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Ivanov V, Marusik Y, Pétillon J, Mutanen M. Relevance of ddRADseq method for species and population delimitation of closely related and widely distributed wolf spiders (Araneae, Lycosidae). Sci Rep 2021; 11:2177. [PMID: 33500478 PMCID: PMC7838170 DOI: 10.1038/s41598-021-81788-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2019] [Accepted: 01/11/2021] [Indexed: 01/30/2023] Open
Abstract
Although species delimitation is often controversial, emerging DNA-based and classical morphology-based methods are rarely compared using large-scale samplings, even less in the case of widely distributed species that have distant, allopatric populations. In the current study, we examined species boundaries within two wolf spider species of the genus Pardosa (Araneae, Lycosidae), P. riparia and P. palustris. Wolf spiders constitute an excellent model for testing the relevance of traditional vs. modern methods in species and population delimitation because several closely related species are distributed over cross-continental geographic ranges. Allopatric populations of the two Pardosa species were sampled across Europe to Far East Russia (latitudinal range > 150°) and several dozen individuals were studied using morphological characters (morphometry of three measures for both sexes, plus five in males only and two in females only), DNA barcoding (COI sequencing) and double-digest restriction site associated DNA sequencing (ddRADseq). The results obtained allow for changing the taxonomic status of two Far East Russian populations to subspecies and ddRADseq proved to be a powerful tool for taxonomic research despite scarce sampling and inherent subjectivity of species delimitation in allopatry. Overall, this study pleads for both multi-criteria and more population-based studies in taxonomy.
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Affiliation(s)
- Vladislav Ivanov
- grid.10858.340000 0001 0941 4873Department of Ecology and Genetics, University of Oulu, Oulu, Finland
| | - Yuri Marusik
- grid.493323.c0000 0004 0399 5314Institute for Biological Problems of the North, RAS, Magadan, Russia ,grid.412219.d0000 0001 2284 638XDepartment of Zoology and Entomology, University of the Free State, Bloemfontein, 9300 South Africa
| | - Julien Pétillon
- grid.410368.80000 0001 2191 9284UMR CNRS ECOBIO, Université de Rennes 1, Rennes, France
| | - Marko Mutanen
- grid.10858.340000 0001 0941 4873Department of Ecology and Genetics, University of Oulu, Oulu, Finland
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Paill W, Koblmüller S, Friess T, Gereben-Krenn BA, Mairhuber C, Raupach MJ, Zangl L. Relicts from Glacial Times: The Ground Beetle Pterostichus adstrictus Eschscholtz, 1823 (Coleoptera: Carabidae) in the Austrian Alps. INSECTS 2021; 12:insects12010084. [PMID: 33478160 PMCID: PMC7835791 DOI: 10.3390/insects12010084] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/20/2020] [Revised: 01/14/2021] [Accepted: 01/15/2021] [Indexed: 12/25/2022]
Abstract
Simple Summary The extant distribution of many plants and animals is the result of the dynamics of the last ice ages with their recurrent advances and retreats of the northern ice sheet and the glaciers in the mountains. The arctic-alpine distribution is a special case where a species occurs in the subarctic/arctic regions and locally restricted in the alpine mountain regions of central or southeastern Europe. Among the ground beetles, several species display this type of distribution, one of which is Pterostichus adstrictus. In Europe, this ground beetle has been thought to have its southernmost occurrences in Wales and southern Scandinavia. In this study, we provide the first reliable record of P. adstrictus from the Austrian Alps based on morphological determination and comparison to other closely related species as well as molecular genetic data. Furthermore, the seasonal occurrence as well as empirical habitat preferences of P. adstrictus in the Austrian Alps are described. Abstract The last ice age considerably influenced distribution patterns of extant species of plants and animals, with some of them now inhabiting disjunct areas in the subarctic/arctic and alpine regions. This arctic-alpine distribution is characteristic for many cold-adapted species with a limited dispersal ability and can be found in many invertebrate taxa, including ground beetles. The ground beetle Pterostichus adstrictus Eschscholtz, 1823 of the subgenus Bothriopterus was previously known to have a holarctic-circumpolar distribution, in Europe reaching its southern borders in Wales and southern Scandinavia. Here, we report the first findings of this species from the Austrian Ötztal Alps, representing also the southernmost edge of its currently known distribution, confirmed by the comparison of morphological characters to other Bothriopterus species and DNA barcoding data. Molecular data revealed a separation of the Austrian and Finish specimens with limited to no gene flow at all. Furthermore, we present the first data on habitat preference and seasonality of P. adstrictus in the Austrian Alps.
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Affiliation(s)
- Wolfgang Paill
- Universalmuseum Joanneum, Studienzentrum Naturkunde, Weinzöttlstraße 16, 8045 Graz, Austria;
- Correspondence: (W.P.); (S.K.)
| | - Stephan Koblmüller
- Institute of Biology, University of Graz, Universitätsplatz 2, 8010 Graz, Austria
- Correspondence: (W.P.); (S.K.)
| | - Thomas Friess
- Ökoteam—Institute for Animal Ecology and Landscape Planning, Bergmanngasse 22, 8010 Graz, Austria;
| | - Barbara-Amina Gereben-Krenn
- Unit Integrative Zoology, Department of Evolutionary Biology, University of Vienna, Althanstraße 14, 1090 Wien, Austria;
| | - Christian Mairhuber
- Amt der Steiermärkischen Landesregierung, Abteilung 16, Baubezirksleitung Steirischer Zentralraum—Naturschutz, Bahnhofgürtel 77, 8020 Graz, Austria;
| | - Michael J. Raupach
- Zoologische Staatssammlung München (SNSB-ZSM), Sektion Hemiptera, Münchhausenstraße 21, 81247 München, Germany;
| | - Lukas Zangl
- Universalmuseum Joanneum, Studienzentrum Naturkunde, Weinzöttlstraße 16, 8045 Graz, Austria;
- Institute of Biology, University of Graz, Universitätsplatz 2, 8010 Graz, Austria
- Ökoteam—Institute for Animal Ecology and Landscape Planning, Bergmanngasse 22, 8010 Graz, Austria;
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Mammola S, Hesselberg T, Lunghi E. A trade‐off between latitude and elevation contributes to explain range segregation of broadly distributed cave‐dwelling spiders. J ZOOL SYST EVOL RES 2020. [DOI: 10.1111/jzs.12432] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Stefano Mammola
- Laboratory for Integrative Biodiversity Research (LIBRe) Finnish Museum of Natural History (LUOMUS) University of Helsinki Helsinki Finland
- Molecular Ecology Group (MEG) Water Research Institute (IRSA) National Research Council (CNR) Verbania Pallanza Italy
| | | | - Enrico Lunghi
- Key Laboratory of the Zoological Systematics and Evolution Institute of Zoology Chinese Academy of Sciences Beijing China
- Museo di Storia Naturale dell'Università degli Studi di Firenze Sezione di Zoologia "La Specola" Firenze Italy
- Natural Oasis Prato Italy
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Smith S, Sandoval-Castellanos E, Lagerholm VK, Napierala H, Sablin M, Von Seth J, Fladerer FA, Germonpré M, Wojtal P, Miller R, Stewart JR, Dalén L. Nonreceding hare lines: genetic continuity since the Late Pleistocene in European mountain hares (Lepus timidus). Biol J Linn Soc Lond 2017. [DOI: 10.1093/biolinnean/blw009] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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Olave M, Avila LJ, Sites JW, Morando M. Model-based approach to test hard polytomies in theEulaemusclade of the most diverse South American lizard genusLiolaemus(Liolaemini, Squamata). Zool J Linn Soc 2015. [DOI: 10.1111/zoj.12231] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Melisa Olave
- Centro Nacional Patagónico - Consejo Nacional de Investigaciones Científicas y Técnicas (CENPAT-CONICET); Boulevard Almirante Brown 2915 ZC: U9120ACD Puerto Madryn Argentina
| | - Luciano J. Avila
- Centro Nacional Patagónico - Consejo Nacional de Investigaciones Científicas y Técnicas (CENPAT-CONICET); Boulevard Almirante Brown 2915 ZC: U9120ACD Puerto Madryn Argentina
| | - Jack W. Sites
- Department of Biology and M. L. Bean Life Science Museum; LSB; Brigham Young University; ZC: 84602 Provo UT USA
| | - Mariana Morando
- Centro Nacional Patagónico - Consejo Nacional de Investigaciones Científicas y Técnicas (CENPAT-CONICET); Boulevard Almirante Brown 2915 ZC: U9120ACD Puerto Madryn Argentina
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De Busschere C, Van Belleghem SM, Hendrickx F. Inter and intra island introgression in a wolf spider radiation from the Galápagos, and its implications for parallel evolution. Mol Phylogenet Evol 2015; 84:73-84. [PMID: 25573742 DOI: 10.1016/j.ympev.2014.11.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2014] [Revised: 11/03/2014] [Accepted: 11/04/2014] [Indexed: 11/30/2022]
Abstract
Parallel radiations within island systems are often assumed to follow a simple scenario in which single colonization events are followed by in situ adaptive divergence. However, subsequent gene exchange after the initial colonization and during the divergence process might have important evolutionary impacts on species radiations. Gene exchange among ecologically similar species from different islands may lead to introgression of adaptive genetic variation and influence the parallel divergence process. In this study, we estimate levels of gene exchange within a wolf spider radiation of the genus Hogna Simon, 1885, from the Galápagos, wherein habitat specialization into 'high elevation' and 'coastal dry' species apparently evolved repeatedly on two islands. By using a multilocus approach we show that low levels of inter-island and relatively higher levels of intra island introgression shaped genetic variation in this species complex. Using these estimates, we demonstrate by means of a coalescence simulation that under these inter- and intra-island migration rates parallel evolution most likely evolves by introgression of adaptive alleles among islands, rather than through independent mutations despite the close genetic relationship of species within islands. As species phylogenies within radiations are frequently used to infer the divergence pattern, even relatively low levels of interspecific gene flow should not be neglected when interpreting parallel trait evolution.
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Affiliation(s)
- Charlotte De Busschere
- Royal Belgian Institute of Natural Sciences, O.D. Taxonomy & Phylogeny, Vautierstraat 29, 1000 Brussels, Belgium; Terrestrial Ecology Unit, Biology Department, Ghent University, K.L. Ledeganckstraat 35, B-9000 Ghent, Belgium.
| | - Steven Marcel Van Belleghem
- Royal Belgian Institute of Natural Sciences, O.D. Taxonomy & Phylogeny, Vautierstraat 29, 1000 Brussels, Belgium; Terrestrial Ecology Unit, Biology Department, Ghent University, K.L. Ledeganckstraat 35, B-9000 Ghent, Belgium.
| | - Frederik Hendrickx
- Royal Belgian Institute of Natural Sciences, O.D. Taxonomy & Phylogeny, Vautierstraat 29, 1000 Brussels, Belgium; Terrestrial Ecology Unit, Biology Department, Ghent University, K.L. Ledeganckstraat 35, B-9000 Ghent, Belgium.
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Lopardo L, Uhl G. Testing mitochondrial marker efficacy for DNA barcoding in spiders: a test case using the dwarf spider genus Oedothorax (Araneae : Linyphiidae : Erigoninae). INVERTEBR SYST 2014. [DOI: 10.1071/is14017] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The present study focusses on comparatively assessing the efficacy for DNA barcoding of the two most commonly used mitochondrial markers (cox1 and 16S) in a genus of erigonine spiders. In total, 53 specimens representing five species, including four multi-sampled species, were sampled from several European localities. Initial evaluation of species monophyly was performed through parsimony and Bayesian phylogenetic analyses. Efficacy of mitochondrial markers was tested using operational (including distance-, tree-based measures and Barcode Gap) and evolutionary criteria (using the General Mixed Yule-coalescent Model) for species delimitation. We propose that the cox1 marker can potentially overestimate analyses of biodiversity and thus might not be the preferred marker for DNA species identification and delimitation methods in Oedothorax. Instead, our results suggest that the 16S marker appears to be a promising candidate for such endeavour. Evaluating the contribution and suitability of markers to the re-identification of species, measured by their recovery of well established morphological species, is critical for future studies and for reliable results in species identification in spiders.
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Garrick RC, Nason JD, Fernández-Manjarrés JF, Dyer RJ. Ecological coassociations influence species' responses to past climatic change: an example from a Sonoran Desert bark beetle. Mol Ecol 2013; 22:3345-61. [DOI: 10.1111/mec.12318] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Ryan C. Garrick
- Department of Biology; University of Mississippi; Oxford; MS; 38677; USA
| | - John D. Nason
- Department of Ecology, Evolution and Organismal Biology; Iowa State University; Ames; IA; 50011; USA
| | - Juan F. Fernández-Manjarrés
- Laboratoire d'Ecologie, Systématique et Evolution; UMR CNRS 8079; Bât 360; Université Paris-Sud 11; 91405; Orsay Cedex; France
| | - Rodney J. Dyer
- Department of Biology; Virginia Commonwealth University; Richmond; VA; 23284; USA
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Ralston J, Kirchman JJ. Predicted range shifts in North American boreal forest birds and the effect of climate change on genetic diversity in blackpoll warblers (Setophaga striata). CONSERV GENET 2012. [DOI: 10.1007/s10592-012-0418-y] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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SCHOVILLE SEAND, LAM ATHENAW, RODERICK GEORGEK. A range-wide genetic bottleneck overwhelms contemporary landscape factors and local abundance in shaping genetic patterns of an alpine butterfly (Lepidoptera: Pieridae:Colias behrii). Mol Ecol 2012; 21:4242-56. [DOI: 10.1111/j.1365-294x.2012.05696.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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McCormack JE, Heled J, Delaney KS, Peterson AT, Knowles LL. CALIBRATING DIVERGENCE TIMES ON SPECIES TREES VERSUS GENE TREES: IMPLICATIONS FOR SPECIATION HISTORY OF APHELOCOMA JAYS. Evolution 2010; 65:184-202. [DOI: 10.1111/j.1558-5646.2010.01097.x] [Citation(s) in RCA: 210] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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12
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Garrick RC, Sunnucks P, Dyer RJ. Nuclear gene phylogeography using PHASE: dealing with unresolved genotypes, lost alleles, and systematic bias in parameter estimation. BMC Evol Biol 2010; 10:118. [PMID: 20429950 PMCID: PMC2880299 DOI: 10.1186/1471-2148-10-118] [Citation(s) in RCA: 105] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2010] [Accepted: 04/30/2010] [Indexed: 01/25/2023] Open
Abstract
Background A widely-used approach for screening nuclear DNA markers is to obtain sequence data and use bioinformatic algorithms to estimate which two alleles are present in heterozygous individuals. It is common practice to omit unresolved genotypes from downstream analyses, but the implications of this have not been investigated. We evaluated the haplotype reconstruction method implemented by PHASE in the context of phylogeographic applications. Empirical sequence datasets from five non-coding nuclear loci with gametic phase ascribed by molecular approaches were coupled with simulated datasets to investigate three key issues: (1) haplotype reconstruction error rates and the nature of inference errors, (2) dataset features and genotypic configurations that drive haplotype reconstruction uncertainty, and (3) impacts of omitting unresolved genotypes on levels of observed phylogenetic diversity and the accuracy of downstream phylogeographic analyses. Results We found that PHASE usually had very low false-positives (i.e., a low rate of confidently inferring haplotype pairs that were incorrect). The majority of genotypes that could not be resolved with high confidence included an allele occurring only once in a dataset, and genotypic configurations involving two low-frequency alleles were disproportionately represented in the pool of unresolved genotypes. The standard practice of omitting unresolved genotypes from downstream analyses can lead to considerable reductions in overall phylogenetic diversity that is skewed towards the loss of alleles with larger-than-average pairwise sequence divergences, and in turn, this causes systematic bias in estimates of important population genetic parameters. Conclusions A combination of experimental and computational approaches for resolving phase of segregating sites in phylogeographic applications is essential. We outline practical approaches to mitigating potential impacts of computational haplotype reconstruction on phylogeographic inferences. With targeted application of laboratory procedures that enable unambiguous phase determination via physical isolation of alleles from diploid PCR products, relatively little investment of time and effort is needed to overcome the observed biases.
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Affiliation(s)
- Ryan C Garrick
- Department of Biology, Virginia Commonwealth University, Richmond, 23284, USA.
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Inference of population history by coupling exploratory and model-driven phylogeographic analyses. Int J Mol Sci 2010; 11:1190-227. [PMID: 20480016 PMCID: PMC2871112 DOI: 10.3390/ijms11041190] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2010] [Revised: 03/18/2010] [Accepted: 03/19/2010] [Indexed: 11/16/2022] Open
Abstract
Understanding the nature, timing and geographic context of historical events and population processes that shaped the spatial distribution of genetic diversity is critical for addressing questions relating to speciation, selection, and applied conservation management. Cladistic analysis of gene trees has been central to phylogeography, but when coupled with approaches that make use of different components of the information carried by DNA sequences and their frequencies, the strength and resolution of these inferences can be improved. However, assessing concordance of inferences drawn using different analytical methods or genetic datasets, and integrating their outcomes, can be challenging. Here we overview the strengths and limitations of different types of genetic data, analysis methods, and approaches to historical inference. We then turn our attention to the potentially synergistic interactions among widely-used and emerging phylogeographic analyses, and discuss some of the ways that spatial and temporal concordance among inferences can be assessed. We close this review with a brief summary and outlook on future research directions.
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Affiliation(s)
- L. Lacey Knowles
- Department of Ecology and Evolutionary Biology, Museum of Zoology, University of Michigan, Ann Arbor, Michigan 48109-1079;
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Strasburg JL, Rieseberg LH. How robust are "isolation with migration" analyses to violations of the im model? A simulation study. Mol Biol Evol 2009; 27:297-310. [PMID: 19793831 DOI: 10.1093/molbev/msp233] [Citation(s) in RCA: 207] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Methods developed over the past decade have made it possible to estimate molecular demographic parameters such as effective population size, divergence time, and gene flow with unprecedented accuracy and precision. However, they make simplifying assumptions about certain aspects of the species' histories and the nature of the genetic data, and it is not clear how robust they are to violations of these assumptions. Here, we use simulated data sets to examine the effects of a number of violations of the "Isolation with Migration" (IM) model, including intralocus recombination, population structure, gene flow from an unsampled species, linkage among loci, and divergent selection, on demographic parameter estimates made using the program IMA. We also examine the effect of having data that fit a nucleotide substitution model other than the two relatively simple models available in IMA. We find that IMA estimates are generally quite robust to small to moderate violations of the IM model assumptions, comparable with what is often encountered in real-world scenarios. In particular, population structure within species, a condition encountered to some degree in virtually all species, has little effect on parameter estimates even for fairly high levels of structure. Likewise, most parameter estimates are robust to significant levels of recombination when data sets are pared down to apparently nonrecombining blocks, although substantial bias is introduced to several estimates when the entire data set with recombination is included. In contrast, a poor fit to the nucleotide substitution model can result in an increased error rate, in some cases due to a predictable bias and in other cases due to an increase in variance in parameter estimates among data sets simulated under the same conditions.
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