Background

Climate changes along with anthropogenic activities are forcing species to move from their
original range to track suitable habitat conditions and these repeated movements leave traces
on the genetic composition of populations and ultimately shapes their adaptive potential to
face climate changes.

One of the most striking impacts is the shift of species distribution, which will vary according to
the species. For instance, if the species are well adapted to cold environments, as boreal
species, they will tend to retract their distribution, however, temperate species, adapted to
warmer climates, will be favoured and will expand their distribution eventually replace other
populations.

Those range replacements when occurring between closely related species that can still
hybridize may enhance hybridization and consequently, gene exchanges between the
interacting species.

This gene flow on the one hand , might pollute the gene pool of both species by introgressive
hybridization but on the other hand, may promote rapid adaption to the new conditions by
introducing new genetic diversity.

Main goals

By using genome-wide single nucleotide polymorphism data, we aim to :

i) Describe the patterns of genetic diversity and genetic structure on two replicates (Sweden
and Scotland) of an ongoing range replacement;

ii) Characterize the patterns of hybridization during the range replacements of species with
contrasting demographic trends;

iii) Describe the patterns of genetic diversity, genetic structure and hybridization of historical
populations (using specimens from Natural History Museums collected before 1940) and
compare with contemporaneous populations;

iv) Describe the demographic history of hybridizing species with opposing demographic trends
and make predictions of future demographic trends under current scenarios of climate change.

Model study

As a model study we will investigate the genetic interactions between the mountain hare,
Lepus timidus, and the European brown hare, Lepus europaeus.

The mountain hare is a boreal-artic species, well adapted to cold environments and high
altitudes and currently, it is distributed in northern Europe and Asia, however, its distribution
has been retracting because of climate changes.

On the other hand, the brown hare is a temperate species that occur in the majority of Europe
and is expanding its distribution to higher latitudes, invading the range occupied by the
mountain hare.

The research will focus on Scotland and Sweden, two contacts areas where an invasion-
retraction dynamics between the species has been described.
Sampling and genetic data collection

My research group already collected contemporary tissue samples from both species, but the
historical samples will be collected later from Natural History Museums.

The sampling covers contact regions (containing individuals thar are currently hybridizing) and
allopatric regions, referring to population without recent contact with the opposing species
that will serve as parental populations.

The genomic DNA will be sequenced by double-digest restriction site-associated sequencing

(ddRAD-seq).

Population structure and Genetic diversity

i) Describe the patterns of genetic diversity and genetic structure on two replicates (Sweden
and Scotland) of an ongoing range replacement;

To achieve this goal,

To evaluate the population structure , we will perform PCAs and run the software Amixture.

Then, standard measures of genetic diversity (deviations for HWE,…) will be calculated within
Lepus species first including all parental populations and after populations from contact
regions.

We will be able to: understand whether the populations are fragmented (structured)

characterize the current population dynamics.

Levels and patterns of genetic admixture

The inspection of levels and patterns of genetic admixture will be performed with populations
from contact regions.

The results from Admixture from the previous task will firstly provide a broader idea regarding
the existence of introgression

The evaluate whether the gene flow occurs between mountain hare and brown hare and
inspect the direction of the gene flow, specific methodologies of Radseq will be used, such as
D-statistic and partitioned D-statistic test

Those analysis will allow evaluate possible hybridization gradients resulting from latitudinal
range replacement along the contact region and identify which species were more affected by
introgression.

Temporal changes of introgression patterns

The gene flow over time between brown hares and mountain hares will be assessed through
analysis of distinct historical collections from the 19th century and compared to our more
recent samples (posterior to 1980).

To do so, we will perform targeted enrichment capture on both types of datasets, by using
probes to capture random SNPs along the genome. Then we will perform the same analysis
that I talked before, including population structure, genetic diversity and detection of
admixture.

Results will allow to infer whether the patterns and levels of hybridization and introgression
remained the same during the last century of climate change. In the case of dissimilarity, the
goal it to understand if it was changes presumably resulting from range replacement caused by
the climate change or only stochastic

Modelling population dynamics and predictions

The presumed history of interaction between the mountain hares and brown hares will be
modelled using spatially explicit simulators (SPLATCH 3, Slim3 and fastsimcoal2) and an
Approximate Bayesian Computation (ABC) framework.

Then, the demographic scenario will be built in accordance with the information about species
distribution (including spatial factors- latitude and longitude), migration rates, bioclimatic
factors and interactions among populations

(Its calibration will be performed using ecological niche modelling from previous works.)

Then, the resulting demographic model will be used to inform the ecological niche models to
predict future demographic trends using current scenarios of future climate change.

Expected results

 In addition, a spatial explicit genetic gradient across the population is expected, with
levels of admixture increasing from the origin of invasion to northern regions, since
introgression typically occurs in hybridization zones at species boundaries.
 Regarding the temporal changes,….
 Concerning the future predictions, is expected that the mountain hares and brown
hares will exhibit a narrower and wider distribution, respectively, resulting from the
loss of suitable habitat caused by climate changes.
o On the other hand, the distributions might remain unaltered, which might be
an evidence that mountain hares gained some beneficial genetic variants from
introgression that allowed them to respond to climatic changes.
IJUP
Climate changes along with anthropogenic activities are forcing species to move from
their original range to track suitable habitat conditions and these repeated movements
leave traces on the genetic composition of populations and ultimately shapes their
adaptive potential to face climate changes.
One of the most relevant impacts is the shift of species distribution, which might result
in a range retraction of vulnerable species or in distribution expansion of favoured
ones, eventually replacing other populations.
Those range replacements when occurring between closely related species that can
still hybridize may enhance hybridization and consequently, gene exchanges between
the interacting species.
Introgression may introduce maladaptive variation and be another source of
aggression but may also add adaptive variation and promote adaptation to new
conditions.
Model Study
As a model study we will investigate the genetic interactions between the mountain hare,
Lepus timidus, and the European brown hare, Lepus europaeus.

The mountain hare is a boreal-artic species, well adapted to cold environments and high
altitudes and currently, it is distributed in northern Europe and Asia, however, its distribution
has been retracting because of climate changes.

On the other hand, the brown hare is a temperate species that occur in the majority of Europe
and is expanding its distribution to higher latitudes, invading the range occupied by the
mountain hare.

Focal regions

The research will focus on Scotland and Sweden, two contacts areas where an invasion-
retraction dynamics between the species has been described.

The presence of the brown hare in Sweden was the result of an introduction in the South of
Sweden in the 20th century and it has been invading the range of the mountain hare towards
north since then.

In Scotland, the range replacement has been slower, and it is a result of the expansion of
agriculture and land use.

Dataset

For that, Double-digestion RAD sequencing was performed on 360 samples, resulting in about
11938 single nucleotide variants.

Main goals

Quantify the demographic trends and genetic exchanges between species in the two
focal areas (Sweden and Scotland).
Regarding the genetic diversity, is expected lower levels of genetic diversity in the retracting
species than in the expanding one.

Higher levels of population structure in the retracting species and lower population structure
on expanding species unless there is allele surfing (when a species expands there is an
amplification of the variants that are in front of the expansion; therefore, I can have different
variants in different areas that will then predominate in the areas later colonized, leading to a
structuring).

Introgressão: In this case of range replacement with hybridization, empirical theoretical work
has shown that higher rates of introgression towards the invasive species are expected.

Dataset

To address the issues in these two models, we performed double-digestion RAD sequencing
among 360 samples mainly distributed in Scotland and Sweden and collected about 12
thousand SNPs.

Genetic diversity

We started by estimating the heterozigoty and the inbreeding coefficient across populations,
within each species. From the results it is possible to see that the mountain hare present
higher levels of diversity, when compared to the brown hare. Regarding the inbreeding
coefficient, it is worth noting that the populations from Scotland present higher levels of
inbreeding that Sweden

Scotland

I will start by contrasting the patterns that we obtained for each species in Scotland in terms of
population structure.

We started by performing principal component analysis which decomposes the diversity of

each individual considering their genotypes over the thousands of snps into coordinates that
explain its variance , with each individual being a point.

The admixture performs an assignment of the genetic composition of each individual (each
fine line) of the sampled populations and seeks to infer the best population structure
according to a predetermined number of populations (K).

• The Scottish population of L. europaeus appears to be fragmented on the PCAs but the
plot from admixture (best k=1) shows no genetic structure within the population.

• The Scottish population of L. timidus, on the other hand, is divided in two main
clusters showing narrow fragmentation, which is corroborated by the plot from
admixture (best k=2), displaying the existence of two genetically different clusters.

EEMS

These are the results of the Estimating Effective Migration Surfaces which a spatially
visualizing based on degrees of genetic similarity. In here, the blue means that the effective
migration between populations are above average, which means more genetic similarity and
the brown refers to an effective migration bellow average, which means less genetic
similarity.
Regarding Lepus europaeus, in the left, it is possible to say that there is evidence of greater
population fragmentation north of the European distribution, which might correspond to the
expansion front. On the right, for Lepus timidus, it is possible to see a thick barrier on the
centre of Scoland, referring to the populations with greater fragmentation.

Sweden

The Swedish population of L. europaeus appears to be fragmented on the PCAs but the plot
from admixture (best k=1) shows no genetic structure within the population.

Regarding the Swedish population of L.timidus, on the right, both analysis suggest that there is
no genetic structuring

EEMS

Regarding Sweden, the plot on the left, referring to Lepus europaeus, suggests that the
existence of a barrier on the west side and a passsageway along the Swedish coast where the
populations might move more easily, thus contacting more frequently with each other. No
sufficient data for Lepus timidus.

ABBA-BABA

The evaluate whether the gene flow occurs between mountain hare and brown hare, we
performed ABBA-BABA tests.

Introgression

Then, we also performed PCAs and admixture in order to inspect whether this evidence of
introgression refers to early generation hybrids and what is the proportion of the genome of
each individual that has evidence of introgression

Está tudo no ppt.

Early conclusions

Esta no ppt

As you can see some of the results do not match predictions, particularly in the case of
Scotland, which might me related with the slower range replacement

Na suecia, invasão mais rapida, mais pronunciada,

Enquanto que na eescócia tenho evidência de introgressão nas duas direções

Next steps

Understand whether patterns of diversity, structure and introgression have varied between
the past and the present, by using and comparing historical and contemporary samples.

Explore the demographic properties that gave rise to the observed rates of diversity and
introgression and make predictions under predictive scenarios of future climate changes to
forecast future demographic trends on both species in Scotland and Sweden.