Reconstruction Of Evolutionary Relationships Research Articles

Phylogenomics

The reconstruction of evolutionary relationships among species is fundamental for our understanding of biodiversity. Today, evolutionary relationships are closely related with the depiction of the tree of life, and research on the topic is underpinned by methods in molecular phylogenetics that have grown in popularity since the 1960s. These methods depend on our understanding of how nucleotide or amino acid sequences evolve through time and in different lineages. Armed with this knowledge, researchers can make inferences about the relationships and amount of genomic divergence among species.

Differentiation of the endemic Greek genus Hymenonema and its relatives of subtribe Scolyminae (Compositae, Cichorieae) based on a multilocus species tree reconstruction

Hymenonema (Compositae, tribe Cichorieae) together with the genera Catananche, Gundelia, and Scolymus forms the subtribe Scolyminae. It is endemic to Greece and consists of two species, Hymenonema laconicum and Hymenonema graecum, which occur in the south Peloponnisos and central Aegean area, respectively. The present contribution aims at a phylogenetic reconstruction of evolutionary relationships among the 12 species of the subtribe, focusing on the temporal and spatial framework for its evolution. The phylogenetic relationships among the members of Scolyminae were inferred from molecular data based on the multi-copy region of the nrDNA internal transcribed spacers ITS1 and ITS2, two intergenic spacers of the cpDNA (trnL-trnF, rpl32-trnL), and one single-copy nuclear region (D10). The gene trees were reconstructed using Bayesian phylogenetic methods. All gene trees support the monophyly of Hymenonema and the sister-group relationship with the genus Scolymus. The further sister-group relationship of this group (Hymenonema–Scolymus) with Catananche is also supported by nrDNA and cpDNA analyses. Finally, a species tree (inferred in a Bayesian coalescent framework) was reconstructed and dates the divergence time between the two Hymenonema species to the Pleistocene (around 1.3 Ma ago). Maximum likelihood-based biogeographical reconstructions suggest a Miocene (pre-Messinian) differentiation of the subtribe on the northern Tethyan platform, followed by Miocene/Pliocene dispersal events to the western Mediterranean and North-African platforms and final, small-scale vicariance events within the genera in the Pleistocene.

A taxonomic framework for emerging groups of ecologically important marine gammaproteobacteria based on the reconstruction of evolutionary relationships using genome-scale data.

In recent years a large number of isolates were obtained from saline environments that are phylogenetically related to distinct clades of oligotrophic marine gammaproteobacteria, which were originally identified in seawater samples using cultivation independent methods and are characterized by high seasonal abundances in coastal environments. To date a sound taxonomic framework for the classification of these ecologically important isolates and related species in accordance with their evolutionary relationships is missing. In this study we demonstrate that a reliable allocation of members of the oligotrophic marine gammaproteobacteria (OMG) group and related species to higher taxonomic ranks is possible by phylogenetic analyses of whole proteomes but also of the RNA polymerase beta subunit, whereas phylogenetic reconstructions based on 16S rRNA genes alone resulted in unstable tree topologies with only insignificant bootstrap support. The identified clades could be correlated with distinct phenotypic traits illustrating an adaptation to common environmental factors in their evolutionary history. Genome wide gene-content analyses revealed the existence of two distinct ecological guilds within the analyzed lineage of marine gammaproteobacteria which can be distinguished by their trophic strategies. Based on our results a novel order within the class Gammaproteobacteria is proposed, which is designated Cellvibrionales ord. nov. and comprises the five novel families Cellvibrionaceae fam. nov., Halieaceae fam. nov., Microbulbiferaceae fam. nov., Porticoccaceae fam. nov., and Spongiibacteraceae fam. nov.

Primates

Primates

Adaptive memory programming: local search parallel algorithms for phylogenetic tree construction

One of the most important aspect of molecular and computational biology is the reconstruction of evolutionary relationships. The area is well explored after decades of intensive research. Despite this fact there remains a need for good and efficient algorithms that are capable of reconstructing the evolutionary relationship in reasonable time. Since the problem is computationally intractable, exact algorithms are used only for small groups of species. In the Maximum Parsimony approach the time of computation grows so fast when number of sequences increases, that in practice it is possible to find the optimal solution for instances containing about 20 sequences only. It is this reason that in practical applications, heuristic methods are used. In this paper, parallel adaptive memory programming algorithms based on Maximum Parsimony and some known neighborhood search methods for phylogenetic tree construction are proposed, and the results of computational experiments are presented. The proposed algorithms achieve a superlinear speedup and find solutions of good quality.

Phylogeny, Introgression, and Character Evolution of Diploid Species in <I>Mentzelia</I> Section <I>Trachyphytum</I> (Loasaceae)

Abstract Mentzelia section Trachyphytum (Loasaceae) has 25–30 species found primarily in the western United States. Species delimitation and reconstruction of evolutionary relationships within Trachyphytum have been difficult due to restricted and continuous morphological variation. We employed phylogeny reconstructions based on morphology and DNA sequences from the plastid trnH-psbA, trnS-trnG, trnS-trnfM, ndhF-rp132, and rp132-trnL regions and the low-copy nuclear gene idh to investigate evolutionary relationships and patterns of hybridization and homoplasy among diploid species in Trachyphytum. Reconstructions indicated surprisingly high levels of genetic introgression among closely and distantly related diploids. Additionally, reconstructions based on molecular data showed that some morphological characters traditionally used to delineate groups exhibit homoplasy. However, both molecular- and morphologically-based reconstructions supported two major clades in section Trachyphytum. In agreement with pr...

Forest monkeys and Pleistocene refugia: a phylogeographic window onto the disjunct distribution of theChlorocebus lhoestispecies group

The reconstruction of evolutionary relationships among a group of closely-related taxa provides a valuable window onto their biogeographic history. This is the first such molecular phylogenetic study to survey all three taxa of the Chlorocebus lhoesti species group, a group of Old World monkeys that includes C. lhoesti, Chlorocebus preussi, and Chlorocebus solatus. Representatives of each species were surveyed for two Y-chromosomal genes, TSPY (∼2240 bp) and SRY (∼780 bp), and one X-chromosomal intergenic region (∼9300 bp) homologous to a portion of human Xq13.3. Maximum likelihood topologies inferred from these sequences confirm that the lhoesti group is monophyletic within the tribe Cercopithecini, as suggested by earlier karyotype studies. Within this group, C. lhoesti (Albertine region) and C. preussi (Cameroon, Nigeria, Bioko) cluster to the exclusion of C. solatus (Gabon). This phylogeographic pattern, evaluated in the context of Pleistocene glacial cycles and lhoesti group ecology, suggests: (1) the common ancestor of the group probably arose in west central Africa, (2) dispersal to the Albertine region is likely to have occurred during a glacial maximum, rather than an interglacial pluvial, and (3) this dispersal probably occurred via a path north of the Congo Basin. Divergence date calculations suggest C. solatus separated from the ancestral stock at ∼2.1 Ma, whereas C. preussi and C. lhoesti bifurcated later, at ∼0.5 Ma. Taken together, these evolutionary analyses draw attention to one period in the Pleistocene (∼0.5 MYA) when a dispersal corridor suitable to montane taxa is likely to have connected the highlands of east central and west central Africa. © 2008 The Linnean Society of London, Zoological Journal of the Linnean Society, 2008, 154, 408–418.

Building Large Phylogenetic Trees on Coarse-Grained Parallel Machines

Phylogenetic analysis is an area of computational biology concerned with the reconstruction of evolutionary relationships between organisms, genes, and gene families. Maximum likelihood evaluation has proven to be one of the most reliable methods for constructing phylogenetic trees. The huge computational requirements associated with maximum likelihood analysis means that it is not feasible to produce large phylogenetic trees using a single processor. We have completed a fully cross platform coarse-grained distributed application, DPRml, which overcomes many of the limitations imposed by the current set of parallel phylogenetic programs. We have completed a set of efficiency tests that show how to maximise efficiency while using the program to build large phylogenetic trees. The software is publicly available under the terms of the GNU general public licence from the system webpage at http://www.cs.nuim.ie/distributed.

Skelton P, Smith A. 2002. Accompanying booklet written by Monks N. Cladistics: a practical primer on CD-ROM

Skelton P, Smith A. 2002. Accompanying booklet written by Monks N. Cladistics: a practical primer on CD-ROM