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Molecular Phylogenetics and Evolution

Catherine L Malone, Víctor Hugo Reynoso, Larry Buckley
Spiny tailed iguanas are highly diverse clade of lizards in Mesoamerica, ranging from northern Mexico through Panama. Utilizing 2 regions of mitochondrial DNA (1948 bp) and 4 nuclear loci (2232 bp) we explored the relationships between these species and the phylogeographic history of the major clades. We discovered that the lineage endemic to the Yucatan Peninsula render the genus Ctenosaura paraphyletic. To resolve this non-m0nophyly, we resurrect the taxon CachryxCope, 1866, and provide a new diagnosis for the genus...
July 14, 2017: Molecular Phylogenetics and Evolution
Ariel Rodríguez, James D Burgon, Mariana Lyra, Iker Irisarri, Denis Baurain, Leon Blaustein, Bayram Göcmen, Sven Künzel, Barbara Mable, Arne W Nolte, Michael Veith, Sebastian Steinfartz, Kathryn R Elmer, Hervé Philippe, Miguel Vences
The rise of high-throughput sequencing techniques provides the unprecedented opportunity to analyse controversial phylogenetic relationships in great depth, but also introduce the risk of being misinterpreted by high node support values influenced by unevenly distributed missing data or unrealistic model assumptions. Here, we use three largely independent phylogenomic data sets to reconstruct the controversial phylogeny of true salamanders of the genus Salamandra. a group of amphibians providing an intriguing model to study the evolution of aposematism and viviparity...
July 14, 2017: Molecular Phylogenetics and Evolution
Luz E Ochoa, Fabio F Roxo, Carlos DoNascimiento, Mark H Sabaj, Aléssio Datovo, Michael Alfaro, Claudio Oliveira
Trichomycteridae is the second most diverse family of the order Siluriformes, its members are widely distributed through the freshwaters of Central and South America, exhibiting an exceptional ecological and phenotypic disparity. The most diverse subfamily, Trichomycterinae, represented mainly by the genus Trichomycterus, historically has been recognized as non-monophyletic and various characters used to unite or divide its constituents are repeatedly called into question. No comprehensive molecular phylogenetic hypothesis regarding relationships of trichomycterids has been produced, and the present study is the first extensive phylogeny for the family Trichomycteridae, based on a multilocus dataset of three mitochondrial loci and two nuclear markers (3284 bp total)...
July 14, 2017: Molecular Phylogenetics and Evolution
H Bradley Shaffer, Evan McCartney-Melstad, Thomas J Near, Genevieve G Mount, Phillip Q Spinks
Accurate time-calibrated phylogenies are the centerpiece of many macroevolutionary studies, and the relationship between the size and scale of molecular data sets and the density and accuracy of fossil calibrations is a key element of time tree studies. Here, we develop a target capture array specifically for living turtles, compare its efficiency to an ultraconserved element (UCE) dataset, and present a time-calibrated molecular phylogeny based on 539 nuclear loci sequenced from 26 species representing the breadth of living turtle diversity plus outgroups...
July 12, 2017: Molecular Phylogenetics and Evolution
M M Soler-Hurtado, P J López-González, A Machordom
No abstract text is available yet for this article.
July 12, 2017: Molecular Phylogenetics and Evolution
Jose Barba-Montoya, Mario Dos Reis, Ziheng Yang
Fossil calibrations are the utmost source of information for resolving the distances between molecular sequences into estimates of absolute times and absolute rates in molecular clock dating analysis. The quality of calibrations is thus expected to have a major impact on divergence time estimates even if a huge amount of molecular data is available. In Bayesian molecular clock dating, fossil calibration information is incorporated in the analysis through the prior on divergence times (the time prior). Here, we evaluate three strategies for converting fossil calibrations (in the form of minimum- and maximum-age bounds) into the prior on times, which differ according to whether they borrow information from the maximum age of ancestral nodes and minimum age of descendent nodes to form constraints for any given node on the phylogeny...
July 11, 2017: Molecular Phylogenetics and Evolution
Marcin Piwczyński, Thomas Pape, Edyta Deja-Sikora, Marcin Sikora, Kamran Akbarzadeh, Krzysztof Szpila
Miltogramminae is one of the phylogenetically most poorly studied taxa of the species-rich family Sarcophagidae (Diptera). Most species are kleptoparasites in nests of solitary aculeate wasps and bees, although parasitoids and saprophagous species are also known, and the ancestral miltogrammine life habit remains unsettled. Here, we present for the first time a comprehensive phylogenetic tree consisting of 58 representatives of Miltogramminae, reconstructed using sequence data from three mitochondrial (COI, cytB, ND4) and one nuclear (Ef-1α) genes...
July 11, 2017: Molecular Phylogenetics and Evolution
Melissa A Johnson, John R Clark, Warren L Wagner, Lucinda A McDade
Cyrtandra (Gesneriaceae) is among the largest genera of flowering plants in the remote oceanic islands of the Pacific, with an estimated 175 species distributed across an area that extends from the Solomon Islands, east to the Marquesas Islands, and north to the Hawaiian Islands. The vast majority of species are single-island endemics that inhabit upland rainforests. Although previous molecular phylogenetic studies greatly advanced our understanding of the diversification of Pacific Cyrtandra, a number of uncertainties remain regarding phylogenetic relationships, divergence times, and biogeographic patterns within this large and widely dispersed group...
July 10, 2017: Molecular Phylogenetics and Evolution
Elliot M Gardner, Paya Sarraf, Evelyn W Williams, Nyree J C Zerega
BACKGROUND AND AIMS: Maclura (ca. 12 spp., Moraceae) is a widespread genus of trees and woody climbers found on five continents. Maclura pomifera, the Osage orange, is considered a classic example of an anachronistic fruit. Native to the central USA, the grapefruit-sized Osage oranges are unpalatable and have no known extant native dispersers, leading to speculation that the fruits were adapted to extinct megafauna. Our aim was to reconstruct the phylogeny, estimate divergence dates, and infer ancestral ranges of Maclura in order to test the monophyly of subgeneric classifications and to understand evolution and dispersal patterns in this globally distributed group...
July 8, 2017: Molecular Phylogenetics and Evolution
Hélène Rousseau, Mathieu Rousseau-Gueutin, Xavier Dauvergne, Julien Boutte, Gaëlle Simon, Nathalie Marnet, Alain Bouchereau, Solène Guiheneuf, Jean-Pierre Bazureau, Jérôme Morice, Stéphane Ravanel, Francisco Cabello-Hurtado, Abdelkader Ainouche, Armel Salmon, Jonathan F Wendel, Malika L Ainouche
DMSP (dimethylsulfoniopropionate) is an ecologically important sulfur metabolite commonly produced by marine algae and by some higher plant lineages, including the polyploid salt marsh genus Spartina (Poaceae). The molecular mechanisms and genes involved in the DMSP biosynthesis pathways are still unknown. In this study, we performed comparative analyses of DMSP amounts and molecular phylogenetic analyses to decipher the origin of DMSP in Spartina that represents one of the major source of terrestrial DMSP in coastal marshes...
July 7, 2017: Molecular Phylogenetics and Evolution
Deborah F Nacer, Fabio Raposo do Amaral
Nuclear copies of mitochondrial genes (numts) are a well-known feature of eukaryotic genomes and a concern in systematics, as they can mislead phylogenetic inferences when inadvertently used. Studies on avian numts initially based on the chicken genome suggest that numts may be uncommon and relatively short among birds. Here we ask how common numts are in falcons, based on recently sequenced genomes of the Saker falcon (Falco cherrug) and Peregrine falcon (F. peregrinus). We identified numts by BLASTN searches and then extracted CYTB, ND2 and COI sequences from them, which were then used for phylogeny inference along with several sequences from other species in Falconiformes...
July 6, 2017: Molecular Phylogenetics and Evolution
Gabriela B Bittencourt-Silva, Lucinda P Lawson, Krystal A Tolley, Daniel M Portik, Christopher D Barratt, Peter Nagel, Simon P Loader
Ecological niche models (ENMs) have been used in a wide range of ecological and evolutionary studies. In biogeographic studies these models have, among other things, helped in the discovery of new allopatric populations, and even new species. However, small sample sizes and questionable taxonomic delimitation can challenge models, often decreasing their accuracy. Herein we examine the sensitivity of ENMs to the addition of new, geographically isolated populations, and the impact of applying different taxonomic delimitations...
July 3, 2017: Molecular Phylogenetics and Evolution
Xin-Mao Zhou, Liang Zhang, Cheng-Wei Chen, Chun-Xiang Li, Yao-Moan Huang, De-Kui Chen, Ngan Thi Lu, Daniele Cicuzza, Ralf Knapp, Thien Tam Luong, Joel H Nitta, Xin-Fen Gao, Li-Bing Zhang
The Old World fern genus Pyrrosia (Polypodiaceae) offers a rare system in ferns to study morphological evolution because almost all species of this genus are well studied for their morphology, anatomy, and spore features, and various hypotheses have been proposed in terms of the phylogeny and evolution in this genus. However, the molecular phylogeny of the genus lags behind. The monophyly of the genus has been uncertain and a modern phylogenetic study of the genus based on molecular data has been lacking. In the present study, DNA sequences of five plastid markers of 220 accessions of Polypodiaceae representing two species of Drymoglossum, 14 species of Platycerium, 50 species of Pyrrosia, and the only species of Saxiglossum (subfamily Platycerioideae), and 12 species of other Polypodiaceae representing the remaining four subfamilies are used to infer a phylogeny of the genus...
July 1, 2017: Molecular Phylogenetics and Evolution
Yonas I Tekle, Fiona C Wood
Longamoebia is one of the most morphologically diverse member of Amoebozoa. It includes the human pathogen Acanthamoeba, which causes minor skin and serious eye infections as well as fatal central nervous system complications. The taxonomy and phylogeny of Longamoebia is poorly understood partly due to the growing number of molecular studies that report unsuspected affiliations of lineages with extremely different morphotypes in the group. A recent molecular study questioned the monophyly of Longamoebia. In this study, we conducted a more comprehensive phylogenomic analysis including all of putative members of Longamoebia to assess its monophyly...
June 29, 2017: Molecular Phylogenetics and Evolution
Felix Vaux, Simon F K Hills, Bruce A Marshall, Steven A Trewick, Mary Morgan-Richards
Under current marine snail taxonomy, the majority of whelks from the Southern Hemisphere (Buccinulidae) are hypothesised to represent a monophyletic clade that has evolved independently from Northern Hemisphere taxa (Buccinidae). Phylogenetic analysis of mitochondrial genomic and nuclear ribosomal DNA sequence data indicates that Southern Hemisphere taxa are not monophyletic, and results suggest that dispersal across the equator has occurred in both directions. New Zealand buccinulid whelks, noted for their high endemic diversity, are also found to not be monophyletic...
June 29, 2017: Molecular Phylogenetics and Evolution
Danielle de Carle, Alejandro Oceguera-Figueroa, Michael Tessler, Mark E Siddall, Sebastian Kvist
Placobdella is a genus of blood-feeding leeches in the family Glossiphoniidae. Historically, species of Placobdella have posed difficulty for systematists owing to a lack of informative morphological characters and the preponderance of inadequate or incomplete species descriptions. Here, we conduct a phylogenetic analysis of 55 individuals representing 20 of the 24 currently recognized nominal taxa using COI, ND1, 12S rDNA and ITS sequences under parsimony, maximum likelihood and Bayesian inference. We also examine the isolated COI phylogeny for the genus using an expanded dataset encompassing three additional species not included in the concatenated dataset...
June 27, 2017: Molecular Phylogenetics and Evolution
Alejandro López-López, Alfried P Vogler
The beetle suborder Adephaga consists of several aquatic ('Hydradephaga') and terrestrial ('Geadephaga') families whose relationships remain poorly known. In particular, the position of Cicindelidae (tiger beetles) appears problematic, as recent studies have found them either within the Hydradephaga based on mitogenomes, or together with several unlikely relatives in Geadephaga based on 18S rRNA genes. We newly sequenced nine mitogenomes of representatives of Cicindelidae and three ground beetles (Carabidae), and conducted phylogenetic analyses together with 29 existing mitogenomes of Adephaga...
June 21, 2017: Molecular Phylogenetics and Evolution
Ian Kendrich Fontanilla, Fred Naggs, Christopher Mark Wade
This study presents a multi-gene phylogenetic analysis of the Achatinoidea and provides an initial basis for a taxonomic re-evaluation of family level groups within the superfamily. A total of 5028 nucleotides from the nuclear rRNA, actin and histone 3 genes and the 1st and 2nd codon positions of the mitochondrial cytochrome c oxidase subunit I gene were sequenced from 24 species, representing six currently recognised families. Results from maximum likelihood, neighbour joining, maximum parsimony and Bayesian inference trees revealed that, of currently recognised families, only the Achatinidae are monophyletic...
June 21, 2017: Molecular Phylogenetics and Evolution
Giovani Hernández-Canchola, Livia León-Paniagua
With 22 species, Sturnira is the most speciose genus of frugivorous Neotropical bats. Sturnira parvidens inhabits lowland tropical areas from Mexico to Central America. The elevation of this taxon to species level was recent, and discrepancies with respect to its geographic limits and phylogenetic position continue to exist. In order to identify genetic and ecological processes likely involved in the diversification and current distribution of S. parvidens, we evaluated relationships, researched phylogeographic and demographic history, and tested the divergence/conservatism of the climatic niche of this bat...
June 21, 2017: Molecular Phylogenetics and Evolution
Tomasz Suchan, Anahí Espíndola, Sereina Rutschmann, Brent C Emerson, Kevin Gori, Christophe Dessimoz, Nils Arrigo, Michał Ronikier, Nadir Alvarez
Determining phylogenetic relationships among recently diverged species has long been a challenge in evolutionary biology. Cytoplasmic DNA markers, which have been widely used, notably in the context of molecular barcoding, have not always proved successful in resolving such phylogenies. However, with the advent of next-generation-sequencing technologies and associated techniques of reduced genome representation, phylogenies of closely related species have been resolved at a much higher detail in the last couple of years...
June 21, 2017: Molecular Phylogenetics and Evolution
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