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Molecular Phylogenetics and Evolution

Jorge Doña, Andrew D Sweet, Kevin P Johnson, David Serrano, Sergey Mironov, Roger Jovani
Host-shift speciation and cospeciation are the two major processes driving symbiont macroevolutionary diversification. Cospeciation is expected to be frequent in vertically transmitted and host-specific symbionts, and leads to congruent host-symbiont phylogenies. However, the cophylogenetic dynamics of many groups of highly specialized host-specific symbionts is largely unstudied. Thus, the relevance of cospeciation vs. host-shift speciation remains largely unknown. Here, we investigated this question by performing the largest cophylogenetic study of feather mites to date, using both distance and event-based cophylogenetic methods...
August 12, 2017: Molecular Phylogenetics and Evolution
Nicolas J Rawlence, Charlotte E Till, Luke J Easton, Hamish G Spencer, Rob Schuckard, David S Melville, R Paul Scofield, Alan J D Tennyson, Matt J Rayner, Jonathan M Waters, Martyn Kennedy
New Zealand's endemic King Shag (Leucocarbo carunculatus) has occupied only a narrow portion of the northeastern South Island for at least the past 240years. However, pre-human Holocene fossil and archaeological remains have suggested a far more widespread distribution of the three Leucocarbo species (King, Otago, Foveaux) on mainland New Zealand at the time of Polynesian settlement in the late 13th Century CE. We use modern and ancient DNA, and morphometric and osteological analyses, of modern King Shags and Holocene fossil Leucocarbo remains to assess the pre-human distribution and taxonomic status of the King Shag on mainland New Zealand, and the resultant conservation implications...
August 10, 2017: Molecular Phylogenetics and Evolution
Maciej Pabijan, Piotr Zieliński, Katarzyna Dudek, Michał Stuglik, Wiesław Babik
Because reproductive isolation often evolves gradually, differentiating lineages may retain the potential for genetic exchange for prolonged periods, providing an opportunity to quantify and to understand the fundamental role of gene flow during speciation. Here we delimit evolutionary lineages, reconstruct the phylogeny and infer gene flow in newts of the Lissotriton vulgaris species complex based on 74 nuclear markers sampled from 127 localities. We demonstrate that distinct lineages along the speciation continuum in newts exchange nontrivial amounts of genes, affecting their evolutionary trajectories...
August 7, 2017: Molecular Phylogenetics and Evolution
Joseph W Brown, Ning Wang, Stephen A Smith
Recent developments in phylogenetic methods and data acquisition have allowed for the construction of large and comprehensive phylogenetic relationships. Published phylogenies represent an enormous resource that not only facilitates the resolution of questions related to comparative biology, but also provides a resource on which to gauge the development of concordance across the tree of life. From the Open Tree of Life, we gathered 290 avian phylogenies representing all major groups that have been published over the last few decades and analyzed how concordance and conflict develop among these trees through time...
August 7, 2017: Molecular Phylogenetics and Evolution
Angelo Poliseno, Christian Feregrino, Stéphane Sartoretto, Didier Aurelle, Gert Wörheide, Catherine S McFadden, Sergio Vargas
Molecular analyses of the ecologically important gorgonian octocoral genus Leptogorgia are scant and mostly deal with few species from restricted geographical regions. Here we explore the phylogenetic relationships and the evolutionary history of Leptogorgia using the complete mitochondrial genomes of six Leptogorgia species from different localities in the Atlantic, Mediterranean and eastern Pacific as well as four other genera of Gorgoniidae and Plexauridae. Our mitogenomic analyses showed high inter-specific diversity, variable nucleotide substitution rates and, for some species, novel genomic features such as ORFs of unknown function...
August 4, 2017: Molecular Phylogenetics and Evolution
Ayed R A Alanzi, James H Degnan
Methods for inferring species trees from gene trees motivated by incomplete lineage sorting typically use either rooted gene trees to infer a rooted species tree, or use unrooted gene trees to infer an unrooted species tree, which is then typically rooted using one or more outgroups. Theoretically, however, it has been known since 2011 that it is possible to consistently infer the root of the species tree directly from unrooted gene trees without assuming an outgroup. Here, we use approximate Bayesian computation to infer the root of the species tree from unrooted gene trees assuming the multispecies coalescent model...
August 2, 2017: Molecular Phylogenetics and Evolution
Toon Janssen, Gerrit Karssen, Valeria Orlando, Sergei A Subbotin, Wim Bert
Root-lesion nematodes of the genus Pratylenchus are an important pest parasitizing a wide range of vascular plants including several economically important crops. However, morphological diagnosis of the more than 100 species is problematic due to the low number of diagnostic features, high morphological plasticity and incomplete taxonomic descriptions. In order to employ barcoding based diagnostics, a link between morphology and species specific sequences has to be established. In this study, we reconstructed a multi-gene phylogeny of the Penetrans group using nuclear ribosomal and mitochondrial gene sequences...
August 1, 2017: Molecular Phylogenetics and Evolution
P A Eyer, R Seltzer, T Reiner-Brodetzki, A Hefetz
Although extensive research has been carried out on the desert ants in the genus Cataglyphis in recent years, some of the specific intra- and interspecific relationships remain elusive. The present study disentangles the phylogenetic relationships among the C. bicolor complex in Israel using an integrative approach based on genetic markers, morphometric measurements, and chemical analyses (cuticular hydrocarbons). Several species delimitation approaches based on four nuclear, two mitochondrial, and eleven microsatellite markers, as well as 16 body measurements and 56 chemical variables, were employed to deciphering the occurrence of cryptic species in our data set...
July 31, 2017: Molecular Phylogenetics and Evolution
Jing Sun, Samuel W James, Jibao Jiang, Bo Yao, Liangliang Zhang, Manqiang Liu, Jiangping Qiu, Feng Hu
Our knowledge of the phylogeny of the earthworm genus Amynthas under the family Megascolecidae, which is comprised of a huge number of species, is very limited compared to the better-known and much smaller family Lumbricidae. In order to investigate the phylogenetic relationships among the species within the genus Amynthas, which is the largest genus of the Megascolecidae family, nuclear and mitochondrial DNA sequences of 77 species, including 76 in-group Amynthas species collected from South China and 1 out-group species, were analyzed...
July 29, 2017: Molecular Phylogenetics and Evolution
Gregorio V Linchangco, David W Foltz, Rob Reid, John Williams, Conor Nodzak, Alexander M Kerr, Allison K Miller, Rebecca Hunter, Nerida G Wilson, William J Nielsen, Christopher L Mah, Greg W Rouse, Gregory A Wray, Daniel A Janies
Multi-locus phylogenetic studies of echinoderms based on Sanger and RNA-seq technologies and the fossil record have provided evidence for the Asterozoa-Echinozoa hypothesis. This hypothesis posits a sister relationship between asterozoan classes (Asteroidea and Ophiuroidea) and a similar relationship between echinozoan classes (Echinoidea and Holothuroidea). Despite this consensus around Asterozoa-Echinozoa, phylogenetic relationships within the class Asteroidea (sea stars or starfish) have been controversial for over a century...
July 27, 2017: Molecular Phylogenetics and Evolution
Belinda Kahnt, Graham A Montgomery, Elizabeth Murray, Michael Kuhlmann, Anton Pauw, Denis Michez, Robert J Paxton, Bryan N Danforth
Despite close ecological interactions between plants and their pollinators, only some highly specialised pollinators adapt to a specific host plant trait by evolving a bizarre morphology. Here we investigated the evolution of extremely elongated forelegs in females of the South African bee genus Rediviva (Hymenoptera: Melittidae), in which long forelegs are hypothesised to be an adaptation for collecting oils from the extended spurs of their Diascia host flowers. We first reconstructed the phylogeny of the genus Rediviva using seven genes and inferred an origin of Rediviva at around 29MYA (95% HPD=19...
July 27, 2017: Molecular Phylogenetics and Evolution
S J Scheffer, K A Davies, G S Taylor, A H Thornhill, M L Lewis, I S Winkler, D K Yeates, M F Purcell, J Makinson, R M Giblin-Davis
This study investigated host-specificity and phylogenetic relationships in Australian galling flies, Fergusonina Malloch (Diptera: Fergusoninidae), in order to assess diversity and explore the evolutionary history of host plant affiliation and gall morphology. A DNA barcoding approach using COI data from 203 Fergusonina specimens from 5gall types on 56 host plant species indicated 85 presumptive fly species. These exhibited a high degree of host specificity; of the 40 species with multiple representatives, each fed only on a single host genus, 29 (72...
July 27, 2017: Molecular Phylogenetics and Evolution
Yunshi Liao, Sammy De Grave, Tsz Wai Ho, Brian H Y Ip, Ling Ming Tsang, Tin-Yam Chan, Ka Hou Chu
Caridean shrimps constitute one of the most diverse groups of decapod crustaceans, notwithstanding their poorly resolved infraordinal relationships. One of the systematically controversial families in Caridea is the predominantly pelagic Pasiphaeidae, comprises 101 species in seven genera. Pasiphaeidae species exhibit high morphological disparity, as well as ecological niche width, inhabiting shallow to very deep waters (>4000m). The present work presents the first molecular phylogeny of the family, based on a combined dataset of six mitochondrial and nuclear gene markers (12S rDNA, 16S rDNA, histone 3, sodium-potassium ATPase α-subunit, enolase and ATP synthase β-subunit) from 33 species belonged to six genera of Pasiphaeidae with 19 species from 12 other caridean families as outgroup taxa...
July 26, 2017: Molecular Phylogenetics and Evolution
Wilson J E M Costa, Pedro F Amorim, José Leonardo O Mattos
The rich biological diversity of South America has motivated a series of studies associating evolution of endemic taxa with the dramatic geologic and climatic changes that occurred during the Cainozoic. The organism here studied is the killifish tribe Cynolebiini, a group of seasonal fishes uniquely inhabiting temporary pools formed during the rainy seasons. The Cynolebiini are found in open vegetation areas inserted in the main tropical and subtropical South American phytogeographical regions east of the Andes...
July 25, 2017: Molecular Phylogenetics and Evolution
Xiuwen Zhang, Peter J Unmack, Gerald Kuchling, Yinan Wang, Arthur Georges
Pseudemydura umbrina is one of the most endangered turtle species in the world, and the imperative for its conservation is its distinctive morphology and relict status among the Chelidae. We use Illumina sequencing to obtain the complete mitogenome for resolving its uncertain phylogenetic position. A novel nuclear paralogue confounded the assembly, and resolution of the authentic mitogenome required further Sanger sequencing. The P. umbrina mitogenome is 16,414bp comprising 37 genes organized in a conserved pattern for other vertebrates...
July 25, 2017: Molecular Phylogenetics and Evolution
Rute B Clemente-Carvalho, Marcos Vaira, Laura E King, Daria Koscinski, Maria I Bonansea, Stephen C Lougheed
The Yungas Redbelly Toad, Melanophryniscus rubriventris, is patchily distributed in Argentina, confined to the upland portion (1000 to 2000 meters above sea level) of the montane forests of northern and central regions of Salta, and in central-eastern and south-eastern Jujuy. This species is known for its striking aposematic color variation across its geographic distribution, and was once treated as a complex of three subspecies based on distinctive color patterns. Here we assess the geographical genetic variation within M...
July 24, 2017: Molecular Phylogenetics and Evolution
Alexander N Schmidt-Lebuhn, Nicola C Aitken, Aaron Chuah
Datasets of hundreds or thousands of SNPs (Single Nucleotide Polymorphisms) from multiple individuals per species are increasingly used to study population structure, species delimitation and shallow phylogenetics. The principal software tool to infer species or population trees from SNP data is currently the BEAST template SNAPP which uses a Bayesian coalescent analysis. However, it is computationally extremely demanding and tolerates only small amounts of missing data. We used simulated and empirical SNPs from plants (Australian Craspedia, Asteraceae, and Pelargonium, Geraniaceae) to compare species trees produced (1) by SNAPP, (2) using SVD quartets, and (3) using Bayesian and parsimony analysis with several different approaches to summarising data from multiple samples into one set of traits per species...
July 22, 2017: Molecular Phylogenetics and Evolution
Christer Erséus, Ida Envall, Pierre De Wit, Lena M Gustavsson
The phylogenetic relationships within Naidinae (Annelida, Clitellata, Naididae) were investigated, using six molecular markers, both mitochondrial (12S rDNA, 16S rDNA, the COI gene) and nuclear (18S rDNA, 28S rDNA, the ITS region). Thirty-seven nominal species, representing 16 of the 22 genera recognized in the subfamily, were included, and the Nais communis/variabilis species complex was represented by six different morphotypes. Ten other species of Naididae were selected as outgroups. The data were analysed by Bayesian inference and Maximum Likelihood...
July 22, 2017: Molecular Phylogenetics and Evolution
Yun-Juan Zuo, Jun Wen, Shi-Liang Zhou
The intercontinental biogeography between eastern Asia and eastern North America has attracted much attention from evolutionary biologists. Further insights into understanding the evolution of the intercontinental disjunctions have been hampered by the lack of studies on the intracontinental biogeography in eastern Asia, a region with complex geology, geography, climates and habitats. Herein we studied the biogeographic history of the eastern Asian-eastern North American disjunct genus Panax with special emphasis on the investigation of its uneven diversification in Asia...
July 22, 2017: Molecular Phylogenetics and Evolution
Matthew Wilding, Matthias Nachtschatt, Robert Speight, Colin Scott
Numerous tools to generate phylogenetic estimates are available, but there is no single protocol that will produce an accurate phylogenetic tree for any dataset. Here, we investigated some of those tools, paying particular attention to different alignment algorithms, in order to produce a phylogeny for the integral membrane fatty acid desaturase (FAD) family. Herein, we report a novel streamlined protocol which utilises peptide pattern recognition (PPR). This protocol can theoretically be applied universally to generate accurate multiple sequence alignments and improve downstream phylogenetic analyses...
July 21, 2017: Molecular Phylogenetics and Evolution
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