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Molecular Phylogenetics and Evolution

Susan Geda, Nathan K Lujan, Michael Perkins, Erin Abernethy, Mark H Sabaj, Michael Gangloff
Dreissenidae is one of the most economically and ecologically important families of freshwater and estuarine mollusks. Fourteen extant species and three genera are currently recognized: Congeria contains three species from karst caves along the eastern Adriatic coast and one from the Orinoco River of Venezuela, Dreissena contains six species native to Eastern European rivers and estuaries, and Mytilopsis contains three species from the Gulf of Mexico, Caribbean, and northwestern coast of South America and one from the Tocantins River of Brazil...
July 14, 2018: Molecular Phylogenetics and Evolution
Erin A Tripp, Yongbin Zhuang, Matthew Schreiber, Heather Stone, Andrea E Berardi
Flavonoids are important secondary metabolites that play an integral role in protecting plants against UV radiation and other forms of environmental stress. Given widespread impacts of environmental effects associated with latitude on a multitude of biological systems and a well-documented increase in solar radiation towards the equator, plant flavonoid production is expected to increase as a response to factors associated with decreasing latitude. Using data from a Neotropical genus (Ruellia) that spans an exceptionally broad latitudinal gradient, we tested a hypothesis of a positive latitudinal gradient in flavonoid concentration and assessed other factors that influence flavonoid production including habitat type (xeric vs...
July 11, 2018: Molecular Phylogenetics and Evolution
R Terry Chesser, Haley Vaseghi, Peter A Hosner, Laura M Bergner, M Nandadevi Cortes-Rodriguez, Andreanna J Welch, Charles T Collins
Phylogenetic relationships among swifts of the morphologically conservative genus Chaetura were studied using mitochondrial and nuclear DNA sequences. Taxon sampling included all species and 21 of 30 taxa (species and subspecies) within Chaetura. Our results indicate that Chaetura is monophyletic and support the division of the genus into the two subgenera previously identified using plumage characters. However, our genetic data, when considered in combination with phenotypic data, appear to be at odds with the current classification of some species of Chaetura...
July 11, 2018: Molecular Phylogenetics and Evolution
Morten Stokkan, José A Jurado-Rivera, Oromí Pedro, Carlos Juan, Damià Jaume, Joan Pons
The amphi-Atlantic distributions exhibited by many thalassoid stygobiont (obligate subterranean) crustaceans have been explained by fragmentation by plate tectonics of ancestral shallow water marine populations. The amphipod stygobiont genus Pseudoniphargus is distributed across the Mediterranean region but also in the North Atlantic archipelagos of Bermuda, Azores, Madeira and the Canaries. We used species delimitation methods and mitogenome phylogenetic analyses to clarify the species diversity and evolutionary relationships within the genus and timing their diversification...
July 9, 2018: Molecular Phylogenetics and Evolution
Habib Ali, Abrar Muhammad, Nafiu Sanda Bala, Guihua Wang, Zhiming Chen, Zhengqiang Peng, Youming Hou
Wolbachia pipientis is a diverse, ubiquitous and most prevalent intracellular bacterial group of alpha-Proteobacteria that is concerned with many biological processes in arthropods. The coconut hispine beetle (CHB), Brontispa longissima (Gestro) is an economically important pest of palm cultivation worldwide. In the present study, we comprehensively surveyed the Wolbachia-infection prevalence and mitochondrial DNA (mtDNA) polymorphism in CHB from five different geographical locations, including China's Mainland and Taiwan, Vietnam, Thailand, Malaysia and Indonesia...
July 5, 2018: Molecular Phylogenetics and Evolution
Xinping Qi, Li-Yaung Kuo, Chunce Guo, Hao Li, Zhongyang Li, Ji Qi, Linbo Wang, Yi Hu, Jianying Xiang, Caifei Zhang, Jing Guo, Chien-Hsun Huang, Hong Ma
Ferns account for 80% of nonflowering vascular plant species and are the sister lineage of seed plants. Recent molecular phylogenetics have greatly advanced understanding of fern tree of life, but relationships among some major lineages remain unclear. To better resolve the phylogenetic relationships of ferns, we generated transcriptomes from 125 ferns and two lycophytes, with three additional public datasets, to represent all 11 orders and 85% of families of ferns. Our nuclear phylogeny provides strong supports for the monophyly of all four subclasses and nearly all orders and families, and for relationships among these lineages...
July 5, 2018: Molecular Phylogenetics and Evolution
Wen-Qing Ye, Zhao-Yan Yap, Pan Li, Hans Peter Comes, Ying-Xiong Qiu
Species of Podophylloideae (Berberidaceae, Ranunculales) are of great pharmacogenetic importance and represent the classic biogeographic disjunction between eastern Asia (EA; 10 ssp.) and eastern North America (ENA; 2 ssp.). However, previous molecular studies of this group suffered from low phylogenetic resolution and/or insufficient marker variability. This study is the first to report whole-plastome sequence data for all 12 species of Podophylloideae (14 individuals) and a close relative, Achlys triphylla...
July 4, 2018: Molecular Phylogenetics and Evolution
Aline C Martins, Thuane Bochorny, Oscar A Pérez-Escobar, Guillaume Chomicki, Silvana H N Monteiro, Eric de Camargo Smidt
The colonization of the epiphytic niche of Neotropical forest canopies played an important role in orchid's extraordinary diversification, with rare reversions to the terrestrial habit. To understand the evolutionary context of those reversals, we investigated the diversification of Galeandra, a Neotropical orchid genus which includes epiphytic and terrestrial species. We hypothesized that reversion to the terrestrial habit accompanied the expansion of savannas. To test this hypothesis we generated a comprehensive time-calibrated phylogeny and employed comparative methods...
June 30, 2018: Molecular Phylogenetics and Evolution
Dominic Evangelista, France Thouzé, Manpreet Kaur Kohli, Philippe Lopez, Frédéric Legendre
Assessing support for molecular phylogenies is difficult because the data is heterogeneous in quality and overwhelming in quantity. Traditionally, node support values (bootstrap frequency, Bayesian posterior probability) are used to assess confidence in tree topologies. Other analyses to assess the quality of phylogenetic data (e.g. Lento plots, saturation plots, trait consistency) and the resulting phylogenetic trees (e.g. internode certainty, parameter permutation tests, topological tests) exist but are rarely applied...
June 30, 2018: Molecular Phylogenetics and Evolution
Hannah M Wood, Vanessa L González, Michael Lloyd, Jonathan Coddington, Nikolaj Scharff
Historical museum specimens are invaluable for morphological and taxonomic research, but typically the DNA is degraded making traditional sequencing techniques difficult to impossible for many specimens. Recent advances in Next-Generation Sequencing, specifically target capture, makes use of short fragment sizes typical of degraded DNA, opening up the possibilities for gathering genomic data from museum specimens. This study uses museum specimens and recent target capture sequencing techniques to sequence both Ultra-Conserved Elements (UCE) and exonic regions for lineages that span the modern spiders, Araneomorphae, with a focus on Palpimanoidea...
June 29, 2018: Molecular Phylogenetics and Evolution
Juan E Uribe, Rafael Zardoya, Nicolas Puillandre
With more than 5,000 species, Conoidea is one of the most diversified superfamilies of Gastropoda. Recently, the family-level classification of these venomous predator snails has undergone substantial changes, on the basis of a phylogenetic tree reconstructed combining partial mitochondrial and nuclear gene sequences, and up to 16 families are now recognized. However, phylogenetic relationships among these families remain largely unresolved. Here, we sequenced 20 complete or nearly complete mitochondrial (mt) genomes, which were combined with mt genomes available in GenBank to construct a dataset that included representatives of 80% of the known families, although for some we had only one species or genus as representative...
June 27, 2018: Molecular Phylogenetics and Evolution
Jacob B Landis, Charles D Bell, Margarita Hernandez, Rosana Zenil-Ferguson, Elizabeth W McCarthy, Douglas E Soltis, Pamela S Soltis
Pollinator-mediated selection is a major driver of evolution in flowering plants, contributing to the vast diversity of floral features. Despite long-standing interest in floral variation and the evolution of pollination syndromes in Polemoniaceae, the evolution of floral traits and known pollinators has not been investigated in an explicit phylogenetic context. Here we explore macroevolutionary patterns of both pollinator specificity and three floral traits long considered important determinants of pollinator attraction across a nearly complete species-level phylogenetic tree for the family...
June 26, 2018: Molecular Phylogenetics and Evolution
Aziz-Ul-Rahman, Muhammad Munir, Muhammad Zubair Shabbir
Avian avulaviruses (avulaviruses or AAvVs) infect a wide range of avian species worldwide with variable clinical outcomes and economic impacts. Owing to broad host spectrum, several novel avulaviruses are being reported from both wild and domesticate birds that highlight the potential of the virus to evolve, adapt and emerge in susceptible population. Pathobiological and phylogenetic characterizations of individual avulaviruses are often demonstrated, however, a cumulative and comparative assessment of avulaviruses remains elusive...
June 26, 2018: Molecular Phylogenetics and Evolution
M Laura Ruiz-Vega, Giovani Hernández-Canchola, Livia León-Paniagua
Osgoodomys banderanus is a recognized and endemic rodent species of western Mexico, an area known for its high biodiversity and number of endemisms. Phylogeographical relationships within this taxon were analyzed based on mitochondrial (ND3, tRNA-Arginine, ND4L and partial ND4) and nuclear (GHR) nucleotide sequences. We obtained a total of 112 samples from 22 localities, covering the complete distribution of the species. Phylogenetic analyses using Maximum Likelihood and Bayesian inference confirmed that Osgoodomys is a monophyletic group...
June 26, 2018: Molecular Phylogenetics and Evolution
Diego Javier Zea, Alexander Miguel Monzon, Gustavo Parisi, Cristina Marino-Buslje
The analysis of evolutionary information in a protein family, such as conservation and covariation, is often linked to its structural information. Multiple sequence alignments of distant homologous sequences are used to measure evolutive variables. Although high structural differences between proteins can be expected in such divergent alignments, most works linking evolutionary and structural information use a single structure ignoring the structural variability inside a protein family. The goal of this work is to elucidate the relevance of structural divergence when sequence-based measures are integrated with structural information...
June 25, 2018: Molecular Phylogenetics and Evolution
James J Shelley, Stephen E Swearer, Mark Adams, Tim Dempster, Matthew C Le Feuvre, Michael P Hammer, Peter J Unmack
The prevalence of unrecognised cryptic species impairs biodiversity estimates, clouds biological research and hinders conservation planning. As the rate of cryptic species detection increases globally, research is needed to determine how frequent cryptic species are, whether they are more common in given management regions, and whether these patterns are consistent across taxonomic groups. The Kimberley region in remote northwestern Australia harbours some of the most speciose, and morphologically and functionally diverse, endemic animal and plant communities on the continent...
June 25, 2018: Molecular Phylogenetics and Evolution
Catriona Munro, Stefan Siebert, Felipe Zapata, Mark Howison, Alejandro Damian Serrano, Samuel H Church, Freya E Goetz, Philip R Pugh, Steven H D Haddock, Casey W Dunn
Siphonophores are a diverse group of hydrozoans (Cnidaria) that are found at most depths of the ocean - from the surface, like the familiar Portuguese man of war, to the deep sea. They play important roles in ocean ecosystems, and are among the most abundant gelatinous predators. A previous phylogenetic study based on two ribosomal RNA genes provided insight into the internal relationships between major siphonophore groups. There was, however, little support for many deep relationships within the clade Codonophora...
June 22, 2018: Molecular Phylogenetics and Evolution
Roger S Thorpe, Axel Barlow, Yann Surget-Groba, Anita Malhotra
Lesser Antillean anoles provide classic examples of island radiations. A detailed knowledge of their phylogeny and biogeography, in particular how the age of species relate to the ages of their respective islands and the age of their radiation, is essential to elucidate the tempo and mechanisms of these radiations. We conduct a large-scale phylogenetic and phylogeographic investigation of the Lesser Antillean anoles using multiple genetic markers and comprehensive geographic sampling of most species. The multilocus phylogeny gives the first well-supported reconstruction of the interspecific relationships, and the densely sampled phylogeography reveals a highly dynamic system, driven by overseas dispersal, with several alternative post-dispersal colonisation trajectories...
June 21, 2018: Molecular Phylogenetics and Evolution
Zahra Nemati, Frank R Blattner, Helmut Kerndorff, Osman Erol, Dörte Harpke
Phylogenetic relationships among the taxa of Crocus series Crocus are still unclear, preventing the understanding of species diversity and the evolution of the important spice saffron (Crocus sativus). Therefore, we analyzed sequences of two chloroplast (trnL-trnF, matK-trnK) and three nuclear (TOPO6, ribosomal DNA ETS and ITS) marker regions to infer phylogenetic relationships among all species belonging to series Crocus. Our phylogenetic analyses resolved the relationships among all taxa of the series. Crocus hadriaticus and the former C...
June 21, 2018: Molecular Phylogenetics and Evolution
Bruno F Melo, Brian L Sidlauskas, Kendra Hoekzema, Richard P Vari, Casey B Dillman, Claudio Oliveira
Curimatidae, the fourth largest family of detritivorous Neotropical characiform fishes, encompasses eight extant genera and over 110 species dwelling in diverse freshwater habitats from Costa Rica to Argentina. Extensive phylogenetic analyses of soft anatomy and osteology provided evidence for intergeneric and most interspecific relationships, and formed the basis of curimatid taxonomy for nearly 40 years. However, that morphological phylogeny demonstrated incomplete phylogenetic resolution at various scales and has never been tested with extensive molecular data...
June 20, 2018: Molecular Phylogenetics and Evolution
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