Microhabitat change drives diversification in pholcid spiders

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Abstract

Background

Microhabitat changes are thought to be among the main drivers of diversification. However, this conclusion is mostly based on studies on vertebrates. Here, we investigate the influence of microhabitat on diversification rates in pholcid spiders (Araneae, Pholcidae). Diversification analyses were conducted in the framework of the largest molecular phylogeny of pholcid spiders to date based on three nuclear and three mitochondrial loci from 600 species representing more than 85% of the currently described pholcid genera.

Results

Assessments of ancestral microhabitat revealed frequent evolutionary change. In particular, within the largest subfamily Pholcinae, numerous changes from near-ground habitats towards leaves and back were found. In general, taxa occupying leaves and large sheltered spaces had higher diversification rates than ground-dwelling taxa. Shifts in speciation rate were found in leaf- and space-dwelling taxa.

Conclusions

Our analyses result in one of the most comprehensive phylogenies available for a major spider family and provide a framework for any subsequent studies of pholcid spider biology. Diversification analyses strongly suggest that microhabitat is an important factor influencing diversification patterns in pholcid spiders.

Electronic supplementary material

The online version of this article (10.1186/s12862-018-1244-8) contains supplementary material, which is available to authorized users.

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Most cited references 101

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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.

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New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0.

Stéphane Guindon, Jean-François Dufayard, Vincent Lefort … (2010)

PhyML is a phylogeny software based on the maximum-likelihood principle. Early PhyML versions used a fast algorithm performing nearest neighbor interchanges to improve a reasonable starting tree topology. Since the original publication (Guindon S., Gascuel O. 2003. A simple, fast and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst. Biol. 52:696-704), PhyML has been widely used (>2500 citations in ISI Web of Science) because of its simplicity and a fair compromise between accuracy and speed. In the meantime, research around PhyML has continued, and this article describes the new algorithms and methods implemented in the program. First, we introduce a new algorithm to search the tree space with user-defined intensity using subtree pruning and regrafting topological moves. The parsimony criterion is used here to filter out the least promising topology modifications with respect to the likelihood function. The analysis of a large collection of real nucleotide and amino acid data sets of various sizes demonstrates the good performance of this method. Second, we describe a new test to assess the support of the data for internal branches of a phylogeny. This approach extends the recently proposed approximate likelihood-ratio test and relies on a nonparametric, Shimodaira-Hasegawa-like procedure. A detailed analysis of real alignments sheds light on the links between this new approach and the more classical nonparametric bootstrap method. Overall, our tests show that the last version (3.0) of PhyML is fast, accurate, stable, and ready to use. A Web server and binary files are available from http://www.atgc-montpellier.fr/phyml/.

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PAML 4: phylogenetic analysis by maximum likelihood.

Ziheng Yang (2007)

PAML, currently in version 4, is a package of programs for phylogenetic analyses of DNA and protein sequences using maximum likelihood (ML). The programs may be used to compare and test phylogenetic trees, but their main strengths lie in the rich repertoire of evolutionary models implemented, which can be used to estimate parameters in models of sequence evolution and to test interesting biological hypotheses. Uses of the programs include estimation of synonymous and nonsynonymous rates (d(N) and d(S)) between two protein-coding DNA sequences, inference of positive Darwinian selection through phylogenetic comparison of protein-coding genes, reconstruction of ancestral genes and proteins for molecular restoration studies of extinct life forms, combined analysis of heterogeneous data sets from multiple gene loci, and estimation of species divergence times incorporating uncertainties in fossil calibrations. This note discusses some of the major applications of the package, which includes example data sets to demonstrate their use. The package is written in ANSI C, and runs under Windows, Mac OSX, and UNIX systems. It is available at -- (http://abacus.gene.ucl.ac.uk/software/paml.html).

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Author and article information

Contributors

Jonas Eberle:

ORCID: http://orcid.org/0000-0003-2519-0640

j.eberle@leibniz-zfmk.de

Dimitar Dimitrov: dimitard.gwu@gmail.com

Alejandro Valdez-Mondragón: lat_mactans@yahoo.com.mx

Bernhard A. Huber: b.huber@leibniz-zfmk.de

Journal

Journal ID (nlm-ta): BMC Evol Biol

Journal ID (iso-abbrev): BMC Evol. Biol

Title: BMC Evolutionary Biology

Publisher: BioMed Central (London )

ISSN (Electronic): 1471-2148

Publication date (Electronic): 19 September 2018

Publication date PMC-release: 19 September 2018

Publication date Collection: 2018

Volume: 18

Electronic Location Identifier: 141

Affiliations

[1 ]Alexander Koenig Research Museum of Zoology, Adenauerallee 160, 53113 Bonn, Germany

[2 ]ISNI 0000 0001 0674 042X, GRID grid.5254.6, Center for Macroecology, Evolution and Climate, Natural History Museum of Denmark, , University of Copenhagen, ; Copenhagen, Denmark

[3 ]ISNI 0000 0004 1936 8921, GRID grid.5510.1, Natural History Museum, , University of Oslo, ; PO Box 1172 Blindern, NO-0318 Oslo, Norway

[4 ]ISNI 0000 0004 1936 7443, GRID grid.7914.b, Department of Natural History, University Museum of Bergen, , University of Bergen, ; PO Box 7800, NO-5020 Bergen, Norway

[5 ]Instituto de Biologia UNAM, sede Tlaxcala. Contiguo FES-Zaragoza Campus III, Ex Fábrica San Manuel de Morcom s/n, San Miguel Contla, Municipio de Santa Cruz Tlaxcala, C.P, 90640 Tlaxcala, Mexico

Author information

Jonas Eberle http://orcid.org/0000-0003-2519-0640

Article

Publisher ID: 1244

DOI: 10.1186/s12862-018-1244-8

PMC ID: 6145181

PubMed ID: 30231864

SO-VID: 2399f022-943d-4168-9a6d-9fb95d359463

License:

Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International License ( http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. 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.

History

Date received : 2 January 2018

Date accepted : 16 August 2018

Funding

Funded by: FundRef http://dx.doi.org/10.13039/501100001659, Deutsche Forschungsgemeinschaft;

Award ID: HU 980/11-1

Award Recipient : Bernhard A. Huber

Funded by: FundRef http://dx.doi.org/10.13039/501100001732, Danmarks Grundforskningsfond;

Award ID: DNRF96

Award Recipient : Dimitar Dimitrov

Funded by: FundRef http://dx.doi.org/10.13039/501100003141, Consejo Nacional de Ciencia y Tecnología;

Award ID: 59

Award Recipient : Alejandro Valdez-Mondragón

Custom metadata

ScienceOpen disciplines: Evolutionary Biology

Keywords: microhabitat,diversification rates,speciation,leaf dwelling,pholcidae,phylogeny

Data availability:

ScienceOpen disciplines: Evolutionary Biology

Keywords: microhabitat, diversification rates, speciation, leaf dwelling, pholcidae, phylogeny

Microhabitat change drives diversification in pholcid spiders

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Electronic supplementary material

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Coleoptera

Most cited references 101

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

New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0.

PAML 4: phylogenetic analysis by maximum likelihood.

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