1
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Murray CS, Karram M, Bass DJ, Doceti M, Becker D, Nunez JCB, Ratan A, Bergland AO. Balancing selection and the functional effects of shared polymorphism in cryptic Daphnia species. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.16.589693. [PMID: 38659826 PMCID: PMC11042267 DOI: 10.1101/2024.04.16.589693] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
The patterns of genetic variation within and between related taxa represent the genetic history of a species. Shared polymorphisms, loci with identical alleles across species, are of unique interest as they may represent cases of ancient selection maintaining functional variation post-speciation. In this study, we investigate the abundance of shared polymorphism in the Daphnia pulex species complex. We test whether shared mutations are consistent with the action of balancing selection or alternative hypotheses such as hybridization, incomplete lineage sorting, or convergent evolution. We analyzed over 2,000 genomes from North American and European D. pulex and several outgroup species to examine the prevalence and distribution of shared alleles between the focal species pair, North American and European D. pulex. We show that while North American and European D. pulex diverged over ten million years ago, they retained tens of thousands of shared alleles. We found that the number of shared polymorphisms between North American and European D. pulex cannot be explained by hybridization or incomplete lineage sorting alone. Instead, we show that most shared polymorphisms could be the product of convergent evolution, that a limited number appear to be old trans-specific polymorphisms, and that balancing selection is affecting young and ancient mutations alike. Finally, we provide evidence that a blue wavelength opsin gene with trans-specific polymorphisms has functional effects on behavior and fitness in the wild. Ultimately, our findings provide insights into the genetic basis of adaptation and the maintenance of genetic diversity between species.
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Affiliation(s)
- Connor S. Murray
- Department of Biology, University of Virginia, Charlottesville, VA, USA
| | - Madison Karram
- Department of Biology, University of Virginia, Charlottesville, VA, USA
| | - David J. Bass
- Department of Biology, University of Virginia, Charlottesville, VA, USA
| | - Madison Doceti
- Department of Biology, University of Virginia, Charlottesville, VA, USA
| | - Dörthe Becker
- Department of Biology, University of Virginia, Charlottesville, VA, USA
- School of Biosciences, Ecology and Evolutionary Biology, University of Sheffield, Sheffield, UK
| | | | - Aakrosh Ratan
- Center of Public Health Genomics, University of Virginia, Charlottesville, VA, USA
- Department of Public Health Sciences, University of Virginia, Charlottesville, VA, USA
| | - Alan O. Bergland
- Department of Biology, University of Virginia, Charlottesville, VA, USA
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2
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Wersebe MJ, Sherman RE, Jeyasingh PD, Weider LJ. The roles of recombination and selection in shaping genomic divergence in an incipient ecological species complex. Mol Ecol 2023; 32:1478-1496. [PMID: 35119153 DOI: 10.1111/mec.16383] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Revised: 01/16/2022] [Accepted: 01/28/2022] [Indexed: 11/24/2022]
Abstract
Speciation genomic studies have revealed that genomes of diverging lineages are shaped jointly by the actions of gene flow and selection. These evolutionary forces acting in concert with processes such as recombination and genome features such as gene density shape a mosaic landscape of divergence. We investigated the roles of recombination and gene density in shaping the patterns of differentiation and divergence between the cyclically parthenogenetic ecological sister-taxa, Daphnia pulicaria and Daphnia pulex. First, we assembled a phased chromosome-scale genome assembly using trio-binning for D. pulicaria and constructed a genetic map using an F2-intercross panel to understand sex-specific recombination rate heterogeneity. Finally, we used a ddRADseq data set with broad geographic sampling of D. pulicaria, D. pulex, and their hybrids to understand the patterns of genome-scale divergence and demographic parameters. Our study provides the first sex-specific estimates of recombination rates for a cyclical parthenogen, and unlike other eukaryotic species, we observed male-biased heterochiasmy in D. pulicaria, which may be related to this somewhat unique breeding mode. Additionally, regions of high gene density and recombination are generally more divergent than regions of suppressed recombination. Outlier analysis indicated that divergent genomic regions are probably driven by selection on D. pulicaria, the derived lineage colonizing a novel lake habitat. Together, our study supports a scenario of selection acting on genes related to local adaptation shaping genome-wide patterns of differentiation despite high local recombination rates in this species complex. Finally, we discuss the limitations of our data in light of demographic uncertainty.
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Affiliation(s)
- Matthew J Wersebe
- Department of Biology, Program in Ecology and Evolutionary Biology, University of Oklahoma, Norman, Oklahoma, USA
| | - Ryan E Sherman
- Department of Integrative Biology, Oklahoma State University, Stillwater, Oklahoma, USA
| | - Punidan D Jeyasingh
- Department of Integrative Biology, Oklahoma State University, Stillwater, Oklahoma, USA
| | - Lawrence J Weider
- Department of Biology, Program in Ecology and Evolutionary Biology, University of Oklahoma, Norman, Oklahoma, USA
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3
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Kotov AA, Taylor DJ. Daphnia japonica sp. nov. (Crustacea: Cladocera) an eastern Palearctic montane species with mitochondrial discordance. PeerJ 2022; 10:e14113. [PMID: 36213509 PMCID: PMC9541614 DOI: 10.7717/peerj.14113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Accepted: 09/02/2022] [Indexed: 01/21/2023] Open
Abstract
The Daphnia longispina complex (Crustacea: Cladocera) contains several keystone freshwater species such as D. longispina O.F. Müller (D. rosea Sars is a junior synonym), D. galeata Sars, D. cucullata Sars, and D. dentifera Forbes. The complex is common throughout the Holarctic, but there are several geographic regions where local forms have been assigned to European species names based on a superficial morphological resemblance. Here we examine the species status of a form that was previously assigned to D. rosea from a montane bog pond on Honshu, Japan. We used two nuclear non-coding loci (nDNA), mitochondrial sequences (the ND2 protein-coding region) and morphology for evidence. The mitochondrial gene evidence supported the existence of a divergent lineage that is more closely related to D. galeata than to D. dentifera. However, morphology and the nuclear DNA data indicated a lineage that is most closely related to D. dentifera. As our evidence supported the existence of a cohesive divergent lineage, we described a new species, Daphnia japonica sp. nov. Recognition of local and subalpine diversity in this group is critical as ongoing anthropogenic disturbance has been associated with introductions, local extirpations, and hybridization.
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Affiliation(s)
- Alexey A. Kotov
- Laboratory of Aquatic Ecology and Invasions, A.N. Severtsov Institute of Ecology and Evolution of Russian Academy of Sciences, Moscow, Russia
| | - Derek J. Taylor
- Biological Sciences, State University of New York at Buffalo, Buffalo, NY, United States
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4
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Fan R, Tang K, Dou L, Fu C, Faiz AUH, Wang X, Wang Y, Chen S, Liu S. Molecular phylogeny and taxonomy of the genus Nectogale (Mammalia: Eulipotyphla: Soricidae). Ecol Evol 2022; 12:e9404. [PMID: 36311392 PMCID: PMC9596327 DOI: 10.1002/ece3.9404] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Revised: 09/17/2022] [Accepted: 09/21/2022] [Indexed: 11/06/2022] Open
Abstract
The elegant water shrew, Nectogale elegans, is one of the small mammal species most adapted to a semi-aquatic lifestyle. The taxonomy of the genus Nectogale has received little attention due to difficulties in specimen collection. In this study, we sequenced one mitochondrial and eight nuclear genes to infer the phylogenetic relationship of Nectogale. Phylogenetic analyses revealed two large clades within Nectogale. One clade represented N. elegans, and the other was regarded as N. sikhimensis. The split between N. elegans and N. sikhimensis dated back to the early Pleistocene (2.15 million years ago [Ma]), which might be relevant to the Qinghai-Tibet Plateau (QTP) uplift. The morphological comparison showed several distinguishing characters within Nectogale: the shape of the mastoids, the first lower unicuspid (a1), and the second upper molar (M2). Overall, the molecular and the morphological evidences supported that the genus Nectogale consists of two valid species: N. elegans and N. sikhimensis.
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Affiliation(s)
- Ronghui Fan
- College of Life SciencesSichuan Normal UniversityChengduChina
| | - Keyi Tang
- College of Life SciencesSichuan Normal UniversityChengduChina
| | - Liang Dou
- Museum of Natural History/School of Life Sciences, Key Laboratory of Bio‐Resources and Eco‐Environment of Ministry of Education, Key Laboratory of Conservation Biology on Endangered Wildlife of Sichuan ProvinceSichuan UniversityChengduChina
| | - Changkun Fu
- College of Life SciencesSichuan Normal UniversityChengduChina
| | - Abu ul Hassan Faiz
- Department of ZoologyWomen University of Azad Jammu and KashmirBaghPakistan
| | | | | | - Shunde Chen
- College of Life SciencesSichuan Normal UniversityChengduChina
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5
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Ye Z, Zhao C, Raborn RT, Lin M, Wei W, Hao Y, Lynch M. Genetic Diversity, Heteroplasmy, and Recombination in Mitochondrial Genomes of Daphnia pulex, Daphnia pulicaria, and Daphnia obtusa. Mol Biol Evol 2022; 39:msac059. [PMID: 35325186 PMCID: PMC9004417 DOI: 10.1093/molbev/msac059] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Genetic variants of mitochondrial DNA at the individual (heteroplasmy) and population (polymorphism) levels provide insight into their roles in multiple cellular and evolutionary processes. However, owing to the paucity of genome-wide data at the within-individual and population levels, the broad patterns of these two forms of variation remain poorly understood. Here, we analyze 1,804 complete mitochondrial genome sequences from Daphnia pulex, Daphnia pulicaria, and Daphnia obtusa. Extensive heteroplasmy is observed in D. obtusa, where the high level of intraclonal divergence must have resulted from a biparental-inheritance event, and recombination in the mitochondrial genome is apparent, although perhaps not widespread. Global samples of D. pulex reveal remarkably low mitochondrial effective population sizes, <3% of those for the nuclear genome. In addition, levels of population diversity in mitochondrial and nuclear genomes are uncorrelated across populations, suggesting an idiosyncratic evolutionary history of mitochondria in D. pulex. These population-genetic features appear to be a consequence of background selection associated with highly deleterious mutations arising in the strongly linked mitochondrial genome, which is consistent with polymorphism and divergence data suggesting a predominance of strong purifying selection. Nonetheless, the fixation of mildly deleterious mutations in the mitochondrial genome also appears to be driving positive selection on genes encoded in the nuclear genome whose products are deployed in the mitochondrion.
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Affiliation(s)
- Zhiqiang Ye
- Center for Mechanisms of Evolution, Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA
| | - Chaoxian Zhao
- Center for Mechanisms of Evolution, Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA
| | - R. Taylor Raborn
- Center for Mechanisms of Evolution, Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA
| | - Man Lin
- Center for Mechanisms of Evolution, Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA
| | - Wen Wei
- Center for Mechanisms of Evolution, Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA
| | - Yue Hao
- Center for Mechanisms of Evolution, Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA
| | - Michael Lynch
- Center for Mechanisms of Evolution, Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA
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6
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Relationship between oxidative stress and lifespan in Daphnia pulex. Sci Rep 2022; 12:2354. [PMID: 35149730 PMCID: PMC8837783 DOI: 10.1038/s41598-022-06279-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Accepted: 01/04/2022] [Indexed: 11/23/2022] Open
Abstract
Macromolecular damage leading to cell, tissue and ultimately organ dysfunction is a major contributor to aging. Intracellular reactive oxygen species (ROS) resulting from normal metabolism cause most damage to macromolecules and the mitochondria play a central role in this process as they are the principle source of ROS. The relationship between naturally occurring variations in the mitochondrial (MT) genomes leading to correspondingly less or more ROS and macromolecular damage that changes the rate of aging associated organismal decline remains relatively unexplored. MT complex I, a component of the electron transport chain (ETC), is a key source of ROS and the NADH dehydrogenase subunit 5 (ND5) is a highly conserved core protein of the subunits that constitute the backbone of complex I. Using Daphnia as a model organism, we explored if the naturally occurring sequence variations in ND5 correlate with a short or long lifespan. Our results indicate that the short-lived clones have ND5 variants that correlate with reduced complex I activity, increased oxidative damage, and heightened expression of ROS scavenger enzymes. Daphnia offers a unique opportunity to investigate the association between inherited variations in components of complex I and ROS generation which affects the rate of aging and lifespan.
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7
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Nickel J, Schell T, Holtzem T, Thielsch A, Dennis SR, Schlick-Steiner BC, Steiner FM, Möst M, Pfenninger M, Schwenk K, Cordellier M. Hybridization Dynamics and Extensive Introgression in the Daphnia longispina Species Complex: New Insights from a High-Quality Daphnia galeata Reference Genome. Genome Biol Evol 2021; 13:6448229. [PMID: 34865004 PMCID: PMC8695838 DOI: 10.1093/gbe/evab267] [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] [Accepted: 11/24/2021] [Indexed: 01/02/2023] Open
Abstract
Hybridization and introgression are recognized as an important source of variation that influence adaptive processes; both phenomena are frequent in the genus Daphnia, a keystone zooplankton taxon in freshwater ecosystems that comprises several species complexes. To investigate genome-wide consequences of introgression between species, we provide here the first high-quality genome assembly for a member of the Daphnia longispina species complex, Daphnia galeata. We further resequenced 49 whole genomes of three species of the complex and their interspecific hybrids both from genotypes sampled in the water column and from single resting eggs extracted from sediment cores. Populations from habitats with diverse ecological conditions offered an opportunity to study the dynamics of hybridization linked to ecological changes and revealed a high prevalence of hybrids. Using phylogenetic and population genomic approaches, we provide first insights into the intra- and interspecific genome-wide variability in this species complex and identify regions of high divergence. Finally, we assess the length of ancestry tracts in hybrids to characterize introgression patterns across the genome. Our analyses uncover a complex history of hybridization and introgression reflecting multiple generations of hybridization and backcrossing in the Daphnia longispina species complex. Overall, this study and the new resources presented here pave the way for a better understanding of ancient and contemporary gene flow in the species complex and facilitate future studies on resting egg banks accumulating in lake sediment.
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Affiliation(s)
- Jana Nickel
- Institute of Zoology, Universität Hamburg, Germany
| | - Tilman Schell
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Frankfurt am Main, Germany
| | - Tania Holtzem
- Department of Ecology, University of Innsbruck, Austria
| | - Anne Thielsch
- Molecular Ecology, Institute for Environmental Sciences, University Koblenz-Landau, Landau in der Pfalz, Germany
| | - Stuart R Dennis
- Department of Aquatic Ecology, EAWAG, Dübendorf, Switzerland
| | | | | | - Markus Möst
- Department of Ecology, University of Innsbruck, Austria
| | - Markus Pfenninger
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Frankfurt am Main, Germany.,Molecular Ecology, Senckenberg Biodiversity and Climate Research Centre, Frankfurt, Germany.,IoME, Gutenberg University, Mainz, Germany
| | - Klaus Schwenk
- Molecular Ecology, Institute for Environmental Sciences, University Koblenz-Landau, Landau in der Pfalz, Germany
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8
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Clark AD, Howell BK, Wilson AE, Schwartz TS. Draft genomes for one Microcystis-resistant and one Microcystis-sensitive strain of the water flea, Daphnia pulicaria. G3 (BETHESDA, MD.) 2021; 11:jkab266. [PMID: 34849790 PMCID: PMC8527513 DOI: 10.1093/g3journal/jkab266] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Accepted: 07/23/2021] [Indexed: 11/17/2022]
Abstract
Daphnia species are well-suited for studying local adaptation and evolutionary responses to stress(ors) including those caused by algal blooms. Algal blooms, characterized by an overgrowth (bloom) of cyanobacteria, are detrimental to the health of aquatic and terrestrial members of freshwater ecosystems. Some strains of Daphnia pulicaria have demonstrated resistance to toxic algae and the ability to mitigate toxic algal blooms. Understanding the genetic mechanism associated with this toxin resistance requires adequate genomic resources. Using whole-genome sequence data mapped to the Daphnia pulex reference genome (PA42), we present reference-guided draft assemblies from one tolerant and one sensitive strain of D. pulicaria, Wintergreen-6 (WI-6), and Bassett-411 (BA-411), respectively. Assessment of the draft assemblies reveal low contamination levels, and high levels (95%) of genic content. Reference scaffolds had coverage breadths of 98.9-99.4%, and average depths of 33X and 29X for BA-411 and WI-6, respectively. Within, we discuss caveats and suggestions for improving these draft assemblies. These genomic resources are presented with a goal of contributing to the resources necessary to understand the genetic mechanisms and associations of toxic prey resistance observed in this species.
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Affiliation(s)
- Amanda D Clark
- Department of Biological Sciences, Auburn University, Auburn, AL 36849, USA
| | - Bailey K Howell
- Bioinformatics REU Program, Department of Biological Sciences, Auburn University, Auburn, AL 36849, USA
- Department of Biological Sciences, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA
| | - Alan E Wilson
- Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL 36849, USA
| | - Tonia S Schwartz
- Department of Biological Sciences, Auburn University, Auburn, AL 36849, USA
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9
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Ye Z, Williams E, Zhao C, Burns CW, Lynch M. The rapid, mass invasion of New Zealand by North American Daphnia " pulex". LIMNOLOGY AND OCEANOGRAPHY 2021; 66:2672-2683. [PMID: 39175934 PMCID: PMC11340258 DOI: 10.1002/lno.11780] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Accepted: 04/08/2021] [Indexed: 08/24/2024]
Abstract
Nonindigenous members of the Daphnia pulex complex have been found in many lakes in New Zealand (NZ) in the past 20 years, suggesting a recent invasion. However, very little is known about the precise phylogenetic origin of invasive Daphnia, whether each lake is invaded by a single clone or multiple clones, the lineage of the invasive clones, and whether they are obligately asexual clones. Furthermore, the source and time of arrival of the invasive genotype(s) are unclear. We address these questions by genomic sequencing of Daphnia populations from 13 lakes in the South Island and 1 lake in the North Island, NZ. All biallelic sites in these NZ populations have similar numbers of reads for the two parental alleles, suggesting each NZ population originates from a single asexual clone. Based on 25,643 monomorphic lineage-specific markers, the invasive Daphnia in the South Island were found to be Daphnia pulicaria Forbes, while those in the North Island are hybrids of D. pulicaria Forbes and D. cf. pulex sensu Hebert. Both the South and North Island Daphnia are phylogenetically clustered with North American Daphnia, thereby suggesting their North American origins. We found also that all South Island clones contain identical mitochondrial genomes, suggesting the origin and proliferation from a single founder clone, which we experimentally verified to be an obligate asexual. Estimates from molecular data imply a colonization time for the South Island clones of ~60 years ago, with a likely invasion route associated with the introduction of salmonids from North America.
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Affiliation(s)
- Zhiqiang Ye
- Biodesign Center for Mechanisms of Evolution, Arizona State University, Tempe, Arizona
| | - Emily Williams
- Biodesign Center for Mechanisms of Evolution, Arizona State University, Tempe, Arizona
| | - Chaoxian Zhao
- Biodesign Center for Mechanisms of Evolution, Arizona State University, Tempe, Arizona
| | - Carolyn W. Burns
- Department of Zoology, University of Otago, Dunedin, New Zealand
| | - Michael Lynch
- Biodesign Center for Mechanisms of Evolution, Arizona State University, Tempe, Arizona
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10
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Chin TA, Cristescu ME. Speciation in Daphnia. Mol Ecol 2021; 30:1398-1418. [PMID: 33522056 DOI: 10.1111/mec.15824] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Revised: 01/11/2021] [Accepted: 01/20/2021] [Indexed: 11/26/2022]
Abstract
The microcrustacean Daphnia is arguably one of the most studied zooplankton species, having a well understood ecology, life history, and a relatively well studied evolutionary history. Despite this wealth of knowledge, species boundaries within closely related species in this genus often remain elusive and the major evolutionary forces driving the diversity of daphniids remain controversial. This genus contains more than 80 species with multiple cryptic species complexes, with many closely related species able to hybridize. Here, we review speciation research in Daphnia within the framework of current speciation theory. We evaluate the role of geography, ecology, and biology in restricting gene flow and promoting diversification. Of the 253 speciation studies on Daphnia, the majority of studies examine geographic barriers (55%). While evidence shows that geographic barriers play a role in species divergence, ecological barriers are also probably prominent in Daphnia speciation. We assess the contribution of ecological and nonecological reproductive isolating barriers between closely related species of Daphnia and found that none of the reproductive isolating barriers are restricting gene flow completely. Research on reproductive isolating barriers has disproportionally focused on two species complexes, the Daphnia pulex and Daphnia longispina species complexes. Finally, we identify areas of research that remain relatively unexplored and discuss future research directions that build our understanding of speciation in daphniids.
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Affiliation(s)
- Tiffany A Chin
- Department of Biology, McGill University, Montreal, QC, Canada
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11
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Boissin E, Neglia V, Baksay S, Micu D, Bat L, Topaloglu B, Todorova V, Panayotova M, Kruschel C, Milchakova N, Voutsinas E, Beqiraj S, Nasto I, Aglieri G, Taviani M, Zane L, Planes S. Chaotic genetic structure and past demographic expansion of the invasive gastropod Tritia neritea in its native range, the Mediterranean Sea. Sci Rep 2020; 10:21624. [PMID: 33303767 PMCID: PMC7730386 DOI: 10.1038/s41598-020-77742-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Accepted: 11/16/2020] [Indexed: 11/21/2022] Open
Abstract
To better predict population evolution of invasive species in introduced areas it is critical to identify and understand the mechanisms driving genetic diversity and structure in their native range. Here, we combined analyses of the mitochondrial COI gene and 11 microsatellite markers to investigate both past demographic history and contemporaneous genetic structure in the native area of the gastropod Tritia neritea, using Bayesian skyline plots (BSP), multivariate analyses and Bayesian clustering. The BSP framework revealed population expansions, dated after the last glacial maximum. The haplotype network revealed a strong geographic clustering. Multivariate analyses and Bayesian clustering highlighted the strong genetic structure at all scales, between the Black Sea and the Adriatic Sea, but also within basins. Within basins, a random pattern of genetic patchiness was observed, suggesting a superimposition of processes involving natural biological effects (no larval phase and thus limited larval dispersal) and putative anthropogenic transport of specimens. Contrary to the introduced area, no isolation-by-distance patterns were recovered in the Mediterranean or the Black Seas, highlighting different mechanisms at play on both native and introduced areas, triggering unknown consequences for species’ evolutionary trajectories. These results of Tritia neritea populations on its native range highlight a mixture of ancient and recent processes, with the effects of paleoclimates and life history traits likely tangled with the effects of human-mediated dispersal.
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Affiliation(s)
- Emilie Boissin
- PSL Research University: EPHE-UPVD-CNRS, USR 3278 CRIOBE, Laboratoire d'Excellence « CORAIL », Université de Perpignan, 52 Avenue Paul Alduy, 66860, Perpignan Cedex, France.
| | - Valentina Neglia
- PSL Research University: EPHE-UPVD-CNRS, USR 3278 CRIOBE, Laboratoire d'Excellence « CORAIL », Université de Perpignan, 52 Avenue Paul Alduy, 66860, Perpignan Cedex, France
| | - Sandra Baksay
- PSL Research University: EPHE-UPVD-CNRS, USR 3278 CRIOBE, Laboratoire d'Excellence « CORAIL », Université de Perpignan, 52 Avenue Paul Alduy, 66860, Perpignan Cedex, France.,Laboratoire Evolution & Diversite Biologique, University TOULOUSE III - Paul Sabatier, 118 route de Narbonne, 31062, Toulouse Cedex 09, France
| | - Dragos Micu
- Romanian Waters National Authority, 127 Mircea cel Batran Blvd., 900592, Constanţa, Romania
| | - Levent Bat
- Department of Hydrobiology, Sinop University Faculty of Fisheries, 57000, Sinop, Turkey
| | - Bulent Topaloglu
- Faculty of Aquatic Sciences, Istanbul University, Ordu St No: 8, 34134, Istanbul, Turkey
| | - Valentina Todorova
- Institute of Oceanology-BAS (IO-BAS), P.O. Box 152, 9000, Varna, Bulgaria
| | - Marina Panayotova
- Institute of Oceanology-BAS (IO-BAS), P.O. Box 152, 9000, Varna, Bulgaria
| | - Claudia Kruschel
- University of Zadar, Ul. Mihovila Pavlinovića, 23000, Zadar, Croatia
| | - Nataliya Milchakova
- Institute of Biology of the Southern Seas, 2 Nakhimov Ave., Sevastopol, Russia, 299011
| | - Emanuela Voutsinas
- Institute of Oceanography, Hellenic Centre for Marine Research, P.O. Box 712, 19013, Anavyssos, Greece
| | - Sajmir Beqiraj
- Faculty of Natural Sciences, Department of Biology, University of Tirana, Bulevardi "Zogu I Parë", 25/1, 1001, Tiranë, Albania
| | - Ina Nasto
- Department of Biology, Faculty of Technical Sciences, Vlora University, 9401, Vlora, Albania
| | - Giorgio Aglieri
- Department of Earth and Marine Sciences (DiSTeM), University of Palermo, via Archirafi 28, 90123, Palermo, Italy.,Consorzio Nazionale Interuniversitario per le Scienze del Mare (CoNISMa), Piazzale Flaminio 9, 00196, Rome, Italy
| | - Marco Taviani
- Institute of Marine Sciences (ISMAR), CNR, via Gobetti 101, 40129, Bologna, Italy.,Stazione Zoologica Anton Dohrn, Villa Comunale, 80121, Napoli, Italy.,Department of Biology, Woods Hole Oceanographic Institution, 266 Woods Hole Road, Woods Hole, MA, 02543, USA
| | - Lorenzo Zane
- Consorzio Nazionale Interuniversitario per le Scienze del Mare (CoNISMa), Piazzale Flaminio 9, 00196, Rome, Italy.,Dipartimento di Biologia, Università di Padova, via U. Bassi/58B, 35121, Padua, Italy
| | - Serge Planes
- PSL Research University: EPHE-UPVD-CNRS, USR 3278 CRIOBE, Laboratoire d'Excellence « CORAIL », Université de Perpignan, 52 Avenue Paul Alduy, 66860, Perpignan Cedex, France
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12
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Environmental conditions as proximate cues of predation risk inducing defensive response in Daphnia pulex. Biologia (Bratisl) 2020. [DOI: 10.2478/s11756-020-00583-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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13
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Wongnikong W, van Brunschot SL, Hereward JP, De Barro PJ, Walter GH. Testing mate recognition through reciprocal crosses of two native populations of the whitefly Bemisia tabaci (Gennadius) in Australia. BULLETIN OF ENTOMOLOGICAL RESEARCH 2020; 110:328-339. [PMID: 31640818 DOI: 10.1017/s0007485319000683] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Bemisia tabaci (Gennadius) represents a relatively large cryptic species complex. Australia has at least two native populations of B. tabaci sensu lato and these were first found on different host plants in different parts of Australia. The species status of these populations has not been resolved, although their mitochondrial sequences differ by 3.82-4.20%. We addressed the question of whether these AUSI and AUSII B. tabaci populations are distinct species. We used reciprocal cross-mating tests to establish whether the insects from these different populations recognize one another as potential mating partners. The results show that the two native Australian populations of B. tabaci have a mating sequence with four phases, each of which is described. Not all pairs in the control crosses mated and the frequency of mating differed across them. Some pairs in the AUSI-M × AUSII-F did mate (15%) and did produce female progeny, but the frequency was extremely low relative to controls. Microsatellite genotyping of the female progeny produced in the crosses showed these matings were successful. None of the AUSII-M × AUSI-F crosses mated although some of the males did search for females. These results demonstrate the critical role of the mate recognition process and the need to assess this directly in cross-mating tests if the species status of different populations is to be tested realistically. In short, AUSI and AUSII B. tabaci populations are distinct species because the individual males and females do not recognize individuals of the alternative population as potential mating partners.
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Affiliation(s)
- W Wongnikong
- School of Biological Sciences, The University of Queensland, Brisbane, Queensland4072, Australia
| | - S L van Brunschot
- School of Biological Sciences, The University of Queensland, Brisbane, Queensland4072, Australia
- Agriculture, Health & Environment Department, Natural Resources Institute, University of Greenwich, Medway Campus, Central Avenue, Chatham Maritime ME4 4TB, UK
| | - J P Hereward
- School of Biological Sciences, The University of Queensland, Brisbane, Queensland4072, Australia
| | - P J De Barro
- CSIRO Health & Biosecurity, GPO Box 2583, Brisbane QLD 4001, Australia
| | - G H Walter
- School of Biological Sciences, The University of Queensland, Brisbane, Queensland4072, Australia
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14
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Lohr JN, Haag CR. Parasite-driven replacement of a sexual by a closely related asexual taxon in nature. Ecology 2020; 101:e03105. [PMID: 32452541 DOI: 10.1002/ecy.3105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Revised: 03/22/2020] [Accepted: 04/15/2020] [Indexed: 11/09/2022]
Abstract
Asexual species are thought to suffer more from coevolving parasites than related sexuals. Yet a variety of studies do not find the patterns predicted by theory. Here, to shine light on this conundrum, we investigate one such case of an asexual advantage in the presence of parasites. We follow the frequency dynamics of sexual and asexual Daphnia pulex in a natural pond that was initially dominated by sexuals. Coinciding with an epidemic of a microsporidian parasite infecting both sexuals and asexuals, the pond was rapidly taken over by the initially rare asexuals. With experiments comparing multiple sexual and asexual clones from across the local metapopulation, we confirm that asexuals are less susceptible and also suffer less from the parasite once infected. These results are consistent with the parasite-driven, ecological replacement of dominant sexuals by closely related, but more resistant asexuals, ultimately leading to the extinction of the formerly superior sexual competitor. Our study is one of the clearest examples from nature, backed up by experimental verification, showing a parasite-mediated reversal of competition dynamics. The experiments show that, across the metapopulation, asexuals have an advantage in the presence of parasites. In this metapopulation, asexuals are relatively rare, likely due to their recent invasion. While we cannot rule out other reasons for the observed patterns, the results are consistent with a temporary parasite-mediated advantage of asexuals due to the fact that they are rare, which is an underappreciated aspect of the Red Queen Hypothesis.
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Affiliation(s)
- Jennifer N Lohr
- Department of Biology, Ecology and Evolution, University of Fribourg, Chemin du Musée 10, 1700, Fribourg, Switzerland.,Tvärminne Zoological Station, J.A. Palménin tie 260, 10900, Hanko, Finland.,Department of Genetics, Evolution and Environment, University College London, Institute of Healthy Ageing, Darwin Building, Gower Street, London, WC1E 6BT, United Kingdom
| | - Christoph R Haag
- Department of Biology, Ecology and Evolution, University of Fribourg, Chemin du Musée 10, 1700, Fribourg, Switzerland.,Tvärminne Zoological Station, J.A. Palménin tie 260, 10900, Hanko, Finland.,CEFE, Univ Montpellier, CNRS, EPHE, IRD, Univ Paul Valéry Montpellier 3, 1919, route de Mende, 34293, Montpellier Cedex 5, France
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15
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Angers B, Leung C, Vétil R, Deremiens L, Vergilino R. The effects of allospecific mitochondrial genome on the fitness of northern redbelly dace ( Chrosomus eos). Ecol Evol 2018; 8:3311-3321. [PMID: 29607026 PMCID: PMC5869299 DOI: 10.1002/ece3.3922] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2018] [Revised: 01/17/2018] [Accepted: 01/23/2018] [Indexed: 11/07/2022] Open
Abstract
Instantaneous mitochondrial introgression events allow the disentangling of the effects of hybridization from those of allospecific mtDNA. Such process frequently occurred in the fish Chrosomus eos, resulting in cybrid individuals composed of a C. eos nuclear genome but with a C. neogaeus mtDNA. This provides a valuable model to address the fundamental question: How well do introgressed individuals perform in their native environment? We infer where de novo production of cybrids occurred to discriminate native environments from those colonized by cybrids in 25 sites from two regions (West-Qc and East-Qc) in Quebec (Canada). We then compared the relative abundance of wild types and cybrids as a measure integrating both fitness and de novo production of cybrids. According to mtDNA variation, 12 introgression events are required to explain the diversity of cybrids. Five cybrid lineages could not be associated with in situ introgression events. This includes one haplotype carried by 93% of the cybrids expected to have colonized West-Qc. These cybrids also displayed a nearly complete allopatric distribution with wild types. We still inferred de novo production of cybrids at seven sites, that accounted for 70% of the cybrids in East-Qc. Wild-type and cybrid individuals coexist in all East-Qc sites while cybrids were less abundant. Allopatry of cybrids restricted to the postglacial expansion suggests the existence of higher fitness for cybrids in specific conditions, allowing for the colonization of different environments and expanding the species' range. However, allospecific mtDNA does not provide a higher fitness to cybrids in their native environment compared to wild types, making the success of an introgressed lineage uncertain.
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Affiliation(s)
- Bernard Angers
- Department of Biological Sciences Université de Montréal Montreal QC Canada
| | - Christelle Leung
- Department of Biological Sciences Université de Montréal Montreal QC Canada
| | - Romain Vétil
- Department of Biological Sciences Université de Montréal Montreal QC Canada
| | - Léo Deremiens
- Department of Biological Sciences Université de Montréal Montreal QC Canada
| | - Roland Vergilino
- Department of Biological Sciences Université de Montréal Montreal QC Canada
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16
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Veale AJ, Russell JC, King CM. The genomic ancestry, landscape genetics and invasion history of introduced mice in New Zealand. ROYAL SOCIETY OPEN SCIENCE 2018; 5:170879. [PMID: 29410804 PMCID: PMC5792881 DOI: 10.1098/rsos.170879] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/11/2017] [Accepted: 12/15/2017] [Indexed: 06/07/2023]
Abstract
The house mouse (Mus musculus) provides a fascinating system for studying both the genomic basis of reproductive isolation, and the patterns of human-mediated dispersal. New Zealand has a complex history of mouse invasions, and the living descendants of these invaders have genetic ancestry from all three subspecies, although most are primarily descended from M. m. domesticus. We used the GigaMUGA genotyping array (approximately 135 000 loci) to describe the genomic ancestry of 161 mice, sampled from 34 locations from across New Zealand (and one Australian city-Sydney). Of these, two populations, one in the south of the South Island, and one on Chatham Island, showed complete mitochondrial lineage capture, featuring two different lineages of M. m. castaneus mitochondrial DNA but with only M. m. domesticus nuclear ancestry detectable. Mice in the northern and southern parts of the North Island had small traces (approx. 2-3%) of M. m. castaneus nuclear ancestry, and mice in the upper South Island had approximately 7-8% M. m. musculus nuclear ancestry including some Y-chromosomal ancestry-though no detectable M. m. musculus mitochondrial ancestry. This is the most thorough genomic study of introduced populations of house mice yet conducted, and will have relevance to studies of the isolation mechanisms separating subspecies of mice.
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Affiliation(s)
- Andrew J. Veale
- Department of Environmental and Animal Sciences, Unitec, 139 Carrington Road, Auckland 1025, New Zealand
| | - James C. Russell
- School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland Mail Centre, Auckland 1142, New Zealand
| | - Carolyn M. King
- Environmental Research Institute, School of Science, University of Waikato, Private Bag 2105, Hamilton 3240, New Zealand
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17
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Thielsch A, Knell A, Mohammadyari A, Petrusek A, Schwenk K. Divergent clades or cryptic species? Mito-nuclear discordance in a Daphnia species complex. BMC Evol Biol 2017; 17:227. [PMID: 29166859 PMCID: PMC5700674 DOI: 10.1186/s12862-017-1070-4] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2017] [Accepted: 11/08/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Genetically divergent cryptic species are frequently detected by molecular methods. These discoveries are often a byproduct of molecular barcoding studies in which fragments of a selected marker are used for species identification. Highly divergent mitochondrial lineages and putative cryptic species are even detected in intensively studied animal taxa, such as the crustacean genus Daphnia. Recently, eleven such lineages, exhibiting genetic distances comparable to levels observed among well-defined species, were recorded in the D. longispina species complex, a group that contains several key taxa of freshwater ecosystems. We tested if three of those lineages represent indeed distinct species, by analyzing patterns of variation of ten nuclear microsatellite markers in six populations. RESULTS We observed a discordant pattern between mitochondrial and nuclear DNA, as all individuals carrying one of the divergent mitochondrial lineages grouped at the nuclear level with widespread, well-recognized species coexisting at the same localities (Daphnia galeata, D. longispina, and D. cucullata). CONCLUSIONS A likely explanation for this pattern is the introgression of the mitochondrial genome of undescribed taxa into the common species, either in the distant past or after long-distance dispersal. The occurrence of highly divergent but rare mtDNA lineages in the gene pool of widespread species would suggest that hybridization and introgression in the D. longispina species complex is frequent even across large phylogenetic distances, and that discoveries of such distinct clades must be interpreted with caution. However, maintenance of ancient polymorphisms through selection is another plausible alternative that may cause the observed discordance and cannot be entirely excluded.
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Affiliation(s)
- Anne Thielsch
- Institute for Environmental Sciences, Molecular Ecology, University of Koblenz-Landau, Landau in der Pfalz, Germany.
| | - Alexis Knell
- Institute for Environmental Sciences, Molecular Ecology, University of Koblenz-Landau, Landau in der Pfalz, Germany
| | - Ali Mohammadyari
- Faculty of Science, Department of Biology, Ferdowsi University of Mashhad, Mashhad, Iran
| | - Adam Petrusek
- Faculty of Science, Department of Ecology, Charles University, Prague, Czechia
| | - Klaus Schwenk
- Institute for Environmental Sciences, Molecular Ecology, University of Koblenz-Landau, Landau in der Pfalz, Germany
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18
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Brown AP, Greenway R, Morgan S, Quackenbush CR, Giordani L, Arias-Rodriguez L, Tobler M, Kelley JL. Genome-scale data reveal that endemic Poecilia populations from small sulphidic springs display no evidence of inbreeding. Mol Ecol 2017; 26:4920-4934. [PMID: 28731545 DOI: 10.1111/mec.14249] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2016] [Revised: 04/04/2017] [Accepted: 06/21/2017] [Indexed: 12/27/2022]
Abstract
Populations with limited ranges can be highly vulnerable to changes in their environment and are, thus, of high conservation concern. Populations that experience human-induced range reductions are often highly inbred and lack genetic diversity, but it is unknown whether this is also the case for populations with naturally small ranges. The fishes Poecilia sulphuraria (listed as critically endangered) and Poecilia thermalis, which are endemic to small hydrogen sulphide-rich springs in southern Mexico, are examples of such populations with inherently small habitats. We used geometric morphometrics and population genetics to quantify phenotypic and genetic variation within and among two populations of P. sulphuraria and one population of P. thermalis. Principal component analyses revealed phenotypic and genetic differences among the populations. Evidence for inbreeding was low compared to populations that have undergone habitat reduction. The genetic data were also used to infer the demographic history of these populations to obtain estimates for effective population sizes and migration rates. Effective population sizes were large given the small habitats of these populations. Our results imply that these three endemic extremophile populations should each be considered separately for conservation purposes. Additionally, this study suggests that populations in naturally small habitats may have lower rates of inbreeding and higher genetic diversity than expected, and therefore may be better equipped to handle environmental perturbations than anticipated. We caution, however, that the inferred lack of inbreeding and the large effective population sizes could potentially be a result of colonization by genetically diverse ancestors.
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Affiliation(s)
- Anthony P Brown
- School of Biological Sciences, Washington State University, Pullman, WA, USA
| | - Ryan Greenway
- Division of Biology, Kansas State University, Manhattan, KS, USA
| | - Samuel Morgan
- Division of Biology, Kansas State University, Manhattan, KS, USA
| | - Corey R Quackenbush
- School of Biological Sciences, Washington State University, Pullman, WA, USA
| | | | - Lenin Arias-Rodriguez
- División Académica de Ciencias Biológicas, Universidad Juárez Autónoma de Tabasco (UJAT), Villahermosa, Tabasco, México
| | - Michael Tobler
- Division of Biology, Kansas State University, Manhattan, KS, USA
| | - Joanna L Kelley
- School of Biological Sciences, Washington State University, Pullman, WA, USA
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19
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Hawlitschek O, Morinière J, Lehmann GUC, Lehmann AW, Kropf M, Dunz A, Glaw F, Detcharoen M, Schmidt S, Hausmann A, Szucsich NU, Caetano-Wyler SA, Haszprunar G. DNA barcoding of crickets, katydids and grasshoppers (Orthoptera) from Central Europe with focus on Austria, Germany and Switzerland. Mol Ecol Resour 2016; 17:1037-1053. [PMID: 27863033 DOI: 10.1111/1755-0998.12638] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2016] [Revised: 10/28/2016] [Accepted: 11/10/2016] [Indexed: 12/21/2022]
Abstract
We present a DNA barcoding study on the insect order Orthoptera that was generated in collaboration between four barcoding projects in three countries, viz. Barcoding Fauna Bavarica (Germany), German Barcode of Life, Austrian Barcode of Life and Swiss Barcode of Life. Our data set includes 748 COI sequences from 127 of the 162 taxa (78.4%) recorded in the three countries involved. Ninety-three of these 122 species (76.2%, including all Ensifera) can be reliably identified using DNA barcodes. The remaining 26 caeliferan species (families Acrididae and Tetrigidae) form ten clusters that share barcodes among up to five species, in three cases even across different genera, and in six cases even sharing individual barcodes. We discuss incomplete lineage sorting and hybridization as most likely causes of this phenomenon, as the species concerned are phylogenetically young and hybridization has been previously observed. We also highlight the problem of nuclear mitochondrial pseudogenes (numts), a known problem in the barcoding of orthopteran species, and the possibility of Wolbachia infections. Finally, we discuss the possible taxonomic implications of our barcoding results and point out future research directions.
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Affiliation(s)
- O Hawlitschek
- Zoologische Staatssammlung München (SNSB-ZSM), Münchhausenstr. 21, 81247, München, Germany.,Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Passeig Maritim de la Barceloneta 37, 08003, Barcelona, Spain
| | - J Morinière
- Zoologische Staatssammlung München (SNSB-ZSM), Münchhausenstr. 21, 81247, München, Germany
| | - G U C Lehmann
- Department of Biology, Behavioural Physiology, Humboldt University Berlin, Invalidenstr. 43, 10115, Berlin, Germany
| | - A W Lehmann
- Orthoptera Working Group Brandenburg and Berlin, Friedensallee 37, 14532, Stahnsdorf, Germany
| | - M Kropf
- Institute for Integrative Nature Conservation Research, University of Natural Resources and Life Sciences (BOKU), Gregor Mendel-Str. 33, 1180, Vienna, Austria
| | - A Dunz
- Zoologische Staatssammlung München (SNSB-ZSM), Münchhausenstr. 21, 81247, München, Germany
| | - F Glaw
- Zoologische Staatssammlung München (SNSB-ZSM), Münchhausenstr. 21, 81247, München, Germany
| | - M Detcharoen
- Zoologische Staatssammlung München (SNSB-ZSM), Münchhausenstr. 21, 81247, München, Germany
| | - S Schmidt
- Zoologische Staatssammlung München (SNSB-ZSM), Münchhausenstr. 21, 81247, München, Germany
| | - A Hausmann
- Zoologische Staatssammlung München (SNSB-ZSM), Münchhausenstr. 21, 81247, München, Germany
| | - N U Szucsich
- 3rd Zoological Dep., Natural History Museum Vienna, Burgring 7, 1010, Vienna, Austria
| | - S A Caetano-Wyler
- Université de Genève, Département de Génétique et Evolution, Quai Ernest Ansermet 30, 1211, Geneva 4, Switzerland
| | - G Haszprunar
- Zoologische Staatssammlung München (SNSB-ZSM), Münchhausenstr. 21, 81247, München, Germany.,Department Biology II and GeoBio-Center of Ludwig-Maximilians-Universität München, Groβhaderner Str. 2, 82152, Planegg-Martinsried, Germany
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20
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Perea S, Vukić J, Šanda R, Doadrio I. Ancient Mitochondrial Capture as Factor Promoting Mitonuclear Discordance in Freshwater Fishes: A Case Study in the Genus Squalius (Actinopterygii, Cyprinidae) in Greece. PLoS One 2016; 11:e0166292. [PMID: 27906993 PMCID: PMC5132402 DOI: 10.1371/journal.pone.0166292] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2016] [Accepted: 10/26/2016] [Indexed: 11/18/2022] Open
Abstract
Hybridization and incomplete lineage sorting are common confounding factors in phylogeny and speciation resulting in mitonuclear disparity. Mitochondrial introgression, a particular case of hybridization, may, in extreme cases, lead to replacement of the mitochondrial genome of one species with that of another (mitochondrial capture). We investigated mitochondrial introgression involving two species of the cyprinid genus Squalius in the western Peloponnese region of Greece using molecular and morphological data. We found evidence of complete mitochondrial introgression of Squalius keadicus into two populations recognized as Squalius peloponensis from the Miras and Pamissos River basins and a divergence of mitochondrial genomes of S. keadicus from the Evrotas basin from that of the introgressed populations dating from the Pleistocene. Secondary contact among basins is a possible factor in connection of the species and the introgression event. Morphological analyses support the hypothesis of mitochondrial introgression, as S. keadicus was different from the other three populations recognized as S. peloponensis, although significant differences were found among the four populations. Isolation by geographical barriers arose during Pleistocene in the western Peloponnese were the source of the evolution of the two reciprocally monophyletic subclades found in the S. keadicus mitochondrial clade, and the morphological differences found among the four populations. Along with the lack of structure in the nuclear genome in the three populations ascribed to S. peloponensis, this suggests an incipient speciation process occurring in these Squalius species in the western Peloponnese.
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Affiliation(s)
- Silvia Perea
- Biodiversity and Evolutionary Group, Museo Nacional de Ciencias Naturales-CSIC, C/José Gutiérrez Abascal, Madrid, Spain
| | - Jasna Vukić
- Department of Ecology, Faculty of Science, Charles University, Viničná, Prague, Czech Republic
| | - Radek Šanda
- Department of Zoology, National Museum, Václavské nám, Prague, Czech Republic
| | - Ignacio Doadrio
- Biodiversity and Evolutionary Group, Museo Nacional de Ciencias Naturales-CSIC, C/José Gutiérrez Abascal, Madrid, Spain
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21
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Wang W, Zhang K, Deng D, Zhang YN, Peng S, Xu X. Genetic Diversity of Daphnia pulex in the Middle and Lower Reaches of the Yangtze River. PLoS One 2016; 11:e0152436. [PMID: 27015539 PMCID: PMC4807850 DOI: 10.1371/journal.pone.0152436] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2015] [Accepted: 03/14/2016] [Indexed: 11/29/2022] Open
Abstract
Increased human activities and environmental changes may lead to genetic diversity variations of Cladocerans in water. Daphnia pulex are distributed throughout the world and often regarded as a model organism. The 16S rDNA, cytochrome c oxidase subunit I (COI), and 18S genes were used as molecular marks. The genetic diversity and phylogeny of D. pulex obtained from 10 water bodies in the middle and lower reaches of the Yangtze River were studied. For 16S rDNA, COI gene, and 18S gene, the A+T content (65.4%, 58.4%, and 54.6%) was significantly higher than the G+C content (34.6%, 41.6% and 45.4%). This result was consistent with higher A and T contents among invertebrates. Based on the genetic distances of 16S rDNA and COI genes, the genetic differences of D. pulex from 10 water bodies located in the middle and lower reaches of the Yangtze River in China was minimal (0%-0.8% for 16S rDNA and 0%-1.5% for COI gene). However, D. pulex evolved into two branches in the phylogenetic trees, which coincided with its geographical distribution. Compared with D. pulex from other countries, the average genetic distance of D. pulex obtained from 10 water bodies in the middle and lower reaches of the Yangtze River reached 9.1%-10.5%, thereby indicating that D. pulex may have evolved into different subspecies.
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Affiliation(s)
- Wenping Wang
- School of Life Science, Huaibei Normal University, Anhui Key Laboratory of Resource and Plant Biology, Huaibei, 235000, China
| | - Kun Zhang
- School of Life Science, Huaibei Normal University, Anhui Key Laboratory of Resource and Plant Biology, Huaibei, 235000, China
| | - Daogui Deng
- School of Life Science, Huaibei Normal University, Anhui Key Laboratory of Resource and Plant Biology, Huaibei, 235000, China
| | - Ya-Nan Zhang
- School of Life Science, Huaibei Normal University, Anhui Key Laboratory of Resource and Plant Biology, Huaibei, 235000, China
| | - Shuixiu Peng
- School of Life Science, Huaibei Normal University, Anhui Key Laboratory of Resource and Plant Biology, Huaibei, 235000, China
| | - Xiaoxue Xu
- School of Life Science, Huaibei Normal University, Anhui Key Laboratory of Resource and Plant Biology, Huaibei, 235000, China
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22
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Alfsnes K, Hobæk A, Weider LJ, Hessen DO. Birds, nutrients, and climate change: mtDNA haplotype diversity of Arctic Daphnia on Svalbard revisited. Polar Biol 2016. [DOI: 10.1007/s00300-015-1868-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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23
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Möst M, Oexle S, Marková S, Aidukaite D, Baumgartner L, Stich HB, Wessels M, Martin-Creuzburg D, Spaak P. Population genetic dynamics of an invasion reconstructed from the sediment egg bank. Mol Ecol 2015; 24:4074-93. [PMID: 26122166 DOI: 10.1111/mec.13298] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2013] [Revised: 06/23/2015] [Accepted: 06/25/2015] [Indexed: 01/16/2023]
Abstract
Biological invasions are a global issue with far-reaching consequences for single species, communities and whole ecosystems. Our understanding of modes and mechanisms of biological invasions requires knowledge of the genetic processes associated with successful invasions. In many instances, this information is particularly difficult to obtain as the initial phases of the invasion process often pass unnoticed and we rely on inferences from contemporary population genetic data. Here, we combined historic information with the genetic analysis of resting eggs to reconstruct the invasion of Daphnia pulicaria into Lower Lake Constance (LLC) in the 1970s from the resting egg bank in the sediments. We identified the invader as 'European D. pulicaria' originating from meso- and eutrophic lowland lakes and ponds in Central Europe. The founding population was characterized by extremely low genetic variation in the resting egg bank that increased considerably over time. Furthermore, strong evidence for selfing and/or biparental inbreeding was found during the initial phase of the invasion, followed by a drop of selfing rate to low levels in subsequent decades. Moreover, the increase in genetic variation was most pronounced during early stages of the invasion, suggesting additional introductions during this period. Our study highlights that genetic data covering the entire invasion process from its beginning can be crucial to accurately reconstruct the invasion history of a species. We show that propagule banks can preserve such information enabling the study of population genetic dynamics and sources of genetic variation in successful invasive populations.
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Affiliation(s)
- Markus Möst
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, CH-8600, Dübendorf, Switzerland.,Institute of Integrative Biology, ETH Zurich, CH-8092, Zurich, Switzerland.,Department of Zoology, University of Cambridge, CB2 3EJ, Cambridge, UK
| | - Sarah Oexle
- Limnological Institute, University of Konstanz, D-78464, Konstanz, Germany.,Laboratory of Aquatic Ecology, Evolution and Conservation, KU Leuven, B-3000, Leuven, Belgium
| | - Silvia Marková
- Laboratory of Molecular Ecology, Institute of Animal Physiology and Genetics, Academy of Sciences of the Czech Republic, Rumburská 89, 27721, Liběchov, Czech Republic
| | - Dalia Aidukaite
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, CH-8600, Dübendorf, Switzerland
| | - Livia Baumgartner
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, CH-8600, Dübendorf, Switzerland
| | | | - Martin Wessels
- Institute for Lake Research, D-88085, Langenargen, Germany
| | | | - Piet Spaak
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, CH-8600, Dübendorf, Switzerland.,Institute of Integrative Biology, ETH Zurich, CH-8092, Zurich, Switzerland
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24
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Dong F, Zou FS, Lei FM, Liang W, Li SH, Yang XJ. Testing hypotheses of mitochondrial gene-tree paraphyly: unravelling mitochondrial capture of the Streak-breasted Scimitar Babbler (Pomatorhinus ruficollis) by the Taiwan Scimitar Babbler (Pomatorhinus musicus). Mol Ecol 2014; 23:5855-67. [DOI: 10.1111/mec.12981] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2014] [Revised: 10/02/2014] [Accepted: 10/14/2014] [Indexed: 01/08/2023]
Affiliation(s)
- Feng Dong
- State Key Laboratory of Genetic Resources and Evolution; Kunming Institute of Zoology; Chinese Academy of Sciences; Kunming 650223 China
| | - Fa-Sheng Zou
- South China Institute of Endangered Animals; Guangzhou 510260 China
| | - Fu-Min Lei
- Key Laboratory of Zoological Systematics and Evolution; Institute of Zoology; Chinese Academy of Sciences; Beijing 100101 China
| | - Wei Liang
- Ministry of Education Key Laboratory for Tropical Plant and Animal Ecology; College of Life Sciences; Hainan Normal University; Haikou 571158 China
| | - Shou-Hsien Li
- Department of Life Science; National Taiwan Normal University; Taipei 116 Taiwan
| | - Xiao-Jun Yang
- State Key Laboratory of Genetic Resources and Evolution; Kunming Institute of Zoology; Chinese Academy of Sciences; Kunming 650223 China
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25
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Filipi K, Marková S, Searle JB, Kotlík P. Mitogenomic phylogenetics of the bank vole Clethrionomys glareolus, a model system for studying end-glacial colonization of Europe. Mol Phylogenet Evol 2014; 82 Pt A:245-57. [PMID: 25450101 DOI: 10.1016/j.ympev.2014.10.016] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2014] [Revised: 10/17/2014] [Accepted: 10/22/2014] [Indexed: 10/24/2022]
Abstract
We have revisited the mtDNA phylogeny of the bank vole Clethrionomys glareolus based on Sanger and next-generation Illumina sequencing of 32 complete mitochondrial genomes. The bank vole is a key study species for understanding the response of European fauna to the climate change following the Last Glacial Maximum (LGM) and one of the most convincing examples of a woodland mammal surviving in cryptic northern glacial refugia in Europe. The genomes sequenced included multiple representatives of each of the eight bank vole clades previously described based on cytochrome b (cob) sequences. All clades with the exception of the Basque - likely a misidentified pseudogene clade - were highly supported in all phylogenetic analyses and the relationships between the clades were resolved with high confidence. Our data extend the distribution of the Carpathian clade, the marker of a northern glacial refugium in the Carpathian Mountains, to include Britain and Fennoscandia (but not adjacent areas of continental Europe). The Carpathian sub-clade that colonized Britain and Fennoscandia had a somewhat different history from the sub-clade currently found in or close to the Carpathians and may have derived from a more north-westerly refugial area. The two bank vole populations that colonized Britain at the end of the last glaciation are for the first time linked with particular continental clades, the first colonists with the Carpathian clade and the second colonists with the western clade originating in a more southerly refugium in the vicinity of the Alps. We however found no evidence that a functional divergence of proteins encoded in the mitochondrial genome promoted the partial genetic replacement of the first colonists by the second colonists detected previously in southern Britain. We did identify one codon site that changed more often and more radically in the tree than expected and where the observed amino acid change may affect the reductase activity of the cytochrome bc1 complex, but the change was not specific to a particular clade. We also found an excess of radical changes to the primary protein structure for geographically restricted clades from southern Italy and Norway, respectively, possibly related to stronger selective pressure at the latitudinal extremes of the bank vole distribution. However, overall, we find little evidence of pervasive effects of deviation from neutrality on bank vole mtDNA phylogeography.
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Affiliation(s)
- Karolína Filipi
- Laboratory of Molecular Ecology, Institute of Animal Physiology and Genetics, Academy of Sciences of the Czech Republic, Rumburská 89, 27721 Liběchov, Czech Republic; Department of Genetics and Microbiology, Faculty of Science, Charles University in Prague, Viničná 5, 12844 Prague 2, Czech Republic
| | - Silvia Marková
- Laboratory of Molecular Ecology, Institute of Animal Physiology and Genetics, Academy of Sciences of the Czech Republic, Rumburská 89, 27721 Liběchov, Czech Republic
| | - Jeremy B Searle
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY 14853, USA
| | - Petr Kotlík
- Laboratory of Molecular Ecology, Institute of Animal Physiology and Genetics, Academy of Sciences of the Czech Republic, Rumburská 89, 27721 Liběchov, Czech Republic.
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26
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Bryson RW, Smith BT, Nieto-Montes de Oca A, García-Vázquez UO, Riddle BR. The role of mitochondrial introgression in illuminating the evolutionary history of Nearctic treefrogs. Zool J Linn Soc 2014. [DOI: 10.1111/zoj.12169] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Robert W. Bryson
- School of Life Sciences; University of Nevada Las Vegas; Las Vegas NV 89154-4004 USA
- Department of Biology and Burke Museum of Natural History and Culture; University of Washington; Seattle WA 98195-1800 USA
| | - Brian Tilston Smith
- Museum of Natural Science; Louisiana State University; Baton Rouge LA 70803 USA
| | - Adrian Nieto-Montes de Oca
- Museo de Zoología Alfonso L. Herrera; Facultad de Ciencias; Universidad Nacional Autónoma de México; Circuito exterior s/n, Cd. Universitaria México 04510 Distrito Federal Mexico
| | - Uri Omar García-Vázquez
- Museo de Zoología Alfonso L. Herrera; Facultad de Ciencias; Universidad Nacional Autónoma de México; Circuito exterior s/n, Cd. Universitaria México 04510 Distrito Federal Mexico
| | - Brett R. Riddle
- School of Life Sciences; University of Nevada Las Vegas; Las Vegas NV 89154-4004 USA
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27
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Bellati A, Tiberti R, Cocca W, Galimberti A, Casiraghi M, Bogliani G, Galeotti P. A dark shell hiding great variability: a molecular insight into the evolution and conservation of melanicDaphniapopulations in the Alps. Zool J Linn Soc 2014. [DOI: 10.1111/zoj.12151] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Adriana Bellati
- Department of Earth and Environmental Sciences; University of Pavia; Via Ferrata 9 27100 Pavia Italy
| | - Rocco Tiberti
- Department of Earth and Environmental Sciences; University of Pavia; Via Ferrata 9 27100 Pavia Italy
- Alpine Wildlife Research Centre; Gran Paradiso National Park; Degioz 11 11010 Valsavarenche Aosta Italy
| | - Walter Cocca
- Department of Earth and Environmental Sciences; University of Pavia; Via Ferrata 9 27100 Pavia Italy
| | - Andrea Galimberti
- ZooPlantLab; Department of Biotechnology and Biosciences; University of Milano-Bicocca; Piazza della Scienza 2 20126 Milano Italy
| | - Maurizio Casiraghi
- ZooPlantLab; Department of Biotechnology and Biosciences; University of Milano-Bicocca; Piazza della Scienza 2 20126 Milano Italy
| | - Giuseppe Bogliani
- Department of Earth and Environmental Sciences; University of Pavia; Via Ferrata 9 27100 Pavia Italy
| | - Paolo Galeotti
- Department of Earth and Environmental Sciences; University of Pavia; Via Ferrata 9 27100 Pavia Italy
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