ORDER within the chaos: Insights into phylogenetic relationships within the Anomura (Crustacea: Decapoda) from mitochondrial sequences and gene order rearrangements
In this study, we performed genome skimming to recover the mitogenome sequences of 12 anomuran species including the world’s largest extant invertebrate, the robber crab (Birgus latro), thereby over doubling these resources for this group, together with 8 new brachyuran mitogenomes. Maximum-likelihood (ML) and Bayesian-inferred (BI) phylogenetic reconstructions based on amino acid sequences from mitogenome protein-coding genes provided strong support for the monophyly of the Anomura and Brachyura and their sister relationship, consistent with previous studies. The majority of relationships within families were suppor...
Source: Molecular Phylogenetics and Evolution - July 13, 2018 Category: Molecular Biology Source Type: research

Connecting Amazonian, Cerrado, and Atlantic forest histories: Paraphyly, old divergences, and modern population dynamics in tyrant-manakins (Neopelma/Tyranneutes, Aves: Pipridae)
Publication date: Available online 12 June 2018Source: Molecular Phylogenetics and EvolutionAuthor(s): João Marcos Guimarães Capurucho, Mary V. Ashley, Camila C. Ribas, John M. BatesAbstractSeveral biogeographic hypotheses have been proposed to explain connections between Amazonian and Atlantic forest biotas. These hypotheses are related to the timing of the connections and their geographic patterns. We performed a phylogeographic investigation of Tyrant-manakins (Aves: Pipridae, Neopelma/Tyranneutes) which include species inhabiting the Amazon and Atlantic forests, as well as gallery forests of the Cerrado. ...
Source: Molecular Phylogenetics and Evolution - July 12, 2018 Category: Molecular Biology Source Type: research

Evolutionary and Ecological Drivers of Plant Flavonoids Across A Large Latitudinal Gradient
This study documents a complex interplay of ecological, historical, phylogenetic relatedness, and pleiotropic factors driving plant flavonoid production.Graphical abstract (Source: Molecular Phylogenetics and Evolution)
Source: Molecular Phylogenetics and Evolution - July 12, 2018 Category: Molecular Biology Source Type: research

Molecular systematics of swifts of the genus Chaetura (Aves: Apodiformes: Apodidae)
Publication date: Available online 11 July 2018Source: Molecular Phylogenetics and EvolutionAuthor(s): R. Terry Chesser, Haley Vaseghi, Peter A. Hosner, Laura M. Bergner, M. Nandadevi Cortes-Rodriguez, Andreanna J. Welch, Charles T. CollinsAbstractPhylogenetic relationships among swifts of the morphologically conservative genus Chaetura were studied using mitochondrial and nuclear DNA sequences. Taxon sampling included all species and 21 of 30 taxa (species and subspecies) within Chaetura. Our results indicate that Chaetura is monophyletic and support the division of the genus into the two subgenera previously identified u...
Source: Molecular Phylogenetics and Evolution - July 12, 2018 Category: Molecular Biology Source Type: research

Renewed classification within Goniurosaurus (Squamata: Eublepharidae) uncovers the dual roles of a continental island (Hainan) in species evolution
Publication date: Available online 12 June 2018Source: Molecular Phylogenetics and EvolutionAuthor(s): Bin Liang, Run-Bang Zhou, Yan-Lin Liu, Bei Chen, L. Lee Grismer, Ning WangAbstractContinental islands are often dynamic in regard to the origin and evolution of their biota. Although colonizations from mainland Southeast Asia to Hainan Island have been reported, the role of Hainan Island as a source for continental biota has not been considered. Goniurosaurus is a genus comprised of nocturnal ground geckos. We reexamined the evolutionary history of Goniurosaurus using both molecular phylogenetics and morphological compari...
Source: Molecular Phylogenetics and Evolution - July 10, 2018 Category: Molecular Biology Source Type: research

Evolutionary relationships and climatic niche evolution in the genus Handleyomys (Sigmodontinae: Oryzomyini)
Publication date: Available online 12 June 2018Source: Molecular Phylogenetics and EvolutionAuthor(s): Ana Laura Almendra, Francisco X. González-Cózatl, Mark D. Engstrom, Duke S. RogersAbstractMesoamerica is considered a biodiversity hot spot with levels of endemism and species diversity likely underestimated. Unfortunately, the region continues to experience some of the highest deforestation rates in the world. For mammals, the evolutionary relationships of many endemic taxa are controversial, as it is the case for members of the genus Handleyomys. Estimation of a time-calibrated hypothesis for the evolution...
Source: Molecular Phylogenetics and Evolution - July 10, 2018 Category: Molecular Biology Source Type: research

The evolutionary history of Lygodactylus lizards in the South American open diagonal
Publication date: Available online 12 June 2018Source: Molecular Phylogenetics and EvolutionAuthor(s): Flávia M. Lanna, Fernanda P. Werneck, Marcelo Gehara, Emanuel M. Fonseca, Guarino R. Colli, Jack W. Sites, Miguel T. Rodrigues, Adrian A. GardaAbstractThe Pleistocenic Arc Hypothesis (PAH) posits that South American Seasonally Dry Tropical Forests (SDTF) were interconnected during Pleistocene glacial periods, enabling the expansion of species ranges that were subsequently fragmented in interglacial periods, promoting speciation. The lizard genus Lygodactylus occurs in Africa, Madagascar, and South America. Compared...
Source: Molecular Phylogenetics and Evolution - July 10, 2018 Category: Molecular Biology Source Type: research

Barcoding and multi-locus phylogeography of the globally distributed calcareous tubeworm genus Hydroides Gunnerus, 1768 (Annelida, Polychaeta, Serpulidae)
Publication date: Available online 12 June 2018Source: Molecular Phylogenetics and EvolutionAuthor(s): Yanan Sun, Eunice Wong, Shane T. Ahyong, Jane E. Williamson, Pat A. Hutchings, Elena K. KupriyanovaAbstractHydroides is a large and diverse group of calcareous tubeworms (Serpulidae, Annelida) recognised by a distinctive but variable two-tiered operculum. Despite considerable research using several species of Hydroides as models in ecological and biofouling studies, phylogenetic and biogeographic relationships within the genus are still poorly understood. Using combined mitochondrial (COI, cytochrome b) and nuclear (18S, ...
Source: Molecular Phylogenetics and Evolution - July 10, 2018 Category: Molecular Biology Source Type: research

Worldwide phylogeny of three-spined sticklebacks
Publication date: Available online 12 June 2018Source: Molecular Phylogenetics and EvolutionAuthor(s): Bohao Fang, Juha Merilä, Filipe Ribeiro, Carlos M. Alexandre, Paolo MomiglianoAbstractStickleback fishes in the family Gasterosteidae have become model organisms in ecology and evolutionary biology. However, even in the case of the most widely studied species in this family – the three-spined stickleback (Gasterosteus aculeatus) – the worldwide phylogenetic relationships and colonization history of the different populations and lineages remain poorly resolved. Using a large collection of samples covering ...
Source: Molecular Phylogenetics and Evolution - July 10, 2018 Category: Molecular Biology Source Type: research

Evolutionary applications of phylogenetically-informed ecological niche modelling (ENM) to explore cryptic diversification over cryptic refugia
Publication date: Available online 12 June 2018Source: Molecular Phylogenetics and EvolutionAuthor(s): Mohsen Ahmadi, Morteza Naderi, Mohammad Kaboli, Masoud Nazarizadeh, Mahmoud Karami, Sara M. BeitollahiAbstractWe used the fat dormouse (Glis glis), a species from a monotypic genus of family Gliridae, as a model to promote the understanding of patterns of cryptic diversification along the ancient Hyrcanian Forests, one of the old-growth relicts of the temperate deciduous forests worldwide. Mitochondrial Cytb data was used to investigate the phylogenetic status of two geographically-different populations of G. glis along t...
Source: Molecular Phylogenetics and Evolution - July 10, 2018 Category: Molecular Biology Source Type: research

Phylogeny and systematics of Chiroxiphia and Antilophia manakins (Aves, Pipridae)
Publication date: Available online 12 June 2018Source: Molecular Phylogenetics and EvolutionAuthor(s): Sofia Marques Silva, Carlos Eduardo Agne, Alexandre Aleixo, Sandro L. BonattoAbstractChiroxiphia and Antilophia manakins are recognized as closely related genera. Nonetheless, Chiroxiphia has been recovered as paraphyletic in some studies with limited taxonomic coverage. This genus currently comprises five species, although this arrangement is still unsettled. Chiroxiphia pareola is the most widespread species, with four recognized subspecies, but their taxonomic status are also uncertain. Finally, the phylogenetic relati...
Source: Molecular Phylogenetics and Evolution - July 10, 2018 Category: Molecular Biology Source Type: research

When did anoles diverge? An analysis of multiple dating strategies
Publication date: Available online 15 June 2018Source: Molecular Phylogenetics and EvolutionAuthor(s): Cristian Román-Palacios, Jose Tavera, María del Rosario CastañedaAbstractWhereas most of the studies that discuss the evolutionary divergence of Anolis lizards have dated the clade’s crown group in between 31 and 64 Ma, a single study has recovered a significantly older age for the same node (87 Ma). These differences also entail notable consequences on the preferred biogeographical hypothesis for the whole clade. Here we analyze a total of seven dating strategies by combining three calibrat...
Source: Molecular Phylogenetics and Evolution - July 10, 2018 Category: Molecular Biology Source Type: research

Cryptic genetic diversity, population structure, and gene flow in the Mojave rattlesnake (Crotalus scutulatus)
Publication date: Available online 15 June 2018Source: Molecular Phylogenetics and EvolutionAuthor(s): Drew R. Schield, Richard H. Adams, Daren C. Card, Andrew B. Corbin, Tereza Jezkova, Nicole R. Hales, Jesse M. Meik, Blair W. Perry, Carol L. Spencer, Lydia L. Smith, Gustavo Campillo García, Nassima M. Bouzid, Jason L. Strickland, Christopher L. Parkinson, Miguel Borja, Gamaliel Castañeda-Gaytán, Robert W. Bryson, Oscar A. Flores-Villela, Stephen P. Mackessy, Todd A. CastoeAbstractThe Mojave rattlesnake (Crotalus scutulatus) inhabits deserts and arid grasslands of the western United States and Mexico....
Source: Molecular Phylogenetics and Evolution - July 10, 2018 Category: Molecular Biology Source Type: research

Lack of host specificity of copepod crustaceans associated with mushroom corals in the Red Sea
Publication date: Available online 15 June 2018Source: Molecular Phylogenetics and EvolutionAuthor(s): Viatcheslav N. Ivanenko, Bert W. Hoeksema, Sofya V. Mudrova, Mikhail A. Nikitin, Alejandro Martínez, Nadezda N. Rimskaya-Korsakova, Michael L. Berumen, Diego FontanetoAbstractThe radiation of symbiotic copepods (Crustacea: Copepoda) living in association with stony corals (Cnidaria: Scleractinia) is considered host-specific and linked to the phylogenetic diversification of their hosts. However, symbiotic copepods are poorly investigated, occurrence records are mostly anecdotal, and no explicit analysis exists regar...
Source: Molecular Phylogenetics and Evolution - July 10, 2018 Category: Molecular Biology Source Type: research

Phylogenetic relationship analyses of complicated class Spirotrichea based on transcriptomes from three diverse microbial eukaryotes: Uroleptopsis citrina, Euplotes vannus and Protocruzia tuzeti
In this study, we obtained the transcriptome data of three typical ciliates, Uroleptopsis citrina, Euplotes vannus, Protocruzia tuzeti using high throughput sequencing. The genetic relationships were revealed by phylogenomic analysis of 109 genes comprising of 34,882 amino acid residues, and analyses based on SSU rDNA of 55 species, as well as the comparison of gene content among spirotricheans and related species. Our phylogenomic analyses show the Spirotrichea is monophyletic when Protocruzia is excluded, in which four subclasses: Oligotrichia, Choreotrichia, Hypotrichia and Euplotia also formed momophyletic groups respe...
Source: Molecular Phylogenetics and Evolution - July 10, 2018 Category: Molecular Biology Source Type: research

Evolutionary lineages of marine snails identified using molecular phylogenetics and geometric morphometric analysis of shells
Publication date: Available online 15 June 2018Source: Molecular Phylogenetics and EvolutionAuthor(s): Felix Vaux, Steven A. Trewick, James S. Crampton, Bruce A. Marshall, Alan G. Beu, Simon F.K. Hills, Mary Morgan-RichardsAbstractThe relationship between morphology and inheritance is of perennial interest in evolutionary biology and palaeontology. Using three marine snail genera Penion, Antarctoneptunea and Kelletia, we investigate whether systematics based on shell morphology accurately reflect evolutionary lineages indicated by molecular phylogenetics. Members of these gastropod genera have been a taxonomic challenge du...
Source: Molecular Phylogenetics and Evolution - July 10, 2018 Category: Molecular Biology Source Type: research

Phylogenetic relationships and classification of the Holarctic family Leuciscidae (Cypriniformes: Cyprinoidei)
Publication date: Available online 18 June 2018Source: Molecular Phylogenetics and EvolutionAuthor(s): Susana Schönhuth, Jasna Vukić, Radek Šanda, Lei Yang, Richard L. MaydenAbstractThe phylogenetic relationships and classification of the freshwater fish order Cypriniformes, like many other species-rich groups of vertebrates, has evolved over time with some consistency and inconsistencies of relationships across various studies. Within Cypriniformes, the Holarctic family Leuciscidae is one of the most widely distributed and highly diverse monophyletic groups of cyprinoids. Despite several studies conducted on ...
Source: Molecular Phylogenetics and Evolution - July 10, 2018 Category: Molecular Biology Source Type: research

Exploring the Udoteaceae diversity (Bryopsidales, Chlorophyta) in the Caribbean region based on molecular and morphological data
Publication date: Available online 18 June 2018Source: Molecular Phylogenetics and EvolutionAuthor(s): Laura Lagourgue, Nicolas Puillandre, Claude E. PayriAbstractThe Udoteaceae family (Bryopsidales, Chlorophyta) is known to be highly diverse morphologically in the Caribbean region, but only few studies have studied its genetic diversity. Using an integrative taxonomic approach, this study aimed at (1) exploring the Udoteaceae species diversity using a combination of five DNA-based species delimitation methods and morpho-anatomical data for confirmation; (2) estimating the discriminatory power of traditional diagnostic cha...
Source: Molecular Phylogenetics and Evolution - July 10, 2018 Category: Molecular Biology Source Type: research

Prevalence of cryptic species in morphologically uniform taxa – Fast speciation and evolutionary radiation in Asian frogs
Publication date: Available online 18 June 2018Source: Molecular Phylogenetics and EvolutionAuthor(s): Zuyao Liu, Guoling Chen, Tianqi Zhu, Zhaochi Zeng, Zhitong Lyu, Jian Wang, Kevin Messenger, Anthony J. Greenberg, Zixiao Guo, Ziheng Yang, Suhua Shi, Yingyong WangAbstractDiversity and distributions of cryptic species have long been a vexing issue. Identification of species boundaries is made difficult by the lack of obvious morphological differences. Here, we investigate the cryptic diversity and evolutionary history of an underappreciated group of Asian frog species (Megophrys) to explore the pattern and dynamic of amph...
Source: Molecular Phylogenetics and Evolution - July 10, 2018 Category: Molecular Biology Source Type: research

Mitogenome phylogeographic analysis of a planktonic crustacean
Publication date: Available online 18 June 2018Source: Molecular Phylogenetics and EvolutionAuthor(s): Peter D. Fields, Darren J. Obbard, Seanna J. McTaggart, Yan Galimov, Tom J. Little, Dieter EbertAbstractPhylogeography places population genetics in an explicitly spatial context, and in doing so attempts to reconstruct the historical and contemporary evolutionary processes acting across a species range through space and time. Here we present the phylogeographical structure of Daphnia magna as determined for full mitochondrial genomes from samples of 60 populations throughout much of the species known range, including Eur...
Source: Molecular Phylogenetics and Evolution - July 10, 2018 Category: Molecular Biology Source Type: research

Phylogenetics of Camelina Crantz. (Brassicaceae) and insights on the origin of gold-of-pleasure (Camelina sativa)
Publication date: Available online 19 June 2018Source: Molecular Phylogenetics and EvolutionAuthor(s): Jordan R. Brock, Ali A. Dönmez, Mark A. Beilstein, Kenneth M. OlsenAbstractCamelina sativa (false flax or gold-of-pleasure) is an Old World oilseed crop that fell out of use in the mid 20th Century but has recently gained renewed interest as a biofuel source. The crop is hexaploid, and its relationship to its diploid and polyploid congeners has remained unresolved. Using 54 accessions representing five species sampled across Camelina’s center of diversity in Turkey and the Caucasus, we performed phylogenetic an...
Source: Molecular Phylogenetics and Evolution - July 10, 2018 Category: Molecular Biology Source Type: research

Molecular phylogenetics of Neotropical detritivorous fishes of the family Curimatidae (Teleostei: Characiformes)
Publication date: Available online 20 June 2018Source: Molecular Phylogenetics and EvolutionAuthor(s): Bruno F. Melo, Brian L. Sidlauskas, Kendra Hoekzema, Richard P. Vari, Casey B. Dillman, Claudio OliveiraAbstractCurimatidae, the fourth largest family of detritivorous Neotropical characiform fishes, encompasses eight extant genera and over 110 species dwelling in diverse freshwater habitats from Costa Rica to Argentina. Extensive phylogenetic analyses of soft anatomy and osteology provided evidence for intergeneric and most interspecific relationships, and formed the basis of curimatid taxonomy for nearly 40 years. How...
Source: Molecular Phylogenetics and Evolution - July 10, 2018 Category: Molecular Biology Source Type: research

Phylogeny of the saffron-crocus species group, Crocus series Crocus (Iridaceae)
Publication date: Available online 21 June 2018Source: Molecular Phylogenetics and EvolutionAuthor(s): Zahra Nemati, Frank R. Blattner, Helmut Kerndorff, Osman Erol, Dörte HarpkeAbstractPhylogenetic relationships among the taxa of Crocus series Crocus are still unclear, preventing the understanding of species diversity and the evolution of the important spice saffron (Crocus sativus). Therefore, we analyzed sequences of two chloroplast (trnL-trnF, matK-trnK) and three nuclear (TOPO6, ribosomal DNA ETS and ITS) marker regions to infer phylogenetic relationships among all species belonging to series Crocus. Our phylogen...
Source: Molecular Phylogenetics and Evolution - July 10, 2018 Category: Molecular Biology Source Type: research

A dated molecular phylogeny of mite harvestmen (Arachnida: Opiliones: Cyphophthalmi) elucidates ancient diversification dynamics in the Australian Wet Tropics
Publication date: Available online 21 June 2018Source: Molecular Phylogenetics and EvolutionAuthor(s): Jill T. Oberski, Prashant P. Sharma, Katya R. Jay, Michelle J. Coblens, Kaelyn A. Lemon, Joanne E. Johnson, Sarah L. BoyerAbstractAustropurcellia, a genus of dispersal-limited arachnids endemic to isolated patches of coastal rainforest in Queensland, Australia, has a remarkable biogeographic history. The genus is a member of the family Pettalidae, which has a classical temperate Gondwanan distribution; previous work has suggested that Austropurcellia is an ancient lineage, with an origin that predates Gondwanan rifting. S...
Source: Molecular Phylogenetics and Evolution - July 10, 2018 Category: Molecular Biology Source Type: research

Multilocus phylogeny, species age and biogeography of the Lesser Antillean anoles
Publication date: Available online 22 June 2018Source: Molecular Phylogenetics and EvolutionAuthor(s): Roger S. Thorpe, Axel Barlow, Yann Surget-Groba, Anita MalhotraAbstractLesser Antillean anoles provide classic examples of island radiations. A detailed knowledge of their phylogeny and biogeography, in particular how the age of species relate to the ages of their respective islands and the age of their radiation, is essential to elucidate the tempo and mechanisms of these radiations. We conduct a large-scale phylogenetic and phylogeographic investigation of the Lesser Antillean anoles using multiple genetic markers and c...
Source: Molecular Phylogenetics and Evolution - July 10, 2018 Category: Molecular Biology Source Type: research

Improved phylogenetic resolution within Siphonophora (Cnidaria) with implications for trait evolution
Publication date: Available online 22 June 2018Source: Molecular Phylogenetics and EvolutionAuthor(s): Catriona Munro, Stefan Siebert, Felipe Zapata, Mark Howison, Alejandro Damian-Serrano, Samuel H. Church, Freya E. Goetz, Philip R. Pugh, Steven H.D. Haddock, Casey W. DunnAbstractSiphonophores are a diverse group of hydrozoans (Cnidaria) that are found at most depths of the ocean - from the surface, like the familiar Portuguese man of war, to the deep sea. They play important roles in ocean ecosystems, and are among the most abundant gelatinous predators. A previous phylogenetic study based on two ribosomal RNA genes prov...
Source: Molecular Phylogenetics and Evolution - July 10, 2018 Category: Molecular Biology Source Type: research

Cryptic biodiversity in the freshwater fishes of the Kimberley endemism hotspot, northwestern Australia
Publication date: Available online 25 June 2018Source: Molecular Phylogenetics and EvolutionAuthor(s): James J. Shelley, Stephen E. Swearer, Mark Adams, Tim Dempster, Matthew C. Le Feuvre, Michael P. Hammer, Peter J. UnmackAbstractThe prevalence of unrecognised cryptic species impairs biodiversity estimates, clouds biological research and hinders conservation planning. As the rate of cryptic species detection increases globally, research is needed to determine how frequent cryptic species are, whether they are more common in given management regions, and whether these patterns are consistent across taxonomic groups. The Ki...
Source: Molecular Phylogenetics and Evolution - July 10, 2018 Category: Molecular Biology Source Type: research

How is structural divergence related to evolutionary information?
Publication date: Available online 25 June 2018Source: Molecular Phylogenetics and EvolutionAuthor(s): Diego Javier Zea, Alexander Miguel Monzon, Gustavo Parisi, Cristina Marino-BusljeAbstractThe analysis of evolutionary information in a protein family, such as conservation and covariation, is often linked to its structural information. Multiple sequence alignments of distant homologous sequences are used to measure evolutionary variables. Although high structural differences between proteins can be expected in such divergent alignments, most works linking evolutionary and structural information use a single structure igno...
Source: Molecular Phylogenetics and Evolution - July 10, 2018 Category: Molecular Biology Source Type: research

Molecular systematics and phylogeography of the endemic Osgood’s deermouse Osgoodomys banderanus (Rodentia: Cricetidae) in the lowlands of western Mexico
Publication date: Available online 26 June 2018Source: Molecular Phylogenetics and EvolutionAuthor(s): M. Laura Ruiz-Vega, Giovani Hernández-Canchola, Livia León-PaniaguaAbstractOsgoodomys banderanus is a recognized and endemic rodent species of western Mexico, an area known for its high biodiversity and number of endemisms. Phylogeographical relationships within this taxon were analyzed based on mitochondrial (ND3, tRNA-Arginine, ND4L and partial ND4) and nuclear (GHR) nucleotide sequences. We obtained a total of 112 samples from 22 localities, covering the complete distribution of the species. Phylogenetic ...
Source: Molecular Phylogenetics and Evolution - July 10, 2018 Category: Molecular Biology Source Type: research

Comparative evolutionary and phylogenomic analysis of Avian avulaviruses 1–20
Publication date: Available online 26 June 2018Source: Molecular Phylogenetics and EvolutionAuthor(s): Aziz-ul-Rahman, Muhammad Munir, Muhammad Zubair ShabbirAbstractAvian avulaviruses (avulaviruses or AAvVs) infect a wide range of avian species worldwide with variable clinical outcomes and economic impacts. Owing to broad host spectrum, several novel avulaviruses are being reported from both wild and domesticated birds that highlight the potential of the virus to evolve, adapt and emerge in susceptible population. Pathobiological and phylogenetic characterizations of individual avulaviruses are often demonstrated, however...
Source: Molecular Phylogenetics and Evolution - July 10, 2018 Category: Molecular Biology Source Type: research

Evolution of floral traits and impact of reproductive mode on diversification in the phlox family (Polemoniaceae)
This study begins to disentangle the individual components that comprise pollination syndromes and lays the foundation for future work on the genetic mechanisms that control each trait.Graphical abstract (Source: Molecular Phylogenetics and Evolution)
Source: Molecular Phylogenetics and Evolution - July 10, 2018 Category: Molecular Biology Source Type: research

Isolation drives increased diversification rates in freshwater amphipods
Publication date: Available online 27 June 2018Source: Molecular Phylogenetics and EvolutionAuthor(s): Nicole E. Adams, Kentaro Inoue, Richard A. Seidel, Brian K. Lang, David J. BergAbstractVicariance and dispersal events affect current biodiversity patterns in desert springs. Whether major diversification events are due to environmental changes leading to radiation or due to isolation resulting in relict species is largely unknown. We seek to understand whether the Gammarus pecos species complex underwent major diversification events due to environmental changes in the area leading either to radiation into novel habitats,...
Source: Molecular Phylogenetics and Evolution - July 10, 2018 Category: Molecular Biology Source Type: research

Phylogenetic relationships of the conoidean snails (Gastropoda: Caenogastropoda) based on mitochondrial genomes
Publication date: Available online 28 June 2018Source: Molecular Phylogenetics and EvolutionAuthor(s): Juan E. Uribe, Rafael Zardoya, Nicolas PuillandreAbstractWith more than 5,000 species, Conoidea is one of the most diversified superfamilies of Gastropoda. Recently, the family-level classification of these venomous predator snails has undergone substantial changes, on the basis of a phylogenetic tree reconstructed combining partial mitochondrial and nuclear gene sequences, and up to 16 families are now recognized. However, phylogenetic relationships among these families remain largely unresolved. Here, we sequenced 20 co...
Source: Molecular Phylogenetics and Evolution - July 10, 2018 Category: Molecular Biology Source Type: research

Topological support and data quality can only be assessed through multiple tests in reviewing Blattodea phylogeny
Publication date: Available online 30 June 2018Source: Molecular Phylogenetics and EvolutionAuthor(s): Dominic Evangelista, France Thouzé, Manpreet Kaur Kohli, Philippe Lopez, Frédéric LegendreAbstractAssessing support for molecular phylogenies is difficult because the data is heterogeneous in quality and overwhelming in quantity. Traditionally, node support values (bootstrap frequency, Bayesian posterior probability) are used to assess confidence in tree topologies. Other analyses to assess the quality of phylogenetic data (e.g. Lento plots, saturation plots, trait consistency) and the resulting phylo...
Source: Molecular Phylogenetics and Evolution - July 10, 2018 Category: Molecular Biology Source Type: research

From tree tops to the ground: Reversals to terrestrial habit in Galeandra orchids (Epidendroideae: Catasetinae)
Publication date: Available online 30 June 2018Source: Molecular Phylogenetics and EvolutionAuthor(s): Aline C. Martins, Thuane Bochorny, Oscar A. Pérez-Escobar, Guillaume Chomicki, Silvana H.N. Monteiro, Eric de Camargo SmidtAbstractThe colonization of the epiphytic niche of Neotropical forest canopies played an important role in orchid’s extraordinary diversification, with rare reversions to the terrestrial habit. To understand the evolutionary context of those reversals, we investigated the diversification of Galeandra, a Neotropical orchid genus which includes epiphytic and terrestrial species. We hypothes...
Source: Molecular Phylogenetics and Evolution - July 10, 2018 Category: Molecular Biology Source Type: research

Next-Generation museum genomics: phylogenetic relationships among palpimanoid spiders using sequence capture techniques (Araneae: Palpimanoidea)
This study uses museum specimens and recent target capture sequencing techniques to sequence both Ultra-Conserved Elements (UCE) and exonic regions for lineages that span the modern spiders, Araneomorphae, with a focus on Palpimanoidea. While many previous studies have used target capture techniques on dried museum specimens (for example, skins, pinned insects), this study includes specimens that were collected over the last two decades and stored in 70% ethanol at room temperature. Our findings support the utility of target capture methods for examining deep relationships within Araneomorphae: sequences from both UCE and ...
Source: Molecular Phylogenetics and Evolution - July 10, 2018 Category: Molecular Biology Source Type: research

Molecular phylogeny of Ischnocnema (Anura: Brachycephalidae) with the redefinition of its series and the description of two new species
We present a new phylogenetic hypothesis for Ischnocnema, a Neotropical brachycephaloid genus of ground-dwelling direct-developing frogs. We performed Bayesian inference, maximum likelihood, and maximum parsimony analyses using two nuclear (RAG1 and Tyr) and three mitochondrial genes (12S rRNA, tRNA-Val, and 16S rRNA) in a matrix comprising more than 80% of the described species. We recover Ischnocnema nanahallux outside the Ischnocnema parva series, and it is now unassigned to any species series, nor are Ischnocnema manezinho and Ischnocnema sambaqui. We propose the Ischnocnema venancioi species series to comprise Ischnoc...
Source: Molecular Phylogenetics and Evolution - July 10, 2018 Category: Molecular Biology Source Type: research

Plastome organization, genome-based phylogeny and evolution of plastid genes in Podophylloideae (Berberidaceae)
This study is the first to report whole-plastome sequence data for all 12 species of Podophylloideae (14 individuals) and a close relative, Achlys triphylla. These 15 plastomes proved highly similar in overall size (156,240–157,370 bp), structure, gene order and content, also when compared to other Ranunculales, but also revealed some structural variations caused by the expansion or contraction of the inverted repeats (IRs) into or out of adjacent single-copy regions. Our phylogenomic analysis, based on 63 plastome-derived protein-coding genes (CDS), supported the monophyly of Podophylloideae and its two major gene...
Source: Molecular Phylogenetics and Evolution - July 10, 2018 Category: Molecular Biology Source Type: research

A well-resolved fern nuclear phylogeny reveals the evolution history of numerous transcription factor families
This study provides a robust phylogenetic and gene family evolution framework, as well as rich molecular resources for understanding the morphological and functional evolution in ferns.Graphical abstract (Source: Molecular Phylogenetics and Evolution)
Source: Molecular Phylogenetics and Evolution - July 10, 2018 Category: Molecular Biology Source Type: research

Genomic evaluations of Wolbachia and mtDNA in the population of coconut hispine beetle, Brontispa longissima (Coleoptera: Chrysomelidae)
Publication date: Available online 6 July 2018Source: Molecular Phylogenetics and EvolutionAuthor(s): Habib Ali, Abrar Muhammad, Nafiu Sanda Bala, Guihua Wang, Zhiming Chen, Zhengqiang Peng, Youming HouAbstractWolbachia pipientis is a diverse, ubiquitous and most prevalent intracellular bacterial group of alpha-Proteobacteria that is concerned with many biological processes in arthropods. The coconut hispine beetle (CHB), Brontispa longissima (Gestro) is an economically important pest of palm cultivation worldwide. In the present study, we comprehensively surveyed the Wolbachia-infection prevalence and mitochondrial DNA (m...
Source: Molecular Phylogenetics and Evolution - July 10, 2018 Category: Molecular Biology Source Type: research

Molecular phylogeny, morphology, and distribution of Polygordius (Class: Polychaeta; Family Polygordiidae) in the Atlantic and Mediterranean
This study presents the first phylogeny of the genus Polygordius and combines molecular data, sequences of COI, 16S and ITS1/2 genes, and morphological data for a systematic re-evaluation focusing on Atlantic species, with an emphasis on populations from European waters. Phylogenetic analyses recovered six valid species (P. appendiculatus, P. lacteus, P. neapolitanus, P. triestinus, P. jouinae, and P. eschaturus) and their distinctness is confirmed by haplotype network analyses. Thus, molecular data supported the validity of the previously recognized morpho-species and no new species were present. P.erythrophthalmus and P....
Source: Molecular Phylogenetics and Evolution - July 10, 2018 Category: Molecular Biology Source Type: research

Species delimitation and mitogenome phylogenetics in the subterranean genus Pseudoniphargus (Crustacea: Amphipoda)
Publication date: Available online 10 July 2018Source: Molecular Phylogenetics and EvolutionAuthor(s): Morten Stokkan, José A. Jurado-Rivera, Oromí Pedro, Carlos Juan, Damià Jaume, Joan PonsAbstractThe amphi-Atlantic distributions exhibited by many thalassoid stygobiont (obligate subterranean) crustaceans have been explained by fragmentation by plate tectonics of ancestral shallow water marine populations. The amphipod stygobiont genus Pseudoniphargus is distributed across the Mediterranean region but also in the North Atlantic archipelagos of Bermuda, Azores, Madeira and the Canaries. We used species ...
Source: Molecular Phylogenetics and Evolution - July 10, 2018 Category: Molecular Biology Source Type: research

Comparative transcriptomics and genomic patterns of discordance in Capsiceae (Solanaceae)
Publication date: September 2018Source: Molecular Phylogenetics and Evolution, Volume 126Author(s): Daniel Spalink, Kevin Stoffel, Genevieve K. Walden, Amanda M. Hulse-Kemp, Theresa A. Hill, Allen Van Deynze, Lynn BohsAbstractThe integration of genomics and phylogenetics allows new insight into the structure of gene tree discordance, the relationships among gene position, gene history, and rate of evolution, as well as the correspondence of gene function, positive selection, and gene ontology enrichment across lineages. We explore these issues using the tribe Capsiceae (Solanaceae), which is comprised of the genera Lyciant...
Source: Molecular Phylogenetics and Evolution - July 10, 2018 Category: Molecular Biology Source Type: research

Editorial Board
Publication date: September 2018Source: Molecular Phylogenetics and Evolution, Volume 126Author(s): (Source: Molecular Phylogenetics and Evolution)
Source: Molecular Phylogenetics and Evolution - July 10, 2018 Category: Molecular Biology Source Type: research

Resolving relationships and phylogeographic history of the Nyssa sylvatica complex using data from RAD-seq and species distribution modeling
Publication date: September 2018Source: Molecular Phylogenetics and Evolution, Volume 126Author(s): Wenbin Zhou, Xiang Ji, Shihori Obata, Andrew Pais, Yibo Dong, Robert Peet, Qiu-Yun (Jenny) XiangAbstractNyssa sylvatica complex consists of several woody taxa occurring in eastern North America. These taxa were recognized as two or three species including three or four varieties by different authors. Due to high morphological similarities and complexity of morphological variation, classification and delineation of taxa in the group have been difficult and controversial. Here we employ data from RAD-seq to elucidate the genet...
Source: Molecular Phylogenetics and Evolution - July 10, 2018 Category: Molecular Biology Source Type: research

Phylogenetic relationships of rollers (Coraciidae) based on complete mitochondrial genomes and fifteen nuclear genes
In this study we examine the phylogenetic relationships of all species currently recognized in the family, including two taxa whose taxonomic status is currently contested. By using shotgun sequencing on degraded DNA from museum study skins we have been able to recover complete mitochondrial genomes as well as 15 nuclear genes for in total 16 taxa. The gene sequences were analyzed both concatenated in a maximum likelihood framework as well in a species tree approach using MP-EST. The different analytical approaches yield similar, highly supported trees and support the current division of the rollers into two genera, Coraci...
Source: Molecular Phylogenetics and Evolution - July 10, 2018 Category: Molecular Biology Source Type: research

Molecular detection of Anaplasma phagocytophilum-like Anaplasma spp. and pathogenic A. Phagocytophilum in cattle from South Korea
This study was conducted to detect A. phagocytophilum and genetically related strains in 764 cattle in South Korea using PCR and restriction fragment length polymorphism assays. APL clade A and A. phagocytophilum were identified in 20 (2.6%) and 16 (2.1%) cattle, respectively, with 16 cattle (2.1%) displaying co-infection. The 16S rRNA sequences of APL clade A were similar (98.3–99.9%) to those clustered in the APL clade A from eastern Asia. The A. phagocytophilum 16S rRNA sequence shared 98.6–100% identity to those of the A. phagocytophilum group. We used PCR to amplify the groEL and msp2 genes from the 20 sam...
Source: Molecular Phylogenetics and Evolution - July 10, 2018 Category: Molecular Biology Source Type: research

Phylogeny and biogeography of the pantropical genus Zanthoxylum and its closest relatives in the proto-Rutaceae group (Rutaceae)
We present the first detailed phylogenetic and biogeographic study of the genus and its close relatives in the proto-Rutaceae group. Our phylogenetic analyses based on two plastid and two nuclear markers show that the genus Toddalia Juss. is nested within Zanthoxylum, that earlier generic and intrageneric classifications need revision, and that the homochlamydeous flowers of the temperate species of Zanthoxylum are the result of a reduction from heterochlamydeous flowers. The biogeographic analyses reveal a Eurasian origin of Zanthoxylum in the Paleocene or Eocene with successive intercontinental or long-range migrations. ...
Source: Molecular Phylogenetics and Evolution - July 10, 2018 Category: Molecular Biology Source Type: research

Species delimitation and biogeography of the gnatcatchers and gnatwrens (Aves: Polioptilidae)
In this study, we delimited species and estimated phylogenetic relationships using multilocus data for the entire family. We then used the inferred diversity along with alternative taxonomic classification schemes to evaluate how lumping and splitting of both taxa and geographical areas influenced biogeographic inference. Species-tree analyses grouped Polioptilidae into four main clades: Microbates, Ramphocaenus, a Polioptila guianensis complex, and the remaining members of Polioptila. Ramphocaenus melanurus was sister to the clade containing M. cinereiventris and M. collaris, which formed a clade sister to all species wit...
Source: Molecular Phylogenetics and Evolution - July 10, 2018 Category: Molecular Biology Source Type: research

Oligocene origin and drivers of diversification in the genus Sticta (Lobariaceae, Ascomycota)
Publication date: September 2018Source: Molecular Phylogenetics and Evolution, Volume 126Author(s): Todd J. Widhelm, Francesca R. Bertoletti, Matt J. Asztalos, Joel A. Mercado-Díaz, Jen-Pan Huang, Bibiana Moncada, Robert Lücking, Nicolas Magain, Emmanuël Sérusiaux, Bernard Goffinet, Nicholas Crouch, Roberta Mason-Gamer, H. Thorsten LumbschAbstractA major challenge to evolutionary biologists is to understand how biodiversity is distributed through space and time and across the tree of life. Diversification of organisms is influenced by many factors that act at different times and geographic locations...
Source: Molecular Phylogenetics and Evolution - July 10, 2018 Category: Molecular Biology Source Type: research