4.2 Article

Widely used, short 16S rRNA mitochondrial gene fragments yield poor and erratic results in phylogenetic estimation and species delimitation of amphibians

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

Gene Flow Increases Phylogenetic Structure and Inflates Cryptic Species Estimations: A Case Study on Widespread Philippine Puddle Frogs (Occidozyga laevis)

Kin Onn Chan et al.

Summary: Genome-wide sequencing of Philippine Puddle Frogs revealed that high levels of genetic diversity are primarily a result of complex patterns of admixture, isolation-by-distance, and isolation-by-environment, rather than species divergence. Additionally, widely adopted tree- and distance-based methods tend to overestimate species diversity in the presence of gene flow.

SYSTEMATIC BIOLOGY (2022)

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 Biochemistry & Molecular Biology

Unexpectedly high levels of lineage diversity in Sundaland puddle frogs (Dicroglossidae: Occidozyga Kuhl and van Hasselt, 1822)

Jana M. Flury et al.

Summary: One of the most urgent tasks for taxonomists and evolutionary biologists today is to estimate the number of species on earth. The study on Occidozyga frogs in Southeast Asia revealed a surprisingly high level of genetic diversity, suggesting that species diversity in this group may have been underestimated. Further research is needed to understand the geographical structure and diversification in this amphibian clade.

MOLECULAR PHYLOGENETICS AND EVOLUTION (2021)

Article Zoology

A taxonomic revision of the genus Phrynoglossus in Indochina with the description of a new species and comments on the classification within Occidozyginae (Amphibia, Anura, Dicroglossidae)

Gunther Koehler et al.

Summary: The study revised the frogs of the genus Phrynoglossus from Indochina and identified three distinct species, one of which is new. These species differ in geographic distribution, external morphology, and genetic distances. The study provides evolutionary evidence for recognizing Phrynoglossus as a genus separate from Occidozyga.

VERTEBRATE ZOOLOGY (2021)

Review Entomology

Mitochondrial DNA as a Molecular Marker in Insect Ecology: Current Status and Future Prospects

Zhaoke Dong et al.

Summary: Molecular techniques are powerful in insect ecology research, with mitochondrial DNA being a widely used molecular marker. While it has favorable biological properties, there are still issues to consider when using mtDNA data. Combining mtDNA with nuclear DNA markers can enhance the power of molecular data in testing phylogenetic and phylogeographic hypotheses.

ANNALS OF THE ENTOMOLOGICAL SOCIETY OF AMERICA (2021)

Article Biochemistry & Molecular Biology

Gene flow creates a mirage of cryptic species in a Southeast Asian spotted stream frog complex

Kin O. Chan et al.

MOLECULAR ECOLOGY (2020)

Article Biochemistry & Molecular Biology

UFBoot2: Improving the Ultrafast Bootstrap Approximation

Diep Thi Hoang et al.

MOLECULAR BIOLOGY AND EVOLUTION (2018)

Article Biochemistry & Molecular Biology

MEGA X: Molecular Evolutionary Genetics Analysis across Computing Platforms

Sudhir Kumar et al.

MOLECULAR BIOLOGY AND EVOLUTION (2018)

Article Biochemistry & Molecular Biology

Cryptic diversity and discordance in single-locus species delimitation methods within horned lizards (Phrynosomatidae: Phrynosoma)

Christopher Blair et al.

MOLECULAR ECOLOGY RESOURCES (2017)

Article Multidisciplinary Sciences

Molecular evolution of a widely-adopted taxonomic marker (COI) across the animal tree of life

Mikko Pentinsaari et al.

SCIENTIFIC REPORTS (2016)

Article Zoology

A comparison of DNA barcoding markers in West African frogs

Heidi J. Rockney et al.

AFRICAN JOURNAL OF HERPETOLOGY (2015)

Article Biochemistry & Molecular Biology

IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies

Lam-Tung Nguyen et al.

MOLECULAR BIOLOGY AND EVOLUTION (2015)

News Item Biochemistry & Molecular Biology

Cold Code: the global initiative to DNA barcode amphibians and nonavian reptiles

Robert W. Murphy et al.

MOLECULAR ECOLOGY RESOURCES (2013)

Article Multidisciplinary Sciences

A DNA-Based Registry for All Animal Species: The Barcode Index Number (BIN) System

Sujeevan Ratnasingham et al.

PLOS ONE (2013)

Article Cell Biology

Biobanked Amphibian Samples Confirmed To Species Level Using 16S rRNA DNA Barcodes

Maria Jose Maya-Soriano et al.

BIOPRESERVATION AND BIOBANKING (2012)

Article Biochemistry & Molecular Biology

COI is better than 16S rRNA for DNA barcoding Asiatic salamanders (Amphibia: Caudata: Hynobiidae)

Yun Xia et al.

MOLECULAR ECOLOGY RESOURCES (2012)

Article Biochemistry & Molecular Biology

Universal COI primers for DNA barcoding amphibians

Jing Che et al.

MOLECULAR ECOLOGY RESOURCES (2012)

Article Biochemical Research Methods

phangorn: phylogenetic analysis in R

Klaus Peter Schliep

BIOINFORMATICS (2011)

Article Evolutionary Biology

Missing Data in Phylogenetic Analysis: Reconciling Results from Simulations and Empirical Data

John J. Wiens et al.

SYSTEMATIC BIOLOGY (2011)

Article Zoology

Phylogenetic signal and the utility of 12S and 16S mtDNA in frog phylogeny

S. Hertwig et al.

JOURNAL OF ZOOLOGICAL SYSTEMATICS AND EVOLUTIONARY RESEARCH (2010)

Article Biochemistry & Molecular Biology

Of Least Concern? Systematics of a cryptic species complex: Limnonectes kuhlii (Amphibia: Anura: Dicroglossidae)

David S. McLeod

MOLECULAR PHYLOGENETICS AND EVOLUTION (2010)

Article Evolutionary Biology

Accelerated Species Inventory on Madagascar Using Coalescent-Based Models of Species Delineation

Michael T. Monaghan et al.

SYSTEMATIC BIOLOGY (2009)

Article Biochemistry & Molecular Biology

CO1 DNA barcoding amphibians: take the chance, meet the challenge

M. Alex Smith et al.

MOLECULAR ECOLOGY RESOURCES (2008)

Article Multidisciplinary Sciences

Underestimation of Species Richness in Neotropical Frogs Revealed by mtDNA Analyses

Antoine Fouquet et al.

PLOS ONE (2007)

Article Multidisciplinary Sciences

DNA barcodes distinguish species of tropical Lepidoptera

M Hajibabaei et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2006)

Article Biology

Deciphering amphibian diversity through DNA barcoding: chances and challenges

M Vences et al.

PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES (2005)

Article Evolutionary Biology

Can incomplete taxa rescue phylogenetic analyses from long-branch attraction?

JJ Wiens

SYSTEMATIC BIOLOGY (2005)

Article Biochemistry & Molecular Biology

Novel relation-ships among hylold frogs inferred from 12S and 16S mitochondrial DNA sequences

CR Darst et al.

MOLECULAR PHYLOGENETICS AND EVOLUTION (2004)

Review Biochemistry & Molecular Biology

Phylogenomics of eukaryotes: Impact of missing data on large alignments

H Philippe et al.

MOLECULAR BIOLOGY AND EVOLUTION (2004)

Article Evolutionary Biology

Missing data, incomplete taxa, and phylogenetic accuracy

JJ Wiens

SYSTEMATIC BIOLOGY (2003)

Article Biology

Biological identifications through DNA barcodes

PDN Hebert et al.

PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES (2003)

Article Biochemistry & Molecular Biology

Testing the utility of partial COI sequences for phylogenetic estimates of gastropod relationships

EA Remigio et al.

MOLECULAR PHYLOGENETICS AND EVOLUTION (2003)