Molecular phylogeny of Caudofoveata (Mollusca) challenges traditional views
Publication date: Available online 10 November 2018Source: Molecular Phylogenetics and EvolutionAuthor(s): Nina T. Mikkelsen, Christiane Todt, Kevin M. Kocot, Kenneth M. Halanych, Endre WillassenAbstractThe shell-less, worm-shaped Caudofoveata (=Chaetodermomorpha) is one of the least known group of molluscs. The taxon consists of 141 recognized species found from intertidal environments to the deep-sea where they live burrowing in sediment. Evolutionary relationships of the group have been debated, but few studies based on morphological or molecular data have investigated the phylogeny of the group. Here we use molecular p...
Source: Molecular Phylogenetics and Evolution - November 11, 2018 Category: Molecular Biology Source Type: research

Core genome phylogenetic analysis of the avian associated Borrelia turdi indicates a close relationship to Borrelia garinii
Publication date: Available online 10 November 2018Source: Molecular Phylogenetics and EvolutionAuthor(s): Gabriele Margos, Noémie S. Becker, Volker Fingerle, Andreas Sing, Jaime Albino Ramos, Isabel Lopes de Carvalho, Ana Claudia NorteAbstractBorrelia burgdorferi sensu lato comprises a species complex of tick-transmitted bacteria that includes the agents of human Lyme borreliosis. Borrelia turdi is a genospecies of this complex that exists in cryptic transmission cycles mainly between ornithophilic tick vectors and their avian hosts. The species has been originally discovered in avian transmission cycles in Asia bu...
Source: Molecular Phylogenetics and Evolution - November 11, 2018 Category: Molecular Biology Source Type: research

The complex study of complexes: The first well-supported phylogeny of two species complexes within genus Caridina (Decapoda: Caridea: Atyidae) sheds light on evolution, biogeography, and habitat
In this study we used next generation sequencing (NGS) to provide new insights into the phylogenetic relationships among the genus Caridina, focusing on two complexes: ‘Caridina nilotica’ and ‘Caridina weberi’. We collected 92 specimens belonging to these two groups from most of their known geographical range, representing 50 species, for which we sequenced seven mitochondrial genes and two nuclear markers using ion torrent NGS. We performed a phylogenetic analysis, which yielded the first well-supported tree for the genus Caridina. On this tree were mapped the geographic ranges and the habitats use...
Source: Molecular Phylogenetics and Evolution - November 11, 2018 Category: Molecular Biology Source Type: research

Four hundred shades of brown: Higher level phylogeny of the problematic Euptychiina (Lepidoptera, Nymphalidae, Satyrinae) based on hybrid enrichment data
This study represents a critical step towards resolving the higher classification and studying the evolution of this highly diverse lineage.Graphical abstract (Source: Molecular Phylogenetics and Evolution)
Source: Molecular Phylogenetics and Evolution - November 11, 2018 Category: Molecular Biology Source Type: research

Integrating phylogenomics, phylogenetics, morphometrics, relative genome size and ecological niche modelling disentangles the diversification of Eurasian Euphorbia seguieriana s. l. (Euphorbiaceae)
In this study, we used a combination of phylogenomic (with RADseq data) and phylogenetic (with sequences of the nuclear internal transcribed spacer, ITS) methods to explore relationships within the taxonomically intricate Euphorbia seguieriana s. l., one of the most widespread Euphorbia taxa inhabiting zonal and extrazonal steppes from Iberia to Central Asia. In the inferred phylogenies the southeastern Balkan and Anatolian populations were clearly separated, supporting the distinction of E. niciciana from E. seguieriana at the species level. Within E. seguieriana, the populations from the Caucasus, Iran, and easternmost A...
Source: Molecular Phylogenetics and Evolution - November 9, 2018 Category: Molecular Biology Source Type: research

Genetic diversity and hybrid formation in Central European club-mosses (Diphasiastrum, Lycopodiaceae) – new insights from cp microsatellites, two nuclear markers and AFLP
Publication date: Available online 9 November 2018Source: Molecular Phylogenetics and EvolutionAuthor(s): Martin Schnittler, Karsten Horn, Rico Kaufmann, Radvilė Rimgailė-Voicik, Anja Klahr, Manuela Bog, Jörg Fuchs, H. Wilfried BennertAbstractIn Europe, the genus Diphasiastrum (Lycopodiophyta) forms a reticulate network of six diploid taxa, including three parent species (D. alpinum, D. complanatum and D. tristachyum) and three hybrids (D. × issleri, D. × oellgaardii and D. × zeilleri). It was not clear if the hybrids arose once or repeatedly, if they have reproductive competence and if backcrossin...
Source: Molecular Phylogenetics and Evolution - November 9, 2018 Category: Molecular Biology Source Type: research

Morphology, geographic distribution, and host preferences are poor predictors of phylogenetic relatedness in the mistletoe genus Viscum L
Publication date: Available online 3 November 2018Source: Molecular Phylogenetics and EvolutionAuthor(s): Karola Maul, Michael Krug, Daniel L. Nickrent, Kai F. Müller, Dietmar Quandt, Susann WickeAbstractBesides their alleged therapeutic effects, mistletoes of the genus Viscum L. (Viscaceae) are keystone species in many ecosystems across Europe, Africa, Asia and Australia because of their complex faunal interactions. We here reconstructed the evolutionary history of Viscum based on plastid and nuclear DNA sequence data. We obtained a highly resolved phylogenetic tree with ten well-supported clades, which we used to un...
Source: Molecular Phylogenetics and Evolution - November 4, 2018 Category: Molecular Biology Source Type: research

Distinct molecular evolution of influenza H3N2 strains in the 2016/17 season and its implications for vaccine effectiveness
Publication date: Available online 3 November 2018Source: Molecular Phylogenetics and EvolutionAuthor(s): Jin Il Kim, Sehee Park, Hyuk Chu, Ilseob Lee, Joon-Yong Bae, Kirim Yoo, Juwon Kim, Joo-Yeon Lee, Namju Lee, Miseon Kim, Jun-Sub Kim, Kyung Wook Hong, Kyung Ran Jun, Jeong Nyeo Lee, Kisoon Kim, Man-Seong ParkAbstractInfluenza virus is a respiratory pathogen that causes seasonal epidemics by resulting in a considerable number of influenza-like illness (ILI) patients. During the 2016/17 season, ILI rates increased unusually earlier and higher than previous seasons in Korea, and most viral isolates were subtyped as H3N2 st...
Source: Molecular Phylogenetics and Evolution - November 4, 2018 Category: Molecular Biology Source Type: research

Mitochondrial phylogenomics of the Hymenoptera
Publication date: Available online 3 November 2018Source: Molecular Phylogenetics and EvolutionAuthor(s): Pu Tang, Jia-chen Zhu, Bo-yin Zheng, Shu-jun Wei, M. Sharkey, Xue-xin Chen, A.P. VoglerAbstractThe insect order Hymenoptera presents marvelous morphological and ecological diversity. Higher-level hymenopteran relationships remain controversial, even after recent phylogenomic analyses, as their taxon sampling was limited. To shed light on the origin and diversification of Hymenoptera, in particular the poorly studied Parasitica, we undertook phylogenetic analyses of 40 newly and 43 previously sequenced mitochondrial gen...
Source: Molecular Phylogenetics and Evolution - November 4, 2018 Category: Molecular Biology Source Type: research

Gene-wise resampling outperforms site-wise resampling in phylogenetic coalescence analyses
Publication date: Available online 2 November 2018Source: Molecular Phylogenetics and EvolutionAuthor(s): Mark P. Simmons, Daniel B. Sloan, Mark S. Springer, John GatesyAbstractIn summary (“two-step”) coalescent analyses of empirical data, researchers typically apply the bootstrap to quantify branch support for clades inferred on the optimal species tree. We tested whether site-wise bootstrap analyses provide consistently more conservative support than gene-wise bootstrap analyses. We did so using data from three empirical phylogenomic studies and employed four coalescent methods (ASTRAL, MP-EST, NJst, and STAR...
Source: Molecular Phylogenetics and Evolution - November 3, 2018 Category: Molecular Biology Source Type: research

Crassula, insights into an old, arid-adapted group of southern African leaf-succulents
Publication date: Available online 2 November 2018Source: Molecular Phylogenetics and EvolutionAuthor(s): P.V. Bruyns, P. Hanáček, C. KlakAbstractThe Crassulaceae is an important family in the Greater Cape Floristic Region of southern Africa and is the seventh largest family in the arid Succulent Karoo Biome. After the Aizoaceae it is the largest group of leaf-succulents in southern Africa.This is the first investigation of a broad selection (68%) of the ± 170 species of Crassula. We used data from three chloroplast and two nuclear gene-regions, which yielded many informative characters and provided good res...
Source: Molecular Phylogenetics and Evolution - November 3, 2018 Category: Molecular Biology Source Type: research

Antarctic and sub-Antarctic Nacella limpets reveal novel evolutionary characteristics of mitochondrial genomes in Patellogastropoda
Publication date: Available online 3 November 2018Source: Molecular Phylogenetics and EvolutionAuthor(s): Juan D. Gaitán-Espitia, Claudio A. González-Wevar, Elie Poulin, Leyla CardenasAbstractMitochondrial genomes (mitogenomes) provide valuable phylogenetic information and genome-level characters that are useful in resolving evolutionary relationships within major lineages of gastropods. However, for more than one decade, these relationships and the phylogenetic position of Patellogastropoda have been inferred based on the genomic architecture as well as the nucleotide and protein sequences of a single repres...
Source: Molecular Phylogenetics and Evolution - November 3, 2018 Category: Molecular Biology Source Type: research

A new Cardinium group of bacteria found in Achipteria coleoptrata (Acari: Oribatida)
Publication date: Available online 1 November 2018Source: Molecular Phylogenetics and EvolutionAuthor(s): Edyta Konecka, Ziemowit OlszanowskiAbstractThe understanding of the biology of arthropods requires an understanding of their bacterial associates. We determined the distribution of bacteria Wolbachia sp., Rickettsia sp., Cardinium sp., Spiroplasma sp., Arsenophonus sp., Hamiltonella sp., and Flavobacterium in oribatid mites (Acari: Oribatida). We identified Cardinium sp. in Achipteria coleoptrata. This is the first report of this bacterium in A. coleoptrata. Approximately 30% of the mite population was infected by Card...
Source: Molecular Phylogenetics and Evolution - November 2, 2018 Category: Molecular Biology Source Type: research

Anchored hybrid enrichment phylogenomics resolves the backbone of erebine moths
This study demonstrates the utility of anchored phylogenomics for resolving relationships within subfamilies of Lepidoptera.Graphical abstract (Source: Molecular Phylogenetics and Evolution)
Source: Molecular Phylogenetics and Evolution - November 2, 2018 Category: Molecular Biology Source Type: research

Near-complete phylogeny and taxonomic revision of the world’s babblers (Aves: Passeriformes)
In this study, we used five mitochondrial and seven nuclear loci to generate a dated phylogeny for babblers. This phylogeny includes 402 species (ca. 89% of the overall clade) from 75 genera (97%) and all five currently recognized families, providing a robust basis for taxonomic revision. Our phylogeny supports seven major clades and reveals several non-monophyletic genera. Divergence time estimates indicate that the seven major clades diverged around the same time (18–20 million years ago, Ma) in the early Miocene. We use the phylogeny in a consistent way to propose a new taxonomy, with seven families and 64 gener...
Source: Molecular Phylogenetics and Evolution - November 2, 2018 Category: Molecular Biology Source Type: research

Exploring Chihuahuan Desert diversification in the gray-banded kingsnake, Lampropeltis alterna (Serpentes: Colubridae)
Publication date: Available online 31 October 2018Source: Molecular Phylogenetics and EvolutionAuthor(s): Edward A. Myers, Robert W. Bryson, Robert W. Hansen, Matthew L. Aardema, David Lazcano, Frank T. BurbrinkAbstractWithin many biomes, the cause of phylogeographic structure remains unknown even across regions throughout North America, including within the biodiverse Chihuahuan Desert. For example, little is known about population structure or the diming of diversification of Chihuahuan endemics. In part, this is due largely to the lack of population genomic studies within this region. We generated ultra-conserved elemen...
Source: Molecular Phylogenetics and Evolution - October 31, 2018 Category: Molecular Biology Source Type: research

Tip-dating and the Origin of Telluraves
Publication date: Available online 29 October 2018Source: Molecular Phylogenetics and EvolutionAuthor(s): Nicholas M.A. Crouch, Karolis Ramanauskas, Boris IgićAbstractDespite a relatively vast accumulation of molecular data, the timing of diversification of modern bird lineages remains elusive. Accurate dating of the origination of Telluraves—a clade of birds defined by their arboreality—is of particular interest, as it contains the most species-rich avian group, the passerines. Historically, neontological studies have estimated a Cretaceous origin for the group, but more recent studies have recovered Cenozoic...
Source: Molecular Phylogenetics and Evolution - October 30, 2018 Category: Molecular Biology Source Type: research

New insights into the Usnea cornuta aggregate (Parmeliaceae, lichenized Ascomycota): Molecular analysis reveals high genetic diversity correlated with chemistry
In this study, we applied an integrative approach based on DNA sequence, chemical, geographic and morphological data to attempt to define species boundaries in the lichen-forming genus Usnea (Parmeliaceae), particularly the U. cornuta aggregate, a cosmopolitan species group. We provide the first species delimitation for this group in the neotropics based on the multispecies coalescent (MSC) model. Using ITS rDNA and two protein-coding genes, Mcm7 and RPB1, we estimated the species tree under the MSC model in a Bayesian framework using STACEY. Our results indicate that at least nine strongly supported distinct lineages coex...
Source: Molecular Phylogenetics and Evolution - October 30, 2018 Category: Molecular Biology Source Type: research

The multiple genotypes of Ophiocordyceps sinensis and the “ITS pseudogene” hypothesis
Publication date: Available online 28 October 2018Source: Molecular Phylogenetics and EvolutionAuthor(s): Jia-Shi Zhu, Yu-Ling Li, Yi-Sang Yao, Wei-Dong Xie (Source: Molecular Phylogenetics and Evolution)
Source: Molecular Phylogenetics and Evolution - October 29, 2018 Category: Molecular Biology Source Type: research

Phylogeography and evolution of infectious hematopoietic necrosis virus in China
In this study, a comprehensive analysis of 40 IHNV viruses isolated from thirteen fish farms in nine geographically dispersed Chinese provinces during 2012 to 2017 is presented. Identity of nucleotide and amino acid sequences among all the complete glycoprotein (G) genes from Chinese isolates was 98.0-100% and 96.7-100%, respectively. Coalescent phylogenetic analyses revealed that all the Chinese IHN virus characterized in this study were in a monophyletic clade that had a most recent common ancestor with the J Nagano (JN) subgroup within the J genogroup of IHNV. Within the Chinese IHNV clade isolates obtained over success...
Source: Molecular Phylogenetics and Evolution - October 26, 2018 Category: Molecular Biology Source Type: research

The phylogenetic placement of the enigmatic Indian Cormorant, Phalacrocorax fuscicollis (Phalacrocoracidae)
Publication date: Available online 25 October 2018Source: Molecular Phylogenetics and EvolutionAuthor(s): Martyn Kennedy, Sampath S. Seneviratne, Nicolas J. Rawlence, Shakila Ratnayake, Hamish G. SpencerAbstractThe Indian Cormorant (Phalacrocorax fuscicollis) is a common avian piscivore that occurs throughout the Indian subcontinent and east to southern Vietnam. Its evolutionary relationships, however, have remained obscure, largely because of a lack of material available for either osteological or genetic analysis. Here we show using DNA-sequence data from both nuclear and mitochondrial genes that this species is sister t...
Source: Molecular Phylogenetics and Evolution - October 26, 2018 Category: Molecular Biology Source Type: research

Multi-allele species reconstruction using ASTRAL
Publication date: Available online 26 October 2018Source: Molecular Phylogenetics and EvolutionAuthor(s): Maryam Rabiee, Erfan Sayyari, Siavash MirarabAbstractGenome-wide phylogeny reconstruction is becoming increasingly common, and one driving factor behind these phylogenomic studies is the promise that the potential discordance between gene trees and the species tree can be modeled. Incomplete lineage sorting is one cause of discordance that bridges population genetic and phylogenetic processes. ASTRAL is a species tree reconstruction method that seeks to find the tree with minimum quartet distance to an input set of inf...
Source: Molecular Phylogenetics and Evolution - October 26, 2018 Category: Molecular Biology Source Type: research

Diversification and historical demography of the rapid racerunner (Eremias velox) in relation to geological history and Pleistocene climatic oscillations in arid Central Asia
Publication date: Available online 26 October 2018Source: Molecular Phylogenetics and EvolutionAuthor(s): Jinlong Liu, Xianguang Guo, Dali Chen, Jun Li, Bisong Yue, Xiaomao ZengAbstractLate Cenozoic stepwise aridification has transformed Central Asia into an arid environment, and the Pleistocene climatic oscillations exerted further ecological impact. Therefore, both aridification and glaciation would have considerably influenced the evolution of many midlatitude species in arid Central Asia (ACA). However, strong biotic evidence supporting this role is still lacking. Here, we test this perspective using a phylogeographic ...
Source: Molecular Phylogenetics and Evolution - October 26, 2018 Category: Molecular Biology Source Type: research

Nuclear introns help unravel the diversification history of the Australo-Pacific Petroica robins
Publication date: Available online 25 October 2018Source: Molecular Phylogenetics and EvolutionAuthor(s): Anna M. Kearns, John F. Malloy, Matthias K. Gobbert, Aude Thierry, Leo Joseph, Amy C. Driskell, Kevin E. OmlandAbstractAustralo-Pacific Petroica robins are known for their striking variability in sexual plumage coloration. Molecular studies in recent years have revised the taxonomy of species and subspecies boundaries across the southwest Pacific and New Guinea. However, these studies have not been able to resolve phylogenetic relationships within Petroica owing to limited sampling of the nuclear genome. Here, we seque...
Source: Molecular Phylogenetics and Evolution - October 25, 2018 Category: Molecular Biology Source Type: research

Ancient DNA of crested penguins: Testing for temporal genetic shifts in the world’s most diverse penguin clade
Publication date: Available online 25 October 2018Source: Molecular Phylogenetics and EvolutionAuthor(s): Theresa L. Cole, Nicolas J. Rawlence, Nicolas Dussex, Ursula Ellenberg, David M. Houston, Thomas Mattern, Colin M. Miskelly, Kyle W. Morrison, R. Paul Scofield, Alan J.D. Tennyson, David R. Thompson, Jamie R. Wood, Jonathan M. WatersAbstractHuman impacts have substantially reduced avian biodiversity in many parts of the world, particularly on isolated islands of the Pacific Ocean. The New Zealand archipelago, including its five subantarctic island groups, holds breeding grounds for a third of the world’s penguin ...
Source: Molecular Phylogenetics and Evolution - October 25, 2018 Category: Molecular Biology Source Type: research

A phylogenetic examination of host use evolution in the quinaria and testacea groups of Drosophila
Publication date: Available online 23 October 2018Source: Molecular Phylogenetics and EvolutionAuthor(s): Clare H. Scott Chialvo, Brooke E. White, Laura K. Reed, Kelly A. DyerAbstractAdaptive radiations provide an opportunity to examine complex evolutionary processes such as ecological specialization and speciation. While a well-resolved phylogenetic hypothesis is critical to completing such studies, the rapid rates of evolution in these groups can impede phylogenetic studies. Here we study the quinaria and testacea species groups of the immigrans-tripunctata radiation of Drosophila, which represent a recent adaptive radia...
Source: Molecular Phylogenetics and Evolution - October 24, 2018 Category: Molecular Biology Source Type: research

Diversifying into the branches: species boundaries in African green and bush snakes, Philothamnus (Serpentes: Colubridae)
Publication date: Available online 23 October 2018Source: Molecular Phylogenetics and EvolutionAuthor(s): Hanlie M. Engelbrecht, William R. Branch, Eli Greenbaum, Graham J. Alexander, Kate Jackson, Marius Burger, Werner Conradie, Chifundera Kusamba, Ange-Ghislain Zassi-Boulou, Krystal A. TolleyAbstractThe African green and bush snakes of the genus Philothamnus currently comprises 21 species and three subspecies and occurs throughout sub-Saharan Africa. The genus has been the subject of previous taxonomic revisions based on traditional morphological characters and limited genetic assessment, and may not reflect their evolut...
Source: Molecular Phylogenetics and Evolution - October 24, 2018 Category: Molecular Biology Source Type: research

Phylogeny, diversity and biogeography of Neotropical sipo snakes (Serpentes: Colubrinae: Chironius)
Publication date: Available online 24 October 2018Source: Molecular Phylogenetics and EvolutionAuthor(s): Omar Torres-Carvajal, Lourdes Y. Echevarría, Simón E. Lobos, Pablo J. Venegas, Philippe J.R. KokAbstractNeotropical sipo snakes (Chironius) are large diurnal snakes with a long tail and big eyes that differ from other Neotropical snakes in having 10 or 12 dorsal scale rows at midbody. The 22 currently recognized species occur from Central America south to Uruguay and northeastern Argentina. Based on the largest geographical sampling to date including ∼90% of all species, we analyzed one nuclear and th...
Source: Molecular Phylogenetics and Evolution - October 24, 2018 Category: Molecular Biology Source Type: research

Insight from an Ultraconserved Element Bait Set Designed for Hemipteran Phylogenetics Integrated with Genomic Resources
We present newly generated UCE data for 36 samples representing three suborders, all seven heteropteran infraorders, 23 families, and 34 genera of Hemiptera and one thysanopteran outgroup. To improve taxon sampling, we also mined additional UCE loci in silico from published hemipteran genomic and transcriptomic data. We obtained 2,271 UCE loci for newly sequenced hemipteran taxa, ranging from 265 to 1,696 (average 904) per sample. These were similar in number to the data mined from transcriptomes and genomes, but with fewer loci overall. The amount of missing data correlates with greater phylogenetic divergence from taxa u...
Source: Molecular Phylogenetics and Evolution - October 23, 2018 Category: Molecular Biology Source Type: research

Do molecular phylogenies unravel the relationships among the evolutionary young “Brafordian” families (Copepoda; Calanoida)?
Publication date: Available online 23 October 2018Source: Molecular Phylogenetics and EvolutionAuthor(s): Silke Laakmann, Elena L. Markhaseva, Jasmin RenzAbstractAmong the most derived calanoid copepod superfamily Clausocalanoidea about half of the genera belong to the so-called “Bradfordian” families that are defined by the presence of sensory setae at the maxilla and maxilliped. Many of these “Bradfordian” taxa are insufficiently well described, because their taxonomy is complicated and phylogenetic relationships are not completely resolved. We therefore aimed to unravel their phylogenetic relatio...
Source: Molecular Phylogenetics and Evolution - October 23, 2018 Category: Molecular Biology Source Type: research

The evolutionary history of the goby Elacatinus puncticulatus in the tropical eastern pacific: effects of habitat discontinuities and local environmental variability
Publication date: Available online 23 October 2018Source: Molecular Phylogenetics and EvolutionAuthor(s): Edgar Raúl Sandoval-Huerta, Rosa Gabriela Beltrán-López, Carmen del Rocío Pedraza-Marrón, María Alejandra Paz-Velásquez, Arturo Angulo, Ross Robertson, Eduardo Espinoza, Omar Domínguez-DomínguezAbstractHabitat discontinuities, temperature gradients, upwelling systems, and ocean currents, gyres and fronts, can affect distributions of species with narrow environmental tolerance or motility and influence the dispersal of pelagic larvae, with effects ranging fr...
Source: Molecular Phylogenetics and Evolution - October 23, 2018 Category: Molecular Biology Source Type: research

What are the roles of taxon sampling and model fit in tests of cyto-nuclear discordance using avian mitogenomic data?
In this study, we examine the mitochondrial phylogeny of Cavitaves to elucidate its congruence with recently published nuclear phylogenies of this group of birds. Cavitaves includes the orders Trogoniformes (trogons), Bucerotiformes (hornbills), Coraciiformes (kingfishers and allies), and Piciformes (woodpeckers and allies). We hypothesized that sparse taxon sampling in previously published mitochondrial trees was responsible for apparent cyto-nuclear discordance. To test this hypothesis, we assembled 27 additional Cavitaves mitogenomes and estimated phylogenies using seven different taxon sampling schemes ranging from fiv...
Source: Molecular Phylogenetics and Evolution - October 23, 2018 Category: Molecular Biology Source Type: research

Multiple connections between Amazonia and Atlantic Forest shaped the phylogenetic and morphological diversity of Chiasmocleis Mehely, 1904 (Anura: Microhylidae: Gastrophryninae)
Publication date: Available online 19 October 2018Source: Molecular Phylogenetics and EvolutionAuthor(s): Rafael O. de Sá, João Filipe Riva Tonini, Hannah van Huss, Alex Long, Travis Cuddy, Mauricio C. Forlani, Pedro L.V. Peloso, Hussam Zaher, Célio F.B. HaddadAbstractChiasmocleis is the most species-rich genus of Neotropical microhylids. Herein, we provide the first comprehensive multilocus phylogeny for the genus, including all but 3 of the 34 recognized species and multiple individuals per species. We discuss cryptic speciation, species discovery, patterns of morphological evolution, and provide a h...
Source: Molecular Phylogenetics and Evolution - October 20, 2018 Category: Molecular Biology Source Type: research

Evolutionary and ecological patterns within the South African Bathyergidae: Implications for taxonomy
Publication date: Available online 17 October 2018Source: Molecular Phylogenetics and EvolutionAuthor(s): Jacobus H. Visser, Nigel C. Bennett, Bettine Jansen van VuurenAbstractThe family Bathyergidae (comprising six genera) is a group of subterranean rodents endemic to sub-Saharan Africa. Our understanding of the evolution and species richness of the South African bathyergid genera Georychus, Bathyergus and Cryptomys is limited, with the majority of species listed as Least Concern by the IUCN Red List of Threatened Species. Genetic data suggest that several cryptic species may be present in these genera. To explore genetic...
Source: Molecular Phylogenetics and Evolution - October 17, 2018 Category: Molecular Biology Source Type: research

Using integrative taxonomy and multispecies coalescent models for phylogeny reconstruction and species delimitation within the “Nastanthus–Gamocarpha” clade (Calyceraceae)
In this study, we reconstructed the phylogeny of the “Nastanthus–Gamocarpha” clade using multispecies coalescent models under BPP and StarBeast2 programs, sampling 63 individuals from 13 of the 14 species recognized to date. We then used this phylogenetic framework to delimit species using BFD and the A11 method implemented in BPP. Species limits suggested through a coalescent approach were then re-evaluated in the light of morphology, geography, and phenology. Coalescent-based methods indicated that most putative lineages could be recognized as distinct species. Morphological, geographical, ecological, a...
Source: Molecular Phylogenetics and Evolution - October 16, 2018 Category: Molecular Biology Source Type: research

Huntsmen of the Caribbean: Multiple tests of the GAARlandia hypothesis
Publication date: Available online 13 October 2018Source: Molecular Phylogenetics and EvolutionAuthor(s): Yanfeng Tong, Greta Binford, Cristina A. Rheims, Matjaž Kuntner, Jie Liu, Ingi AgnarssonAbstractThe origin of the Caribbean biota remains debated, but amassing evidence suggests important roles of both dispersal and vicariance events in the colonization the archipelago. The most prominent vicariance hypothesis is colonization over the GAARlandia land bridge that putatively connected the Greater Antilles to South America around 33 mya. This hypothesis has received support from studies of individual lineages, but its ma...
Source: Molecular Phylogenetics and Evolution - October 14, 2018 Category: Molecular Biology Source Type: research

Phylogeny of Schinus L. (Anacardiaceae) with a new infrageneric classification and insights into evolution of spinescence and floral traits
Publication date: Available online 13 October 2018Source: Molecular Phylogenetics and EvolutionAuthor(s): Cíntia Luíza Silva-Luz, José Rubens Pirani, John Daniel Mitchell, Douglas Daly, Natalie do Valle Capelli, Diego Demarco, Susan K. Pell, Gregory M. PlunkettAbstractSchinus, best known by its few cultivated and invasive species, is the largest genus of Anacardiaceae in southern South America. It is remarkably diverse compared to closely related genera, with approximately 42 species, most ofwhich occur in several arid vegetation types and extend into Andean and Atlantic moist forests. The most compreh...
Source: Molecular Phylogenetics and Evolution - October 14, 2018 Category: Molecular Biology Source Type: research

Combining transcriptomes and ultraconserved elements to illuminate the phylogeny of Apidae
In this study, we evaluate the combination of UCEs and transcriptomes in a single analysis using genome-, transcriptome-, and UCE data for 79 bees in the largest and most biologically diverse bee family, Apidae. Using existing tools, we first developed a workflow to assemble phylogenomic data from different sources and produced two large nucleotide matrices of combined data. We then reconstructed the phylogeny of the Apidae using concatenation- and coalescent-based methods, and critically evaluated the resulting phylogenies in the context of previously published genetic, genomic, and morphological data sets. Our estimated ...
Source: Molecular Phylogenetics and Evolution - October 14, 2018 Category: Molecular Biology Source Type: research

Near-complete phylogeny and taxonomic revision of the world’s babbler (Aves: Passeriformes)
In this study, we used five mitochondrial and seven nuclear loci to generate a dated phylogeny for babblers. This phylogeny includes 402 species (ca. 89% of the overall clade) from 75 genera (97%) and all five currently recognized families, providing a robust basis for taxonomic revision. Our phylogeny supports seven major clades and reveals several non-monophyletic genera. Divergence time estimates indicate that the seven major clades diverged around the same time (18–20 million years ago, Ma) in the early Miocene. We use the phylogeny in a consistent way to propose a new taxonomy, with seven families and 64 genera ...
Source: Molecular Phylogenetics and Evolution - October 13, 2018 Category: Molecular Biology Source Type: research

What are the roles of taxon sampling and model fit in tests of cyto-nuclear discordance using avian mitogenomic data?
In this study, we examine the mitochondrial phylogeny of Cavitaves to elucidate its congruence with recently published nuclear phylogenies of this group of birds. Cavitaves includes the orders Trogoniformes (trogons), Bucerotiformes (hornbills), Coraciiformes (kingfishers and allies), and Piciformes (woodpeckers and allies). We hypothesized that sparse taxon sampling in previously published mitochondrial trees was responsible for apparent cyto-nuclear discordance. To test this hypothesis, we assembled 27 additional Cavitaves mitogenomes and estimated phylogenies using seven different taxon sampling schemes ranging from fiv...
Source: Molecular Phylogenetics and Evolution - October 13, 2018 Category: Molecular Biology Source Type: research

The origin of the world’s smallest flightless bird, the Inaccessible Island Rail Atlantisia rogersi (Aves: Rallidae)
Publication date: Available online 12 October 2018Source: Molecular Phylogenetics and EvolutionAuthor(s): Martin Stervander, Peter G. Ryan, Martim Melo, Bengt HanssonAbstractRails (Aves: Rallidae) are renowned for their extreme dispersal capability, which has given rise to numerous island lineages. Many insular species lost the ability to fly as a response to release from predator pressure—a feature causing rapid extinction when humans subsequently introduced mammals. The world’s smallest extant flightless bird, the Inaccessible Island Rail Atlantisia rogersi, is endemic to Inaccessible Island, Tristan da Cunha...
Source: Molecular Phylogenetics and Evolution - October 13, 2018 Category: Molecular Biology Source Type: research

Hemocyanin genes as indicators of habitat shifts in Panpulmonata?
Publication date: Available online 13 October 2018Source: Molecular Phylogenetics and EvolutionAuthor(s): Gabriela Giannina Schäfer, Veronika Pedrini-Martha, Raimund Schnegg, Reinhard Dallinger, Daniel John Jackson, Bernhard LiebAbstractHemocyanin is the primary respiratory protein for the majority of the Mollusca and therefore directly interfaces with the physiological requirements of each species and the environments to which they are adapted. Hemocyanin is therefore likely to have been evolutionarily imprinted by significant habitat shifts. In the gastropod clade Panpulmonata (>30,000 species) major realm transi...
Source: Molecular Phylogenetics and Evolution - October 13, 2018 Category: Molecular Biology Source Type: research

Reassessment of the classification of Bryopsidales (Chlorophyta) based on chloroplast genome phylogenomic analyses
In this study, we re-assess the phylogeny of the order with datasets derived from chloroplast genomes, drastically increasing the taxon sampling by sequencing 32 new chloroplast genomes. The phylogenies presented here provided good support for the major lineages (suborders and most families) in Bryopsidales. In Bryopsidineae, Pseudobryopsis hainanensis was inferred as a distinct lineage from the three established families allowing us to establish the family Pseudobryopsidaceae. The Antarctic species Lambia antarctica was shown to be an early-branching lineage in the family Bryopsidaceae. In Halimedineae, we revealed severa...
Source: Molecular Phylogenetics and Evolution - October 13, 2018 Category: Molecular Biology Source Type: research

A phylogeny and the evolution of epizoism within the family Hydrozoanthidae with description of a new genus and two new species
In this study, two new Hydrozoanthidae species, Aenigmanthus segoi gen. n., sp. n. and Hydrozoanthus sils sp. n., are described from Japanese and Palauan waters based on combined morphological and molecular phylogenetic analyses utilizing multiple genetic markers. Additionally, Hydrozoanthidae consists of species with an obligate epizoic relationship with hydroids (Hydrozoanthus) and of species with facultative epizoic relationships (Aenigmanthus gen. n. and Terrazoanthus). Results of ancestral state reconstruction analyses indicate that Hydrozoanthus gained obligate epizoic relationships in their evolutionary history perh...
Source: Molecular Phylogenetics and Evolution - October 13, 2018 Category: Molecular Biology Source Type: research

Phylogenomics supports the monophyly of the Cercozoa
Publication date: Available online 11 October 2018Source: Molecular Phylogenetics and EvolutionAuthor(s): Nicholas A.T. Irwin, Denis V. Tikhonenkov, Elisabeth Hehenberger, Alexander P. Mylnikov, Fabien Burki, Patrick J. KeelingAbstractThe phylum Cercozoa consists of a diverse assemblage of amoeboid and flagellated protists that forms a major component of the supergroup, Rhizaria. However, despite its size and ubiquity, the phylogeny of the Cercozoa remains unclear as morphological variability between cercozoan species and ambiguity in molecular analyses, including phylogenomic approaches, have produced ambiguous results an...
Source: Molecular Phylogenetics and Evolution - October 13, 2018 Category: Molecular Biology Source Type: research

Allopatric diversification and evolutionary melting pot in a North African Palearctic relict: The biogeographic history of Salamandra algira
Publication date: Available online 12 October 2018Source: Molecular Phylogenetics and EvolutionAuthor(s): Marco Dinis, Khaled Merabet, Fernando Martínez-Freiría, Sebastian Steinfartz, Miguel Vences, James D. Burgon, Kathryn R. Elmer, David Donaire, Arlo Hinckley, Soumia Fahd, Ulrich Joger, Adnane Fawzi, Tahar Slimani, Guillermo Velo-AntónAbstractNorth Africa is a climatically and topographically complex region with unique biotic assemblages resulting from the combination of multiple biogeographic realms. Here, we assess the role of climate in promoting intra-specific diversification in a Palearctic rel...
Source: Molecular Phylogenetics and Evolution - October 13, 2018 Category: Molecular Biology Source Type: research

Evolution of the Grey-bellied pygmy mouse group: highly structured molecular diversity with predictable geographic ranges but morphological crypsis
Publication date: Available online 12 October 2018Source: Molecular Phylogenetics and EvolutionAuthor(s): Jarmila Krásová, Ondřej Mikula, Vladimír Mazoch, Josef Bryja, Oldřich Říčan, Radim ŠumberaAbstractThe grey-bellied pygmy mouse (Mus triton) from the endemic African subgenus Nannomys is a widespread rodent species inhabiting the highlands of eastern and central Africa. Although it has long been considered as a single species, recent data has suggested the existence of a species complex. In order to evaluate the geographical structure and current taxonomy of M. triton, we analysed ...
Source: Molecular Phylogenetics and Evolution - October 13, 2018 Category: Molecular Biology Source Type: research

From Himalayas to Continental Island: Integrative species delimitation in the Brownish-flanked Bush Warbler Horornis fortipes complex
Publication date: Available online 12 October 2018Source: Molecular Phylogenetics and EvolutionAuthor(s): Chentao Wei, Lu Dong, Shou-Hsien Li, Per Alström, Yang Liu, Canwei Xia, Cheng-Te Yao, Yanyun ZhangAbstractAs species serve as basic units of study in many fields of biology, assessments of species limits are fundamental for such studies. Here, we used a multilocus dataset and different coalescent-based methods to analyze species delimitation and phylogenetic relationships in the Brownish-flanked Bush Warbler Horornis fortipes complex, which is widespread in the Sino-Himalayan region. We also examined the vocal and...
Source: Molecular Phylogenetics and Evolution - October 13, 2018 Category: Molecular Biology Source Type: research

Conservation of mitochondrial genome arrangements in brittle stars (Echinodermata, Ophiuroidea)
In this study, 17 mitochondrial genomes spanning the taxonomic breadth of Ophiuroidea were utilized to explore evolutionary relationships through maximum likelihood analyses, Bayesian inference and comparative assessment of gene order. Our phylogenetic analyses, based on both nucleotide and amino acid residues, support recent findings based on multilocus nuclear data and morphology, in that the brittle star clades Ophintegrida and Euryophiurida were recovered as monophyletic with the latter comprising Euyalida, Ophiuridae and Ophiopyrgidae. Only three different arrangements of the 13 protein coding and 2 ribosomal RNA gene...
Source: Molecular Phylogenetics and Evolution - October 12, 2018 Category: Molecular Biology Source Type: research

Unraveling the intricate biodiversity of the benthic harpacticoid genus Nannopus (Copepoda, Harpacticoida, Nannopodidae) in Korean waters
In this study, we aimed to identify Nannopus species using an integrative approach including molecular taxonomy. We adopted a non-destructive DNA extraction method so that morphological and molecular data could be obtained from the same specimen. We analyzed the molecular diversity and distributions of Nannopus using a sample of 190 individuals. We sequenced the mtCOI, 53 mtCYTB, 25 18SrDNA, and 43 28SrDNA genes of all 190 individuals. Several species delimitation approaches were applied, including uncorrected p-distances for mtCOI, mtCYTB, 18SrDNA, and 28SrDNA, and Automatic Barcode Gap Discovery and Bayesian implemented ...
Source: Molecular Phylogenetics and Evolution - October 9, 2018 Category: Molecular Biology Source Type: research