Flight over the Proto-Caribbean seaway: Phylogeny and macroevolution of Neotropical Anaeini leafwing butterflies
We present the first comprehensive molecular phylogeny for the Neotropical Anaeini leafwing butterflies (Nymphalidae, Charaxinae) and, applying likelihood-based methods, we test the impact of major abiotic (Andean orogeny, Central American highland orogeny, Proto-Caribbean seaway closure, Quaternary glaciations) and biotic (host plant association) factors on their macroevolution. We infer a robust phylogenetic hypothesis for the tribe despite moderate support in some derived clades. Our phylogenetic inference recovers the genus Polygrapha Staudinger, [1887] as polyphyletic, rendering the genera Fountainea Rydon, 1971 and M...
Source: Molecular Phylogenetics and Evolution - April 23, 2019 Category: Molecular Biology Source Type: research

3RAD-based systematics of the transitional Nearctic-Neotropical lubber grasshopper genus Taeniopoda (Orthoptera: Romaleidae)
This study demonstrates the utility of 3RAD to detect gene flow and to resolve species limits and phylogenetic relationships among closely related taxa.Graphical abstract (Source: Molecular Phylogenetics and Evolution)
Source: Molecular Phylogenetics and Evolution - April 22, 2019 Category: Molecular Biology Source Type: research

Mechanisms of allopatric speciation in an Antillean damselfly genus (Odonata, Zygoptera): vicariance or long-distance dispersal?
Publication date: Available online 21 April 2019Source: Molecular Phylogenetics and EvolutionAuthor(s): Yusdiel Torres-Cambas, Sónia Ferreira, Adolfo Cordero-Rivera, M. Olalla Lorenzo-CarballaAbstractWe have examined divergence times of the Antillean damselfly genus Hypolestes, to elucidate which mechanism of allopatric speciation, vicariance or long-distance dispersal, could better explain the currently observed disjunct distributions of this genus. Samples of the three extant species of the genus, Hypolestes clara (Jamaica), H. hatuey (Hispaniola) and H. trinitatis (Cuba), were collected. Mitochondrial and nuclear...
Source: Molecular Phylogenetics and Evolution - April 22, 2019 Category: Molecular Biology Source Type: research

Phylogenomics of the longitarsal Colossendeidae: The evolutionary history of an Antarctic sea spider radiation
Publication date: Available online 16 April 2019Source: Molecular Phylogenetics and EvolutionAuthor(s): Lars Dietz, Jana S. Dömel, Florian Leese, Andrew R. Mahon, Christoph MayerAbstractSea spiders (Pycnogonida) constitute a group of marine benthic arthropods that has a particularly high species diversity in the Southern Ocean. The “longitarsal” group of the sea spider family Colossendeidae is especially abundant in this region. However, this group also includes some representatives from other oceans, which raises the question where the group originates from. Therefore, we here investigated the phylogeny o...
Source: Molecular Phylogenetics and Evolution - April 17, 2019 Category: Molecular Biology Source Type: research

Synteny footprints provide clearer phylogenetic signal than sequence data for prokaryotic classification
ConclusionsThis work exhibits three separate yet related contributions. In terms of phylogenetics, it demonstrates quantitatively the advantage of the SI-based approach over the standard sequence based marker. Evolutionarily, the tree we produce is unique both in its specificity and broadness. Methodologically, the U-shape approach we developed, from synthetic realm, to real life and back to simulation, is novel and allow us to simulate the exact realistic conditions.Graphical abstract (Source: Molecular Phylogenetics and Evolution)
Source: Molecular Phylogenetics and Evolution - April 17, 2019 Category: Molecular Biology Source Type: research

Phylogenomics clarifies biogeographic and evolutionary history, and conservation status of West Indian tremblers and thrashers (Aves: Mimidae)
Publication date: Available online 15 April 2019Source: Molecular Phylogenetics and EvolutionAuthor(s): Jeffrey M. DaCosta, Matthew J. Miller, Jennifer L. Mortensen, J. Michael Reed, Robert L. Curry, Michael D. SorensonAbstractThe West Indian avifauna has provided fundamental insights into island biogeography, taxon cycles, and the evolution of avian behavior. Our interpretations, however, should rely on robust hypotheses of evolutionary relationships and consistent conclusions about taxonomic status in groups with many endemic island populations. Here we present a phylogenetic study of the West Indian thrashers, tremblers...
Source: Molecular Phylogenetics and Evolution - April 16, 2019 Category: Molecular Biology Source Type: research

A brainstorm on the systematics of Turnera (Turneraceae, Malpighiales) caused by insights from molecular phylogenetics and morphological evolution
Publication date: Available online 15 April 2019Source: Molecular Phylogenetics and EvolutionAuthor(s): Lamarck Rocha, Patrícia Luz Ribeiro, Peter K. Endress, Alessandro RapiniAbstractWith 145 species, Turnera is the largest genus of Turneraceae (Malpighiales). Despite several morphotaxonomic and cytogenetic studies, our knowledge about the phylogenetic relationships in Turnera remains mainly based on morphological data. Here, we reconstruct the most comprehensive phylogeny of Turnera with molecular data to understand the morphological evolution within this group and to assess its circumscription and infrageneric cl...
Source: Molecular Phylogenetics and Evolution - April 16, 2019 Category: Molecular Biology Source Type: research

Dark offshoot: phylogenomic data sheds light on the evolutionary history of a new species of cave brittle star
In this study, we reassess the species boundaries of this putative cave species using a phylogenomic dataset (20 specimens in 13 species, 100 exons, 18.7 kbp). We perform species delimitation analyses using robust full-coalescent methods for discovery and validation of hypotheses on species boundaries, as well as infer its phylogenetic relationships with species distributed in adjacent marine regions, in order to investigate the origin of this cave-adapted species. We assess which hypotheses on the origin of subterranean taxa can be applied to this species by taking into account its placement within the genus Ophionereis a...
Source: Molecular Phylogenetics and Evolution - April 13, 2019 Category: Molecular Biology Source Type: research

Introgressive hybridisation between two widespread sharks in the east Pacific Region
Publication date: Available online 11 April 2019Source: Molecular Phylogenetics and EvolutionAuthor(s): Diana A. Pazmiño, Lynne vanHerwerden, Colin A. Simpfendorfer, Claudia Junge, Stephen C. Donnellan, E. Mauricio Hoyos-Padilla, Clinton A.J. Duffy, Charlie Huveneers, Bronwyn Gillanders, Paul A. Butcher, Gregory E. MaesAbstractWith just a handful of documented cases of hybridisation in cartilaginous fishes, shark hybridisation remains poorly investigated. Small amounts of admixture have been detected between Galapagos (Carcharhinus galapagensis) and dusky (Carcharhinus obscurus) sharks previously, generating a hypot...
Source: Molecular Phylogenetics and Evolution - April 13, 2019 Category: Molecular Biology Source Type: research

Evolution of the human cold/menthol receptor, TRPM8
In this study, we investigate whether alternative transcription has been a driving force in the evolution of the human forms of the cold receptor TRPM8.We identified 33 TRPM8 alternative mRNAs (24 new sequences) and their associated protein isoforms in human tissues. Using comparative genomics, we described the evolution of the human TRPM8 sequences in eight ancestors since the origin of Amniota, and estimated in which ancestors the new TRPM8 variants originated. In order to validate the estimated origins of this receptor, we performed experimental validations of predicted exons in mouse tissues. Our results suggest a firs...
Source: Molecular Phylogenetics and Evolution - April 11, 2019 Category: Molecular Biology Source Type: research

A comprehensive kelp phylogeny sheds light on the evolution of an ecosystem
Publication date: Available online 10 April 2019Source: Molecular Phylogenetics and EvolutionAuthor(s): S. Starko, M. Soto Gomez, H. Darby, K.W. Demes, H. Kawai, N. Yotsukura, S.C. Lindstrom, P.J. Keeling, S.W. Graham, P.T. MartoneAbstractReconstructing phylogenetic topologies and divergence times is essential for inferring the timing of radiations, the appearance of adaptations, and the historical biogeography of key lineages. In temperate marine ecosystems, kelps (Laminariales) drive productivity and form essential habitat but an incomplete understanding of their phylogeny has limited our ability to infer their evolution...
Source: Molecular Phylogenetics and Evolution - April 11, 2019 Category: Molecular Biology Source Type: research

The genetic structure of flax illustrates environmental and anthropogenic selections that gave rise to its eco-geographical adaptation
Publication date: Available online 9 April 2019Source: Molecular Phylogenetics and EvolutionAuthor(s): Demissew Sertse, Frank M. You, Sridhar Ravichandran, Sylvie CloutierAbstractFlax, one of the eight founder crops of agriculture, has been cultivated for its oil and/or fiber for millennia. Understanding genetic divergence and geographic origins of germplasm in line with their cultivation history and ecological adaptation are essential for conservation and breeding. Here we performed a genome-wide assessment based on more than 51,000 single nucleotide polymorphic sites defining 383 flax accessions from a core collection re...
Source: Molecular Phylogenetics and Evolution - April 10, 2019 Category: Molecular Biology Source Type: research

Molecular phylogeny of Oreochromis (Cichlidae: Oreochromini) reveals mito-nuclear discordance and multiple colonisation of adverse aquatic environments
Publication date: Available online 8 April 2019Source: Molecular Phylogenetics and EvolutionAuthor(s): Antonia G.P. Ford, Thomas R. Bullen, Longson Pang, Martin J. Genner, Roger Bills, Tomáš Flouri, Benjamin P. Ngatunga, Lukas Rüber, Ulrich K. Schliewen, Ole Seehausen, Asilatu Shechonge, Melanie L.J. Stiassny, George F. Turner, Julia J. DayAbstractAlthough the majority of cichlid diversity occurs in the African Great Lakes, these fish have also diversified across the African continent. Such continental radiations, occurring in both rivers and lakes have received far less attention than lacustrine radiati...
Source: Molecular Phylogenetics and Evolution - April 10, 2019 Category: Molecular Biology Source Type: research

Assessing the diversity of Western North American Juga (Semisulcospiridae, Gastropoda)
Publication date: Available online 8 April 2019Source: Molecular Phylogenetics and EvolutionAuthor(s): Ellen E. Strong, Nathan V. WhelanAbstractJuga is a genus of freshwater gastropods distributed in Pacific and Interior drainages of the Pacific Northwest from central California to northern Washington. The current classification has relied heavily on features of the shell, which vary within and across drainages, and often intergrade without sharp distinctions between species. The only previous molecular analysis included limited population sampling, which did not allow robust assessment of intra- versus interspecific level...
Source: Molecular Phylogenetics and Evolution - April 10, 2019 Category: Molecular Biology Source Type: research

A species-level phylogeny of Trachylepis (Scincidae: Mabuyinae) provides insight into their reproductive mode evolution
Publication date: Available online 6 April 2019Source: Molecular Phylogenetics and EvolutionAuthor(s): Jeffrey L. Weinell, William R. Branch, Timothy J. Colston, Todd R. Jackman, Arianna Kuhn, Werner Conradie, Aaron M. BauerAbstractTrachylepis (Mabuyinae) includes ∼80 species of fully-limbed skinks found primarily in Africa and Madagascar, but a robust species-level phylogeny for this genus is lacking and this impedes studies on a wide-range of topics from biogeography to character evolution. Trachylepis and its close relatives (which together form the Mabuya group or Mabuyinae) are notable in that they have undergone ...
Source: Molecular Phylogenetics and Evolution - April 7, 2019 Category: Molecular Biology Source Type: research

New insights from nuclear and mitochondrial markers on the genetic diversity and structure of the Indian white shrimp Fenneropenaeus indicus among the marginal seas in the Indian Ocean
Publication date: Available online 4 April 2019Source: Molecular Phylogenetics and EvolutionAuthor(s): K.A. Sajeela, A. Gopalakrishnan, V.S. Basheer, A. Mandal, K.K. Bineesh, G. Grinson, S.D. GopakumarAbstractGenetic variation in wild stocks of a major commercial shrimp, Fenneropenaeus indicus, from the marginal seas in the Indian Ocean was analysed using polymorphic microsatellite loci and mitochondrial COI gene. The average observed heterozygosity (Ho=0.44±0.02) and the expected heterozygosity (He=0.73±0.01) were high across loci and populations indicating high microsatellite variation. Pairwise FST and Bay...
Source: Molecular Phylogenetics and Evolution - April 5, 2019 Category: Molecular Biology Source Type: research

Hunting the wolf: A molecular phylogeny of the wolf spiders (Araneae, Lycosidae)
We present a broad phylogenetic analysis of the Lycosidae including a wide geographic sampling of representatives and all the subfamilies described to date. Additionally, we extend the amount of molecular data used in previous studies (28S, 12S and NADH) through the inclusion of two additional markers, the nuclear H3 and the mitochondrial COI. We estimated the divergence times through the inclusion of fossils as calibration points and used the phylogenetic hypothesis obtained to explore the evolution of particular traits associated with dispersal capabilities. We recovered most of the currently recognized subfamilies with ...
Source: Molecular Phylogenetics and Evolution - April 5, 2019 Category: Molecular Biology Source Type: research

Chloroplast genome analysis of box-ironbark Eucalyptus
We report four new complete chloroplast genomes of Eucalyptus, including three genomes from species previously lacking any chloroplast reference sequences. Plastomes of E. albens, E. conica, E. crebra and E. melliodora assembled using a de novo approach were shown to be largely identical to each other, and similar in size and structure to previously published chloroplast genomes from Eucalyptus. A total of 132 genes (114 single-copy genes and 18 duplicated genes in the IR regions) were identified, and shown to be highly conserved in terms of gene order, content and organization. Slightly higher divergence in the intergenic...
Source: Molecular Phylogenetics and Evolution - April 5, 2019 Category: Molecular Biology Source Type: research

A multi-locus phylogeny for the Neotropical Anomospermeae (Menispermaceae): Implications for taxonomy and biogeography
In this study, we used six chloroplast and two nuclear DNA markers to reconstruct phylogenetic relationships within the Neotropical Anomospermeae (Menispermaceae). The phylogeny of this group was then used as basis to reconstruct its biogeographical history. The phylogenetic framework reconstructed here strongly supports the monophyly of the Neotropical Anomospermeae and recovers the species of Anomospermum in three different clades: (i) Anomospermum sect. Anomospermum plus Orthomene; (ii) Anomospermum grandifolium and A. solimoesanum (Anomospermum sect. Elissarrhena); and (iii) Anomospermum bolivianum (Anomospermum sect. ...
Source: Molecular Phylogenetics and Evolution - April 3, 2019 Category: Molecular Biology Source Type: research

From seascape ecology to population genomics and back. Spatial and ecological differentiation among cryptic species of the red algae Lithophyllum stictiforme/L. cabiochiae, main bioconstructors of coralligenous habitats
Publication date: Available online 2 April 2019Source: Molecular Phylogenetics and EvolutionAuthor(s): Aurélien De Jode, Romain David, Anne Haguenauer, Abigail E. Cahill, Zinovia Erga, Dorian Guillemain, Stéphane Sartoretto, Caroline Rocher, Marjorie Selva, Line Le Gall, Jean-Pierre Féral, Anne ChenuilAbstractEcosystem engineering species alter the physical structure of their environment and can create or modify habitats, having a massive impact on local biodiversity. Coralligenous reefs are highly diverse habitats endemic to the Mediterranean Sea built by calcareous benthic organisms among which Crust...
Source: Molecular Phylogenetics and Evolution - April 3, 2019 Category: Molecular Biology Source Type: research

Contrasting phylogeographic histories between the continent and islands of East Asia: Massive mitochondrial introgression and long-term isolation of hares (Lagomorpha: Lepus)
Publication date: Available online 2 April 2019Source: Molecular Phylogenetics and EvolutionAuthor(s): Gohta Kinoshita, Mitsuo Nunome, Alexey P Kryukov, Irina V. Kartavtseva, San-Hoon Han, Fumio Yamada, Hitoshi SuzukiAbstractHares of the genus Lepus are distributed worldwide, and introgressive hybridization is thought to be pervasive among species, leading to reticulate evolution and taxonomic confusion. Here, we performed phylogeographic analyses of the following species of hare across East Asia: L. timidus, L. mandshuricus, L. coreanus, and L. brachyurus collected from far-eastern Russia, South Korea, and Japan. Nucleoti...
Source: Molecular Phylogenetics and Evolution - April 3, 2019 Category: Molecular Biology Source Type: research

Saffron (Crocus sativus) is an autotriploid that evolved in Attica (Greece) from wild Crocus cartwrightianus
Publication date: Available online 1 April 2019Source: Molecular Phylogenetics and EvolutionAuthor(s): Zahra Nemati, Dörte Harpke, Almila Gemicioglu, Helmut Kerndorff, Frank R. BlattnerAbstractCrocus sativus, the saffron crocus, is the source of saffron, which is made from the dried stigmas of the plant. It is a male-sterile triploid lineage that ever since its origin has been propagated vegetatively. Its mode of evolution and area of origin are matters of long-lasting debates. Here we analyzed chloroplast genomes and genome-wide DNA polymorphisms obtained through genotyping-by-sequencing (GBS) to infer the parent and...
Source: Molecular Phylogenetics and Evolution - April 2, 2019 Category: Molecular Biology Source Type: research

Synteny Footprints Provide Clearer Phylogenetic Signal than Sequence Data for Prokayotic Classification
ConclusionsThis work exhibits three separate yet related contributions. In terms of phylogenetics, it demonstrates quantitatively the advantage of the SI-based approach over the standard sequence based marker. Evolutionarily, the tree we produce is unique both in its specificity and broadness. Methodologically, the U-shape approach we developed, from synthetic realm, to real life and back to simulation, is novel and allow us to simulate the exact realistic conditions.Graphical abstract (Source: Molecular Phylogenetics and Evolution)
Source: Molecular Phylogenetics and Evolution - April 2, 2019 Category: Molecular Biology Source Type: research

Museum genomics reveals the speciation history of Dendrortyx wood-partridges in the Mesoamerican highlands
Publication date: Available online 28 March 2019Source: Molecular Phylogenetics and EvolutionAuthor(s): Whitney L.E. Tsai, Claudio Mota-Vargas, Octavio Rojas-Soto, Ravi Bhowmik, Emily Y. Liang, James M. Maley, Eugenia Zarza, John E. McCormackAbstractNatural history collections are increasingly valued as genomic resources. Their specimens reflect the combined efforts of collectors and curators over hundreds of years. For many rare or endangered species, specimens are the only readily available source of DNA. We leveraged specimens from a historical collection to study the evolutionary history of wood-partridges in the genus...
Source: Molecular Phylogenetics and Evolution - March 29, 2019 Category: Molecular Biology Source Type: research

Molecular phylogeny of Paraonidae (Annelida)
Publication date: Available online 29 March 2019Source: Molecular Phylogenetics and EvolutionAuthor(s): Joachim Langeneck, Michele Barbieri, Ferruccio Maltagliati, Alberto CastelliAbstractA molecular phylogeny of the family Paraonidae was reconstructed on the basis of 16S rDNA, COI and 18S rDNA sequences obtained from 66 individuals belonging to 38 nominal species and subspecies. In agreement with previous findings, Paraonidae represent a monophyletic group, closely related to Sternaspidae. The topology obtained by the Bayesian and Maximum Likelihood analyses on the combined dataset was not consistent with the traditional ...
Source: Molecular Phylogenetics and Evolution - March 29, 2019 Category: Molecular Biology Source Type: research

On the uniqueness of the maximum parsimony tree for data with up to two substitutions: an extension of the classic Buneman theorem in phylogenetics
Publication date: Available online 27 March 2019Source: Molecular Phylogenetics and EvolutionAuthor(s): Mareike FischerAbstractOne of the main aims of phylogenetics is the reconstruction of the correct evolutionary tree when data concerning the underlying species set are given. These data typically come in the form of DNA, RNA or protein alignments, which consist of various characters (also often referred to as sites). Often, however, tree reconstruction methods based on criteria like maximum parsimony may fail to provide a unique tree for a given dataset, or, even worse, reconstruct the ‘wrong’ tree (i.e. a tr...
Source: Molecular Phylogenetics and Evolution - March 28, 2019 Category: Molecular Biology Source Type: research

Plastome based phylogenetics and younger crown node age in Pelargonium
In this study, we reconstructed a phylogenetic tree based on 74 plastome exons and nuclear rDNA ITS regions for 120 species, which represents 43 % taxon coverage for Pelargonium. We also performed a dating analysis to examine the timing of the major radiations in the genus.Phylogenetic analyses of nucleotide, amino acid, and ITS alignments confirmed the previously-documented subgeneric split into five main clades ((C1,C2),(B(A1,A2))) although clade only A1 received low bootstrap support.Using calibration evidence from a range of sources the Pelargonium crown age was estimated to be 9.7 My old, much younger than previous es...
Source: Molecular Phylogenetics and Evolution - March 27, 2019 Category: Molecular Biology Source Type: research

The mystery of the phylogeographic structural pattern in rodent-borne hantaviruses
Publication date: Available online 23 March 2019Source: Molecular Phylogenetics and EvolutionAuthor(s): Alexandro Guterres, Renata Carvalho de Oliveira, Jorlan Fernandes, Elba Regina Sampaio de LemosAbstractHantaviruses (order Bunyavirales, family Hantaviridae) are important zoonotic pathogens. Because of the great diversity of their reservoir hosts, hantaviruses are excellent models to evaluate the dynamics of virus-host co-evolution. To understand the mechanisms behind the evolutionary history of hantaviruses through virus-reservoir interactions, it is important to know how the radiation and diversity of hantaviruses occ...
Source: Molecular Phylogenetics and Evolution - March 24, 2019 Category: Molecular Biology Source Type: research

Wolbachia of phylogenetic supergroup E identified in oribatid mite Gustavia microcephala (Acari: Oribatida)
We report for the first time Wolbachia in oribatid mite Gustavia microcephala. The sequences of 16S rDNA, gltA, and ftsZ genes of the endosymbiont from the mite showed the highest similarity to Wolbachia found in Collembola. Phylogenetic analysis based on single gene and concatenated alignments of three genes revealed that the bacteria from G. microcephala and Collembola were related and clustered together with supergroup E. Relatively close relationship of Wolbachia from oribatid and collembolan hosts might mean at the evolutionary scale that horizontal transfer of bacteria between these two groups of invertebrates may ta...
Source: Molecular Phylogenetics and Evolution - March 24, 2019 Category: Molecular Biology Source Type: research

Phylogenomics shows lignotuber state is taxonomically informative in closely related eucalypts
Publication date: Available online 23 March 2019Source: Molecular Phylogenetics and EvolutionAuthor(s): Carl R. Gosper, Tara Hopley, Margaret Byrne, Stephen D. Hopper, Suzanne M. Prober, Colin J. YatesAbstractPlant taxa can be broadly divided based on the mechanisms enabling persistence through whole-crown disturbances, specifically whether individuals resprout, populations reseed, or both or neither of these mechanisms are employed. At scales from species through to communities, the balance of disturbance-response types has major ramifications for ecological function and biodiversity conservation. In some lineages, morpho...
Source: Molecular Phylogenetics and Evolution - March 24, 2019 Category: Molecular Biology Source Type: research

Plastome reduction and gene content in New World Pilostyles (Apodanthaceae) unveils high similarities to African and Australian congeners
We present data on plastome assembly, transcriptomic data that confirm the transcriptional activity of all genes and describe for the first time six transcript variants of a putative ORF likely having oxidoreductase activity. Our data show that such extreme reduction in P. boyacensis is similar but not identical to that reported in one Australian and one African species of the genus. Such intercontinental similarity suggests that the legume-Pilostyles holoparasitism was already in place during the main African-Australian-South American break-up. We compare plastome content and synteny between the three sequenced species, p...
Source: Molecular Phylogenetics and Evolution - March 24, 2019 Category: Molecular Biology Source Type: research

Complete subspecies-level phylogeny of the Oriolidae (Aves: Passeriformes): Out of Australasia and return
We present a new complete molecular (mtDNA) subspecies level phylogeny of the Oriolidae including all 113 taxa (35 species) together with a backbone phylogeny of 19 taxa from the main Oriolus clades based on i) 21 nuclear genes, ii) whole mito-genomes, and iii) genome-wide ultraconserved elements. We use this phylogeny to assess systematic relationships and the biogeographical history of this avian family. Furthermore, we use morphological measurements to investigate the relationship between size and shape axes and upstream or back-colonization of this extensive island region from Asia. We show that several subspecies or g...
Source: Molecular Phylogenetics and Evolution - March 24, 2019 Category: Molecular Biology Source Type: research

Restriction-site associated DNA sequencing supports a sister group relationship of Nigritella and Gymnadenia (Orchidaceae)
Publication date: Available online 23 March 2019Source: Molecular Phylogenetics and EvolutionAuthor(s): Marie K. Brandrud, Ovidiu Paun, Richard Lorenz, Juliane Baar, Mikael HedrénAbstractThe orchid genus Nigritella is closely related to Gymnadenia and has from time to time been merged with the latter. Although Nigritella is morphologically distinct, it has been suggested that the separating characters are easily modifiable and subject to rapid evolutionary change. So far, molecular phylogenetic studies have either given support for the inclusion of Nigritella in Gymnadenia, or for their separation as different gener...
Source: Molecular Phylogenetics and Evolution - March 24, 2019 Category: Molecular Biology Source Type: research

Phylogenetic delineation of regional biota: a case study of the Chinese flora
Publication date: Available online 22 March 2019Source: Molecular Phylogenetics and EvolutionAuthor(s): Jianfei Ye, Limin Lu, Bing Liu, Tuo Yang, Jinlong Zhang, Haihua Hu, Rong Li, Anming Lu, Huiyuan Liu, Lingfeng Mao, Zhiduan ChenAbstractBiogeographical regionalization schemes have traditionally been constructed based on taxonomic endemism of families, genera, and/or species, and rarely incorporated the phylogenetic relationships between taxa. However, phylogenetic relationships are important for understanding historical connections within and among biogeographical regions. Phylogeny-based delineation of biota is a burgeo...
Source: Molecular Phylogenetics and Evolution - March 22, 2019 Category: Molecular Biology Source Type: research

Spatio-temporal evolution of climbing habit in the Dahlia-Hidalgoa group (Coreopsidae, Asteraceae)
Publication date: Available online 20 March 2019Source: Molecular Phylogenetics and EvolutionAuthor(s): Erandi Sánchez-Chávez, Aaron Rodríguez, Arturo Castro-Castro, Miguel Angel Pérez- Farrera, Victoria SosaAbstractIn this paper we focus on Hidalgoa, a small genus distributed in cloud forest from Mexico to Colombia with the uncommon climbing habit of enlarging its petioles. This genus belongs to tribe Coreopsideae (Asteraceae), a group mostly from the Neotropics with a few taxa in Oceania and Polynesia. The phylogenetic position of Hidalgoa has not yet been determined though it will most probab...
Source: Molecular Phylogenetics and Evolution - March 21, 2019 Category: Molecular Biology Source Type: research

Mechanisms of Antiviral Resistance in Influenza Neuraminidase Revealed by a Mass Spectrometry Based Phylonumerics Approach
Publication date: Available online 20 March 2019Source: Molecular Phylogenetics and EvolutionAuthor(s): Elma H. Akand, Kevin.M. DownardAbstractA mass based phylonumerics approach is shown to be able to investigate the origins of the emergence of antiviral resistance mutations in influenza neuraminidase through a global view of mutational trends. Frequent ancestral and descendant mutations that precede and follow the manifestation of antiviral resistance mutations are identified in N2 neuraminidase. The majority occur in the head region around the active site and drive hydrophilicity changes, primarily through the incorpora...
Source: Molecular Phylogenetics and Evolution - March 21, 2019 Category: Molecular Biology Source Type: research

Multiple new species: Cryptic diversity in the widespread mite species Cymbaeremaeus cymba (Oribatida, Cymbaeremaeidae)
In this study we aimed at characterizing the molecular diversity of the Palearctic arboreal oribatid mite species Cymbaeremaeus cymba across large parts of Europe. Phylogenetic analyses of three molecular markers, including the COI barcoding region, identified eight well supported, fairly divergent clades within C. cymba, which we consider to represent distinct species based on molecular species delimitation methods. Intraspecific variation of the COI gene was extremely low in all putative species, contradicting previous assumptions of high intraspecific diversity in oribatid mites. The frequent co-occurrence of two specie...
Source: Molecular Phylogenetics and Evolution - March 18, 2019 Category: Molecular Biology Source Type: research

Inferring hypothesis-based transitions in clade-specific models of chromosome number evolution in sedges (Cyperaceae)
Publication date: Available online 15 March 2019Source: Molecular Phylogenetics and EvolutionAuthor(s): José Ignacio Márquez-Corro, Santiago Martín-Bravo, Daniel Spalink, Modesto Luceño, Marcial EscuderoAbstractLarge-scale changes in chromosome number have been associated with diversification rate shifts in many lineages of plants. For instance, several ancient rounds of polyploidization events have been inferred to promote genomic differentiation and/or isolation and, consequently, angiosperm diversification. Dysploidy, although less studied, has been suggested to also play an important role in...
Source: Molecular Phylogenetics and Evolution - March 16, 2019 Category: Molecular Biology Source Type: research

Digging for the spiny rat and hutia phylogeny using a gene capture approach, with the description of a new mammal subfamily
Publication date: Available online 15 March 2019Source: Molecular Phylogenetics and EvolutionAuthor(s): Maxime Courcelle, Marie-ka Tilak, Yuri L.R. Leite, Emmanuel J.P. Douzery, Pierre-Henri FabreAbstractNext generation sequencing (NGS) and genomic database mining allow biologists to gather and select large molecular datasets well suited to address phylogenomics and molecular evolution questions. Here we applied this approach to a mammal family, the Echimyidae, for which generic relationships have been difficult to recover and often referred to as a star phylogeny. These South-American spiny rats represent a family of cavi...
Source: Molecular Phylogenetics and Evolution - March 16, 2019 Category: Molecular Biology Source Type: research

The Phylogeny and Evolutionary Timescale of stoneflies (Insecta: Plecoptera) inferred from Mitochondrial Genomes
Publication date: Available online 12 March 2019Source: Molecular Phylogenetics and EvolutionAuthor(s): Shuangmei Ding, Weihai Li, Ying Wang, Stephen L. Cameron, Dávid Murányi, Ding YangAbstractPhylogenetic analysis based on mitochondrial genomic data from 25 stonefly species recovered a well-supported tree resolving higher-level relationships within Plecoptera (stoneflies). The monophyly of both currently recognized suborders was strongly supported, concordant with previous molecular analyses of Plecoptera. The southern hemisphere suborder Antarctoperlaria formed two clades: Eustheniidae +Diamphipnoidae and ...
Source: Molecular Phylogenetics and Evolution - March 13, 2019 Category: Molecular Biology Source Type: research

A novel gene arrangement among the Stylommatophora by the complete mitochondrial genome of the terrestrial slug Meghimatium bilineatum (Gastropoda, Arionoidea)
Publication date: Available online 8 March 2019Source: Molecular Phylogenetics and EvolutionAuthor(s): Guang-Long Xie, Frank Köhler, Xiao-Chen Huang, Rui-Wen Wu, Chun-Hua Zhou, Shan Ouyang, Xiao-Ping WuAbstractStylommatophora is a main clade of Gastropoda that encompasses approximately 112 gastropod families and may exceed a total of 30,000 species. Twenty-four complete stylommatophoran mitogenomes have been sequenced to date, yet our understanding of mitochondrial evolution in stylommatophorans is still in its infancy. To further expand the set of available mitogenomes, we sequenced the mitogenome of Meghimatium bili...
Source: Molecular Phylogenetics and Evolution - March 10, 2019 Category: Molecular Biology Source Type: research

Unraveling patterns and processes of diversification in the South Andean-Patagonian Nassauvia subgenus Strongyloma (Asteraceae, Nassauvieae)
This study emphasizes that adding more than one sequence per species, not combining data with dissimilar inheritance patterns without first performed incongruence tests, exploring data through different methodologies, considering the timing of events, and searching for the causes of poorly resolved and/or incongruent phylogenies help to reveal complex biological underlying processes, which might otherwise remain hidden.Graphical abstract (Source: Molecular Phylogenetics and Evolution)
Source: Molecular Phylogenetics and Evolution - March 8, 2019 Category: Molecular Biology Source Type: research

Editorial Board
Publication date: May 2019Source: Molecular Phylogenetics and Evolution, Volume 134Author(s): (Source: Molecular Phylogenetics and Evolution)
Source: Molecular Phylogenetics and Evolution - March 8, 2019 Category: Molecular Biology Source Type: research

Incorporation of deep-sea and small-sized species provides new insights into gastropods phylogeny
In this study, we aimed at correcting this bias by reconstructing the phylogeny with new mitogenomes of deep-sea gastropods including Anatoma sp., Bathysciadiidae sp., Bayerotrochus teramachii, Calliotropis micraulax, Coccocrater sp., Cocculina subcompressa, Lepetodrilus guaymasensis, Peltospira smaragdina, Perotrochus caledonicus, Pseudococculinidae sp., and Shinkailepas briandi. This dataset provided the first reports of the mitogenomes for the Cocculiniformia, three vetigastropod superfamilies: Pleurotomarioidea, Lepetelloidea, and Scissurelloidea, and the neritimorph family Phenacolepadidae. The addition of deep-sea re...
Source: Molecular Phylogenetics and Evolution - March 8, 2019 Category: Molecular Biology Source Type: research

Frozen Antarctic path for dispersal initiated parallel host-parasite evolution on different continents
Publication date: Available online 6 March 2019Source: Molecular Phylogenetics and EvolutionAuthor(s): Daniel Benda, Yuta Nakase, Jakub StrakaAbstractAfter the break-up of Gondwana dispersal of organisms between America, Australia and Africa became more complicated. One of the possible remaining paths led through Antarctica, that was not yet glaciated and it remained habitable for many organisms. This favourable climate made Antarctica an important migration corridor for organisms with good dispersal ability, such as Aculeata (Hymenoptera), till the Oligocene cooling. Here we tested how cooling of Antarctica impacted globa...
Source: Molecular Phylogenetics and Evolution - March 6, 2019 Category: Molecular Biology Source Type: research

Molecular Phylogeny of the Ghost Knifefishes (Gymnotiformes: Apteronotidae)
Publication date: Available online 4 March 2019Source: Molecular Phylogenetics and EvolutionAuthor(s): Maxwell J. Bernt, Victor A. Tagliacollo, James S. AlbertGraphical abstract (Source: Molecular Phylogenetics and Evolution)
Source: Molecular Phylogenetics and Evolution - March 5, 2019 Category: Molecular Biology Source Type: research

Phylogeny, phylogeography and hybridization of Caucasian barbels of the genus Barbus (Actinopterygii, Cyprinidae)
Publication date: Available online 4 March 2019Source: Molecular Phylogenetics and EvolutionAuthor(s): Boris A. Levin, Alexander A. Gandlin, Evgeniy S. Simonov, Marina A. Levina, Anna E. Barmintseva, Bella Japoshvili, Nikolai S. Mugue, Levan Mumladze, N.J. Mustafayev, Andrey N. Pashkov, Haikaz R. Roubenyan, Maxim I. Shapovalov, Ignacio DoadrioAbstractPhylogenetic relationships and phylogeography of six species of Caucasian barbels, the genus Barbus s. str., were studied based on extended geographic coverage and using mtDNA and nDNA markers. Based on 26 species studied, matrilineal phylogeny of the genus Barbus is composed ...
Source: Molecular Phylogenetics and Evolution - March 5, 2019 Category: Molecular Biology Source Type: research

Evolutionary history of the Pasque-flowers (Pulsatilla, Ranunculaceae): molecular phylogenetics, systematics and rDNA evolution
Publication date: Available online 1 March 2019Source: Molecular Phylogenetics and EvolutionAuthor(s): Gábor Sramkó, Levente Laczkó, Polina A. Volkova, Richard M. Bateman, Jelena MlinarecAbstractPulsatilla (Anemoneae, Ranunculaceae) is sister to Anemone s.s. and contains ca 40 perennial species of considerable horticultural and medical importance. We sequenced 31 of those species, plus nine subspecies, two cultivars and six outgroups, for two nuclear regions (high-copy nrITS and low-copy MLH1) and three plastid regions (rbcL, accD–psaI, trnL intron) in order to generate the first comprehensive sp...
Source: Molecular Phylogenetics and Evolution - March 5, 2019 Category: Molecular Biology Source Type: research

Phylogenomics facilitates stable scorpion systematics: Reassessing the relationships of Vaejovidae and a new high-level classification of Scorpiones (Arachnida)
Publication date: Available online 1 March 2019Source: Molecular Phylogenetics and EvolutionAuthor(s): Carlos E. Santibáñez-López, Edmundo González-Santillán, Lionel Monod, Prashant P. SharmaAbstractThe Neartic family Vaejovidae (Scorpiones: Chactoidea) has long been treated as a diverse and systematically cohesive group of scorpions, but its monophyly and relationship to other scorpion families have historically been questioned. Morphological data have supported its monophyly and a variety of phylogenetic placements within the superfamily Chactoidea. Recent phylogenomic analyses have ins...
Source: Molecular Phylogenetics and Evolution - March 5, 2019 Category: Molecular Biology Source Type: research

Positive Selection of Cereblon Modified Function Including its E3 Ubiquitin Ligase Activity and Binding Efficiency with AMPK
Publication date: Available online 2 March 2019Source: Molecular Phylogenetics and EvolutionAuthor(s): Wataru Onodera, Toru Asahi, Naoya SawamuraAbstractCereblon (CRBN) is a substrate receptor for an E3 ubiquitin ligase that directly binds to target proteins resulting in cellular activities, such as energy metabolism, membrane potential regulation, and transcription factor degradation. Genetic mutations in human CRBN lead to intellectual disabilities. In addition, it draws pathological attention because direct binding with immunomodulatory drugs can cure multiple myeloma (MM) and lymphocytic leukemia. To further explore th...
Source: Molecular Phylogenetics and Evolution - March 5, 2019 Category: Molecular Biology Source Type: research