4.6 Article

Integrative species delimitation helps to find the hidden diversity of the leaf-litter frog Ischnocnema manezinho (Garcia, 1996) (Anura, Brachycephalidae), endemic to the southern Atlantic Forest

相关参考文献

注意:仅列出部分参考文献,下载原文获取全部文献信息。
Article Evolutionary Biology

StarBeast3: Adaptive Parallelized Bayesian Inference under the Multispecies Coalescent

Jordan Douglas et al.

Summary: This paper introduces StarBeast3, a software package for efficient Bayesian inference under the multispecies coalescent model. By utilizing cutting-edge proposal kernels and adaptive operators, StarBeast3 is particularly efficient when a relaxed clock model is applied, and it can handle large data sets with hundreds of genes.

SYSTEMATIC BIOLOGY (2022)

Article Zoology

Genetic and morphometric analyses of historical type specimens clarify the taxonomy of the Ethiopian Leptopelis gramineus species complex (Anura, Arthroleptidae)

Sandra Goutte et al.

Summary: In this study, genetic and morphological analyses were conducted to investigate the diversity and taxonomy of Leptopelis frogs in the Ethiopian Highlands. The results revealed the existence of multiple unnamed taxa within the endemic species L. gramineus. The recently resurrected L. montanus was found to be a junior synonym of L. rugosus, and a distinct undescribed species was identified east of the Great Rift Valley. Additionally, re-descriptions of L. rugosus and descriptions of two new species were provided, along with an identification key and call descriptions.

ZOOKEYS (2022)

Article Remote Sensing

Aerodynamics Effect of Holes in UAV Wings Modified for VTOL Capability

Laith S. Sawaqed et al.

Summary: This research explores the possibility of modifying the X8 Skywalker from a fixed-wing unmanned aerial vehicle into a convertiplane. Computational fluid dynamics and wind tunnel experiments were conducted to analyze the performance of different wing configurations. The results indicate that the proposed modifications can generate enough lift despite reducing the wing area, with the filleted hole configuration demonstrating less drag and turbulence effects at low angles of attack.

DRONE SYSTEMS AND APPLICATIONS (2022)

Article Evolutionary Biology

Phylogenomics Reveals Ancient Gene Tree Discordance in the Amphibian Tree of Life

Paul M. Hime et al.

Summary: This study provides a phylogenomic perspective on amphibian relationships by developing a taxon-specific Anchored Hybrid Enrichment protocol targeting conserved exons. It clarifies relationships among amphibians and identifies gene tree-species tree conflict. The results strongly support amphibian monophyly and a sister relationship between frogs and salamanders, with a surprisingly younger timescale for crown and ordinal amphibian diversification.

SYSTEMATIC BIOLOGY (2021)

Article Biochemistry & Molecular Biology

ASAP: assemble species by automatic partitioning

Nicolas Puillandre et al.

Summary: ASAP is a fast and efficient method for constructing species partitions from single locus sequence alignments. It offers a new scoring system without prior biological insight, and can be used through a graphical web interface or downloaded for local usage.

MOLECULAR ECOLOGY RESOURCES (2021)

Article Biochemical Research Methods

Adaptive dating and fast proposals: Revisiting the phylogenetic relaxed clock model

Jordan Douglas et al.

Summary: This article investigates the relaxed clock model and explores optimizations to improve its statistical inference performance, achieving up to 65 times efficiency compared to previous setups, particularly suitable for processing long biological sequences.

PLOS COMPUTATIONAL BIOLOGY (2021)

Article Zoology

A new species of Ischnocnema (Anura: Brachycephalidae) from the mountainous region of Atlantic Forest, southeastern Brazil, with a new phylogeny and diagnose for Ischnocnema parva series

Thiago Silva-Soares et al.

Summary: A new species of Rain Frog has been discovered in Brazil's Atlantic Forest, specifically in the montane rainforest of Santa Teresa, state of Espirito Santo, southeastern Brazil. This unique species, Ischnocnema crassa sp. nov., is known for its moderate hand webbing between fingers, which distinguishes it from other Ischnocnema species. Additionally, it is part of the I. parva series and important for amphibian conservation efforts in Brazil, particularly in Santa Teresa where it is home to 109 species of anurans.

ZOOTAXA (2021)

Article Biochemistry & Molecular Biology

MEGA11 Molecular Evolutionary Genetics Analysis Version 11

Koichiro Tamura et al.

Summary: MEGA software, a mature tool for computational molecular evolution, has been enhanced with new additions for building timetrees of species, pathogens, and gene families using rapid relaxed-clock methods. These additions include methods for estimating divergence times, confidence intervals, and new options for tagging sequences with spatiotemporal sampling information. The enhancements aim to improve user experience, result quality, and the pace of biological discovery.

MOLECULAR BIOLOGY AND EVOLUTION (2021)

Article Biochemistry & Molecular Biology

GenBank

Eric W. Sayers et al.

NUCLEIC ACIDS RESEARCH (2020)

Article Evolutionary Biology

Improving the performance of Bayesian phylogenetic inference under relaxed clock models

Rong Zhang et al.

BMC EVOLUTIONARY BIOLOGY (2020)

Article Biochemistry & Molecular Biology

Outstanding diversity and microendemism in a clade of rare Atlantic Forest montane frogs

Maria Tereza C. Thome et al.

MOLECULAR PHYLOGENETICS AND EVOLUTION (2020)

Article Biochemical Research Methods

ape 5.0: an environment for modern phylogenetics and evolutionary analyses in R

Emmanuel Paradis et al.

BIOINFORMATICS (2019)

Article Evolutionary Biology

The Spectre of Too Many Species

Adam D. Leache et al.

SYSTEMATIC BIOLOGY (2019)

Article Biodiversity Conservation

More grist for the mill? Species delimitation in the genomic era and its implications for conservation

David W. G. Stanton et al.

CONSERVATION GENETICS (2019)

Article Biochemical Research Methods

BEAST 2.5: An advanced software platform for Bayesian evolutionary analysis

Remco Bouckaert et al.

PLOS COMPUTATIONAL BIOLOGY (2019)

Article Biodiversity Conservation

Integrative taxonomy helps to assess the extinction risk of anuran species

Rafael Felix de Magalhaes et al.

JOURNAL FOR NATURE CONSERVATION (2018)

Article Biochemistry & Molecular Biology

MEGA X: Molecular Evolutionary Genetics Analysis across Computing Platforms

Sudhir Kumar et al.

MOLECULAR BIOLOGY AND EVOLUTION (2018)

Review Biochemistry & Molecular Biology

Cryptic species as a window into the paradigm shift of the species concept

Cene Fiser et al.

MOLECULAR ECOLOGY (2018)

Article Biochemistry & Molecular Biology

The hitchhiker's guide to single-locus species delimitation

Simon Dellicour et al.

MOLECULAR ECOLOGY RESOURCES (2018)

Article Biochemistry & Molecular Biology

Molecular phylogeny of Ischnocnema (Anura: Brachycephalidae) with the redefinition of its series and the description of two new species

Pedro P. G. Taucce et al.

MOLECULAR PHYLOGENETICS AND EVOLUTION (2018)

Article Evolutionary Biology

Posterior Summarization in Bayesian Phylogenetics Using Tracer 1.7

Andrew Rambaut et al.

SYSTEMATIC BIOLOGY (2018)

Review Ecology

Finding Evolutionary Processes Hidden in Cryptic Species

Torsten H. Struck et al.

TRENDS IN ECOLOGY & EVOLUTION (2018)

Article Ecology

RRPP: An R package for fitting linear models to high-dimensional data using residual randomization

Michael L. Collyer et al.

METHODS IN ECOLOGY AND EVOLUTION (2018)

Article Multidisciplinary Sciences

Phylogenomics reveals rapid, simultaneous diversification of three major clades of Gondwanan frogs at the Cretaceous-Paleogene boundary

Yan-Jie Feng et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2017)

Article Multidisciplinary Sciences

Multispecies coalescent delimits structure, not species

Jeet Sukumaran et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2017)

Article Multidisciplinary Sciences

The importance of naming cryptic species and the conservation of endemic subterranean amphipods

Teo Delic et al.

SCIENTIFIC REPORTS (2017)

Article Evolutionary Biology

bModelTest: Bayesian phylogenetic site model averaging and model comparison

Remco R. Bouckaert et al.

BMC EVOLUTIONARY BIOLOGY (2017)

Article Biology

Taxonomic distribution of cryptic diversity among metazoans: not so homogeneous after all

Gerardo Perez-Ponce de Leon et al.

BIOLOGY LETTERS (2016)

Article Multidisciplinary Sciences

Neotropical forest expansion during the last glacial period challenges refuge hypothesis

Yuri L. R. Leite et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2016)

Article Ecology

Flexible methods for estimating genetic distances from single nucleotide polymorphisms

Simon Joly et al.

METHODS IN ECOLOGY AND EVOLUTION (2015)

Article Biodiversity Conservation

Guidelines for DNA taxonomy, with a focus on the meiofauna

Diego Fontaneto et al.

MARINE BIODIVERSITY (2015)

Article Biochemical Research Methods

RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies

Alexandros Stamatakis

BIOINFORMATICS (2014)

Article Biodiversity Conservation

Where is positional uncertainty a problem for species distribution modelling?

Babak Naimi et al.

ECOGRAPHY (2014)

Article Biochemistry & Molecular Biology

Unguided Species Delimitation Using DNA Sequence Data from Multiple Loci

Ziheng Yang et al.

MOLECULAR BIOLOGY AND EVOLUTION (2014)

Review Biochemistry & Molecular Biology

How to fail at species delimitation

Bryan C. Carstens et al.

MOLECULAR ECOLOGY (2013)

Article Biodiversity Conservation

Implications of different species concepts for conserving biodiversity

Richard Frankham et al.

BIOLOGICAL CONSERVATION (2012)

Article Biology

High levels of cryptic species diversity uncovered in Amazonian frogs

W. Chris Funk et al.

PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES (2012)

Article Ecology

Coalescent-based species delimitation in an integrative taxonomy

Matthew K. Fujita et al.

TRENDS IN ECOLOGY & EVOLUTION (2012)

Article Biochemistry & Molecular Biology

SpedeSTEM: a rapid and accurate method for species delimitation

Daniel D. Ence et al.

MOLECULAR ECOLOGY RESOURCES (2011)

Editorial Material Biology

A coalescent perspective on delimiting and naming species: a reply to Bauer et al.

Matthew K. Fujita et al.

PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES (2011)

Article Biochemical Research Methods

pegas: an R package for population genetics with an integrated-modular approach

Emmanuel Paradis

BIOINFORMATICS (2010)

Review Zoology

The integrative future of taxonomy

Jose M. Padial et al.

FRONTIERS IN ZOOLOGY (2010)

Article Biochemistry & Molecular Biology

SEQPHASE: a web tool for interconverting phase input/output files and fasta sequence alignments

J-F. Flot

MOLECULAR ECOLOGY RESOURCES (2010)

Article Biodiversity Conservation

Cryptic species diversity should not be trivialised

Peter Trontelj et al.

SYSTEMATICS AND BIODIVERSITY (2009)

Article Biology

The conditioned reconstructed process

Tanja Gernhard

JOURNAL OF THEORETICAL BIOLOGY (2008)

Article Biochemical Research Methods

Decoding of Superimposed Traces Produced by Direct Sequencing of Heterozygous Indels

Dmitry A. Dmitriev et al.

PLOS COMPUTATIONAL BIOLOGY (2008)

Article Evolutionary Biology

Delimiting species without monophyletic gene trees

L. Lacey Knowles et al.

SYSTEMATIC BIOLOGY (2007)

Article Evolutionary Biology

Species concepts and species delimitation

Kevin De Queiroz

SYSTEMATIC BIOLOGY (2007)

Article Biochemical Research Methods

Clustal W and clustal X version 2.0

M. A. Larkin et al.

BIOINFORMATICS (2007)

Article Multidisciplinary Sciences

Underestimation of Species Richness in Neotropical Frogs Revealed by mtDNA Analyses

Antoine Fouquet et al.

PLOS ONE (2007)

Article Multidisciplinary Sciences

Major Caribbean and Central American frog faunas originated by ancient oceanic dispersal

Matthew P. Heinicke et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2007)

Review Ecology

Cryptic species as a window on diversity and conservation

David Bickford et al.

TRENDS IN ECOLOGY & EVOLUTION (2007)

Article Biochemistry & Molecular Biology

Application of phylogenetic networks in evolutionary studies

DH Huson et al.

MOLECULAR BIOLOGY AND EVOLUTION (2006)

Article Biology

The role of taxonomy in species conservation

GM Mace

PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES (2004)

Article Biochemistry & Molecular Biology

Neighbor-Net: An agglomerative method for the construction of phylogenetic networks

D Bryant et al.

MOLECULAR BIOLOGY AND EVOLUTION (2004)

Article Genetics & Heredity

A new statistical method for haplotype reconstruction from population data

M Stephens et al.

AMERICAN JOURNAL OF HUMAN GENETICS (2001)