Showing papers in "Molecular Phylogenetics and Evolution in 2015"

TL;DR: Reconstruct Ancestral State in Phylogenies (RASP), a user-friendly software package for inferring historical biogeography through reconstructing ancestral geographic distributions on phylogenetic trees and generates high-quality exportable graphical results.

TL;DR: This robust phylogeny of turtle phylogeny shows that proposed phylogenetic names correspond to well-supported clades, and this topology is more consistent with the temporal appearance of clades and paleobiogeography.

TL;DR: The hexaploid African Labeobarbus & allies and Western Asian Capoeta are likely derived from two independent hybridization events between their respective maternal tetraploid ancestors and Cyprinion.

TL;DR: The data offer support for the riverine hypothesis and for a Plio-Pleistocene time of origin for Amazonian drainage system and show that Rio Branco was an important geographical barrier, limiting the distribution of six primate genera: Cacajao, Callicebus, Cebus to the west and Pithecia, Saguinus, Sapajus to the east.

TL;DR: Most of the transoceanic distribution patterns in Myrtaceae have occurred since the Miocene due to LDDE, whereas inferred vicariance events all occurred before the Late Eocene.

TL;DR: This evolutionary history is most consistent with a Young Amazon Flooded Forest Taxa model, suggesting Saimiri has always maintained a lowland wetlands niche and was able to greatly expand its range with the transition from a lacustrine to a riverine system in Amazonia.

TL;DR: The characterization of arthropod TRP channels revealed that Daphnia pulex and insects have specifically expanded the TRPA subfamily, which diverged from the ancient TRPA1 channel gene.

TL;DR: It is suggested that current implementations of tip dating may overestimate ages of divergence in calibrated phylogenies, and the precision of clade age estimates using tip dating increases with the number of fossils analyzed and with the proximity of fossil taxa to the node under assessment.

TL;DR: Future studies should prioritize the alpha taxonomy of most Neotropical primate groups, and the use of phylogenetic and geographic data, combined with reliable estimates of divergence times, to clarify the taxonomic status at species and genus level, as well as to help understand the evolutionary history of this remarkable and highly diversified group.

TL;DR: Results of the analysis, which included type- and non-type species for every valid genus in Hypostominae, support the reevaluation and restriction of several historically problematic genera, including Baryancistrus, Cordylancistsrus, Hemiancistrus and Peckoltia.

TL;DR: This work assembled multi-gene matrices of chloroplast, mitochondrial, and nuclear sequences, as well as large single- and multi-copy nuclear gene data sets, to elucidate the position of the Celastrales-Oxalidales-Malpighiales clade within Rosidae and emphasize the importance of genomic data sets for revealing deep incongruence and complex patterns of evolution.

TL;DR: A new heuristic-hierarchical Bayesian approach is described and used to construct a species-level phylogeny for all extant and late Quaternary extinct mammals; species with large quantities of genetic data are placed nearly freely in the mammalian phylogeny according to these data, whereas the placement of species with lower quantities of data is performed with steadily stricter restrictions for decreasing data quantities.

TL;DR: The results indicate that the amount of sequence data currently available is sufficient to produce a robust estimate of the avian tree of life using current methods of inference, and the availability of a tree that is unconstrained by prior information should be useful for comparative methods, taxonomic revisions, and prioritizing taxa that should be targeted for additional data collection.

TL;DR: The outline of a universal TE classification is proposed, a set of methods and classification rules that could be used by all scientific communities involved in the study of TEs are proposed, and a 5-year schedule for the establishment of an International Committee for Taxonomy of Transposable Elements (ICTTE) is proposed.

TL;DR: Phylogenetic relationships inferred by different tree reconstruction methods were largely congruent and showed a general agreement between concatenated tree topologies, Yet, local conflicts in phylogenetic signals evidenced a number of critical sectors in the phylogeny of Dacini fruit flies.

TL;DR: It is demonstrated that genes with minimal phylogenetic information can produce unreliable gene trees, which may in turn reduce the accuracy of species tree estimation using gene-tree-based coalescent methods, which can be alleviated by sampling more genes.

TL;DR: It is probable that the crown platyrrhine clade did not originate before about 20-24 Ma, a conclusion consistent with the phylogenetic analysis of fossil taxa presented here and with recent molecular clock estimates.

TL;DR: The monophyly of Amoebozoa is unequivocally established, showing a primary dichotomy between the previously contested subphyla Lobosa and Conosa, and phylogenetic features are entirely congruent with the most recent major amoEBozoan classification.

TL;DR: Targeted sequence capture of multiple loci in conjunction with both concatenated and Bayesian concordance analyses are used to reevaluate the phylogeny of allopolyploid cotton species and provide robust support for the Gossypium polyploid clade.

TL;DR: It is suggested that wood-feeding, and the resultant need to conserve nitrogen, may have been an important factor in the development of termite eusociality.

TL;DR: A time-calibrated multi-locus phylogeny from GenBank data and the callitrichid literature for 38 taxa is constructed and shows support for a 9 million year old split between a small-bodied group and large- bodied group of tamarins.

TL;DR: In this article, the authors presented a new tribal level phylogenetic hypothesis for the cichlid fishes of Lake Tanganyika that is based on the so far largest set of nuclear markers and a total alignment length of close to 18kb.

TL;DR: Genome-wide RAD-Seq data confirm the pattern of one-way introgressive hybridization among TEP Pocillopora, suggesting that introgression may play a role in generating shared, polyphyletic lineages among currently recognized Pocillipora species.

TL;DR: It is suggested that even if many traditional diversification hypotheses remain untestable, investigations using genomic datasets will provide greater resolution of species histories in the Neotropics and elsewhere.

TL;DR: Evidence is found for a significant increase in diversification rate at the basal phylogenetic node for the genus Falco, and the timing for this rate shift correlates generally with expansion of C4 grasslands beginning around the Miocene/Pliocene transition.

TL;DR: This study highlights the utility of target enrichment using multiple accessions to resolve relationships in recently radiated taxa and suggests an Appalachian massif biogeographic origin of the genus Sarracenia.

TL;DR: A molecular phylogenetic study based on a comprehensive taxon sampling of 259 flea taxa, suggesting that Theria (placental mammals and marsupials) represent the most likely ancestral host group of extant Siphonaptera, with marsupial occupying a more important role than previously assumed.

TL;DR: It is suggested that most primates currently inhabiting drier open habitats are relatively recent arrivals, having expanded from rainforest habitats in the Pleistocene.

TL;DR: Results from biogeographic analyses and divergence time estimation suggested an origin and early diversification of Abies in an area of high latitude around the Pacific during the Eocene and an 'out-of-America' migration, for the origin of an eastern Asian and western North American disjunct species pairs in section Amabilis.

TL;DR: It is hypothesize that the origin of European brambles can be attributed to both Holocene species range expansion and Pleistocene climate fluctuations, and revealed an extreme reticulation in bramble evolution.