A phylogeny of the genus <i>Limia</i> (Teleostei: Poeciliidae) suggests a single-lake radiation nested in a Caribbean-wide allopatric speciation scenario

There is no author summary for this article yet. Authors can add summaries to their articles on ScienceOpen to make them more accessible to a non-specialist audience.

Abstract

Objective

The Caribbean is an important global biodiversity hotspot. Adaptive radiations there lead to many speciation events within a limited period and hence are particularly prominent biodiversity generators. A prime example are freshwater fish of the genus Limia, endemic to the Greater Antilles. Within Hispaniola, nine species have been described from a single isolated site, Lake Miragoâne, pointing towards extraordinary sympatric speciation. This study examines the evolutionary history of the Limia species in Lake Miragoâne, relative to their congeners throughout the Caribbean.

Results

For 12 Limia species, we obtained almost complete sequences of the mitochondrial cytochrome b gene, a well-established marker for lower-level taxonomic relationships. We included sequences of six further Limia species from GenBank (total N = 18 species). Our phylogenies are in concordance with other published phylogenies of Limia. There is strong support that the species found in Lake Miragoâne in Haiti are monophyletic, confirming a recent local radiation. Within Lake Miragoâne, speciation is likely extremely recent, leading to incomplete lineage sorting in the mtDNA. Future studies using multiple unlinked genetic markers are needed to disentangle the relationships within the Lake Miragoâne clade.

Supplementary Information

The online version contains supplementary material available at 10.1186/s13104-021-05843-x.

Related collections

Most cited references 73

Record: found
Abstract: found
Article: not found

MEGA X: Molecular Evolutionary Genetics Analysis across Computing Platforms.

Sudhir Kumar, Glen Stecher, Michael KaWah Li … (2018)

The Molecular Evolutionary Genetics Analysis (Mega) software implements many analytical methods and tools for phylogenomics and phylomedicine. Here, we report a transformation of Mega to enable cross-platform use on Microsoft Windows and Linux operating systems. Mega X does not require virtualization or emulation software and provides a uniform user experience across platforms. Mega X has additionally been upgraded to use multiple computing cores for many molecular evolutionary analyses. Mega X is available in two interfaces (graphical and command line) and can be downloaded from www.megasoftware.net free of charge.

0 comments Cited 10893 times – based on 0 reviews      Review now

Bookmark

Record: found
Abstract: found
Article: found

Is Open Access

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

Alexandros Stamatakis (2014)

Motivation: Phylogenies are increasingly used in all fields of medical and biological research. Moreover, because of the next-generation sequencing revolution, datasets used for conducting phylogenetic analyses grow at an unprecedented pace. RAxML (Randomized Axelerated Maximum Likelihood) is a popular program for phylogenetic analyses of large datasets under maximum likelihood. Since the last RAxML paper in 2006, it has been continuously maintained and extended to accommodate the increasingly growing input datasets and to serve the needs of the user community. Results: I present some of the most notable new features and extensions of RAxML, such as a substantial extension of substitution models and supported data types, the introduction of SSE3, AVX and AVX2 vector intrinsics, techniques for reducing the memory requirements of the code and a plethora of operations for conducting post-analyses on sets of trees. In addition, an up-to-date 50-page user manual covering all new RAxML options is available. Availability and implementation: The code is available under GNU GPL at https://github.com/stamatak/standard-RAxML. Contact: alexandros.stamatakis@h-its.org Supplementary information: Supplementary data are available at Bioinformatics online.

0 comments Cited 8586 times – based on 0 reviews      Review now

Bookmark

Record: found
Abstract: found
Article: found

Is Open Access

MrBayes 3.2: Efficient Bayesian Phylogenetic Inference and Model Choice Across a Large Model Space

Fredrik Ronquist, Maxim Teslenko, Paul van der Mark … (2012)

Since its introduction in 2001, MrBayes has grown in popularity as a software package for Bayesian phylogenetic inference using Markov chain Monte Carlo (MCMC) methods. With this note, we announce the release of version 3.2, a major upgrade to the latest official release presented in 2003. The new version provides convergence diagnostics and allows multiple analyses to be run in parallel with convergence progress monitored on the fly. The introduction of new proposals and automatic optimization of tuning parameters has improved convergence for many problems. The new version also sports significantly faster likelihood calculations through streaming single-instruction-multiple-data extensions (SSE) and support of the BEAGLE library, allowing likelihood calculations to be delegated to graphics processing units (GPUs) on compatible hardware. Speedup factors range from around 2 with SSE code to more than 50 with BEAGLE for codon problems. Checkpointing across all models allows long runs to be completed even when an analysis is prematurely terminated. New models include relaxed clocks, dating, model averaging across time-reversible substitution models, and support for hard, negative, and partial (backbone) tree constraints. Inference of species trees from gene trees is supported by full incorporation of the Bayesian estimation of species trees (BEST) algorithms. Marginal model likelihoods for Bayes factor tests can be estimated accurately across the entire model space using the stepping stone method. The new version provides more output options than previously, including samples of ancestral states, site rates, site d N /d S rations, branch rates, and node dates. A wide range of statistics on tree parameters can also be output for visualization in FigTree and compatible software.

0 comments Cited 5487 times – based on 0 reviews      Review now

Bookmark

All references

Author and article information

Contributors

Montrai Spikes: spikesm@ou.edu

Rodet Rodríguez-Silva: Rodet.Rodriguez.Silva-1@ou.edu

Kerri-Ann Bennett: kerriann.bennett@gmail.com

Stefan Bräger: Stefan.Braeger@gmx.net

James Josaphat: james.josaphat@yahoo.fr

Patricia Torres-Pineda: ptorresp@umich.edu

Anja Ernst: schneida@uni-potsdam.de

Katja Havenstein: katja.havenstein@uni-potsdam.de

Ingo Schlupp: schlupp@ou.edu

Ralph Tiedemann:

ORCID: http://orcid.org/0000-0002-2604-6336

tiedeman@uni-potsdam.de

Journal

Journal ID (nlm-ta): BMC Res Notes

Journal ID (iso-abbrev): BMC Res Notes

Title: BMC Research Notes

Publisher: BioMed Central (London )

ISSN (Electronic): 1756-0500

Publication date (Electronic): 25 November 2021

Publication date PMC-release: 25 November 2021

Publication date Collection: 2021

Volume: 14

Electronic Location Identifier: 425

Affiliations

[1 ]GRID grid.11348.3f, ISNI 0000 0001 0942 1117, Unit of Evolutionary Biology/Systematic Zoology, Institute of Biochemistry and Biology, , University of Potsdam, ; Karl-Liebknecht-Straße 24-25, Haus 26, 14476 Potsdam, Germany

[2 ]GRID grid.266900.b, ISNI 0000 0004 0447 0018, Department of Biology, , University of Oklahoma, ; 730 Van Vleet Oval, Norman, OK 73019 USA

[3 ]GRID grid.12916.3d, ISNI 0000 0001 2322 4996, Department of Life Sciences, , The University of the West Indies (Mona Campus), ; Kingston, Jamaica

[4 ]GRID grid.506169.d, ISNI 0000 0001 1019 0424, German Oceanographic Museum (DMM), ; Katharinenberg 14-20, 18439 Stralsund, Germany

[5 ]Caribaea Intitiative and Université Des Antilles, Guadeloupe, Kingston, Jamaica

[6 ]Museo Nacional de Historia Natural Prof. “Eugenio de Jesús Marcano”, Avenida Cesar Nicolás Penson, 10204 Santo Domingo, República Dominicana

Author information

Ralph Tiedemann http://orcid.org/0000-0002-2604-6336

Article

Publisher ID: 5843

DOI: 10.1186/s13104-021-05843-x

PMC ID: 8613956

PubMed ID: 34823576

SO-VID: de46722a-8e19-41e8-8abc-360cd911a0b2

License:

Open AccessThis article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/. The Creative Commons Public Domain Dedication waiver ( http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data.

History

Date received : 3 August 2021

Date accepted : 10 November 2021

Funding

Funded by: university of potsdam

Custom metadata

ScienceOpen disciplines: Medicine

Keywords: cytochrome b,island biogeography,fresh water fish,phylogeny

Data availability:

ScienceOpen disciplines: Medicine

Keywords: cytochrome b, island biogeography, fresh water fish, phylogeny

Comments

Comment on this article

scite_

Smart Citations

Citing PublicationsSupportingMentioningContrasting

View Citations

See how this article has been cited at scite.ai

scite shows how a scientific paper has been cited by providing the context of the citation, a classification describing whether it supports, mentions, or contrasts the cited claim, and a label indicating in which section the citation was made.

Cited by 4

See all cited by

Most referenced authors 1,182

See all reference authors

A phylogeny of the genus Limia (Teleostei: Poeciliidae) suggests a single-lake radiation nested in a Caribbean-wide allopatric speciation scenario

Read this article at

Abstract

Objective

Results

Supplementary Information

Related collections

Karger: Nephrology

Most cited references 73

MEGA X: Molecular Evolutionary Genetics Analysis across Computing Platforms.

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

MrBayes 3.2: Efficient Bayesian Phylogenetic Inference and Model Choice Across a Large Model Space

Author and article information

Contributors

Journal

Affiliations

Author information

Article

History

Funding

Categories

Custom metadata

Comments

Comment on this article

Similar content 80

Cited by 4

Most referenced authors 1,182