As stated in the Law of Homologous series in variation, Vavilov (1922) suggested that the

similarities between species within a taxon are due to their homologous factors. Through decades of

research, numerous studies dwelled on similarities and differences across taxa. In the study of Paterson

et al., (2000), they linked plant genomes belonging to the same family using comparative genomics.

From then on, numerous investigative studies also suggested that in most plants, the evolution of

essential portions of the genome has proceeded slowly thus recognizable intragenic DNA sequences

were retained in taxa that have been reproductively isolated for a long period of time (Paterson et al.,

2000). As such, a common set of orthologous genes that links the species within families have been

easily detected since then. (Fulton et al., 2002). Together with the basis of phylogenetic analyses, which

offers the means of estimating evolutionary relationships (Choudhuri,2014) we can further understand

the relationship of the genomes of species within families. That’s why in this activity we hope to show

the phylogenetic relationship of the atpB gene sequences of the selected gymnosperm and angiosperm

species. The resulting phylogenetic tree is shown in Fig_

Fig._
 The resulting tree produced 2 major groups or clades, the first clade contains the gymnosperm

species only while the second clade contains all the angiosperm species, the remaining of the

gymnosperm species, and the outgroups.

In the first clade which contains gymnosperms species, it can be observed that these species

belong to cycads, pines, and ginkgo. Zamia furfuracea, Encephalartos lehmannii, and Cycas

segmentifida can be seen to group together with a bootstrap value of 100. This coincides with their

taxonomic classification as they belong to order Cycadales. Ginko biloba can be observed in this tree to

be closely related to the cycads species. In taxonomic classification, Gingko and cycads are said to be

sisters (WFO, 2021) and in some analyses, they form a clade that has a sister relationship to other

gymnosperm clades (Soltis and Soltis, 2003) The remaining gymnosperm species in this clade are Pinus

thunbergia, Picea asperata, Juniperus communis. Pinus thunbergia and Picea asperata can be observed

to group together with a bootstrap value of 100. This coincides with their taxonomic classification as

they both belong to the family Pinaceae (WFO, 2021). The Juniperus communis species belong to the

taxonomic order Cupressales (WFO, 2021) so that must be the reason why it is separated on its own.

As mentioned above, the second clade contains the angiosperm species, some gymnosperm

species, and the outgroup species. The gymnosperm and outgroup species formed a subclade or

subgroup while the angiosperms formed a separate one. In the first subgroup, gymnosperm species and

outgroups species from respective groups. The gymnosperm group contains the Ephedra californica,

Gnetum luofuense, and Gnetum gnemon species. In the taxonomic classification, they belong to the

order Gnetales while the outgroups species belong to the taxonomic classification Divisions Bryophyta

and Polypodiophyta respectively. Generally, based on taxonomy and nomenclature, Gymnosperm seems

distant to earth moss and ferns. But there are phylogenetic analyses that argue that some gymnosperm

taxa are close relative to ferns. In the study of Pryer et al., (2001), they performed phylogenetic analysis

using DNA sequences of selected species from monophyletic lineages of land plants. Their result shows
that horsetails and ferns form a monophyletic group with Pinales and Gnetales species. In the second

subgroup, the angiosperm species are divided further into two subgroups, the first one consists mostly

of angiosperm species under taxonomic class Liliopsida, and the second contains all angiosperm species

that belong to the taxonomic class Magnoliopsida. The Liliopsida sub subgroup, contains Zea mays,

Oryza sativa, Cocos nucifera, and Phoenix dactylifera. Zea mays and Oryza sativa are both under the

taxonomic family Poales (WFO, 2021). It is also shown in the phylogeny tree that despite Phoenix

dactylifera belonging to the taxonomic class Magnoliopsida, it still grouped with the Liliopsida species.

Both Cocos nucifera and Phoenix dactylifera belong to the taxonomic class Arecaceles commonly known

as palm trees (WFO, 2021). Their relatedness is reflected in this phylogeny tree Fig. which is also most

likely the reason for the inclusion of Phoenix dactylifera in this sub subgroup. The Magnoliopsida

subgroup contains Brassica oleracea var. italica, Brassica rapa, Solanum melongena, Solanum

lycopersicum, Helianthus annuus, and Dahlia pinnata species. The species Brassica oleracea var. italica,

Brassica rapa paired together with a boostrap value 100 which coincides with their taxonomic

classification order Brassicales (WFO, 2021). The species Solanum melongena and Solanum

lycopersicum paired together with a boostrap value 100 which coincides with their taxonomic

classification family Solanales (WFO, 2021). The species Helianthus annuus and Dahlia pinnata paired

together also with a bootstrap value 100 which also coincides with their taxonomic classification family

Asterales (WFO, 2021). It can also be observed that the Solanaceae species pair and Asteraceae species

pair grouped. This aligns with the APG IV classification system where Solanales species and Asterales

species family belongs to the Asterid group or clade of flowering plants, whereas the Brassicales species

belongs to the Rosid group of flowering plants (The Angiosperm Phylogeny Group et al., 2016).
Literature Cited

Choudhuri, S. (2014). Chapter 9 - Phylogenetic Analysis Bioinformatics for Beginners (bll 209–218).
doi:10.1016/B978-0-12-410471-6.00009-8

Finet, C., Timme, R. E., Delwiche, C. F., & Marlétaz, F. (2010). Multigene phylogeny of the green lineage
reveals the origin and diversification of land plants. Current Biology, 20(24), 2217-2222.

Fulton, T. M., Van der Hoeven, R., Eannetta, N. T., & Tanksley, S. D. (2002). Identification, analysis, and
utilization of conserved ortholog set markers for comparative genomics in higher plants. The
Plant cell, 14(7), 1457–1467. https://doi.org/10.1105/tpc.010479

Paterson, A. H., Bowers, J. E., Burow, M. D., Draye, X., Elsik, C. G., Jiang, C. X., Katsar, C. S., Lan, T. H., Lin,
Y. R., Ming, R., & Wright, R. J. (2000). Comparative genomics of plant chromosomes. The Plant
cell, 12(9), 1523–1540. https://doi.org/10.1105/tpc.12.9.1523

Pryer, K. M., Schneider, H., Smith, A. R., Cranfill, R., Wolf, P. G., Hunt, J. S., & Sipes, S. D. (2001).
Horsetails and ferns are a monophyletic group and the closest living relatives to seed
plants. Nature, 409(6820), 618-622.

The Angiosperm Phylogeny Group, Chase, M. W., Christenhusz, M. J. M., Fay, M. F., Byng, J. W., Judd, W.
S., … Stevens, P. F. (2016). An update of the Angiosperm Phylogeny Group classification for the
orders and families of flowering plants: APG IV. Botanical Journal of the Linnean Society, 181(1),
1–20. doi:10.1111/boj.12385

WFO (2021): World Flora Online. Published on the Internet; http://www.worldfloraonline.org. Accessed
on: 03 Nov 2021'