abstract：:The field of phylogenetics is changing rapidly with the application of high-throughput sequencing to non-model organisms. Cost-effective use of this technology for phylogenetic studies, which often include a relatively small portion of the genome but several taxa, requires strategies for genome partitioning and sequen...

journal_title：Molecular phylogenetics and evolution

authors： Barrow LN,Ralicki HF,Emme SA,Lemmon EM

更新日期：2014-06-01 00:00:00

abstract：:Stochastic models of sequence evolution have been developed to reflect many biologically important processes, allowing for accurate phylogenetic reconstruction when an appropriate model is selected. However, commonly used models do not incorporate several potentially important biological processes. Spurious phylogenet...

journal_title：Molecular phylogenetics and evolution

authors： Doyle VP,Andersen JJ,Nelson BJ,Metzker ML,Brown JM

更新日期：2014-06-01 00:00:00

abstract：:Polycyclic triterpenoids, such as sterols and hopanoids, are essential components of plasmatic membrane in eukaryotic organisms. Although it is generally assumed that ciliates do not synthesize sterols, and many of them are indeed auxotrophic, a large set of annotated genomic sequences and experimental data from recen...

journal_title：Molecular phylogenetics and evolution

authors： Tomazic ML,Poklepovich TJ,Nudel CB,Nusblat AD

更新日期：2014-05-01 00:00:00

abstract：:Lake Tanganyika (LT) is a biodiversity hotspot supporting many endemic radiations that provide comparative systems in which to investigate if there are common factors leading to the build-up of its considerable diversity. Despite LT containing the highest diversity of lacustrine catfishes on Earth, the evolutionary re...

journal_title：Molecular phylogenetics and evolution

authors： Peart CR,Bills R,Wilkinson M,Day JJ

更新日期：2014-04-01 00:00:00

abstract：:The catfish family Diplomystidae is one of the earliest branching lineages within the diverse order Siluriformes and shows a deep phylogenetic split from all other extant and extinct major catfish groups. Despite its relevance in the evolution of siluriforms, phylogenetic relationships within the Diplomystidae are poo...

journal_title：Molecular phylogenetics and evolution

authors： Muñoz-Ramírez CP,Unmack PJ,Habit E,Johnson JB,Cussac VE,Victoriano P

更新日期：2014-04-01 00:00:00

abstract：:In animals and plants, non-coding small RNAs regulate the expression of many genes at the post-transcriptional level. Recently, many non-coding small RNAs (sRNAs) have also been found to regulate a variety of important biological processes in bacteria, including social traits, but little is known about the phylogeneti...

journal_title：Molecular phylogenetics and evolution

authors： Chen IC,Griesenauer B,Yu YT,Velicer GJ

更新日期：2014-04-01 00:00:00

abstract：:Eight current species of snakes of the Bothrops neuwiedi group are widespread in South American open biomes from northeastern Brazil to southeastern Argentina. In this paper, 140 samples from 93 different localities were used to investigate species boundaries and to provide a hypothesis of phylogenetic relationships a...

journal_title：Molecular phylogenetics and evolution

authors： Machado T,Silva VX,Silva MJ

更新日期：2014-02-01 00:00:00

abstract：:Phylogenetic analyses based on small to moderately sized sets of sequential data lead to overestimating mutation rates in influenza hemagglutinin (HA) by at least an order of magnitude. Two major underlying reasons are: the incomplete lineage sorting, and a possible absence in the analyzed sequences set some of key mi...

journal_title：Molecular phylogenetics and evolution

authors： Radomski JP,Płoński P,Zagórski-Ostoja W

更新日期：2014-01-01 00:00:00

abstract：:Rapid radiations have long been regarded as the most challenging issue for elucidating poorly resolved phylogenies in evolutionary biology. The eight diploid AA- genome species in the genus Oryza represent a typical example of a closely spaced series of recent speciation events in plants. However, questions regarding ...

journal_title：Molecular phylogenetics and evolution

authors： Zhu T,Xu PZ,Liu JP,Peng S,Mo XC,Gao LZ

更新日期：2014-01-01 00:00:00

abstract：:The systematics of Eutardigrada, the largest lineage among the three classes of the phylum Tardigrada, is based mainly on the morphology of the leg claws and of the buccal apparatus. However, three members of the rarely recorded and poorly known limno-terrestrial eutardigrade genus Apodibius have no claws on their str...

journal_title：Molecular phylogenetics and evolution

authors： Dabert M,Dastych H,Hohberg K,Dabert J

更新日期：2014-01-01 00:00:00

abstract：:BaCoCa (BAse COmposition CAlculator) is a user-friendly software that combines multiple statistical approaches (like RCFV and C value calculations) to identify biases in aligned sequence data which potentially mislead phylogenetic reconstructions. As a result of its speed and flexibility, the program provides the poss...

journal_title：Molecular phylogenetics and evolution

authors： Kück P,Struck TH

更新日期：2014-01-01 00:00:00

abstract：:Reconstructing species trees by incorporating information from many independent gene trees reduces the confounding influence of stochastic lineage sorting. Such analyses are particularly important for taxa that share polymorphisms due to incomplete lineage sorting or introgressive hybridization. We investigated phylog...

journal_title：Molecular phylogenetics and evolution

authors： Lavretsky P,McCracken KG,Peters JL

更新日期：2014-01-01 00:00:00

abstract：:The Ciminalis section of Gentiana comprises seven species, two of them growing on siliceous substrates (G. alpina and G. acaulis), the other ones being calcareous taxa (G. clusii, G. angustifolia, G. ligustica, G. occidentalis and G. dinarica). A total of 515 individuals from 183 populations over the entire Ciminalis ...

journal_title：Molecular phylogenetics and evolution

authors： Christe C,Caetano S,Aeschimann D,Kropf M,Diadema K,Naciri Y

更新日期：2014-01-01 00:00:00

abstract：:Species boundaries are traditionally inferred using morphological characters, although morphology sometimes fails to correctly delineate species. To overcome this limitation, researchers have widely taken advantage of alternative methods such as DNA barcoding or analysis of cuticular hydrocarbons (CHs) profiles, but r...

journal_title：Molecular phylogenetics and evolution

authors： Bourguignon T,Šobotník J,Hanus R,Krasulová J,Vrkoslav V,Cvačka J,Roisin Y

更新日期：2013-12-01 00:00:00

abstract：:We present a phylogenetic analysis and comparison of structural features of chloroplast genomes for 39 species of the eucalypt group (genera Eucalyptus, Corymbia, Angophora, and outgroups Allosyncarpia and Stockwellia). We use 41 complete chloroplast genome sequences, adding 39 finished-quality chloroplast genomes to ...

journal_title：Molecular phylogenetics and evolution

authors： Bayly MJ,Rigault P,Spokevicius A,Ladiges PY,Ades PK,Anderson C,Bossinger G,Merchant A,Udovicic F,Woodrow IE,Tibbits J

更新日期：2013-12-01 00:00:00

abstract：:The Ruschieae is a large tribe of about 1600 species of succulent perennials. They form a major component of the arid parts of the Greater Cape Floristic Region, both in numbers of species and in their density of coverage. So far phylogenetic relationships within the tribe have been unresolved, largely through the pau...

journal_title：Molecular phylogenetics and evolution

authors： Klak C,Bruyns PV,Hanáček P

更新日期：2013-12-01 00:00:00

abstract：:Typically anadromous, the twaite shad (Alosa fallax) can become landlocked and adapt to a fully freshwater life. The only landlocked shad population in Northwestern Europe is found in a lake in Ireland, Lough Leane. The Killarney shad, Alosa killarnensis (or Alosa fallax killarnensis, as it is mostly referred to) disp...

journal_title：Molecular phylogenetics and evolution

authors： Coscia I,McDevitt AD,King JJ,Roche WK,McLoughlin C,Mariani S

更新日期：2013-12-01 00:00:00

abstract：:Increasing evidence has shown the complex and dynamic nature of polyploids. Two single copy nuclear genes were used to explore genome evolutionary dynamics and the origin of tetraploid E. ciliaris: the phosphoglycerate kinase (PGK1) and the second largest subunit of RNA polymerase II (RPB2) together with a chloroplast...

journal_title：Molecular phylogenetics and evolution

authors： Hu Q,Yan C,Sun G

更新日期：2013-12-01 00:00:00

abstract：:To better understand the underlying causes of rarity and extinction risk in Acropora (staghorn coral), we contrast the minimum divergence ages and nucleotide diversity of an array of species with different range sizes and levels of threat. Time-calibrated Bayesian analyses based upon concatenated nuclear and mitochond...

journal_title：Molecular phylogenetics and evolution

authors： Richards ZT,Miller DJ,Wallace CC

更新日期：2013-12-01 00:00:00

abstract：:Urticaceae is one of the larger Angiosperm families, but relationships within it remain poorly known. This study presents the first densely sampled molecular phylogeny of Urticaceae, using maximum likelihood (ML), maximum parsimony (MP) and Bayesian inference (BI) to analyze the DNA sequence data from two nuclear (ITS...

journal_title：Molecular phylogenetics and evolution

authors： Wu ZY,Monro AK,Milne RI,Wang H,Yi TS,Liu J,Li DZ

更新日期：2013-12-01 00:00:00

abstract：:Molecular methods have been used for the first time to determine the phylogeny of families, genera and species within the Pennatulacea (sea pens). Variation in ND2 and mtMutS mitochondrial protein-coding genes proved adequate to resolve phylogenetic relationships among pennatulacean families. The gene mtMutS is more v...

journal_title：Molecular phylogenetics and evolution

authors： Dolan E,Tyler PA,Yesson C,Rogers AD

更新日期：2013-12-01 00:00:00

abstract：:Hydrobiidae is one of the largest families of freshwater gastropods comprised of approximately 400 genera and 1000 species. Despite this high level of diversity, most hydrobiid species inhabit fragile ecosystems in restricted distribution areas. In this work, we analyze modes of speciation and causes of diversificatio...

journal_title：Molecular phylogenetics and evolution

authors： Delicado D,Machordom A,Ramos MA

更新日期：2013-09-01 00:00:00

abstract：:Inferring evolutionary relationships between recently diverged taxa is still challenging, especially taking into account the likely occurrence of incomplete lineage sorting and/or introgression. The Xiphorhynchus pardalotus/ocellatus species complex includes between two to three polytypic species and eight to nine sub...

journal_title：Molecular phylogenetics and evolution

authors： Sousa-Neves T,Aleixo A,Sequeira F

更新日期：2013-09-01 00:00:00

abstract：:The miniaturized frogs of the Eleutherodactylus limbatus group, endemic to Cuba, have recently been shown to contain alkaloids in their skin, representing the fifth independent evolutionary origin of alkaloid sequestering in anurans. Based on a comprehensive sampling of all known species of the group we here assess th...

journal_title：Molecular phylogenetics and evolution

authors： Rodríguez A,Poth D,Schulz S,Gehara M,Vences M

更新日期：2013-09-01 00:00:00

abstract：:The Yellow-shouldered bats, Genus Sturnira, are widespread, diverse, and abundant throughout the Neotropical Region, but little is known of their phylogeny and biogeography. We collected 4409 bp of DNA from three mitochondrial (cyt-b, ND2, D-loop) and two nuclear (RAG1, RAG2) sequences from 138 individuals representin...

journal_title：Molecular phylogenetics and evolution

authors： Velazco PM,Patterson BD

更新日期：2013-09-01 00:00:00

abstract：:Cyananthus (Campanulaceae) is a small genus consisting of ca. 20 species endemic to the Sino-Himalayan region. Based on phylogenetic analysis using nuclear ribosomal ITS and four plastid markers (matK, rbcL, psbA-trnH and trnG-S), our results strongly support the monophyly of Cyananthus and its close relationship with...

journal_title：Molecular phylogenetics and evolution

authors： Zhou Z,Hong D,Niu Y,Li G,Nie Z,Wen J,Sun H

更新日期：2013-09-01 00:00:00

abstract：:Phylogenetic trees are a starting point for the study of further evolutionary and ecological questions. We show that for avian evolutionary relationships, improved taxon sampling, longer sequences and additional data sets are giving stability to the prediction of the grouping of pelecaniforms and ciconiiforms, thus al...

journal_title：Molecular phylogenetics and evolution

authors： Gibb GC,Kennedy M,Penny D

更新日期：2013-08-01 00:00:00

abstract：:Andean Pholidobolus and Macropholidus lizards contain seven and two species, respectively, as currently recognized. We analyze three mitochondrial loci (12S, 16S, ND4) using Bayesian methods to clarify the phylogenetic relationships between these genera based on a well-supported phylogenetic hypothesis. The phylogenet...

journal_title：Molecular phylogenetics and evolution

authors： Torres-Carvajal O,Mafla-Endara P

更新日期：2013-08-01 00:00:00

abstract：:Recent conceptual and methodological advances have increased the ability to apply multifaceted approaches to species delimitation, which is particularly useful in delimiting recently diversified species where single lines of evidence lead to incorrect species delimitation or assignment of individuals to species (e.g. ...

journal_title：Molecular phylogenetics and evolution

authors： Sistrom M,Donnellan SC,Hutchinson MN

更新日期：2013-07-01 00:00:00

abstract：:We present the most comprehensive time-calibrated, species-level hypothesis of the timing of Acanthuridae (surgeonfishes and allies) evolution based on 76% of the extant diversity and nine genes. We recover two major acanthurid clades, Nasinae and Acanthurinae, and infer a much more recent Nasinae crown age (17 Ma) co...

journal_title：Molecular phylogenetics and evolution

authors： Sorenson L,Santini F,Carnevale G,Alfaro ME

更新日期：2013-07-01 00:00:00

abstract：:Antilopini (gazelles and their allies) are one of the most diverse but phylogenetically controversial groups of bovids. Here we provide a molecular phylogeny of this poorly understood taxon using combined analyses of mitochondrial (CYTB, COIII, 12S, 16S) and nuclear (KCAS, SPTBN1, PRKCI, MC1R, THYR) genes. We explore ...

journal_title：Molecular phylogenetics and evolution

authors： Bärmann EV,Rössner GE,Wörheide G

更新日期：2013-05-01 00:00:00

abstract：:Afrocanarian blue tits (Cyanistes teneriffae) have a scattered distribution on the Canary Islands and on the North African continent. To date, the Canary Islands have been considered the species' main Pleistocene evolutionary center, but their colonization pathways remain uncertain. We set out to reconstruct a dated m...

journal_title：Molecular phylogenetics and evolution

authors： Päckert M,Martens J,Hering J,Kvist L,Illera JC

更新日期：2013-05-01 00:00:00

abstract：:Apathya is a lacertid genus occurring mainly in south-east Turkey and its adjacent regions (part of Iran and Iraq). So far two morphological species have been attributed to the genus; A. cappadocica (with five subspecies, A. c.cappadocica, A. c.muhtari, A. c.schmidtlerorum, A. c. urmiana and A. c.wolteri) and A.yassuj...

journal_title：Molecular phylogenetics and evolution

authors： Kapli P,Botoni D,Ilgaz C,Kumlutaş Y,Avcı A,Rastegar-Pouyani N,Fathinia B,Lymberakis P,Ahmadzadeh F,Poulakakis N

更新日期：2013-03-01 00:00:00

abstract：:We inferred the phylogenetic relationships among members of the Poecilia sphenops species complex to resolve the colonization process and radiation of this group in Central America. We analyzed 2550 base pairs (bp) of mitochondrial DNA (mtDNA), including ATP synthase 6 and 8, cytochrome oxidase subunit I and NADH dehy...

journal_title：Molecular phylogenetics and evolution

authors： Alda F,Reina RG,Doadrio I,Bermingham E

更新日期：2013-03-01 00:00:00

abstract：:Cyclestheria hislopi is thought to be the only extant species of Cyclestherida. It is the sister taxon of all Cladocera and displays morphological characteristics intermediate of Spinicaudata and Cladocera. Using one mitochondrial (COI) and two nuclear (EF1α and 28S rRNA) markers, we tested the hypothesis that C. hisl...

journal_title：Molecular phylogenetics and evolution

authors： Schwentner M,Clavier S,Fritsch M,Olesen J,Padhye S,Timms BV,Richter S

更新日期：2013-03-01 00:00:00

abstract：:Argonaute proteins (AGOs) are mediators of gene silencing via recruitment of small regulatory RNAs to induce translational regression or degradation of targeted molecules. Platyhelminths have been reported to express microRNAs but the diversity of AGOs in the phylum has not been explored. Phylogenetic relationships of...

journal_title：Molecular phylogenetics and evolution

authors： Zheng Y

更新日期：2013-03-01 00:00:00

abstract：:Recombinations are known to disrupt bifurcating tree structure of gene genealogies. Although recently occurred recombinations are easily detectable by using conventional methods, recombinations may have occurred at any time. We devised a new method for detecting ancient recombinations through phylogenetic network anal...

journal_title：Molecular phylogenetics and evolution

authors： Saitou N,Kitano T

更新日期：2013-02-01 00:00:00

abstract：:The emergence of Cetacea in the Paleogene represents one of the most profound macroevolutionary transitions within Mammalia. The move from a terrestrial habitat to a committed aquatic lifestyle engendered wholesale changes in anatomy, physiology, and behavior. The results of this remarkable transformation are extant w...

journal_title：Molecular phylogenetics and evolution

authors： Gatesy J,Geisler JH,Chang J,Buell C,Berta A,Meredith RW,Springer MS,McGowen MR

更新日期：2013-02-01 00:00:00

abstract：:The paper reviews the current state of low and single copy nuclear markers that have been applied successfully in plant phylogenetics to date, and discusses case studies highlighting the potential of massively parallel high throughput or next-generation sequencing (NGS) approaches for molecular phylogenetic and evolut...

journal_title：Molecular phylogenetics and evolution

authors： Zimmer EA,Wen J

更新日期：2013-02-01 00:00:00

abstract：:The so-called "Taygetis clade" is a group of exclusively Neotropical butterflies classified within Euptychiina, one of the largest subtribes in the subfamily Satyrinae. Since the distribution of the ten genera belonging to this group ranges throughout the entire Neotropics, from lowlands to lower montane habitats, it ...

journal_title：Molecular phylogenetics and evolution

authors： Matos-Maraví PF,Peña C,Willmott KR,Freitas AV,Wahlberg N

更新日期：2013-01-01 00:00:00