3 (3)
Nicaragua n = 1 (n = 1)
Nueva Segovia Department 1 (1)
Costa Rica n = 3 (n = 3)
Alajuela Province 2 (2)
Puntarenas Province 1(1)
Panama n = 1 (n = 1)
Colón Province 1 (1)
Chocó Department 2
Guayas Department 2 (2)
Morona-Santiago Department 1
These samples were sequenced for the mtCOI and COII genes. The samples and
localities for the mitogenome dataset can be seen in Ruiz-García et al. (2018).
For the second taxon studied, P. flavus, a total of 46 specimens were sequenced
for entire mitogenomes. These samples were obtained in Mexico, Guatemala,
Honduras, Colombia, Ecuador, Peru, and Bolivia and represented Mexico (n = 1),
Guatemala (n = 4), Honduras (n = 1), Colombia (n = 15), Ecuador (n = 9), Peru
(n = 14), and Bolivia (n = 2) (Table 6.1). The samples were pieces of skins, muscle,
blood, teeth, and hairs with bulbs obtained directly in the wild. The samples and
localities for the five-mitochondrial genes dataset can be seen in Ruiz-García et al.
(2019a).
For the third taxa studied, 205 coatis were sequenced for mitogenomes
(108 N. nasua, 40 N. olivacea, and 57 N. narica), together with 2 Bassarycion neb-
lina (Ecuador) as outgroup. For N. nasua, the following countries were sampled:
Colombia (n = 20), Ecuador (n = 8), Peru (n = 45), Bolivia (n = 16), Brazil (n = 7),
Chile (n = 1), Paraguay (n = 7), and Uruguay (n = 4). For N. narica, the following
countries were sampled: Mexico (n = 21), Guatemala (n = 15), Belize (n = 3),
Honduras (n = 7), El Salvador (n = 3), Nicaragua (n = 1), Costa Rica (n = 3), Panama
(n = 1), Colombia (n = 1), Ecuador (n = 2). For N. olivacea, the following countries
were sampled: Colombia (n = 35), Ecuador (n = 4), and Peru (n = 1) (Table 6.1). The
samples were pieces of skins, teeth, bones, blood, muscle, and hairs with bulbs
obtained directly in the wild. The samples and localities for the three-mitochondrial
genes dataset can be seen in Ruiz-García et al. (2020b), including 345 coatis
(222 N. nasua, 51 N. olivacea, and 72 N. narica). In that study, the outgroups
sequenced were 1 Procyon cancrivorus (Colombia), 5 Bassarycion neblina
(Colombia and Ecuador), 5 Bassarycion medius (Colombia and Ecuador), and 14

Bassarycion aleni (Ecuador, Peru, and Bolivia).
2.2 Laboratory Procedures
Cebus albifrons: The primers and the PCR conditions for the mitogenome dataset
are in Ruiz-García et al. (2018). The total length of the sequences studied for this
dataset was 13,662 bp. For the current work, we sequenced two mitochondrial genes
of the three mitochondrial DNA encoded subunits of respiratory complex IV
(Cytochrome Oxidase; COI, COII and COIII). This complex is the third and final
enzyme of the electron transport chain of mitochondrial oxidative phosphorylation
(Capaldi 1990).
The mtCOI gene has emerged as the standard barcode region for animals (www.
mammaliabol.org). Hebert et al. (2003, 2004) strongly argued in favor of using a
fragment of this mitochondrial gene as a barcoding marker. It has been shown to
provide sufficient resolution and robustness in distinguishing species within some
groups of organisms, such as arthropods, fish, birds and mammals (Borisenko et al.
2008; Agrizzi et al. 2012; Elmeer et al. 2012). The mtCOII gene has been studied
extensively in primate phylogenetics within the Hominoidea (Adkins and Honeycutt
1991; Ruvolo et al. 1991), Cercopithecoidea (Disotell et al. 1992), and Strepsirrhini
(Adkins and Honeycutt 1994). This gene has also been well studied in many
Neotropical Primate genera and species, such as Aotus (Ashley and Vaughn 1995;
Plautz et al. 2009; Ruiz-García et al. 2011, 2013, 2016a), Alouatta (Figueiredo et al.
1998; Cortés-Ortiz et al. 2003; Ruiz-García et al. 2016b, 2017), Ateles (Collins and
Dubach 2000; Ruiz-García et al. 2016c), Lagothrix (Ruiz-García and Pinedo-Castro
2010; Ruiz-García et al. 2014a, 2019b, 2020c), Cebus apella (Ruiz-García et al.
2012a), C. albifrons (Ruiz-García et al. 2010a, b, 2018, 2019c), C. capucinus (Ruiz-
García et al. 2012b), Saimiri (Ruiz-García et al. 2015), Saguinus leucopus (Ruiz-
García et al. 2014b) and other Callitrichinae (Sena et al. 2002). Ascunce et al. (2003)
showed that a phylogenetic signal (g1) was present in all codon positions of mtCOII,
despite having transitional saturation at the third position. The bootstrap support
values were very high below the genus level but abruptly decreased above this level.
These authors concluded that mtCOII could be very useful in molecular platyrrhine
systematics, both at intra-generic and intra-specific levels.
DNA from skins was extracted using the phenol–chloroform procedure
(Sambrock et al. 1989), whereas DNA samples from hair and teeth were extracted
with 10% Chelex resin (Walsh et al. 1991). For the mtCOI amplification (poly-
merase chain reaction, PCR), we used the forward primer LCO1490
(5′-GGTCAACAAATCATAAAGATATTGG-3′), and the reverse primer HCO2198
(5′-TAAACTTCAGGGTGACCAAAAAATCA-3′) (657 bp) (Folmer et al. 1994)
under the following PCR profile: 94 °C for 5 min, followed by 39 cycles of 94 °C
for 30 s, 44 °C for 45 s, 72 °C for 45 s, and a final cycle of 72 °C for 5 min. For the
amplification of the mtCOII gene (located in the lysine and asparagine tRNAs) we
used the forward primer L6955 (5′-AACCATTTCATAACTTTGTCAA-3′) and the
reverse primer H7766 (5′-CTCTTAATCTTTAACTTAAAAG-3′) (720 bp) (Ashley
and Vaughn 1995). We used the following temperatures: 95 °C for 5 min, 35 cycles
of 45 s at 95 °C, 30 s at 50 °C and 30 s at 72 °C and a final extension time for 5 min
at 72 °C. For both genes, the PCRs were performed in a 25 μL volume with reaction
mixtures including 4 μL of 10× buffer, 6 μL of 3 mM MgCl2, 2 μL of 1 mM dNTPs,
2 μL (8 pmol) of each primer, 2 units of Taq DNA polymerase, 5 μL of H2O and
2 μL (20–80 ng/μL) of DNA. PCR reactions were carried out in a BioRad thermo-
cycler. All amplifications, including positive and negative controls, were checked in
2% agarose gels, using the molecular weight marker ϕ174 DNA digested with Hind
III and Hinf I. The amplified samples were purified using membrane-binding spin
columns (Qiagen). The double-stranded DNA was directly sequenced in a 377A
(ABI) automated DNA sequencer. The samples were sequenced in both directions
using the BigDye TM kit and all the samples were repeated to ensure sequence
accuracy.
Potos flavus, Nasua, and Nasuella: The primers and the PCR conditions for the
five mitochondrial genes sequenced in P. flavus (Cytb, COI, ND4, ND5, and D-loop;
3899 bp) and for the three mitochondrial genes (ND5, Cyt-b, and D-loop; 978 bp)
sequenced for the three species of coatis are in Ruiz-García et al. (2019a, 2020b).
For the mitogenomic analyses of all these carnivores, DNA was extracted and
isolated from hair, skins, or muscle samples using the QIAamp DNA Micro Kit
(Qiagen, Inc.) following the protocol provided by the manufacturer. Muscle extrac-
tions followed the protocol “DNA Purification from Tissues”. Mitochondrial
genomes were sequenced by long-template PCR, which minimizes the chance of
amplifying mitochondrial pseudogenes from the nuclear genome (numts) (Thalmann
et al. 2004; Raaum et al. 2005). PCR amplification of mitochondrial DNA was car-
ried out using a LongRange PCR Kit (Qiagen, Inc.), with a reaction volume of
25 μL and a reaction mix consisting of 2.5 μL of 10× LongRange PCR Buffer,
500 μM of each dNTP, 0.6 μM of each primer, 1 unit of Long-Range PCR Enzyme,
and 50–250 ng of template DNA. Cycling conditions were as follows: 94 °C for
5 min, followed by 45 cycles denaturing at 94 °C for 30 s, primer annealing at
50–57 °C (depending on primer set) for 30 s, and an extension at 72 °C for 8 min,
followed by 30 cycles of denaturing at 93 °C for 30 s, annealing at 45–52 °C
(depending on primer set) for 30 s, and extension at 72 °C for 5 min, with a final
extension at 72 °C for 8 min. Four sets of primers were used to generate overlap-
ping amplicons [PROCYONID1F (5′-ATGAGTAATCAGCCCTTGAT-3′) and
PROCYONID1R (5′-ATGCATCCCACGTCAATCAT-3′) (around 5000 bp),
PROCYONID2F (5′-AAGTAATATGTCTGACATAA-3′) and PROCYONID2R
(5′-TCATCTGCATCTATTCTGA-3′) (around 4000 bp), PROCYONID3F
(5′-CATTTAGAAGCTAATTAAGC-3′) and PROCYONID3R (5′-GTGCAACTC
GAAATAAATGT-3′) (around 4000 bp), PROCYONID4F (5′-TAATTGTAATA
AAGCTATTT-3′) and PROCYONID4R (5′-TGGCACATCTCGATGGAGTA-3′)
(around 3200 bp)] from around 3200 to 5000 bp in length, thereby enabling a qual-
ity test for genome circularity (Bensasson et al. 2001; Thalmann et al. 2004). Both
mtDNA strands were sequenced directly using BigDye Terminator v3.1 (Applied
Biosystems, Inc.). Sequencing products were analyzed on an ABI 3730 DNA
Analyzer system (Applied Biosystems, Inc.). Sequences were then assembled and
edited using Sequencher 4.7 software (Gene Codes, Corp., Ann Arbor, MI).
Overlapping regions were examined for irregularities such as frameshift mutations
and premature stop codons. A lack of such irregularities indicates an absence of
contaminating numt sequences.
Alignments of the genes (around 16,089 bp for P. flavus and 16,200 bp for Nasua
and Nasuella) were concatenated after removing problematic regions using Gblocks
0.91 (Talavera and Castresana 2007) under a relaxed approach. This software
removes all poorly aligned regions and has been shown to be particularly effective
in phylogenetic studies including very divergent sequences (Castresana 2000;
Talavera and Castresana 2007). The individual alignments were then concatenated
by means of the SequenceMatrix v1.7.6 software (Vaidya et al. 2011) to create a
master alignment.
2.3 Phylogenetic Analyses
The sequence alignments were carried out manually as well as with the DNA
Alignment program (Fluxus Technology Ltd.). The best evolutionary nucleotide
substitution model for each dataset was estimated by PartitionFinder 2.1.1 software
(Lanfear et al. 2012) and jModeltest v2.0 (Darriba et al. 2012). Akaike’s informa-
tion criterion (AIC, Akaike 1974; Posada and Buckley 2004) and the Bayesian
information criterion (BIC, Schwarz 1978) were used to determine the best evolu-
tionary nucleotide model.
Phylogenetic trees for C. albifrons, P. flavus, and Nasua and Nasuella were con-
structed by using the procedure of Maximum Likelihood trees (ML) with the
RAxML v8.2.10 software (Stamatakis 2014). We used the partitioning scheme and
best-fit models chosen by the PartitionFinder 2.1.1 software (Lanfear et al. 2012).
This program was used to objectively determine the optimal model of evolution and
partitioning scheme simultaneously (for the partitions, codons 1 + 2 combined, and
codon 3, for each gene, and including control region and RNAs). Best-fit models
were selected using Bayesian information criteria under a ‘greedy’ search scheme
using a subset of models specific to RAxML. The GTR + G model (General Time
Reversible model + gamma-distributed rate variation among sites, Lanave et al.
1984) was the most used to search for the ML tree. We estimated support for nodes
using the rapid-bootstrapping algorithm (_f a-x option) for 1000 non-parametric
bootstrap replicates (Stamatakis et al. 2008).
2.4 Genetic Heterogeneity
In the case of the coatis, we used FST tests with Markov chains, 10,000 dememoriza-
tions parameters, 20 batches, and 5000 iterations per batch to determine possible
genetic heterogeneity among the different groups or clades detected. These signifi-
cances were compared with those obtained for Ruiz-García et al. (2020d) for the
three mitochondrial gene dataset. All of these statistics were calculated with the
DNAsp 5.1 (Librado and Rozas 2009) and Arlequin 3.5.1.2 programs (Excoffier
and Lischer 2010).
2.5 Spatial Genetic Structure
For C. albifrons in Ecuador, we employed SAMOVA 1.0 (Dupanloup et al. 2002)

(SAMOVA, spatial analysis of molecular variance) to investigate population subdi-
vision using analysis of molecular variance for the mtCOI and COII dataset and
compare these results with those obtained by Ruiz-García et al. (2018) with the
mitogenome dataset. SAMOVA 1.0 defines groups of populations that are geo-
graphically homogeneous and maximally differentiated from each other and identi-
fies genetic barriers between these population groups. The method is based on a
simulated annealing procedure that aims to maximize the proportion of total genetic
variance due to differences between groups of populations. We set k (number of
different populations) to 2–10 and estimated statistical significance using 1000
permutations.
For C. albifrons in Ecuador, for P. flavus in Latin America, and for N. olivacea in
Colombia and Ecuador, we used a Mantel test (Mantel 1967) to test for an overall
geographical relationship between the Kimura 2P genetic distance and the geo-
graphic distance in the 65 Ecuadorian C. albifrons individuals analyzed for the
mtCOI and COII dataset, in the 46 Latin American P. flavus individuals analyzed for
mitogenomes, and in the 39 Colombian and Ecuadorian N. olivacea analyzed for
mitogenomes. We normalized Mantel’s statistic according to Smouse et al. (1986)
to yield a correlation coefficient. The results obtained were compared with those
obtained by Ruiz-García et al. (2018) for the mitogenome dataset in C. albifrons,
with Ruiz-García et al. (2019a) for the five mitochondrial genes in P. flavus, and
with those obtained by Ruiz-García et al. (2020a) for the three mitochondrial genes
in Nasuella, respectively.
Also for C. albifrons in Ecuador, for P. flavus in Latin America, and for Nasuella
olivacea in Colombia and Ecuador, we used the Ay statistic (Miller 2005) for each
distance class (DC) calculated in the spatial autocorrelation analysis. Ay can be
interpreted as the average genetic distance between pairs of individuals that fall
within a specified distance class. Ay takes a value of 0 when all individuals within a
distance class are genetically identical and a value of 1 when all individuals within
a distance class are completely dissimilar. The probability of each distance class is
obtained using 10,000 randomizations. For the mtCOI-COII gene dataset of C. albi-
frons shown here, we used five DCs each of different size but with an equal number
of individual comparisons (0–64; 64–122, 122–185; 185–280; 280–605 km). Ruiz-
García et al. (2018) defined 10 distance classes of equal size (0–60; 60–121;
121–181; 181–242; 242–302; 302–362; 362–423, 423–483, 483–544; 544–605 km).
For the mitogenome dataset of P. flavus, we carried out two spatial correlation anal-
yses. In the first, we employed five DC using equal distances with unequal sample
sizes (0–596; 596–1191; 1191–1787, 1787–2383; 2383–2979 km, respectively). In
the second, we employed 10 DCs using unequal distances with equal sample sizes
(0–166; 166–262, 262–344, 344–427, 427–530, 530–678, 678–1011, 1011–1398,
1398–1712, 1712–2979 km). For the five mitochondrial dataset, Ruiz-García et al.
(2019a) also used five DCs (0–629; 629–1259; 1259–1888; 1888–2517; 2517–3147)
and ten DC (0–123; 123–250, 250–341; 341–411; 411–489; 489–631; 631–830;
830–1131; 1131–1397; 1397–3147 km), respectively. For the mitogenome dataset
of N. olivacea, we defined six DCs (0–46, 46–144, 144–206, 206–268, 268–429,
429–753 km, respectively) each of different size but with an equal number of indi-
vidual comparisons. Ruiz-García et al. (2020d) also employed six DCs for the three-
mitochondrial gene dataset (0–50; 50–150; 150–210; 210–270; 270–440;
440–800 km). For both primates and carnivores, we used AIS for this analysis
(Miller 2005).
We also used the Monmonier’s algorithm for further spatial analysis (Monmonier
1973) with AIS (Miller 2005) for both C. albifrons and N. olivacea. This geographi-
cal regionalization procedure detects the locations of putative barriers to gene flow
by iteratively identifying sets of contiguous, large genetic distances along connec-
tivity networks (Dupanloup et al. 2002; Manel et al. 2003; Manni et al. 2004). We
used a Delaunay triangulation (Brouns et al. 2003; Watson 1992) to generate the
connectivity network among sampling points. This procedure superimposes a
graphical representation of putative “barriers” inferred by the algorithm over the
connectivity network to identify important geographical features that reflect the
genetic data set. We compare the results obtained here with those obtained by Ruiz-
García et al. (2018, 2020b).
3 Results
3.1 The Case of C. albifrons in Ecuador

3.1.1 Nucleotide Substitution Model in C. albifrons
For the mtCOI + COII dataset, the best nucleotide substitution model for BIC and
AIC was GTR + G (26,819.529 and 23,818.597, respectively). Ruiz-García et al.
(2018) also showed that for the mitogenomes the best nucleotide substitution model
was GTR + G. Thus, the best nucleotide substitution model was insensitive to the
use of mitogenomes or only two mitochondrial genes.
3.1.2 Phylogenetic Analysis with the mtCOI and COII Database

in the Ecuadorian C. albifrons
The ML tree that included 65 individuals with only the mtCOI and COII genes
could be seen in Fig. 6.1. It also detected the nine groups of C. albifrons in Ecuador
observed for mitogenomes (Ruiz-García et al. 2018) [H1 (100%), that in this case
included H3; H2 (99%); H4 (61%); H5 (41%); H6 (60%); H7 (97%); H8 (62%,
including the two sub-groups detected for mitogenomes, 99% and 98%, respec-
tively); and H9 (60%)]. However, two additional small haplogroups were detected
in this analysis. One of them contained an individual from the Pastaza Province
(67%; H10) and the second one was integrated by two individuals from the Tiguino
area (Napo province; 100%; H11), and was the most divergent haplogroup detected
in this analysis. Henceforth, with more individuals analyzed, although with only
two mitochondrial genes, the number of different haplogroups for C. albifrons in the
current territory of Ecuador could be increased to at least 11. Furthermore, the other
nine haplogroups detected with mitogenomes were also detected with only two
mitochondrial genes. However, for both datasets, individuals from the Pacific trans-
Andean and the Amazon cis-Andean areas were intermixed in some of these hap-
logroups. Therefore, mitogenomics and individual mitochondrial gene analyses do
not consistently support that there are only two different monophyletic taxa of
C. albifrons on each side of the Ecuadorian Andes (C. a. aequatorialis at the trans-
Pacific area and C. a. yuracus at the cis-Amazonian area). Our data support an
extremely more complex situation independently of the dataset employed.
3.1.3 Spatial Genetic Structure in the Ecuadorian C. albifrons
Both dataset analyses yielded similar results with scarce geographic structuration.
However the mtCOI-COII sequence dataset with more individuals analyzed detected
a slightly higher level of genetic structure than the mitogenomics analysis.
SAMOVA showed the same results for both datasets. Six different groups was
the most probable result (for the mtCOI-COII data set: k = 6, FCT = 0.294,
p = 0.00078; Table 6.2).
The Mantel’s test for the mitogenome dataset showed that geographical distance
only explained 0.45% of the genetic distance (r = 0.067, p = 0.121; Ruiz-García
et al. 2018). However, for the mtCOI-COII gene dataset (Fig. 6.2), this test was
significant, although the correlation was also low (r = 0.143, p = 0.0045), and the
geographical distance only explained 2.05% of the genetic distance.
The ten DCs spatial autocorrelation analysis for the mitogenome dataset did not
show any evidence of significant structure (Ruiz-García et al. 2018). Similarly, the
same analysis with five DCs for the mtCOI-COII gene dataset did not yield a sig-
nificant correlogram (V = 0.00311, p = 0.337; Fig. 6.3). Only the first DC indicated
significance (0–67 km, p = 0.0397). This means that, there was a higher genetic
similarity among the closest animals. Nonetheless, the animals sampled further
away did not show a significant decrease in genetic similarity.
Fig. 6.1 Maximum-likelihood tree of 65 Ecuadorian Cebus albifrons specimens sequenced at the
mitochondrial COI-COII genes. The different haplogroups detected in Ecuador were note as H
(H1-H11). In the nodes, bootstrap percentages
Table 6.2 SAMOVA for the % variance % variance within

11 haplogroups (65 Geographical clusters among groups populations
specimens) detected in the
2 groups 9.34 79.24**
Ecuadorian C. albifrons
analyzed at the mtCOI-COII 3 groups 16.98** 77.83**
genes. Six geographical 4 groups 20.45** 80.12**
clusters showed the highest 5 groups 20.63** 81.11**
% variance among the 6 groups 29.43** 86.97**
geographical groups for 7 groups 18.43 87.34**
C. albifrons in Ecuador for
both analyses. **P < 0.001
Fig. 6.2 Mantel’s test applied at the mitochondrial COI-COII genes of 65 Ecuadorian specimens
of Cebus albifrons
Monmonier’s algorithm revealed six detectable geographical areas with genetic

differences for the mitogenome dataset (Ruiz-García et al. 2018). We detected also
six regions with the mtCOI-COII gene analysis (Fig. 6.4). They are listed here in
order of importance. The first showed an area that contained part of the Pichincha
and Manabí provinces, including the majority of the H8 (Pacific trans-Andean area)
individuals. The second region is in the northern Ecuadorian Amazon (zone of
Tiguino at the Napo River near to the frontier between Ecuador and Peru) (H11).
The third region is an area within another part of the Pichincha and Cotacachi-
Cayapas provinces (Pacific trans-Andean area). The fourth region contains exem-
plars of H8 in the southern Manabí province together with cis-Andean Amazon
Fig. 6.3 Spatial autocorrelation analysis with five distance classes at the mitochondrial COI-COII
genes of 65 Ecuadorian specimens of Cebus albifrons
Fig. 6.4 Monmonier’s algorithm analysis to detect the six most important geographical barriers
for 65 Ecuadorian Cebus albifrons sequenced at the mitochondrial COI-COII genes
individuals from the Loja and Zamora-Chinchipe provinces. The fifth region is an
Amazonian area typically containing H7 individuals, whereas the sixth boundary
enclosed an Ecuadorian Amazonian zone area with individuals from H1, H4, and
H5. Thus, both analyses detected three different zones with differentiated genetic
characteristics in the Pacific trans-Andean area as well as three different zones with
differentiated genetic characteristics in the Amazonian cis-Andean area of Ecuador.
The main haplotype of the Pacific trans-Andean area was also found in the cis-
Andean area, and in the three Amazonian cis-Andean zones. Therefore, we detected
different haplogroups coexisting sympatrically in each zone.
3.2 The Case of P. flavus in Latin America
3.2.1 Nucleotide Substitution Model in P. flavus
The top-ranked nucleotide substitution model (lowest AIC score) for the dataset of
five mtDNA genes analyzed was GTR + G (100,345.84) (Ruiz-García et al. 2019a),
meanwhile for the mitogenome dataset, it was HKY + G (3,463,625.14). Thus, in
this case, the best nucleotide substitution model was different depending on the use
of five mtDNAs or complete mitogenomes.
3.2.2 Phylogenetic Analysis with the Mitogenome Dataset from P. flavus

in Latin America
The ML tree for the five mtDNA gene datasets obtained by Ruiz-García et al.
(2019a) showed eight clusters with geographical significance for P. flavus. The first
haplogroup of P. flavus (H1) was composed of all the specimens from northern
Central America (97% bootstrap support). The second haplogroup (H2) was inte-
grated by specimens from trans-Andean Ecuador and Pacific Colombia, and from
northern and central Colombia (73% bootstrap support). Two sub-haplogroups were
detected. The first one contained specimens from trans-Andean Ecuador (Provinces
of Cotopaxi, Esmeraldas, Imbabura, Manabí, and Pichincha), from Pacific Colombia
(Departments of Cauca, Chocó, Nariño, Risaralda, and Valle del Cauca), and the
Colombian Caribbean (Cesar Department) (H2a). The second one had specimens
from central and northern Colombia (Antioquia, Caldas, and Cundinamarca) as well
as one specimen from Ecuador (Imbabura Province) (H2b). Two specimens from
Pando (northern Bolivian Amazon) were enclosed in H2 as well as one specimen
from the Casanare Department in the Colombian Eastern Llanos. H3 contained two
specimens from central-southern Colombia (Cueva de Los Guacharos National
Park, Huila Department, central-southern Colombia; 91% bootstrap support). H4
(82% bootstrap support) was a mix of all the individuals sampled in the north-
central Andes and in the Peruvian southern Amazon (Departments of Cajamarca,
Huánuco, Pasco, San Martín, and Ucayali). Similarly, H5 (77% bootstrap support)
was composed of mostly specimens sampled in Bolivia (Departments of Beni,
Cochabamba, and Santa Cruz), with the exception of two samples from Pando,
which clustered as sister taxa of the H2a clade. H6 (92% bootstrap support) was
composed of two specimens sampled in the Colombian Eastern Llanos, specifically
from the Vichada Department. The last cluster (H7; 84% bootstrap support) con-
tained the majority of individuals sampled coming from the northern Peruvian,
Colombian, and Ecuadorian Amazon (Loreto Department in Peru; Amazonas,
Caquetá, and Vaupés Departments in Colombia; Morona-Santiago, Napo, and
Pastaza Provinces in Ecuador). There was also representation from other areas of
Colombia (northern Colombia: Norte de Santander Department; central Colombia:
Tolima Department; Eastern Llanos: Meta Department).
The ML tree for the 46 individuals sequenced for their complete mitogenomes
(Fig. 6.5) detected four main significant clades plus one individual not associated
with any of these clades. The first clade (72% bootstrap support) agrees quite well
with the H1 of the five mitochondrial genes dataset. The individuals were from
Mexico, Guatemala, and Honduras. The second clade (86% bootstrap support) had
two sub-groups. One of them (95% bootstrap support) was composed of two indi-
viduals from the Cueva de Los Guacharos National Park (Huila Department, central-
southern Colombia) and one from the Antioquia Department (central-northern
Colombia) and the other sub-group (54% bootstrap support) was composed of indi-
viduals from the trans-Andean Ecuador (Provinces of Esmeraldas, Manabí, and
Pichincha), and from the Pacific Colombia (Departments of Cauca, Chocó, Nariño,
and Valle del Cauca). Henceforth, the first sub-group of this second clade included
specimens from H3 and H2b and the second sub-group included specimens from
H2a. The third clade (96% bootstrap support) was also composed of two sub-groups.
The first one (96% bootstrap support) was composed of two Bolivian individuals,
which agrees quite well with H5 of the previous dataset. The second sub-group
(88% bootstrap support) was mainly integrated by individuals from central Andean
Peru and southern Peruvian Amazon, which is in agreement with the H4 of the pre-
vious analyzed dataset.
However, one specimen from the Risaralda Department (central Colombia) and
another from the Colombian Amazon were also enclosed in this cluster. The fourth
clade contained individuals from the northern Peruvian, Colombian, and Ecuadorian
Amazon, which perfectly agrees with the H7 from the dataset analyzed by Ruiz-
García et al. (2019a). The individual not associated with any of these clades was
from the Vichada Department in the Eastern Colombian Llanos, and this corre-
sponds to the H6 from the previous analysis. Therefore, the mitogenome dataset
detected the same haplogroups as that of the five mtDNA gene dataset. However,
they were less defined and, in some cases, as in the second clade, specimens for
three haplogroups were intermixed and not differentiated.
Fig. 6.5 Maximum-likelihood tree of 46 Potos flavus specimens from seven Latin American coun-
tries (Mexico, Guatemala, Honduras, Colombia, Ecuador, Peru, and Bolivia) sequenced at their
mitogenomes. In the nodes, bootstrap percentages
Fig. 6.6 Mantel’s test applied at the mitogenomes of 46 specimens of Potos flavus from 7 Latin
American countries (Mexico, Guatemala, Honduras, Colombia, Ecuador, Peru, and Bolivia)
3.2.3 Spatial Genetic Structure in P. flavus
The Mantel’s test for the mitogenome dataset showed that geographical distance
significantly explained 25.20% of the genetic distance (r = 0.502, p = 0.00009;
Fig. 6.6). Similarly, Ruiz-García et al. (2019a) determined a significant relationship
between geographical and genetic distances for the five mitochondrial genes dataset
(r = 0.458, p = 0.00009) with geographical distances explaining 20.97% of genetic
distances. Thus, the use of one or other dataset yielded the same results.
Figure 6.7 shows the overall correlograms for both five and ten DCs carried out
for the mitogenome dataset in P. flavus. For five DCs, the overall correlogram was
highly significant (V = 0.0147, p = 0.004), with the one DC significantly positive
(p = 0.000001), and the three, four, and five DCs significantly negative (p = 0.000001,
p = 0.000001, and p = 0.0067, respectively). This is correlated with isolation by
distance. For the ten DCs, the overall correlogram was highly significant (V = 0.0124,
p = 0.000001), with the one, two, three, five, and six DCs significantly positive
(p = 0.000001, p = 0.0268, p = 0.0196, p = 0.0044, p = 0.0018, respectively), and
the eight, nine, and ten DCs significantly negative (p = 0.0009, p = 0.000001, and
p = 0.000001, respectively). This correlogram is more detailed than the previous
one. Two geographical patterns are shown. The first one consists of genetic patches
with an average diameter of around 430 km and the other is basically isolation by
distance or a monotonic cline from 700 to 3000 km. Therefore, the spatial genetic
structure for P. flavus is outstanding. The results obtained with the mitogenome
Fig. 6.7 Spatial autocorrelation analysis with 5 (top panel) and 10 (bottom panel) distance classes
at the mitogenomess of 46 specimens of Potos flavus from 7 Latin American countries (Mexico,
Guatemala, Honduras, Colombia, Ecuador, Peru, and Bolivia)
dataset are almost identical to those obtained by Ruiz-García et al. (2019a) for the
five-mitochondrial genes database.
3.3 The Case of the Coatis, Nasua and Nasuella

in Latin America
3.3.1 Nucleotide Substitution Model in Coatis (Nasua and Nasuella)
For mitogenomes, the best nucleotide substitution models were TN93 + G + I

(254,960.981) and GTR + G + I (212,220.462) for BIC and AIC, respectively. The
same nucleotide substitution models were found at the three-mitochondrial genes
dataset by Ruiz-García et al. (2020b). Therefore, the nucleotide substitution models
were scarcely affected by using a fragment of a mitochondrial gene or the entire
mitogenome for the coatis.
3.3.2 Phylogenetic Analysis with the Mitogenome Dataset in Nasua

and Nasuella in Latin America
The ML tree with mitogenomes can be observed in Fig. 6.8. In contrast, to that
observed by Ruiz-García et al. (2020b) for the ML tree with the three-mitochondrial
genes dataset, the ML tree with mitogenomes detected a closer relationship between
N. nasua and N. narica, and determined N. olivacea to be the most differenti-
ated taxon.
Haplogroups in N. nasua
The first haplogroup (MH1-NAS; 97% bootstrap support) contained 3 sub-

haplogroups with specimens from Bolivia and a large fraction of southern Peru as
well as some specimens from the central Peruvian Amazon (first sub-haplogroup,
MH1-sh1-NAS; 90%), with specimens from the Andean area of southern Peru
(Cuzco Department) and Ucayali River (second sub-haplogroup, MH1-sh2-NAS;
83%), and specimens of the central Brazilian Amazon (Negro River; sub-haplogroup,
MH1-sh3-NAS; 85%). This haplogroup, MH1-NAS, was also detected at the three-
mitochondrial genes dataset.
The second haplogroup (MH2-NAS; 99%) contained specimens of the Peruvian
Amazon and some Peruvian Andean areas in transition to the Amazon (San Martin
Department). MH2-NAS was also detected at the three-mitochondrial genes dataset.
The third haplogroup (MH3-NAS; 100%) included specimens from the Peruvian
Amazon and the southern Peruvian Andes (Cuzco Department) and it also expanded
into the Colombian Amazon (Leticia). A couple of small and significant clusters
Fig. 6.8 Maximum-

likelihood tree based on
mitogenomes of 205
specimens of 3 species of
coatis (Nasua nasua, Nasua
narica, and Nasuella
olivacea) sampled in 16
Latin American countries
(Mexico, Guatemala, Belize,
Honduras, El Salvador,
Nicaragua, Costa Rica,
Panama, Colombia, Ecuador,
Peru, Brazil, Bolivia, Chile,
Paraguay, and Uruguay).
Nodes are labeled with
bootstrap percentages.
Significant haplogroups
were marked
Fig. 6.8 (continued)

were detected (86%, and 94%, respectively). MH3-NAS was also detected at the
three-mitochondrial genes dataset.
The fourth haplogroup (MH4-NAS; 92%) contained a single specimen from
Robinson Crusoe Island (Chile). This haplogroup was detected at the three-
mitochondrial genes dataset. However, Ruiz-García et al. (2020b) had discovered
that this haplogroup was centered on the trans-Andean Ecuador, but with the
mitogenomes, the origin of this haplogroup was not recovered.
The fifth haplogroup (MH5-NAS; 100%) consisted of specimens from southern
South America (southern Brazil, Paraguay, and Uruguay). MH5-NAS was also
detected with the three-mitochondrial genes dataset.
The sixth haplogroup (MH6-NAS; 91%) was integrated by specimens of the
Andean Cordilleras from Colombia (Norte de Santander, Antioquia, and Risaralda
Departments) and Ecuador (Imbabura and Esmeraldas Provinces). Associated to
this haplogroup appeared one specimen of N. olivacea from the Chocó Department
(Colombia). MH6-NAS was also detected at the three-mitochondrial genes dataset.
Nonetheless, there were some differences between datasets. Some of the specimens
from the Colombian Eastern Llanos at the three-mitochondrial genes dataset
belonged to another haplogroup, whereas with the mitogenomes, these specimens
were within MH6-NAS. Additionally, at the three-mitochondrial genes dataset, we
determined that this haplogroup reached until Turbo (Antioquia Department) very
near to the Colombian-Panamanian frontier, whereas with mitogenomes this infor-
mation was not recovered.
The seventh haplogroup (MH7-NAS; 100%) mainly consisted of specimens of
the Colombian and Ecuadorian Amazon together with some specimens from Andean
Colombia (Cundinamarca and Valle del Cauca Department) and trans-Andean
Pacific Ecuador (Esmeraldas Province). MH7-NAS was also detected with the
three-mitochondrial genes dataset, but a difference between the datasets was discov-
ered. In this case, two sub-haplogroups were better differentiated with the mitoge-
nome dataset than with the three-mitochondrial genes dataset. These two
sub-haplogroups were MH7-sh1-NAS (82%), which was integrated by specimens
from the Colombian Amazon (Amazonas and Guaviare Departments), and Napo
River in Peru, and MH7-sh2-NAS (100%), which consisted of specimens of the
Ecuadorian Amazon, Colombian Eastern Llanos, Cundinamarca, and Valle del
Cauca Departments (Colombia).
Haplogroups in N. narica
For N. narica, the situation was very similar to that detected at the three-mitochondrial
genes dataset, with only one outstanding difference.
The first diverging haplogroup (MH0-NARI; 91%) only contained one specimen
from Costa Rica. The three-mitochondrial genes dataset did not detect the notewor-
thy differentiation of this specimen (Ruiz-García et al. 2020b).
The second haplogroup (MH1-NARI; 99%) contained two specimens of the

Guayas Province (Ecuador). This agrees quite well with the results of the three-
mitochondrial genes dataset shown in Ruiz-García et al. (2020b).
The third haplogroup (MH2-NARI; 94%) consisted of three specimens from the
Yucatan (Mexico), as it was detected by the three-mitochondrial genes dataset.
The fourth haplogroup (MH3-NARI; 100%) was the largest detected in Central
America, including three sub-haplogroups. The first sub-haplogroup (MH3-sh1-
NARI; 99%) consisted of specimens from Guatemala, Honduras, El Salvador,
Nicaragua, and northcentral Costa Rica. This haplogroup was also detected with the
three-mitochondrial genes dataset. The second sub-haplogroup (MH3-sh2-NARI;
94%) contained specimens from Guatemala and Belize. This haplogroup was also
detected using the three-mitochondrial genes dataset. The third sub-haplogroup
(MH3-sh3-NARI; 92%) contained specimens from southern Mexico (including
Cozumel Island) and Guatemala. This haplogroup was also detected with the three-
mitochondrial genes dataset. In this case, however, the mitogenome analysis better
discriminated certain sub-structure within this sub-haplogroup since some small
geographical groups were detected (Chiapas, 95%; Tabasco, 85%; Tabasco, 100%)
that were not detected with the three-mitochondrial genes dataset.
The fifth haplogroup (MH4-NARI; 100%) was associated with N. olivacea, such
as was determined by Ruiz-García et al. (2020b) at the three-mitochondrial genes
dataset. It consisted of specimens from southern Costa Rica, Panama, and northern
Colombia (Antioquia Department).
Haplogroups in N. olivacea
For N. olivacea, Ruiz-García et al. (2020b) detected a haplogroup that they named
H1-OLI with the three-mitochondrial genes dataset. In the current study with
mitogenomes, this group was split. One specimen from the Chocó Department
(Colombia) was associated with the MH6-NAS, but the remaining specimens
belonging to H1-OLI formed a separated haplogroup for mitogenomes, which was
associated with the other haplogroups of N. olivacea obtained with this dataset.
With mitogenomes, the haplotypes of N. olivacea for this haplogroup (MH1-OLI;
100%) were less related to the haplotypes of Nasua than with the three-mitochondrial
genes dataset. Therefore, the mitogenome analysis seems to detect more heteroge-
neity within this haplogroup than did the three-mitochondrial genes dataset.
However, the specimens analyzed for mitogenomes were centered in southern
Andean Colombia (Cauca and Nariño Departments) and northern Andean Ecuador
(Carchi Department), whereas, with the three-mitochondrial genes dataset, this hap-
logroup expanded throughout the Colombian Andes.
H2-OLI, evident in the three-mitochondrial genes dataset, was absent with the
mitogenome dataset.
The second haplogroup detected with mitogenomes (we named MH3-OLI to
conserve the correlation with the three-mitochondrial genes dataset; 100%) included
specimens of N. olivacea from the Western and Central Colombian (Caldas,
Risaralda, Tolima, Chocó Departments) and Ecuadorian (Pichincha, and Cotopaxi

Departments) Andean Cordilleras. MH3-OLI was also detected with the three-
mitochondrial genes dataset. Nonetheless, with mitogenomes, we found a specimen
with an intermediate morphotype between N. nasua and N. olivacea from Alba
(Urubamba River, Cuzco) highly similar to the other mitogenomes of N. olivacea of
this haplogroup. This provides validation of the presence of N. olivacea in Peru, a
species which has not yet been reported at this country.
The third haplogroup (MH4-OLI; 100%) consisted of specimens from the
Eastern Colombian Andean Cordillera. This haplogroup was also detected with the
three-mitochondrial genes dataset.
Another haplogroup detected at the three-mitochondrial genes dataset (H5-OLI)
was not detected with mitogenomes.
Henceforth, with 205 coati specimens and entire mitogenomes, we detected 15
main haplogroups (7 N. nasua, 5 N. narica, and 3 N. olivacea) and 8 sub-haplogroups
(5 N. nasua, and 3 N. narica). Ruiz-García et al. (2020b) detected 19 main hap-
logroups (10 haplogroups in N. nasua, 4 haplogroups in N. narica, and 5 hap-
logroups in N. olivacea) and 8–10 sub-haplogroups (5–7 in N. nasua, and 3 in
N. narica) with the three-mitochondrial genes dataset of 345 coati specimens.
Therefore, the mitogenome dataset, with less individuals and less geographical area
covered, detected less significant clusters or groups than the three-mitochondrial
genes dataset with a larger sample size and also more geographical areas considered.
3.3.3 Genetic Heterogeneity Between Haplogroups of Coatis
For the mitogenomes, a large fraction of the comparison pairs between these hap-
logroups and sub-haplogroups were significant (considered 17 groups and 136 com-
parison pairs; 89.71%; 122 out 136 comparison pairs with p < 0.05) (Table 6.3),
although with a percentage lower than that found by Ruiz-García et al. (2020b) at
the three-mitochondrial genes dataset. The percentage was 98.19% (24 considered
groups and 276 comparison pairs; 271 out 276 comparison pairs with p < 0.05) for
this last dataset. With mitogenomes, the comparison pairs which were not signifi-
cant were MH1-sh3-NAS with a divergent specimen of N. olivacea from Chocó
(Colombia), and with MH1-NARI, MH2-NARI, MH1-OLI, and MH4-OLI, the
specimen of N. olivacea from Chocó with MH1-NARI, MH2-NARI, and MH4-
OLI, MH1-NARI with MH2-NARI, MH1-OLI, and MH4-NARI, and finally MH1-
OLI with MH4-NARI. Likely, as in Ruiz-García et al. (2020b) at the
three-mitochondrial genes dataset, some of the oldest haplotypes and the most
divergent within N. olivacea were not sufficiently differentiated from the oldest
haplotypes of N. narica, and the haplotypes of N. narica from southern Central
America that were introgressed by N. olivacea. The absence of significant differ-
ences between MH1-sh3-NAS and other haplogroups was due to the very small
sample size of that haplogroup for the mitogenome analysis (n = 2).
Table 6.3 FST pair statistics (below main diagonal; significance upper main diagonal) among 17
groups of coatis [7 groups of Nasua nasua (1 = MH1-sh1-NAS; 2 = MH1-sh2-NAS; 3 = MH2-
NAS; 4 = MH3-NAS; 5 = MH5-NAS; 6 = MH6-NAS; 8 = M7-NAS), 4 groups of Nasuella
olivacea (7 = one specimen of N. olivacea from Chocó Department associated to N. nasua;
14 = MH1-OLI; 15 = MH3-OLI, 17 = MH4-OLI), and 6 groups of Nasua narica (9 = MH1-NARI;
10 = MH2-NARI; 11 = MH3-sh1-NARI; 12 = MH3-sh2-NARI; 13 = MH3-sh3-NARI), and
16 = MH4-NARI] analyzed by means of mitogenomes. *P < 0.05, **P < 0.001
Coati
Taxa 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17
1 * ** ** ** ** * ** ** ** ** ** ** ** ** ** **
2 0.60 * * * * * * * * * *
3 0.56 0.40 ** ** ** * ** * * ** ** ** * ** * **
4 0.65 0.45 0.48 ** ** * ** * * ** ** ** ** ** ** **
5 0.88 0.83 0.83 0.76 ** * ** * ** ** ** ** ** ** * **
6 0.88 0.67 0.74 0.77 0.81 * ** * * ** ** ** * * * **
7 0.95 0.95 0.93 0.87 0.93 0.36 * * * * * *
8 0.90 0.82 0.83 0.82 0.85 0.59 0.78 * ** ** ** ** ** ** ** **
9 0.95 0.90 0.92 0.86 0.91 0.66 0.94 0.81 * * * * *
10 0.94 0.80 0.87 0.86 0.90 0.69 0.81 0.84 0.46 * * ** * **
11 0.96 0.96 0.95 0.92 0.94 0.83 0.96 0.89 0.80 0.73 ** ** * ** * **
12 0.95 0.93 0.93 0.89 0.92 0.79 0.93 0.87 0.60 0.63 0.74 ** * ** * **
13 0.96 0.96 0.95 0.93 0.94 0.87 0.96 0.90 0.78 0.72 0.71 0.62 ** ** ** **
14 0.96 0.89 0.92 0.89 0.93 0.73 0.88 0.86 0.86 0.80 0.94 0.91 0.94 * **
15 0.95 0.88 0.90 0.89 0.92 0.80 0.87 0.87 0.84 0.81 0.90 0.88 0.92 0.60 * **
16 0.96 0.93 0.94 0.91 0.94 0.79 0.95 0.88 0.91 0.82 0.95 0.93 0.96 0.71 0.47 **
17 0.94 0.90 0.91 0.90 0.92 0.85 0.89 0.89 0.88 0.86 0.90 0.89 0.96 0.69 0.56 0.56
3.3.4 Spatial Genetic Structure in N. olivacea
The Mantel’s test for the mitogenome dataset (Fig. 6.9) showed an overall signifi-
cant relationship between geographical and genetic distances for N. olivacea
(r = 0.457; p = 0.000099). This means that the geographic distance significantly
explained around 20.92% of the genetic distances. The Mantel’s test carried out at
the three-mitochondrial genes dataset carried out by Ruiz-García et al. (2020d) also
showed a significant relationship between distances (r = 0.371; p = 0.000099; geo-
graphic distance significantly explained around 13.79% of the genetic distances).
Therefore, both genetic datasets showed a significant and overall relationship
between geographic and genetic distances, although the mitogenome dataset yielded
a slightly greater relationship.
The spatial autocorrelation analysis with six DCs for the mitogenome dataset
showed an overall significant correlogram (V = 0.0117; p = 0.001) (Fig. 6.10). The
two first DCs had a significant positive autocorrelation (1 DC: 0–46 km,
p = 0.000001; 2 DC: 46–144 km, p = 0.0234). The three and four DCs did not show
evidence of a significant autocorrelation, meanwhile the five and six DCs yielded
significant negative autocorrelation (5 DC: 268–429 km, p = 0.0002; 6 DC:
Fig. 6.9 Mantel’s test applied at the mitogenomes of 40 specimens of Nasuella olivacea from 3
Latin American countries (Colombia, Ecuador, and Peru)
Fig. 6.10 Spatial autocorrelation analysis with 6 distance classes at the mitogenomess of 40 speci-
mens of Nasuella olivacea from 3 Latin American countries (Colombia, Ecuador, and Peru)
Fig. 6.11 Monmonier’s algorithm analysis to detect the 5 most important geographical barriers
for 40 Nasuella olivacea from Colombia, Ecuador, and Peru and sequenced at their mitogenomes
429–754 km, p = 0.0349). The overall correlogram showed a spatial monotonic

cline. Ruiz-García et al. (2020d) also detected a significant correlogram at the three-
mitochondrial genes dataset for N. olivacea. Thus, both spatial autocorrelation anal-
yses with both three genes and mitogenome datasets offered a significant spatial
structure for N. olivacea. Nevertheless, we detected regional patches (200 km) and
isolation by distance from 200 to 800 km with the three-mitochondrial genes data-
set. In contrast, we detected a monotonic cline more than patches and isolation by
distance at the mitogenome dataset.
The MMDA procedure for the mitogenome dataset for N. olivacea is shown in
Fig. 6.11. Five possible geographical barriers were analyzed. The first barrier (blue)
detected a geographical area including individuals from the Risaralda and Chocó
Departments (central and western Colombian Andean Cordilleras). The second bar-
rier (green) also determined a small geographic area in the Risaralda, Chocó, and
Cauca Departments (central and western Colombian Andean Cordilleras). The third
barrier (bluish green) displays the geographical area where we sampled the majority
of the specimens of the central Colombian Andean Cordillera in the southern area
of the group’s distribution. The fourth barrier (brown) marked the most northern
area of distribution in the central Colombian Andean Cordillera, whilst the fifth bar-
rier (lilac) represented the geographical area of the eastern Colombian Andean
Cordillera. The first, second, and five barriers agree well with the barriers detected
by Ruiz-García et al. (2020d) with the three-mitochondrial genes dataset.
4 Discussion
4.1 The Main Differences Between the Two Genetic Datasets

Analyzed for the Primates and Carnivores Studied
For the nucleotide substitution models, the use of the two molecular datasets for
C. albifrons, P. flavus, and the three species of coatis were somewhat contradictory.
For both C. albifrons and coatis, it doesn’t matter if a few mitochondrial genes are
used or the complete mitogenomes: the results are the same. However, in the case of
P. flavus, there were differences depending on the molecular dataset. Thus, some
differences should be evident in some taxa, although we believe that in many cases
the results should be similar and therefore it does not matter if a few mitochondrial
genes or complete mitogenomes are used.
In reference to the number of groups or clades detected for each taxon studied, it
is clear that in the three cases, the molecular dataset with fewer mitochondrial mark-
ers, but with larger sample sizes collected across wide geographical areas, detected
the highest number of different genetic groups or units. In the case of C. albifrons in
Ecuador, the 2-mitochondrial genes dataset detected 11 groups, including the 9
groups shown by Ruiz-García et al. (2018) with mitogenomes plus 2 small groups
in the Ecuadorian Amazon not detected with the mitogenome dataset. In the case of
P. flavus, the five-mitochondrial genes dataset (Ruiz-García et al. 2019a) discrimi-
nated eight groups or units in different regions of Latin America. With the mitoge-
nome dataset, these eight groups were detected but only in four main clades and
some of these groups were intermixed in some clades. Therefore, there was substan-
tially less discrimination in the mitogenome dataset than in the five-mitochondrial
genes dataset. In an identical sense, the three-mitochondrial genes dataset in the
coatis detected a higher number of groups or units than the mitogenome dataset. In
the first case, 19 main groups (10 for N. nasua, 4 for N. narica, and 5 for N. oliva-
cea) and 10 sub-groups (7 for N. nasua, and 3 for N. narica) were determined. For
the mitogenome dataset herein analyzed, 15 main groups (7 for N. nasua, 5 for
N. narica, and 3 for N. olivacea) and 8 sub-groups (5 for N. nasua, and 3 for N. nar-
ica) were recovered. Henceforth, for the first dataset, 29 genetic units were detected
and only 23 genetic units were recovered. Six genetic units were lost with the
mitogenomes due to reduced sample size and smaller geographical area analyzed.
For the spatial genetic analysis, for the three cases analyzed, the results were
insensitive to the use of either if the molecular datasets. For C. albifrons, there was
no spatial genetic structure in Ecuador. In contrast, for the kinkajou and for N. oli-
vacea (also for the two Nasua species, shown elsewhere) the spatial genetic struc-
ture in Latin America is quite robust. In other words, to detect spatial genetic
structure the molecular dataset used is irrelevant.
If we want to determine how many groups, MUs, ESUs or even subspecies
(Moritz, 1994) are within a species, it is strongly recommended to study large sam-
ple sizes with one or few mitochondrial genes than complete mitogenomes with
smaller sample sizes. For instance, with mitogenomes we have not detected the five
important haplogroups, some of which are crucial for the reconstruction of the ori-
gins of the coatis. Obviously better mitogenomes are needed, if we want to recover
the most precise phylogenetic, or phylogeographic, relationships among different
species. This is especially true if they are related but well differentiated. We also
need them in order to enhance the discrimination of internal structure in some
clades, or groups, (higher bootstrap percentages), but using similar sample sizes
with mitogenomes and with a few mitochondrial genes. Nevertheless, for two prac-
tical reasons, we recommend the use of one, or a few mitochondrial genes, but with
large sample sizes, trying to represent all of the geographical areas where the taxon
under study lives. These reasons were: (1) At least, with medium and large wild
mammals, samples are not easy to obtain and many times when samples are obtained
they could be of low quality to extract DNA, which makes it impossible to procure
entire mitogenomes for many of them. Thus, it is important not to waste these sam-
ples; and (2) It is much more economical to analyze one or a few mitochondrial
genes with large sample sizes than entire mitogenomes with a few specimens.
4.2 The Case of C. albifrons in Ecuador
The main difference in comparing the results of Ruiz-García et al. (2018) that used
mitogenomes of C. albifrons collected from Ecuador and the current analysis that
only used two mitochondrial genes (mtCOI-COII), but with a larger sample size,
was the detection of two additional haplogroups. They were not observed with the
mitogenomes. One was in the Pastaza province and other in Tiguino (Napo
Province), both in the Amazon area of this country. Apparently, the more geographi-
cally restricted haplogroups and/or the haplogroups with smaller sizes tend to go
unnoticed, although many genes should be sequenced. The conservation and phylo-
geograph of C. albifrons depends on a determination of the number of groups or
units. It is also essential to analyze the largest and broadest sample as possible
although the number of genes sequenced can be low.
In Ecuador, authors traditionally consider two taxa: C. a. aequatorialis in the
Pacific area of the trans-Andean (western) Ecuador and C. a. yuracus (C. c. cusci-
nus for Groves 2001, 2005) for the cis-Andean Amazonian (eastern) Ecuador. Some
authors regard these two taxa as full species (C. aequatorialis and C. yuracus;
Rylands and Mittermeier 2013). Boubli et al. (2012) found one unique haplogroup
(they named A) for the Ecuadorian Amazon and a large part of the Peruvian Amazon.
In Ecuador, they only sampled two specimens. However, we detected 11 different
haplogroups in the Ecuadorian Amazon living sympatrically in many areas when
we increased the sample size to 65 with many (54) from the Ecuadorian Amazon.
The genetic distances among the groups H4-H11 were small (1.9–3.7%),
although the groups H1-H3 showed higher genetic distances regarding the other
haplogroups (6–7%). The last genetic distances involved ancestral haplogroups of
the current C. albifrons and/or they were introgressed with robust capuchins
(C. apella). They are not different ESUs nor subspecies for C. albifrons in Ecuador
based on: (1) the relative small genetic distances among the majority of the hap-
logroups, (2) many of the haplogroups detected in the western area of Ecuador were
also in the eastern area of this country and vice versa, and (3) there were a limited
degree of differences with nuclear microsatellites among specimens of these hap-
logroups (Ruiz-García et al. unpublished). These haplogroups should theoretically
be MUs. Nevertheless, many of them are geographically overlapped. For instance,
within the Pastaza Province, we found seven haplogroups (H1, H4, H5, H7, H8, H9,
and H10) overlapped in many localities and even in different troops of C. albifrons.
Thus, it is impossible to distinguish in the field to which haplogroup, or theoretical
MUs, a given specimen belongs. C. albifrons aequatorialis is classified by IUCN as
critically endangered (Cornejo and De la Torre 2015), meanwhile C. albifrons yura-
cus is classified by IUCN as least concern, although Tirira (2011) classified it as
almost threatened for Ecuador. It is now clear that with only molecular genetics
results it is practically impossible to apply the concept of MUs for different popula-
tions of C. albifrons to create specific conservation plans for different populations
of this species within this South American country. Thus, from a molecular perspec-
tive, a unique conservation plan should be preferable. Maybe specific conservation
plans for certain local population could be created and carried out if the specimens
of these populations had some phenotypic characteristic trait or some dynamic
demographic pattern differentiated from the remaining populations.
4.3 The Case of P. flavus in Latin America
The results obtained both in Ruiz-García et al. (2019a) and here show the existence
of eight well differentiated groups of P. flavus. The genetic distances among them
are considerably large, with many of these values ranging from 8% to 16%. These
values are even higher that those estimated between well-established procyonid spe-
cies. For instance, the genetic distances determined with mitochondrial markers,
ranged from 6% to 7% between Bassaricyon gabbii, B. medius, and B. alleni, and
from 9.6% to 11.3% between B. neblina and other Bassaricyon species (Helgen
et al. 2013). Although we only have some nuclear microsatellite results for some of
these groups, these preliminary results significantly differentiated some of them in
the same way that mitochondrial results did. Henceforth, we can affirm that these
eight groups are clearly ESUs (the genetic differences obtained were considerably
greater than required for MUs), some of them agreeing quite well with established
morphological subspecies. Theoretically, these very elevated genetic distances
would indicate cryptic species within the kinkajous.
H1 from southern Mexico and northern Central America agrees with the putative
subspecies P. f. prehensilis. H2a agrees with the geographic holotype of the subspe-
cies P. f. modestus (Daule River, Guayas Province, Ecuador). This haplogroup is
expanded in southern Central America (at least Panama) and the trans-Andean Area
of Colombia and Ecuador. One interesting and noteworthy point is that in Ruiz-
García et al. (2019a), with the five-mitochondrial genes dataset, H1 clearly seemed
to be the first population and all remaining ones were derived. With some mitoge-
nome analyses, H1 also seems to be the original population, but some other analyses
indicated that H2a should be the original P. flavus population. H2b is distributed by
central and northern Colombia, and some specimen in the Casanare Department
(Colombia) near Venezuela. Currently, we don’t exactly know if these ESUs corre-
spond to any undescribed subspecies (if so, it should be tentatively named P. f.
antioquensis) or correspond to the Venezuelan subspecies, P. f. meridensis (type
locality: Merida State, Venezuela). H3 (from the Huila Department in central-south
Colombia) is well differentiated from other Colombian haplogroups. However, the
potential ESUs do not correspondent to any defined morphological subspecies.
Tentatively, we propose the name P. f. huilensis. H4 (central and southern Andean
Peru and southern Peruvian Amazon) was also well differentiated. Similar to other
ESUs, it does not correspond to any defined morphological subspecies. Tentatively,
we propose the name P. f. peruvensis. H5 (basically, the major part of Bolivia) is a
very congruent geographical ESU. P. f. chapadensis (type locality: Chapada dos
Guimaraes, Matto Grosso State, Brazil) is the geographically nearest putative sub-
species. However, we do not have sufficient results to establish if the Bolivian speci-
mens belong to this subspecies or if they are really a differentiated subspecies. If so,
we tentatively named it as P. f. boliviensis. H6 (Vichada Department, Colombia),
together the specimens analyzed by Nascimento et al. (2017) from Negro River in
Brazil (the named C5) make up another well characterized ESU with no connec-
tions with any defined morphological subspecies. Tentatively, it should be named
P. f. vichadensis. H7 (Colombian, Ecuadorian, and northern Peruvian Amazon) is a
very well defined ESUs. Wozencraft (2005) and Kays (2009) designated P. f. cha-
padensis as the subspecies with a distribution across the totality of the Amazon.
However, if P. f. chapadensis has connections with the Bolivian ESUs, then, the
Colombian, Ecuadorian, and northern Peruvian Amazon P. flavus population should
be named as P. f. amazonensis. Nascimento et al. (2017) found another two hap-
logroups in Brazil. One of them was the haplogroup C5b. It is located in the Atlantic
side of Brazil and it supports the geographical holotype of the subspecies, P. f. noc-
turnus (type locality: Sao Miguel dos Campos, Alagoas State, Brazil). The other
haplogroup, C2, extends to the Guiana Shield region, and includes areas in south-
eastern Venezuela, Guyana, Surinam, French Guiana, and the Brazilian states of
Amazonas, Roraima, and Amapá (Holowell and Reynolds 2005). P. f. flavus (type
locality: Surinam) corresponds to this ESU.
Therefore, the current work, together with the works of Nascimento et al. (2017)
and Ruiz-García et al. (2019a), showed the existence, at least, of ten well differenti-
ated ESUs and subspecies (or even cryptic species) for P. flavus in Latin America.
This means that, at least, ten conservation plans should be developed for the
kinkajous.
4.4 The Case of the Coatis, Nasua and Nasuella

in Latin America
One outstanding difference to using the three-mitochondrial genes dataset and the
mitogenome dataset for coatis was that for the first dataset, N. narica was more
related to N. olivacea than to N. nasua, whilst, in the current study, N. nasua and
N. narica were more related to each other than to N. olivacea. This information has
great significance for the systematics of the coatis.
In the case of the coatis, the mitogenome dataset had a considerable sample size.
This probably explains why the advantages we observed for C. albifrons and in
P. flavus regarding a small mitochondrial genes dataset over a mitogenome dataset
were not so obvious. For the coatis, the three-mitochondrial genes dataset showed
the following interesting features which were not observed with mitogenomes: (1)
The mitogenome dataset did not recover three important haplogroups of N. nasua,
and two important haplogroups of N. olivacea. Some of these haplogroups, which
were not recovered with mitogenomes, were transcendental in the reconstruction of
the origins of the current coatis. (2) Very likely, the real geographical extension of
some significant groups is more detectable with a three-mitochondrial genes dataset
than with the mitogenome dataset. Some examples are as follows: (a) MH3-NAS
did not recover specimens that were expanded by the trans-Andean and Pacific
Ecuador, but these same specimens were detected by H3-NAS with the three-
mitochondrial genes dataset; (b) MH4-NAS only included the specimen of Robinson
Crusoe Island (Chile). This dataset showed that mitogenomes detected that this
specimen was not a N. narica, such as it was traditionally thought, but a N. nasua.
However, this same dataset was not able to determine the geographical origin of the
last specimen. In contrast, the three-mitochondrial genes dataset (Ruiz-García et al.
2020b) also identified this specimen as N. nasua, but it identified its geographical
origin as well as what kind of relationship maintained this specimen with other
specimens of its own haplogroup (H7-NAS; Ruiz-García et al. 2020b); (c) The
mitogenome dataset did not include the specimen of N. nasua from Goias State in
Brazil (MH5-NAS) and therefore this analysis did not detect that this haplogroup of
N. nasua from southern South America expanded to northern areas of Brazil. In
contrast, the three-mitochondrial genes dataset showed this specimen, although
showing certain genetic differences from the specimens from southern Brazil
(Parana State), Paraguay, and Uruguay, clearly related to them (H4-NAS in Ruiz-
García et al. 2020b); (d) Mitogenomes detected N. nasua in the central area of the
Antioquia Department (MH6-NAS). However, with the three-mitochondrial genes
dataset, this haplogroup expanded up to the frontier of Panama (H6-NAS; Ruiz-
García et al. 2020b); (e) With mitogenomes, MH1-OLI (N. olivacea) was exclu-
sively centered in southern Andean Colombia and northern Andean Ecuador.
However, the three-mitochondrial genes dataset detected that H1-OLI (Ruiz-García
et al., 2020b) was expanded throughout the entire Colombian Andes as well as a
large fraction of the Ecuadorian Andes; (f) With mitogenomes, MH4-OLI was
exclusively placed in the Eastern Colombian Andean Cordillera. However, the
three-mitochondrial genes dataset (H4-OLI; Ruiz-García et al. 2020b) showed that

specimens of this haplogroup were also expanded outside this area (in at least one
locality of the Central Colombian Andean Cordillera as well as in the Sangay NP in
Ecuador); (g) With mitogenomes, MH1-NARI recovered the presence of the old
haplotypes of N. narica in the trans-Andean and Pacific area of Ecuador.
Nevertheless, as a specimen of Fatimas (Ecuadorian Amazon) was not included (but
included in Ruiz-García et al. 2020b for the three-mitochondrial genes dataset),
mitogenomes did not detect that this ancestral haplogroup of N. narica in South
America expanded from the trans-Andean Pacific Ecuadorian area into the Amazon
area of this country.
However, some important details were detected with the mitogenome dataset,
but not with the three-mitochondrial genes dataset: (1) As Jaramillo et al. (2020)
showed using different phylogenetic procedures and different sets of out-groups, the
mitogenome dataset offered more stable phylogenies than those obtained with the
three-mitochondrial genes dataset; (2) The percentages of bootstrap were usually
much higher for the main clades with mitogenomes than with the three-mitochondrial
genes dataset, which is important for determining “real” taxa; (3) When the number
of specimens were similar for some groups, mitogenomes tended to detect finer
internal structure. Some examples are as follows: (a) The three-mitochondrial genes
dataset did not do a good job of differentiating sub-haplogroups in H10-NAS (two
possible haplogroups were detected, although bootstrap percentages were low),
whilst mitogenomes clearly distinguished differentiated sub-haplogroups (with ele-
vated percentages of bootstraps) inside MH7-NAS; (b) Mitogenomes did show
more heterogeneity within MH1-OLI than detected by the three-mitochondrial
genes dataset; (c) Mitogenomes helped to show the strongest evidence of an exem-
plar of N. olivacea in Peru (Alba, Urubamba River, Cuzco Department). Other spec-
imens detected in Peru and Bolivia, which should belong to N. olivacea or some
form of N. nasua, adapted to live in high altitudes (with convergent morphotypes
with N. olivacea), were unnoticed with mitogenomes but detected with the three-
mitochondrial genes dataset (H5-OLI; Ruiz-García et al. 2020b); (d) Mitogenomes
discriminated better within sub-haplogroups of MH3-NARI than in the case of the
three-mitochondrial genes dataset (H3-NARI; Ruiz-García et al. 2020b); (4)
Mitogenomes detected one divergent haplotype of N. nasua in Costa Rica (MH0-
NARI), which was not detected with the three-mitochondrial genes dataset and
which could have important consequences in the origin of N. narica.
Thus, when the sample size for mitogenomes increases, some traits begin to
appear that are not revealed by other datasets with only a few mitochondrial genes.
Similar to what we observed for P. flavus, the different haplogroups detected for
Nasua and Nasuella showed elevated genetic distances. For instance, some com-
parisons among different haplogroups of N. nasua had genetic differentiation of
approximately 8–12%, which is on the border of different species. Additionally, in
a preliminary analysis with nuclear microsatellites, some of the mitochondrial hap-
logroups were analyzed and the differences were significant. Therefore, the main
haplogroups detected in the three coati species should be considered, at least, ESUs.
The sub-haplogroups detected in some main haplogroups should be considered, at

least, MUs.
Now, we review which relationship could exist between these detected ESUs and
the morphological putative subspecies considered in N. nasua and in N. narica.
For N. nasua, traditionally ten geographical and morphological subspecies have
been considered (Gompper and Decker, 1998). For the ESUs found for N. nasua,
only a small fraction agrees well with the traditional morphological subspecies.
Two cases seem to be in absolute agreement. These were the cases of MH5-NAS
with N. nasua spadicea (type locality: Paraguay) and MH1-sh1-NAS with N. nasua
boliviensis (type locality: Chaparé, Cochabamba, Bolivia). The possible remaining
agreement among ESUs of N. nasua and traditional subspecies is more complex
and, even, dubious. Two additional morphological subspecies agree with ESUs
although our data is not as clear as in the two previous cases. For the three-mito-
chondrial genes dataset, one specimen of Goias (Brazil) that we analyzed was the
most divergent within H4-NAS. Probably, if we could have analyzed more speci-
mens from this Brazilian area (or relatively neighbor zones), we could have detected
a new haplogroup or sub-haplogroup which could agree with N. nasua nasua (type
locality: Pernanbuco, Brazil). Tsuchiya-Jerep (2009) detected five haplogroups
(four in Brazil), one of them in the central Brazilian Atlantic forest, which probably
corresponded to N. nasua solitaria (type locality: Bahia, Brazil).
In Colombia, N. n. candace (type locality: Medellín, Antioquia, Colombia) and
N. n. judex (type locality: Bogotá, Cundinamarca, Colombia) have been defined.
However, they are considered synonyms (Gompper and Decker 1998). Thus, for
these authors only a subspecies is present in Colombia (N. n. candace). Our mitoge-
nome results showed that, at least, two different ESUs of N. nasua were present at
this country (MH6-NAS, and MH7-NAS), whereas the three-mitochondrial genes
dataset identified, at least, six ESUs in this country: H1-NAS (Amazon Department),
H3-NAS (Amazon Department), H6-NAS (Colombian Andes), H8-NAS (Amazon
and Colombian Eastern Llanos), H9-NAS (Risaralda, Chocó, and Valle del Cauca
Department, and Colombian Eastern Llanos), and H10-NAS (Antioquia,
Cundinamarca, Valle del Cauca, and Colombian Eastern Llanos). This indicates—
as the molecular results showed—a more complex reality than that described by the
putative morphological subspecies. In fact, there was no connection between the
two morphological subspecies and the six ESUs detected. From a conservation
point of view, this also introduces a technical complication because many of these
haplogroups were geographically overlapped. For instance, we only found three
ESUs in the Colombian Eastern Llanos.
A similar situation occurred in Peru with only two subspecies defined, N. n. mon-
tana (type locality: Umanpuqio, Ceja Region, Peru) in the Andes and N. n. dorsalis
(type locality: Peru and Ecuador) in the Amazon. With the mitogenome dataset, we
detected four ESUs (one of these ESUs probably including two MUs), meanwhile
with the three-mitochondrial genes dataset we detected six ESUs: H1-NAS with
three potential MUs [the first in southern Peru (Madre de Dios River basin; this is
the ESU which corresponded to N. nasua boliviensis), the second in northern and
southern Peruvian Amazon, and the third also in northern and southern Peruvian
Amazon], H2-NAS (northern and southern Peruvian Amazon and Peruvian Andes
in Cuzco, Pasco, and San Martín Departments), H3-NAS (northern and southern
Peruvian Amazon and Peruvian Andes in Apurimac, Cuzco, and San Martín
Departments), H5-NAS (northern Peruvian Amazon), H7-NAS (Apurimac
Department), and H10-NAS (northern Peruvian Amazon). There were even haplo-
types of transition of N. nasua to N. olivacea in the Peruvian Andes, which further
complicates the situation. For instance, only in the northern Peruvian Amazon, did
four ESUs of this species converge and all of them overlap geographically. This
introduces considerable complications in using traditional systematic nomenclature
as well as for relying on them for conservation purposes and for delimitating geo-
graphical conservation plans for each one of these potential ESUs.
The case of Ecuador is even more complex. Three morphological subspecies
have been defined for Ecuador: N. n. manium (type locality: Balzar, Guayaquil,
Ecuador), N. n. quichua (type locality: Jima, Azuay Province, Ecuador), and the
cited N. n. dorsalis. With the mitogenome dataset, two potential ESUs were detected;
however, with the three-mitochondrial genes dataset, at least, seven ESUs were
found. They were H3-NAS (Guayas, Manabi Provinces), H5-NAS (Santo Domingo
de Tsáchilas Province), H6-NAS (Imbabura, Pichincha, and Esmeraldas Provinces),
H7-NAS (Carchi, Manabi, Pichincha Provinces), H8-NAS (Esmeraldas Province),
H9-NAS (Esmeraldas Province), and H10-NAS (Guayas, Pichincha, Santo Domingo
de Tsáchilas). Three different ESU were detected in specimens from the trans-
Andean Ecuadorian Province of Esmeraldas.
Thus, of the ten morphological subspecies defined for N. nasua, only four could
be related to the molecular ESUs detected with the three-mitochondrial genes data-
set. Two were clear examples and there was some evidence for the other two,
although only minor. Nevertheless, the other six subspecies had no clear connec-
tion with the remaining ESUs. Therefore, the number of ESUs and MUs were
considerably greater that the number of proposed subspecies. The kinkajou and the
N. nasua cases were similar in one aspect. ESUs, subspecies, or even cryptic spe-
cies were characterized by large genetic distances among these genetic units, but
they were substantially different in other aspects. In the case of the kinkajous, the
ESUs were placed in given geographical areas which did not generally overlap.
Therefore, it was relatively easy to see the correspondence between these ESUs
and the morphological subspecies proposed. When an ESU was detected in an area
where no subspecies was previously proposed, it was also easy to create a subspe-
cies nomenclature for that ESU. The case of N. nasua was considerably more com-
plex because there were many more ESUs and MUs than morphological subspecies
and many of these units geographically overlapped. This made it impossible to
distinguish specimens in the field of a determined locality to belong to determine
ESUs or MUs (should be necessary in a molecular probe). It was also impossible
to determine which of the sympatric ESUs corresponded to the morphological sub-
species defined for a particular area (only the sequencing of the holotypes could
solve the problem).
Finally, we analyzed the taxonomy of N. narica and the ESUs and MUs found
for this species. Traditionally, four morphological subspecies of N. narica have
been described (Gompper 1995): N. narica molaris (type locality: Manzanillo,

Colima State, northern Pacific Mexico), N. narica yucatanica (type locality:
Chichen-Itza, Yucatan, Mexico), N. narica nelsoni (type locality: Cozumel Island,
Mexico), and N. narica narica (type locality: Isthmus of Tehuantepec, Veracruz
State, Caribbean Mexico). The first subspecies was not represented in our samples.
Thus, we cannot make any taxonomical inference between the haplogroups, or
ESUs, detected and this morphological subspecies. With the mitogenome dataset
(very similar results were detected with the three-mitochondrial genes dataset), five
haplogroups were found. In this case, the genetic distances were considerably lower
than those obtained among many haplogroups of N. nasua. The values ranged from
1.6% to 4.5%, typical of different populations or incipient subspecies. This agrees
quite well with the fact that N. narica is considerably younger than N. nasua. This
also correlates with the evolution of the current coatis and its presence first in South
America and then in Central America. The conclusion is antithesis to the traditional
paleontological vision that coatis migrated from North America to South America at
the beginning of the Pleistocene. Additionally, no nuclear DNA results were
obtained for our haplogroups of N. narica. Thus, it is considerably less clear that
these haplogroups were ESUs or subspecies like in the cases of P. flavus and
N. nasua. We consider that these groups make better MUs. We detected two or three
specimens (depending on the analyses) that formed MH2-NARI from the Yucatan
Peninsula (Mexico). This group agrees quite well with the second subspecies men-
tioned and it was the most differentiated haplogroups of N. narica detected with the
exception of MH4-NARI (from southern Costa Rica, Panama, and northern
Colombia introgressed with mtDNA of N. olivacea). Very likely, the Yucatan group
is more of an ESU more than a MU because it crossed a bottleneck or a strong
founder effect or it represents a different coati migration wave to Central America.
Aforementioned, at Cozumel Island, there is a third morphological subspecies. We
analyzed one specimen from this island and it was not differentiated from the major
part of the coatis from southern Mexico and part of Guatemala (MH3-sh3-NARI).
This sub-haplogroup of MH3-NARI, together with two others (MH3-sh1-NARI,
part of Guatemala, Honduras, El Salvador, Nicaragua, and northern-central Costa
Rica and MH3-sh2-NARI, in different part of Guatemala, and Belize) corresponded
to the fourth subspecies of N. narica traditionally considered. All of these groups
should be considered as MUs. The situation of the quoted MH4-NARI is complex
because its mtDNA is from an introgression with N. olivacea. However, we don’t
know about its nuclear DNA. Thus, until this haplogroup is comparatively studied
with other groups of N. narica using nuclear DNA, we cannot determine if it is an
ESU or a subspecies. Finally, two other haplogroups were detected in this species.
One, MH0-NARI from Costa Rica, consisted of one unique individual. Its haplo-
type is one of the original ones that gave origin to the remaining haplotypes found
in N. narica. The second, MH1-NARI, from Ecuador, is an extremely interesting
group because it contained the oldest haplotypes found for this species. It demon-
strates that the origin of N. narica was in South-America, although the major part of
the distribution of this species is in Central America. We don’t exactly know how to
classify MH0-NARI and MH1-NARI, but the second haplogroup should be an ESU
by its geographical situation.
In conclusion, this work showed that the most important condition in determin-
ing the exact number of ESUs or MUs to develop correct conservation plans for
many species is the exhaustive sampling including as many specimens possible as
well as including the wide geographical area where these species inhabit. This is
more important than the number of mitochondrial genes sequenced (two or three
mitochondrial genes should be enough). In the case of C. albifrons in Ecuador, we
determined a considerable number of different lineages which could agree with
MUs, but in many areas of Ecuador these MUs were mixed and geographically
overlapped. Thus, it is practically impossible to carry out differentiated conserva-
tion plans for this species in that country. Then, a unique flexible conservation plan
could be preferable. In the case, of P. flavus, the genetic differentiation among the
haplogroups detected was very high and they were situated in discrete geographical
areas without overlapping in the major number of cases. Therefore, the determina-
tion of ESUs and different conservation plans is relatively easy to carry out for this
species. In the case of the coatis, for N. nasua and N. olivacea (for this species see
Ruiz-García et al. 2020d), the genetic differentiation among the haplogroups
detected is also very high and numerous ESUs could be defined. However, many of
them converged in the same sympatric geographical areas. This could make it
extremely challenging to create specific conservation plans for each ESU detected.
For N. narica, due to its more recent origin, the detection of MUs or ESUs, and the
creation of specific conservation plains, seems to be easier than for the other two
coati species. Nevertheless, more specimens and areas of Central America and
northern South America are in need of sampling and analysis. Ideally, studies of this
nature will be extended to the many additional Latin American species that suffer
from seizure or hunting.
Acknowledgments Thanks to Dr. Diana Alvarez, Pablo Escobar-Armel, Nicolás Lichilín, Luisa
Fernanda Castellanos-Mora, Dr. Clara Saldamando, Armando Castellanos, and Jorge Brito for
their respective help during the last 20 years. This work was financed by the Project 6839 (Pontificia
Universidad Javeriana). Thanks to the Ministerio del Ambiente Ecuatoriano (MAE) in Santo
Domingo de Tsáchilas and in Coca, to the Instituto von Humboldt (Colombia), to the Peruvian
Ministry of Environment, PRODUCE (Dirección Nacional de Extracción y Procesamiento
Pesquero), Consejo Nacional del Ambiente and the Instituto Nacional de Recursos Naturales
(INRENA) from Peru, to the Colección Boliviana de Fauna (Dr. Julieta Vargas), and to CITES
Bolivia for their role in facilitating the obtainment of the collection permits in Ecuador, Colombia,
Peru and Bolivia. The first author also thanks the many people of diverse Indian tribes in Ecuador
(Kichwa, Huaorani, Shuar and Achuar), in Colombia (Jaguas, Ticunas, Huitoto, Cocama, Tucano,
Nonuya, Yuri and Yucuna), in Peru (Bora, Ocaina, Shipigo-Comibo, Capanahua, Angoteros,
Orejón, Cocama, Kishuarana and Alamas), in Bolivia (Sirionó, Canichana, Cayubaba and
Chacobo) for their assistance in obtaining samples of C. albifrons, P. flavus, N. nasua, and N. oli-
vacea in South America, and multiple colonos and peasants in Andean areas of Colombia, Ecuador,
Peru, and Bolivia, and multiple Mayan communities and peasants from Honduras, El Salvador,
Belize, Guatemala, and southern Mexico for their assistance in obtaining samples of P. flavus and
N. narica in Central America.
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Chapter 6

Effects of Sample Size in the Determination

Manuel Ruiz-García, María Fernanda Jaramillo, Sebastián Sánchez-Castillo,

The identification and conservation of local differentiated genetic populations is of

© Springer Nature Switzerland AG 2021 101

2 Materials and Methods

2.1 Sampling Strategy

Table 6.1 (continued)

Table 6.1 (continued)

Table 6.1 (continued)

Table 6.1 (continued)

(Colombia and Ecuador), 5 Bassarycion medius (Colombia and Ecuador), and 14

2.2 Laboratory Procedures

2.3 Phylogenetic Analyses

2.4 Genetic Heterogeneity

2.5 Spatial Genetic Structure

For C. albifrons in Ecuador, we employed SAMOVA 1.0 (Dupanloup et al. 2002)

3.1 The Case of C. albifrons in Ecuador

3.1.2 Phylogenetic Analysis with the mtCOI and COII Database

3.1.3 Spatial Genetic Structure in the Ecuadorian C. albifrons

Table 6.2 SAMOVA for the % variance % variance within

Monmonier’s algorithm revealed six detectable geographical areas with genetic

3.2 The Case of P. flavus in Latin America

3.2.1 Nucleotide Substitution Model in P. flavus

3.2.2 Phylogenetic Analysis with the Mitogenome Dataset from P. flavus

3.2.3 Spatial Genetic Structure in P. flavus

3.3 The Case of the Coatis, Nasua and Nasuella

For mitogenomes, the best nucleotide substitution models were TN93 + G + I

3.3.2 Phylogenetic Analysis with the Mitogenome Dataset in Nasua

The first haplogroup (MH1-NAS; 97% bootstrap support) contained 3 sub-

Fig. 6.8 Maximum-

Fig. 6.8 (continued)

The second haplogroup (MH1-NARI; 99%) contained two specimens of the

Risaralda, Tolima, Chocó Departments) and Ecuadorian (Pichincha, and Cotopaxi

3.3.3 Genetic Heterogeneity Between Haplogroups of Coatis

3.3.4 Spatial Genetic Structure in N. olivacea

429–754 km, p = 0.0349). The overall correlogram showed a spatial monotonic

4.1 The Main Differences Between the Two Genetic Datasets

4.2 The Case of C. albifrons in Ecuador

4.3 The Case of P. flavus in Latin America

4.4 The Case of the Coatis, Nasua and Nasuella

three-mitochondrial genes dataset (H4-OLI; Ruiz-García et al. 2020b) showed that

The sub-haplogroups detected in some main haplogroups should be considered, at

been described (Gompper 1995): N. narica molaris (type locality: Manzanillo,

Emmons LH (1990) Carnivores (Procyonidae). In: Hickock-Emmons L (ed) Neotropical rainforest

Ruiz-García M, Escobar-Armel P, Leguizamón N et al (2014b) Genetic characterization and

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