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Molecular Phylogenetics and Evolution

Ashley E Sproles, Nathan L Kirk, Sheila A Kitchen, Clinton A Oakley, Arthur R Grossman, Virginia M Weis, Simon K Davy
Metabolic exchange between cnidarians and their symbiotic dinoflagellates is central to maintaining their mutualistic relationship. Sugars are translocated to the host, while ammonium and nitrate are utilized by the dinoflagellates (Symbiodinium spp.). We investigated membrane protein sequences of each partner to identify potential transporter proteins that move sugars into cnidarian cells and nitrogen products into Symbiodinium cells. We examined the facilitated glucose transporters (GLUT), sodium/glucose cotransporters (SGLT), and aquaporin (AQP) channels in the cnidarian host as mechanisms for sugar uptake, and the ammonium and high-affinity nitrate transporters (AMT and NRT2, respectively) in the algal symbiont as mechanisms for nitrogen uptake...
December 9, 2017: Molecular Phylogenetics and Evolution
Lincoln Carneiro, Gustavo A Bravo, Natalia Aristizábal, Andrés M Cuervo, Alexandre Aleixo
We infer phylogenetic relationships, divergence times, and the diversification history of the avian Neotropical antpitta genera Hylopezus and Myrmothera (Grallariidae), based on sequence data (3139 base pairs) from two mitochondrial (ND2 and ND3) and three nuclear markers (TGFB2, MUSK and FGB-I5) from 142 individuals of the 12 currently recognized species in Hylopezus and Myrmothera and 5 outgroup species. Phylogenetic analyses recovered 19 lineages clustered into two major clades, both distributed in Central and South America...
December 9, 2017: Molecular Phylogenetics and Evolution
Jeffrey L Weinell, Aaron M Bauer
A systematic study of the Trachylepis varia complex was conducted using mitochondrial and nuclear DNA markers for individuals sampled across the species range. The taxonomic history of T. varia has been complicated and its broad geographic distribution and considerable phenotypic variation has made taxonomic revision difficult, leading earlier taxonomists to suggest that T. varia is a species complex. We used maximum likelihood and Bayesian inference to estimate gene trees and a multilocus time-tree, respectively, and we used these trees to identify the major clades (putative species) within T...
December 9, 2017: Molecular Phylogenetics and Evolution
Liz Milla, Erik J van Nieukerken, Ruben Vijverberg, Camiel Doorenweerd, Stephen A Wilcox, Mike Halsey, David A Young, Therésa M Jones, Axel Kallies, Douglas J Hilton
Heliozelidae are a widespread, evolutionarily early diverging family of small, day-flying monotrysian moths, for which a comprehensive phylogeny is lacking. We generated the first molecular phylogeny of the family using DNA sequences of two mitochondrial genes (COI and COII) and two nuclear genes (H3 and 28S) from 130 Heliozelidae specimens, including eight of the twelve known genera: Antispila, Antispilina, Coptodisca, Heliozela, Holocacista, Hoplophanes, Pseliastis, and Tyriozela. Our results provide strong support for five major Heliozelidae clades: (i) a large widespread clade containing the leaf-mining genera Antispilina, Coptodisca and Holocacista and some species of Antispila, (ii) a clade containing most of the described Antispila, (iii) a clade containing the leaf-mining genus Heliozela and the monotypic genus Tyriozela, (iv) an Australian clade containing Pseliastis and (v) an Australian clade containing Hoplophanes...
December 8, 2017: Molecular Phylogenetics and Evolution
Sergei V Drovetski, Andrew B Reeves, Yaroslav A Red'kin, Igor V Fadeev, Evgeniy A Koblik, Vladimir N Sotnikov, Gary Voelker
Resolving relationships among members of the yellow and citrine wagtail species complexes is among the greatest challenges in avian systematics due to arguably the most dramatic disagreements between traditional taxonomy and mtDNA phylogeny. Each species complex is divided into three geographically cohesive mtDNA clades. Each clade from one species complex has a sister from the other complex. Furthermore, one cross-complex pair is more distantly related to the remaining two pairs than are several other wagtail species...
December 7, 2017: Molecular Phylogenetics and Evolution
Michael San Jose, Camiel Doorenweerd, Luc Leblanc, Norman Barr, Scott Geib, Daniel Rubinoff
Molecular and morphological research often suggest conflicting results. Selective pressure on certain morphologies can confound understanding of evolutionary relationships. Dacini is one of the most diverse tribes of tephritid flies and contains many economically important pest species. Their black and yellow patterned body markings are presumed to act as wasp mimicry, and the characters separating species and groups are limited and in some cases phenotypically plastic. The traditional taxonomy of the tribe is controversial because groupings are based on unique combinations of morphological characters without the use of cladistic methods, though recent phylogenetic and taxonomic analyses have resulted in significant changes to their taxonomy...
December 7, 2017: Molecular Phylogenetics and Evolution
Hugo Vianna Silva Rody, Luiz Orlando de Oliveira
Plants are successful paleopolyploids. The wide diversity of land plants is driven strongly by their gene duplicates undergoing distinct evolutionary fates after duplication. We used genomic resources from 35 model plant species to unravel the evolutionary fate of gene copies (paralogs) of the cobalamin-independent methionine synthase (metE) gene family across the land plants. To explore genealogical relationships and characterize positive selection as a driving force in the evolution of metE paralogs within a single species, we carried out complementary analyses on genomic data of 32 genotypes of soybean...
December 6, 2017: Molecular Phylogenetics and Evolution
Marcelo Fernando Devecchi, William Wayt Thomas, Gregory M Plunkett, José Rubens Pirani
Generic circumscriptions in the mostly pantropical family Simaroubaceae are somewhat controversial. Simaba is the largest genus, currently defined as exclusively neotropical, with around 25 species of trees and shrubs, but both its limits and infrageneric classification have been a matter of discussion and divergence. Traditionally, species of the genus have been treated in three sections: Simaba sect. Tenuiflorae, S. sect. Floribundae and S. sect. Grandiflorae, but a phylogenetic analysis suggested that the latter two may not be monophyletic...
December 5, 2017: Molecular Phylogenetics and Evolution
Félicien Tosso, Olivier J Hardy, Jean-Louis Doucet, Kasso Daïnou, Esra Kaymak, Jérémy Migliore
Tropical rain forests support a remarkable diversity of tree species, questioning how and when this diversity arose. The genus Guibourtia (Fabaceae, Detarioideae), characterized by two South American and 13 African tree species growing in various tropical biomes, is an interesting model to address the role of biogeographic processes and adaptation to contrasted environments on species diversification. Combining whole plastid genome sequencing and morphological characters analysis, we studied the timing of speciation and diversification processes in Guibourtia through molecular dating and ancestral habitats reconstruction...
December 5, 2017: Molecular Phylogenetics and Evolution
Rafael Medina, Matthew Johnson, Yang Liu, Nicholas Wilding, Terry A Hedderson, Norman Wickett, Bernard Goffinet
Rapid diversifications of plants are primarily documented and studied in angiosperms, which are perceived as evolutionarily dynamic. Recent studies have, however, revealed that bryophytes have also undergone periods of rapid radiation. The speciose family Funariaceae, including the model taxon Physcomitrella patens, is one such lineage. Here, we infer relationships among major lineages within the Entosthodon-Physcomitrium complex from virtually complete organellar exomes (i.e., 123 genes) obtained through high throughput sequencing of genomic libraries enriched in these loci via targeted locus capture...
December 5, 2017: Molecular Phylogenetics and Evolution
Daniel F Hughes, Krystal A Tolley, Mathias Behangana, Wilber Lukwago, Michele Menegon, J Maximilian Dehling, Jan Stipala, Colin R Tilbury, Arshad M Khan, Chifundera Kusamba, Eli Greenbaum
Several biogeographic barriers in the Central African highlands have reduced gene flow among populations of many terrestrial species in predictable ways. Yet, a comprehensive understanding of mechanisms underlying species divergence in the Afrotropics can be obscured by unrecognized levels of cryptic diversity, particularly in widespread species. We implemented a multilocus phylogeographic approach to examine diversity within the widely distributed Central African pygmy chameleon, Rhampholeon boulengeri. Gene-tree analyses coupled with a comparative coalescent-based species delimitation framework revealed R...
November 30, 2017: Molecular Phylogenetics and Evolution
Israel Solano-Zavaleta, Adrián Nieto-Montes de Oca
The widely distributed, Central American anguid lizard Mesaspis moreletii is currently recognized as a polytypic species with five subspecies (M. m. fulvus, M. m. moreletii, M. m. rafaeli, M. m. salvadorensis, and M. m. temporalis). We reevaluated the species limits within Mesaspis moreletii using DNA sequences of one mitochondrial and three nuclear genes. The multi-locus data set included samples of all of the subspecies of M. moreletii, the other species of Mesaspis in Central America (M. cuchumatanus and M...
November 30, 2017: Molecular Phylogenetics and Evolution
Jade Bruxaux, Maëva Gabrielli, Hidayat Ashari, Robert Prŷs-Jones, Leo Joseph, Borja Milá, Guillaume Besnard, Christophe Thébaud
Assessing the relative contributions of immigration and diversification into the buildup of species diversity is key to understanding the role of historical processes in driving biogeographical and diversification patterns in species-rich regions. Here, we investigated how colonization, in situ speciation, and extinction history may have generated the present-day distribution and diversity of Goura crowned pigeons (Columbidae), a group of large forest-dwelling pigeons comprising four recognized species that are all endemic to New Guinea...
November 30, 2017: Molecular Phylogenetics and Evolution
Knud Andreas Jønsson, Mozes P K Blom, Martin Päckert, Per G P Ericson, Martin Irestedt
Molecular studies have revealed a number of cases in which traditional assessments of evolutionary relationships have been incorrect. This has implications not only for systematics and taxonomy but also for our understanding of how diversity patterns on Earth have been formed. Here, we use high-throughput sequencing technology to obtain molecular data from the holotype specimen of the elusive Eutrichomyias rowleyi, which is endemic to the Indonesian island of Sangihe. We show that E. rowleyi unexpectedly is a member of the family Lamproliidae, which dates back some 20 Million years and only include two other species, Lamprolia victoriae from Fiji and Chaetorhynchus papuensis from New Guinea...
November 30, 2017: Molecular Phylogenetics and Evolution
V Deepak, Praveen Karanth
The establishment of monsoon climate and the consequent aridification has been one of the most important climate change episodes in the Indian subcontinent. However, little is known about how these events might have shaped the diversification patterns among the widely distributed taxa. Fan-throated lizards (FTL) (Genus: Sitana, Sarada) are widespread, diurnal and restricted to the semi-arid zones of the Indian subcontinent. We sampled FTL in 107 localities across its range. We used molecular species delimitation method and delineated 15 species including six putative species...
November 29, 2017: Molecular Phylogenetics and Evolution
Manisha Priyam, Mamta Tripathy, Umesh Rai, Soma Mondal Ghorai
No abstract text is available yet for this article.
November 28, 2017: Molecular Phylogenetics and Evolution
Cintia Débora Medina, Luciano Javier Avila, Jack Walter Sites, Juan Santos, Mariana Morando
We present different approaches to a multi-locus phylogeny for the Liolaemus elongatus-kriegi group, including almost all species and recognized lineages. We sequenced two mitochondrial and five nuclear gene regions for 123 individuals from 35 taxa, and compared relationships resolved from concatenated and species tree methods. The L. elongatus-kriegi group was inferred as monophyletic in three of the five analyses (concatenated mitochondrial, concatenated mitochondrial + nuclear gene trees, and SVD quartet species tree)...
November 28, 2017: Molecular Phylogenetics and Evolution
Daniele Salvi, Ana Perera, Filipa L Sampaio, Salvador Carranza, D James Harris
Biogeographic and evolutionary patterns in the North African portion of the Western Palaearctic are poorly known. A high fraction of undescribed diversity is expected in this region, especially in groups such as reptiles. Here we used mitochondrial (12S, 16S, cytb) and nuclear (pomc, rag2, cmos) markers and morphological data to investigate phyletic diversification and phylogeographical structure in the amphisbaenian Trogonophis wiegmanni endemic to the Maghreb. Phylogenetic and molecular dating analyses based on gene trees and species trees support three deeply divergent lineages of Pliocene origin, two in Morocco and one in central Algeria and Tunisia...
November 28, 2017: Molecular Phylogenetics and Evolution
Li-En Yang, Wei Zhou, Chuan-Ming Hu, Yin-Yin Deng, Guang-Ping Xu, Tao Zhang, Stephen Russell, Jian-Yi Zhu, Qin-Qin Lu, Juliet Brodie
A molecular taxonomic study was undertaken for the first time of the bladed Bangiales of the mainland coast of China (Northwest Pacific) based on sequence data of 201 plastid rbcL and 148 nuclear 18S sequences of historical and contemporary specimens. The results revealed that only one genus of bladed Bangiales, Pyropia, was present along Chinese coast. Species delimitation was determined using two empirical methods: the Automatic Barcode Gap Discovery (ABGD) and General Mixed Yule Coalescence (GMYC) coupled with detection of monophyly in tree reconstruction...
November 24, 2017: Molecular Phylogenetics and Evolution
Jean P Boubli, Maria N F da Silva, Anthony B Rylands, Stephen D Nash, Fabrício Bertuol, Mário Nunes, Russell A Mittermeier, Hazel Byrne, Felipe E da Silva, Fábio Röhe, Iracilda Sampaio, Horacio Schneider, Izeni P Farias, Tomas Hrbek
The pygmy marmoset, Cebuella pygmaea, the smallest of the New World monkeys, has one of the largest geographical distributions of the Amazonian primates. Two forms have been recognized: Cebuella pygmaea pygmaea (Spix, 1823), and C. p. niveiventrisLönnberg, 1940. In this study, we investigated if the separation of pygmy marmosets into these two clades can be corroborated by molecular data. We also examine and compare coloration of the pelage in light of the new molecular results. We analyzed the mtDNA cytochrome b gene and, for the first time for any Neotropical primate, we used a reduced representation genome sequencing approach (ddRADseq) to obtain data for recently collected, geographically representative samples from the Rio Japurá, a northern tributary of the Rio Solimões and from the Javarí, Jutaí, Juruá, Madeira and Purus river basins, all tributaries south of the Solimões...
November 23, 2017: Molecular Phylogenetics and Evolution
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