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Molecular Phylogenetics and Evolution

Katriina L Ilves, Dax Torti, Hernán López-Fernández
The phenotypic, geographic, and species diversity of cichlid fishes have made them a group of great interest for studying evolutionary processes. Here we present a targeted-exon next-generation sequencing approach for investigating the evolutionary relationships of cichlid fishes (Cichlidae), with focus on the Neotropical subfamily Cichlinae using a set of 923 primarily single-copy exons designed through mining of the Nile tilapia (Oreochromis niloticus) genome. Sequence capture and assembly were robust, leading to a complete dataset of 415 exons for 139 species (147 terminals) that consisted of 128 Neotropical species, six African taxa, and five Indo-Malagasy cichlids...
October 12, 2017: Molecular Phylogenetics and Evolution
Daniel F Mokodongan, Javier Montenegro, Koji Mochida, Shingo Fujimoto, Asano Ishikawa, Ryo Kakioka, Lengxob Yong, Mulis, Renny K Hadiaty, Ixchel F Mandagi, Kawilarang W A Masengi, Nakatada Wachi, Yasuyuki Hashiguchi, Jun Kitano, Kazunori Yamahira
The Oryzias woworae species group, composed of O. asinua, O. wolasi, and O. woworae, is widely distributed in southeastern Sulawesi, an island in the Indo-Australian Archipelago. Deep-elongated body shape divergence is evident among these three species to the extent that it is used as a species-diagnostic character. These fishes inhabit a variety of habitats, ranging from upper streams to ponds, suggesting that the body shape divergence among the three species may reflect adaptation to local environments. First, our geometric morphometrics among eight local populations of this species group revealed that the three species cannot be separated by body shape and that riverine populations had more elongated bodies and longer caudal parts than lacustrine populations...
October 9, 2017: Molecular Phylogenetics and Evolution
Clark A Danderson, Stephen R Downie, Michael Hermann
The Arracacia clade (Apiaceae, Apioideae) is a heterogeneous assemblage of 12 genera, comprising 111 known species distributed in high montane temperate and sub-alpine habitats of meso- and South America. Previous studies have indicated that the genera Arracacia, Coulterophytum, and Prionosciadium are polyphyletic, but for the most part relationships among the members of the clade are largely unknown. Initially, cladistic analyses of nrDNA ITS sequences were carried out on 212 accessions (122 taxa), representing 92 species of the Arracacia clade and outgroups from the closely-related páramo genera Cotopaxia, Niphogeton, and Perissocoeleum and members of the Perennial Endemic North American clade and its allies...
October 7, 2017: Molecular Phylogenetics and Evolution
Guilherme S T Garbino, Antonio M G Martins-Junior
Marmosets and tamarins (Cebidae, Callitrichinae) constitute the most species-rich subfamily of New World monkeys and one of the most diverse phenotypically. Despite the profusion of molecular phylogenies of the group, the evolution of phenotypic characters under the rapidly-emerging consensual phylogeny of the subfamily has been little studied, resulting in taxonomic proposals that have limited support from other datasets. We examined the evolution of 18 phenotypic traits (5 continuous and 13 discrete), including pelage, skull, dentition, postcrania, life-history and vocalization variables in a robust molecular phylogeny of marmoset and tamarin monkeys, quantifying their phylogenetic signal and correlations among some of the traits...
October 6, 2017: Molecular Phylogenetics and Evolution
Annie R Lindgren, Frank E Anderson
Historically, deep-level relationships within the molluscan class Cephalopoda (squids, cuttlefishes, octopods and their relatives) have remained elusive due in part to the considerable morphological diversity of extant taxa, a limited fossil record for species that lack a calcareous shell and difficulties in sampling open ocean taxa. Many conflicts identified by morphologists in the early 1900s remain unresolved today in spite of advances in morphological, molecular and analytical methods. In this study we assess the utility of transcriptome data for resolving cephalopod phylogeny, with special focus on the orders of Decapodiformes (open-eye squids, bobtail squids, cuttlefishes and relatives)...
October 5, 2017: Molecular Phylogenetics and Evolution
H Peter Linder, Yanis Bouchenak-Khelladi
Although much of extant diversity is probably the product of evolutionary radiations, the special case of adaptive radiations has not yet been thoroughly explored. Adaptive radiations are postulated to occur when a lineage is exposed to new ecological opportunities, where it can diversify ecologically. We argue that adaptive radiations have two characteristics. Firstly, the diversification rate accelerates initially, and is then followed by a density-dependent slow-down. Secondly, traits relevant to the new ecological opportunity should evolve at or just before the radiation...
October 5, 2017: Molecular Phylogenetics and Evolution
Yun-Yun Lv, Kai He, Sebastian Klaus, Rafe M Brown, Jia-Tang Li
Currently, the genus Kurixalus comprises 14 species distributed in Southern, Southeast and East Asia. Because of their relatively low dispersal capability and intolerance of seawater, this group may be an ideal one for the study of terrestrial range evolution, especially that portion of its distributional range that extends into the island archipelagos of southern Asia. We assembled a large dataset of mitochondrial and nuclear genes, and estimated phylogeny by maximum likelihood and Bayesian methods, and we explored the history of each species via divergence-time estimation based on fossil-calibrations...
October 5, 2017: Molecular Phylogenetics and Evolution
Eugenio Valderrama Escallon, James E Richardson, Catherine A Kidner, Santiago Madriñán, Graham S Stone
The reconstruction of species rich groups that have recently evolved in biodiversity hotspots is hampered by a lack of phylogenetically informative markers. It is also made difficult by the lack of sampling necessary to reconstruct a species-level phylogeny. We use transcriptome mining to search for markers to reconstruct a phylogeny of the amphi-Atlantic genus Renealmia L. f. (Zingiberaceae). We recover seven introns from single copy genes and use them to reconstruct the phylogeny of the genus together with a commonly used phylogenetic marker, internal transcribed spacers of ribosomal DNA (ITS) that has previously been used to reconstruct the phylogeny of the genus...
October 4, 2017: Molecular Phylogenetics and Evolution
Irene Villalta, Fernando Amor, Juan A Galarza, Simon Dupont, Patrocinio Ortega, Abraham Hefetz, Abdallah Dahbi, Xim Cerdá, Raphaël Boulay
The creation of geographic barriers has long been suspected to contribute to the formation of new species. We investigated the phylogeography of desert ants in the western Mediterranean basin in order to elucidate their mode of diversification. These insects which have a low dispersal capacity are recently becoming important model systems in evolutionary studies. We conducted an extensive sampling of species belonging to the Cataglyphis albicans group in the Iberian Peninsula (IP) and the northern Morocco (North Africa; NA)...
October 3, 2017: Molecular Phylogenetics and Evolution
Yingqi Liu, Fan Song, Pei Jiang, John-James Wilson, Wanzhi Cai, Hu Li
Mitochondrial phylogenomics is often controversial, in particular for inferring deep relationships. The recent rapid increase of mitochondrial genome data provides opportunities for better phylogenetic estimates and assessment of potential biases resulting from heterogeneity in nucleotide composition and mutation rates. Here, we gathered 76 mitochondrial genome sequences for Heteroptera representing all seven infraorders, including 17 newly sequenced mitochondrial genomes. We found strong heterogeneity in base composition and contrasting evolutionary rates among heteropteran mitochondrial genomes, which affected analyses with various datasets and partitioning schemes under site-homogeneous models and produced false groupings of unrelated taxa exhibiting similar base composition and accelerated evolutionary rates...
October 3, 2017: Molecular Phylogenetics and Evolution
Daniela Matenaar, Marcus Fingerle, Eva Heym, Sarah Wirtz, Axel Hochkirch
Vicariance and dispersal are two important processes shaping biodiversity patterns. The South African Cape Floristic Region (CFR) is known for its high biotic diversity and endemism. However, studies on the phylogeography of endemic invertebrates in this biodiversity hotspot are still scarce. Here, we present a phylogenetic study of the flightless grasshopper genus Betiscoides, which is endemic to the CFR and strongly associated with restio plants (Restionaceae). We hypothesized that the genus originated in the southwestern part of the CFR, that differentiation within the genus is mainly an effect of vicariance and that the three known species only represent a minor fraction of the real genetic diversity of the genus...
October 3, 2017: Molecular Phylogenetics and Evolution
Han Ming Gan, Mun Hua Tan, Yin Peng Lee, Mark B Schultz, Pierre Horwitz, Quinton Burnham, Christopher M Austin
To further understand the evolutionary history and mitogenomic features of Australia's highly distinctive freshwater crayfish fauna, we utilized a recently described rapid mitogenome sequencing pipeline to generate 24 new crayfish mitogenomes including a diversity of burrowing crayfish species and the first for Astacopsis gouldi, the world's largest freshwater invertebrate. Whole mitogenome-based phylogeny estimates using both Bayesian and Maximum Likelihood methods substantially strengthen existing hypotheses for systematic relationships among Australian freshwater crayfish with evidence of pervasive diversifying selection and accelerated mitochondrial substitution rate among the members of the clade representing strongly burrowing crayfish that may reflect selection pressures for increased energy requirement for adaptation to terrestrial environment and a burrowing lifestyle...
September 28, 2017: Molecular Phylogenetics and Evolution
Florian Jabbour, Myriam Gaudeul, Josie Lambourdière, Guillaume Ramstein, Alexandre Hassanin, Jean-Noël Labat, Corinne Sarthou
The nearly cosmopolitan tribe Desmodieae (Fabaceae) includes many important genera for medicine and forage. However, the phylogenetic relationships among the infratribal groups circumscribed using morphological traits are still poorly known. In this study, we used chloroplast (rbcL, psbA-trnH) and nuclear (ITS-1) DNA sequences to investigate the molecular phylogeny and historical biogeography of Desmodieae, and infer ancestral states for several vegetative and reproductive traits. Three groups, corresponding to the Desmodium, Lespedeza, and Phyllodium groups sensu Ohashi were retrieved in the phylogenetic analyses...
September 28, 2017: Molecular Phylogenetics and Evolution
Yuan Zhuang, John C Clamp, Zhenzhen Yi, Daode Ji
Peritrichs are a major group of ciliates with worldwide distribution, and they play important roles in many habitats. Intrafamilial phylogeny of some peritrichs was investigated using information from three genes, which provided more robust interpretations than single-gene analyses. Sixty-seven new sequences including SSU rDNA, ITS1-5.8S-ITS2 and LSU rDNA were aligned with available sequences in GenBank to infer phylogenetic relationships within the families Zoothamniidae and Epistylididae. Results reveal the following relationships: (1) Epistylididae is polyphyletic, consisting of two clades that nest within the Zoothamniidae as part of the crown clade of peritrichs (order Vorticellida) and a third one that is part of the basal clade of peritrichs (order Opercularida); (2) Epistylis elongata falls within one of the clades of Zoothamnium rather than with congeners; (3) Zoothamnium is probably paraphyletic, consisting of three divergent clades, with the genera Myoschiston and Zoothamnopsis intermingled with species of Zoothamnium...
September 28, 2017: Molecular Phylogenetics and Evolution
Josef Bryja, Danila Kostin, Yonas Meheretu, Radim Šumbera, Anna Bryjová, Mohammed Kasso, Ondřej Mikula, Leonid A Lavrenchenko
The Ethiopian highlands are the most extensive complex of mountainous habitats in Africa. The presence of the Great Rift Valley (GRV) and the striking elevational ecological gradients inhabited by recently radiated Ethiopian endemics, provide a wide spectrum of model situations for evolutionary studies. The extant species of endemic rodents, often markedly phenotypically differentiated, are expected to possess complex genetic features which evolved asa consequence of the interplay between geomorphology and past climatic changes...
September 27, 2017: Molecular Phylogenetics and Evolution
Matthew P Heinicke, Alan R Lemmon, Emily Moriarty Lemmon, Kathleen McGrath, S Blair Hedges
Phylogenomic approaches have proven able to resolve difficult branches in the tree of life. New World direct-developing frogs (Terraranae) represent a large evolutionary radiation in which interrelationships at key points in the phylogeny have not been adequately determined, affecting evolutionary, biogeographic, and taxonomic interpretations. We employed anchored hybrid enrichment to generate a data set containing 389 loci and >600,000 nucleotide positions for 30 terraranan and several outgroup frog species encompassing all major lineages in the clade...
September 27, 2017: Molecular Phylogenetics and Evolution
Ryan A Eldridge, Anang S Achmadi, Thomas C Giarla, Kevin C Rowe, Jacob A Esselstyn
Phylogeographic research on endemic primates and amphibians inhabiting the Indonesian island of Sulawesi revealed the existence of seven areas of endemism (AoEs). Here, we use phylogenetic and population genetic analyses of one mitochondrial gene and 15 nuclear loci to assess geographic patterns of genetic partitioning in a shrew (Crocidura elongata) that is endemic to Sulawesi, but occurs across the island. We uncover substantial genetic diversity in this species both between and within AoEs, but we also identify close relationships between populations residing in different AoEs...
September 26, 2017: Molecular Phylogenetics and Evolution
Liang Zhang, Li-Bing Zhang
The braken fern genus Pteris belongs to Pteridaceae subfamily Pteridoideae. It is one of the largest fern genera and has been estimated to contain 200-250 species distributed on all continents except Antarctica. Previous studies were either based on plastid data only or based on both plastid and nuclear data but the sampling was small. In addition, an infrageneric classification of Pteris based on morphological and molecular evidence has not been available yet. In the present study, based on molecular data of eight plastid markers and one nuclear marker (gapCp) of 256 accessions representing ca...
September 23, 2017: Molecular Phylogenetics and Evolution
Navaneethan Palanisamy, Dario Akaberi, Johan Lennerstrand
Viruses belonging to the Flaviviridae family have been an important health concern for humans, animals and birds alike. No specific treatment is available yet for many of the viral infections caused by the members of this family. Lack of specific drugs against these viruses is mainly due to lack of protein structure information. It has been known that protein backbone fluctuation pattern is highly conserved in protein pairs with similar folds, in spite of the lack of sequence similarity. We hypothesized that this concept should also hold true for proteins (especially enzymes) of viruses included in different genera of the Flaviviridae family, as we know that the sequence similarity between them is low...
September 22, 2017: Molecular Phylogenetics and Evolution
Lukas J Musher, Joel Cracraft
Phylogeographic studies within the Neotropics continue to uncover hidden diversity, the extent of which remains poorly known. In birds, molecular studies are producing evidence that species-level diversity is substantially underestimated. Many avian taxa comprise large complexes of subspecies that often represent species-level taxa by various criteria. One such group of Neotropical suboscine birds, the becards (Pachyramphus), ranges from Argentina through northern Mexico. Their taxonomic limits have been complex and controversial as the genus has bounced around a number of suboscine families...
September 22, 2017: Molecular Phylogenetics and Evolution
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