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Molecular Phylogenetics and Evolution

Tauana Junqueira Cunha, Sarah Lemer, Philippe Bouchet, Yasunori Kano, Gonzalo Giribet
Fissurellidae are marine gastropods with a worldwide distribution and a rich fossil record. We integrate molecular, geographical and fossil data to reconstruct the fissurellid phylogeny, estimate divergence times and investigate historical routes of oceanic dispersal. With five molecular markers for 143 terminals representing 27 genera, we resolve deep nodes and find that many genera (e.g., Emarginula, Diodora, Fissurella) are not monophyletic and need systematic revision. Several genera classified as Emarginulinae are recovered in Zeidorinae...
February 16, 2019: Molecular Phylogenetics and Evolution
Christophe Dufresnes, Menad Beddek, Dmitriy V Skorinov, Luca Fumagalli, Nicolas Perrin, Pierre-André Crochet, Spartak N Litvinchuk
Comparative molecular studies emphasized a new biogeographic paradigm for the terrestrial fauna of North Africa, one of the last uncharted ecoregions of the Western Palearctic: two independent east-west divisions across the Maghreb. Through a comprehensive nuclear phylogeography, we assessed how this model suits the genetic diversification documented for the tree frog Hyla meridionalis sensu lato. Analyses of mtDNA variation and thousands of nuclear loci confirmed the old split (low-Pliocene) between Tunisian and Algerian populations...
February 15, 2019: Molecular Phylogenetics and Evolution
Andrea A Cabrera, Jeroen P A Hoekendijk, Alex Aguilar, Susan G Barco, Simon Berrow, Dorete Bloch, Asunción Borrell, Haydée A Cunha, Luciano Dalla Rosa, Carolina P Dias, Pauline Gauffier, Wensi Hao, Scott Landry, Finn Larsen, Vidal Martín, Sally Mizroch, Tom Oosting, Nils Øien, Christophe Pampoulie, Simone Panigada, Rui Prieto, Christian Ramp, Vania E Rivera-Léon, Jooke Robbins, Conor Ryan, Elena Schall, Richard Sears, Mónica A Silva, Jorge Urbán, Frederick W Wenzel, Per J Palsbøll, Martine Bérubé
The advent of massive parallel sequencing technologies has resulted in an increase of studies based upon complete mitochondrial genome DNA sequences that revisit the taxonomic status within and among species. Spatially distinct monophyly in such mitogenomic genealogies, i.e., the sharing of a recent common ancestor among con-specific samples collected in the same region has been viewed as evidence for subspecies. Several recent studies in cetaceans have employed this criterion to suggest subsequent intraspecific taxonomic revisions...
February 13, 2019: Molecular Phylogenetics and Evolution
Andrew J Perkins
Hydrocotyle L. is a cosmopolitan genus, with approximately 150 species, of mostly perennial herbs in the family Araliaceae. The genus includes around 115 perennial and 35 annual species, with all annual species endemic to Australia. In this study, I used sequences of a nDNA marker (ETS) and two cpDNA markers (psbA-trnH and trnL-trnF) to reconstruct phylogenetic relationships among the annual species of Hydrocotyle. The final sampling included 21 species of Hydrocotyle and seven outgroup taxa. The phylogenetic analyses of the combined molecular dataset (i...
February 13, 2019: Molecular Phylogenetics and Evolution
Yunshi Liao, Ka Yan Ma, Sammy De Grave, Tomoyuki Komai, Tin-Yam Chan, Ka Hou Chu
One of the systematically controversial superfamilies in Caridea is the predominately deep-sea or cold water Pandaloidea, largely because this species-rich group of nearly 200 species in 25 genera exhibits a very high diversity of body forms and ecology. Although the relationships amongst the taxa within Pandaloidea have been repeatedly discussed based on morphology, no comprehensive molecular phylogeny exists. In this study, we present the first molecular phylogeny of the group, based on a combined dataset of two mitochondrial (12S and 16S rRNA) and six nuclear (ATP synthase β-subunit, enolase, glyceraldehyde-3-phosphate dehydrogenase, histone 3, phosphoenolpyruvate carboxykinase and sodium-potassium ATPase α-subunit) markers, based on 62 species (about 1/3 of known biodiversity) in 22 genera (88% of genera) of two pandaloid families (Pandalidae, Thalassocarididae) and outgroups from seven other caridean families...
February 12, 2019: Molecular Phylogenetics and Evolution
Yamama Naciri, Camille Christe, Sébastien Bétrisey, Yi-Gang Song, Min Deng, Giuseppe Garfì, Gregor Kozlowski
Zelkova species, trees of the elm family (Ulmaceae), are part of the Cenozoic relict flora. In western Eurasia, the genus comprises three species that are restricted to disjunct areas (Z. sicula on Sicily, Z. abelicea on Crete and Z. carpinifolia in Transcaucasia). The situation is different in East Asia, where three species (Z. serrata, Z. schneideriana and Z. sinica) have at least partly overlapping distributions. The phylogenetic and phylogeographic status of these East Asian species is still not well understood, mainly since all previous studies used almost exclusively plant material collected in botanical gardens and were based on very small numbers of individuals...
February 12, 2019: Molecular Phylogenetics and Evolution
Michael J Jowers, Santiago Sánchez-Ramírez, Susana Lopes, Igor Karyakin, Valery Dombrovski, Abdeljebbar Qninba, Thijs Valkenburg, Nuno Onofre, Nuno Ferrand, Pedro Beja, Luís Palma, Raquel Godinho
Population range expansions and contractions as a response to climate and habitat change throughout the Quaternary are known to have contributed to complex phylogenetic and population genetic events. Speciation patterns and processes in Palearctic buzzards (genus Buteo) are a long-standing example of morphological and genetic data incongruence, attributed to panmixia, habitat range shifts, contact zones, and climate change. Here we assess the systematics, phylogeography and population genetic structure of three nominal species of Palearctic buzzards, Buteo buteo (including B...
February 11, 2019: Molecular Phylogenetics and Evolution
Ka Yan Ma, Jing Qin, Chia-Wei Lin, Tin-Yam Chan, Peter K L Ng, Ka Hou Chu, Ling Ming Tsang
Recent fossil calibrated molecular phylogenies have revealed that the Brachyura underwent rapid radiation during the Cretaceous and Early Tertiary, resulting in many early diverging lineages separated by short internodes that remain difficult to resolve. Here we present the first phylogenomic analyses of Brachyura using transcriptome data from 30 brachyuran species and 22 families. Analyses were carried out on a dataset containing 372 putative homologous loci (246,590 bps) and included data from 22 newly generated transcriptomes...
February 11, 2019: Molecular Phylogenetics and Evolution
Yijun Ni, Xiaolin Ma, Wei Hu, David Blair, Mingbo Yin
The distribution and genetic diversity of freshwater zooplankton is understudied in the Eastern Palearctic. Here, we explored the lineage diversity and regional distribution of the genus Moina in China. Members of this genus are often keystone components of freshwater ecosystems and have been frequently subjected to toxicological and physiological studies. Four species of Moina were identified, based on morphology, in 50 of 113 Chinese water bodies examined, and their phylogenetic position was analyzed using both a mitochondrial (mitochondrial cytochrome c oxidase subunit I; COI) and a nuclear marker (the nuclear internal transcribed spacer; ITS-1)...
February 9, 2019: Molecular Phylogenetics and Evolution
Michael Knapp, Jessica E Thomas, James Haile, Stefan Prost, Simon Y W Ho, Nicolas Dussex, Sophia Cameron-Christie, Olga Kardailsky, Ross Barnett, Michael Bunce, M Thomas P Gilbert, R Paul Scofield
Prior to human arrival in the 13th century, two large birds of prey were the top predators in New Zealand. In the absence of non-volant mammals, the extinct Haast's eagle (Hieraaetus moorei), the largest eagle in the world, and the extinct Eyles' harrier (Circus teauteensis) the largest harrier in the world, had filled ecological niches that are on other landmasses occupied by animals such as large cats or canines. The evolutionary and biogeographic history of these island giants has long been a mystery. Here we reconstruct the origin and evolution of New Zealand's giant raptors using complete mitochondrial genome data...
February 9, 2019: Molecular Phylogenetics and Evolution
Jana Štundlová, Jiří Šmíd, Petr Nguyen, František Šťáhlavský
Over time, mountain biota has undergone complex evolutionary histories that have left imprints on its genomic arrangement, geographical distribution and diversity of contemporary lineages. Knowledge on these biogeographical aspects still lags behind for invertebrates inhabiting the Alpine region. In the present study, we examined three scorpion species of the subgenus Euscorpius (Alpiscorpius) from the European Alps using cytogenetic and molecular phylogenetic approaches to determine the variation and population structure of extant lineages at both chromosome and genetic level, and to provide an insight into the species diversification histories...
February 8, 2019: Molecular Phylogenetics and Evolution
Lucas C Marinho, Liming Cai, Xiaoshan Duan, Brad R Ruhfel, Pedro Fiaschi, André M Amorim, Cássio van den Berg, Charles C Davis
Clusieae is an exclusively Neotropical tribe in the family Clusiaceae sensu stricto. Although tribes within Clusiaceae are morphologically and phylogenetically well-delimited, resolution among genera within these tribes remains elusive. The tribe Clusieae includes an estimated ∼500 species distributed among five genera: Chrysochlamys, Clusia, Dystovomita, Tovomita, and Tovomitopsis. In this study, we used nearly complete plastid genomes from 30 exemplar Clusieae species representing all genera recognized, plus two outgroups to infer the phylogeny of the tribe using Maximum Likelihood and Bayesian Inference...
February 8, 2019: Molecular Phylogenetics and Evolution
Marek L Borowiec, Christian Rabeling, Seán G Brady, Brian L Fisher, Ted R Schultz, Philip S Ward
Knowledge of the internal phylogeny and evolutionary history of ants (Formicidae), the world's most species-rich clade of eusocial organisms, has dramatically improved since the advent of molecular phylogenetics. A number of relationships at the subfamily level, however, remain uncertain. Key unresolved issues include placement of the root of the ant tree of life and the relationships among the so-called poneroid subfamilies. Here we assemble a new data set to attempt a resolution of these two problems and carry out divergence dating, focusing on the age of the root node of crown Formicidae...
February 7, 2019: Molecular Phylogenetics and Evolution
Gang Yao, Jian-Jun Jin, Hong-Tao Li, Jun-Bo Yang, Venkata Shiva Mandala, Matthew Croley, Rebecca Mostow, Norman A Douglas, Mark W Chase, Maarten J M Christenhusz, Douglas E Soltis, Pamela S Soltis, Stephen A Smith, Samuel F Brockington, Michael J Moore, Ting-Shuang Yi, De-Zhu Li
The Caryophyllales includes 40 families and 12,500 species, representing a large and diverse clade of angiosperms. Collectively, members of the clade grow on all continents and in all terrestrial biomes and often occupy extreme habitats (e.g., xeric, salty). The order is characterized by many taxa with unusual adaptations including carnivory, halophytism, and multiple origins of C4 photosynthesis. However, deep phylogenetic relationships within the order have long been problematic due to putative rapid divergence...
February 5, 2019: Molecular Phylogenetics and Evolution
Tuliana O Brunes, André Justino da Silva, Sergio Marques-Souza, Miguel T Rodrigues, Katia C M Pellegrino
In vertebrates, true parthenogenesis is found only in squamate reptiles and (mostly) originates via interspecific hybridization after a secondary contact. In many cases, parthenogenesis is followed by an increase of ploidy, resulting in triploid lineages. Phylogenetic analyses derived from nuclear and maternally inherited markers can help to clarify the mechanisms of origin and the potential parental species involved. In the Amazon region, parthenogenetic lizards of the Loxopholis percarinatum complex are widely distributed, comprising both diploid and triploid clones...
February 4, 2019: Molecular Phylogenetics and Evolution
Elyse Parker, Alex Dornburg, Omar Domínguez-Domínguez, Kyle R Piller
A major emerging challenge to resolution of a stable phylogenetic Tree of Life has been incongruent inference among studies. Given the increasing ubiquity of incongruent studies, analyzing the predicted phylogenetic utility and quantitative evidence regarding contributions toward resolution of commonly-used markers in historical studies over the last decade represents an important, yet neglected, component of phylogenetics. Here we examine the phylogenetic utility of two sets of commonly-used legacy markers for understanding the evolutionary relationships among goodeines, a group of viviparous freshwater fishes endemic to central Mexico...
February 4, 2019: Molecular Phylogenetics and Evolution
Robert C Jadin, Christopher Blair, Michael J Jowers, Anthony Carmona, John C Murphy
The Brown Vine Snake, Oxybelis aeneus, is considered a single species despite the fact its distribution covers an estimated 10% of the Earth's land surface, inhabiting a variety of ecosystems throughout North, Central, and South America and is distributed across numerous biogeographic barriers. Here we assemble a multilocus molecular dataset (i.e. cyt b, ND4, cmos, PRLR) derived from Middle American populations to examine for the first time the evolutionary history of Oxybelis and test for evidence of cryptic lineages using Bayesian and maximum likelihood criteria...
February 1, 2019: Molecular Phylogenetics and Evolution
Christina Schilde, Hajara M Lawal, Koryu Kin, Ikumi Shibano-Hayakawa, Kei Inouye, Pauline Schaap
The Dictyostelid social amoebas are a popular model system for cell- and developmental biology and for evolution of sociality. Small subunit (SSU) ribosomal DNA-based phylogenies subdivide the known 150 species into four major and some minor groups, but lack resolution within groups, particularly group 4, and, as shown by genome-based phylogenies of 11 species, showed errors in the position of the root and nodes separating major clades. We are interested in the evolution of cell-type specialization, which particularly expanded in group 4...
January 31, 2019: Molecular Phylogenetics and Evolution
Piotr Wasąg, Tomasz Grajkowski, Anna Suwińska, Marta Lenartowska, Robert Lenartowski
Calreticulin (CRT) is a multifunctional resident endoplasmic reticulum (ER) luminal protein implicated in regulating a variety of cellular processes, including Ca2+ storage/mobilization and protein folding. These multiple functions may be carried out by different CRT genes and protein isoforms. The plant CRT family consist of three genes: CRT1 and CRT2 classified in the common subclass (CRT1/2), and CRT3. These genes are highly conserved during evolution end encode three different protein products (CRT1, 2 and 3)...
January 31, 2019: Molecular Phylogenetics and Evolution
Rima Soli, Belhassen Kaabi, Mourad Barhoumi, Chokri Maktoof, Sami Ben-Hadj Ahmed
The influenza-A virus (IAV) causes seasonal epidemics and presents a pandemic risk with the possibility of genetic re-assortment, allowing the emergence of new strains. The evolution of IAVes is done most often by relatively frequent re-assortment between gene segments, but the hypothesis of their evolution by recombination between RNA segments has not been justified to this date. Here, we examine this hypothesis by Bayesian phylogenetic analysis, to test if recombination events have occurred between genomic RNA segments...
January 29, 2019: Molecular Phylogenetics and Evolution
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