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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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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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Weider LJ, Hobaek A, Colbourne JK, Crease TJ, Dufresne F, Hebert PDN. HOLARCTIC PHYLOGEOGRAPHY OF AN ASEXUAL SPECIES COMPLEX I. MITOCHONDRIAL DNA VARIATION IN ARCTIC DAPHNIA. Evolution 2017; 53:777-792. [DOI: 10.1111/j.1558-5646.1999.tb05372.x] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/1997] [Accepted: 02/04/1999] [Indexed: 11/30/2022]
Affiliation(s)
| | - Anders Hobaek
- Norwegian Institute for Water Research; Nordnesboder 5 N-5005 Bergen Norway
| | - John K. Colbourne
- Department of Zoology; University of Guelph; Guelph Ontario N1G 2W1 Canada
| | - Teresa J. Crease
- Department of Zoology; University of Guelph; Guelph Ontario N1G 2W1 Canada
| | - France Dufresne
- Département de Biologie; Université de Laval, Pavilion Vachon; Ste-Foy Québec G5L 3A1 Canada
| | - Paul D. N. Hebert
- Department of Zoology; University of Guelph; Guelph Ontario N1G 2W1 Canada
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Abstract
Polyploidy-the increase in the number of whole chromosome sets-is an important evolutionary force in eukaryotes. Polyploidy is well recognized throughout the evolutionary history of plants and animals, where several ancient events have been hypothesized to be drivers of major evolutionary radiations. However, fungi provide a striking contrast: while numerous recent polyploids have been documented, ancient fungal polyploidy is virtually unknown. We present a survey of known fungal polyploids that confirms the absence of ancient fungal polyploidy events. Three hypotheses may explain this finding. First, ancient fungal polyploids are indeed rare, with unique aspects of fungal biology providing similar benefits without genome duplication. Second, fungal polyploids are not successful in the long term, leading to few extant species derived from ancient polyploidy events. Third, ancient fungal polyploids are difficult to detect, causing the real contribution of polyploidy to fungal evolution to be underappreciated. We consider each of these hypotheses in turn and propose that failure to detect ancient events is the most likely reason for the lack of observed ancient fungal polyploids. We examine whether existing data can provide evidence for previously unrecognized ancient fungal polyploidy events but discover that current resources are too limited. We contend that establishing whether unrecognized ancient fungal polyploidy events exist is important to ascertain whether polyploidy has played a key role in the evolution of the extensive complexity and diversity observed in fungi today and, thus, whether polyploidy is a driver of evolutionary diversifications across eukaryotes. Therefore, we conclude by suggesting ways to test the hypothesis that there are unrecognized polyploidy events in the deep evolutionary history of the fungi.
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Dufresne F, Hebert PDN. Temperature-related differences in life-history characteristics between diploid and polyploid clones of the Daphnia pulex complex. ECOSCIENCE 2016. [DOI: 10.1080/11956860.1998.11682481] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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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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Rautio M, Dufresne F, Laurion I, Bonilla S, Vincent WF, Christoffersen KS. Shallow freshwater ecosystems of the circumpolar Arctic. ECOSCIENCE 2015. [DOI: 10.2980/18-3-3463] [Citation(s) in RCA: 160] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Milla Rautio
- Centre d'études nordiques and Département des sciences fondamentales, Université du Québec à Chicoutimi, Chicoutimi, Québec, Canada,
| | - France Dufresne
- Centre d'études nordiques and Département de biologie, chimie, géographie, Université du Québec à Rimouski, Rimouski, Québec, Canada
| | - Isabelle Laurion
- Centre d'études nordiques and INRS—Centre Eau Terre Environnement, Québec, Québec, Canada
| | - Sylvia Bonilla
- Grupo de Ecología y Fisiología de Fitoplancton, Sección Limnología, Facultad de Ciencias, 11400-Montevideo, Uruguay
| | - Warwick F. Vincent
- Centre d'études nordiques and Département de biologie, Université Laval, Québec, Québec, Canada
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Przytulska A, Bartosiewicz M, Rautio M, Dufresne F, Vincent WF. Climate Effects on High Latitude Daphnia via Food Quality and Thresholds. PLoS One 2015; 10:e0126231. [PMID: 25970289 PMCID: PMC4430472 DOI: 10.1371/journal.pone.0126231] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2014] [Accepted: 03/31/2015] [Indexed: 11/18/2022] Open
Abstract
Climate change is proceeding rapidly at high northern latitudes and may have a variety of direct and indirect effects on aquatic food webs. One predicted effect is the potential shift in phytoplankton community structure towards increased cyanobacterial abundance. Given that cyanobacteria are known to be a nutritionally poor food source, we hypothesized that such a shift would reduce the efficiency of feeding and growth of northern zooplankton. To test this hypothesis, we first isolated a clone of Daphnia pulex from a permafrost thaw pond in subarctic Québec, and confirmed that it was triploid but otherwise genetically similar to a diploid, reference clone of the same species isolated from a freshwater pond in southern Québec. We used a controlled flow-through system to investigate the direct effect of temperature and indirect effect of subarctic picocyanobacteria (Synechococcus) on threshold food concentrations and growth rate of the high latitude clone. We also compared the direct effect of temperature on both Daphnia clones feeding on eukaryotic picoplankton (Nannochloropsis). The high latitude clone had a significantly lower food threshold for growth than the temperate clone at both 18 and 26°C, implying adaptation to lower food availability even under warmer conditions. Polyunsaturated fatty acids were present in the picoeukaryote but not the cyanobacterium, confirming the large difference in food quality. The food threshold for growth of the high latitude Daphnia was 3.7 (18°C) to 4.2 (26°C) times higher when fed Synechococcus versus Nannochloropsis, and there was also a significant negative effect of increased temperature and cyanobacterial food on zooplankton fatty acid content and composition. The combined effect of temperature and food quality on the performance of the high latitude Daphnia was greater than their effects added separately, further indicating the potentially strong indirect effects of climate warming on aquatic food web processes.
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Affiliation(s)
- Anna Przytulska
- Centre d’études nordiques (CEN), Université Laval, Québec, Québec, Canada
- Département de biologie, Université Laval, Québec, Québec, Canada
- * E-mail:
| | - Maciej Bartosiewicz
- Centre d’études nordiques (CEN), Université Laval, Québec, Québec, Canada
- Centre Eau Terre Environnement, Institut National de la Recherche Scientifique, Québec, Québec, Canada
| | - Milla Rautio
- Centre d’études nordiques (CEN), Université Laval, Québec, Québec, Canada
- Department of Fundamental Sciences, Université du Québec à Chicoutimi, Chicoutimi, Québec, Canada
| | - France Dufresne
- Biology, Chemistry and Geography Department, Université du Québec à Rimouski, Rimouski, Québec, Canada
| | - Warwick F. Vincent
- Centre d’études nordiques (CEN), Université Laval, Québec, Québec, Canada
- Département de biologie, Université Laval, Québec, Québec, Canada
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Innes DJ, Ginn M. A population of sexual Daphnia pulex resists invasion by asexual clones. Proc Biol Sci 2015; 281:20140564. [PMID: 24943366 DOI: 10.1098/rspb.2014.0564] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Asexual reproduction avoids the costs associated with sex, predicting that invading asexual clones can quickly replace sexual populations. Daphnia pulex populations in the Great Lakes area are predominately asexual, but the elimination of sexual populations by invading clones is poorly understood. Asexual clones were detected at low frequency in one rare sexual population in 1995, with some increase in frequency during 2003 and 2004. However, these clones remained at low frequency during further yearly sampling (2005-2013) with no evidence that the resident sexual population was in danger of elimination. There was evidence for hybridization between rare males produced by asexual clones and sexual females with the potential to produce new asexual genotypes and spread the genetic factors for asexuality. In a short-term laboratory competition experiment, the two most common asexual clones did not increase in frequency relative to a genetically diverse sexual population due in part to a greater investment in diapausing eggs that trades-off current population growth for increased contribution to the egg bank. Our results suggest that a successful invasion can be prolonged, requiring a combination of clonal genotypes with high fitness, persistence of clones in the egg bank and negative factors affecting the sexual population such as inbreeding depression resulting from population bottlenecks.
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Affiliation(s)
- David J Innes
- Department of Biology, Memorial University, St John's, Newfoundland and Labrador, Canada A1B 3X9
| | - Michael Ginn
- Department of Biology, Memorial University, St John's, Newfoundland and Labrador, Canada A1B 3X9
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Vergilino R, Eagle SH, Crease TJ, Dufresne F. Impact of ploidy level on the distribution of Pokey element insertions in the Daphnia pulex complex. Mob DNA 2014; 5:1. [PMID: 24382139 PMCID: PMC3882798 DOI: 10.1186/1759-8753-5-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2013] [Accepted: 11/20/2013] [Indexed: 11/22/2022] Open
Abstract
Background Transposable elements (TEs) play a major role in genome evolution. Their capacity to move and/or multiply in the genome of their host may have profound impacts on phenotypes and dramatic consequences on genome structure. The population dynamics and distribution of TEs are influenced by their mode of transposition, the availability of niches in host genomes, and host population dynamics. Theories predict an increase in the number of TE insertions following hybridization or polyploidization. Evolution of TEs in hybrids and polyploids has mostly been studied in plants; few studies have examined the impacts of hybridization and/or polyploidization on TEs in animals. Hybrids and polyploids have arisen multiple times in the Daphnia pulex complex and are thought to reproduce by obligate parthenogenesis. Our study examines the effects of ploidy level on polymorphism and number of Pokey element insertions in diploid and polyploid hybrid isolates from the Daphnia pulex complex. Results The polymorphism of Pokey insertion sites did not depend solely on either the ploidy level or the genetic background of their host; therefore, it may be the result of interactions between these parameters and other parameters such as Pokey activity, selection and/or drift. No significant effect of ploidy level was found on the number of Pokey insertions using TE display and qPCR. However, the load of Pokey insertion sites and the number of unique insertion sites were slightly (but not significantly) higher in polyploids than in diploids. Conclusions These results suggest a lack of increase in the number of Pokey insertions following polyploidization but higher availability of Pokey insertion sites in polyploids than in diploids. Compared to previous TE display and qPCR results, the load of Pokey insertions in hybrid diploids was higher than in non-hybrid sexual and asexual diploids, which suggests an increase in the density of Pokey insertions following hybridization.
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Affiliation(s)
- Roland Vergilino
- Département de Biologie, Chimie et Géographie, Université du Québec à Rimouski, Rimouski, Québec G5L 3A1, Canada.
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11
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Marková S, Dufresne F, Manca M, Kotlík P. Mitochondrial capture misleads about ecological speciation in the Daphnia pulex complex. PLoS One 2013; 8:e69497. [PMID: 23869244 PMCID: PMC3711805 DOI: 10.1371/journal.pone.0069497] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2013] [Accepted: 06/11/2013] [Indexed: 11/18/2022] Open
Abstract
The North American ecological species Daphniapulicaria and Daphniapulex are thought to have diverged from a common ancestor by adaptation to sympatric but ecologically distinct lake and pond habitats respectively. Based on mtDNA relationships, European D. pulicaria is considered a different species only distantly related to its North American counterpart, but both species share a lactate dehydrogenase (Ldh) allele F supposedly involved in lake adaptation in North America, and the same allele is also carried by the related Holarctic Daphniatenebrosa. The correct inference of the species' ancestral relationships is therefore critical for understanding the origin of their adaptive divergence. Our species tree inferred from unlinked nuclear loci for D. pulicaria and D. pulex resolved the European and North American D. pulicaria as sister clades, and we argue that the discordant mtDNA gene tree is best explained by capture of D. pulex mtDNA by D. pulicaria in North America. The Ldh gene tree shows that F-class alleles in D. pulicaria and D. tenebrosa are due to common descent (as opposed to introgression), with D. tenebrosa alleles paraphyletic with respect to D. pulicaria alleles. That D. tenebrosa still segregates the ancestral and derived amino acids at the two sites distinguishing the pond and lake alleles suggests that D. pulicaria inherited the derived states from the D. tenebrosa ancestry. Our results suggest that some adaptations restricting the gene flow between D. pulicaria and D. pulex might have evolved in response to selection in ancestral environments rather than in the species' current sympatric habitats. The Arctic (D. tenebrosa) populations are likely to provide important clues about these issues.
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Affiliation(s)
- Silvia Marková
- Institute of Animal Physiology and Genetics, Laboratory of Molecular Ecology, Academy of Sciences of the Czech Republic, Liběchov, Czech Republic
| | - France Dufresne
- Département de Biologie, Centre d’Études Nordiques, Université du Québec à Rimouski, Québec, Canada
| | - Marina Manca
- CNR Istituto per lo Studio degli Ecosistemi, Verbania, Italy
| | - Petr Kotlík
- Institute of Animal Physiology and Genetics, Laboratory of Molecular Ecology, Academy of Sciences of the Czech Republic, Liběchov, Czech Republic
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Vergilino R, Elliott TA, Desjardins-Proulx P, Crease TJ, Dufresne F. Evolution of a transposon in Daphnia hybrid genomes. Mob DNA 2013; 4:7. [PMID: 23384095 PMCID: PMC3575242 DOI: 10.1186/1759-8753-4-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2012] [Accepted: 11/06/2012] [Indexed: 11/17/2022] Open
Abstract
Background Transposable elements play a major role in genome evolution. Their capacity to move and/or multiply in the genome of their host may have profound impacts on phenotypes, and may have dramatic consequences on genome structure. Hybrid and polyploid clones have arisen multiple times in the Daphnia pulex complex and are thought to reproduce by obligate parthenogenesis. Our study examines the evolution of a DNA transposable element named Pokey in the D. pulex complex. Results Portions of Pokey elements inserted in the 28S rRNA genes from various Daphnia hybrids (diploids and polyploids) were sequenced and compared to sequences from a previous study to understand the evolutionary history of the elements. Pokey sequences show a complex phylogenetic pattern. We found evidence of recombination events in numerous Pokey alleles from diploid and polyploid hybrids and also from non-hybrid diploids. The recombination rate in Pokey elements is comparable to recombination rates previously estimated for 28S rRNA genes in the congener, Daphnia obtusa. Some recombinant Pokey alleles were encountered in Daphnia isolates from multiple locations and habitats. Conclusions Phylogenetic and recombination analyses showed that recombination is a major force that shapes Pokey evolution. Based on Pokey phylogenies, reticulation has played and still plays an important role in shaping the diversity of the D. pulex complex. Horizontal transfer of Pokey seems to be rare and hybrids often possess Pokey elements derived from recombination among alleles encountered in the putative parental species. The insertion of Pokey in hotspots of recombination may have important impacts on the diversity and fitness of this transposable element.
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Affiliation(s)
- Roland Vergilino
- Department of Integrative Biology, University of Guelph, Science complex, N1G 2 W1, Guelph, ON, Canada.
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Collares-Pereira M, Matos I, Morgado-Santos M, Coelho M. Natural Pathways towards Polyploidy in Animals: TheSqualius alburnoidesFish Complex as a Model System to Study Genome Size and Genome Reorganization in Polyploids. Cytogenet Genome Res 2013; 140:97-116. [DOI: 10.1159/000351729] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
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Crease TJ, Floyd R, Cristescu ME, Innes D. Evolutionary factors affecting Lactate dehydrogenase A and B variation in the Daphnia pulex species complex. BMC Evol Biol 2011; 11:212. [PMID: 21767386 PMCID: PMC3231769 DOI: 10.1186/1471-2148-11-212] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2011] [Accepted: 07/18/2011] [Indexed: 11/29/2022] Open
Abstract
BACKGROUND Evidence for historical, demographic and selective factors affecting enzyme evolution can be obtained by examining nucleotide sequence variation in candidate genes such as Lactate dehydrogenase (Ldh). Two closely related Daphnia species can be distinguished by their electrophoretic Ldh genotype and habitat. Daphnia pulex populations are fixed for the S allele and inhabit temporary ponds, while D. pulicaria populations are fixed for the F allele and inhabit large stratified lakes. One locus is detected in most allozyme surveys, but genome sequencing has revealed two genes, LdhA and LdhB. RESULTS We sequenced both Ldh genes from 70 isolates of these two species from North America to determine if the association between Ldh genotype and habitat shows evidence for selection, and to elucidate the evolutionary history of the two genes. We found that alleles in the pond-dwelling D. pulex and in the lake-dwelling D. pulicaria form distinct groups at both loci, and the substitution of Glutamine (S) for Glutamic acid (F) at amino acid 229 likely causes the electrophoretic mobility shift in the LDHA protein. Nucleotide diversity in both Ldh genes is much lower in D. pulicaria than in D. pulex. Moreover, the lack of spatial structuring of the variation in both genes over a wide geographic area is consistent with a recent demographic expansion of lake populations. Neutrality tests indicate that both genes are under purifying selection, but the intensity is much stronger on LdhA. CONCLUSIONS Although lake-dwelling D. pulicaria hybridizes with the other lineages in the pulex species complex, it remains distinct ecologically and genetically. This ecological divergence, coupled with the intensity of purifying selection on LdhA and the strong association between its genotype and habitat, suggests that experimental studies would be useful to determine if variation in molecular function provides evidence that LDHA variants are adaptive.
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Affiliation(s)
- Teresa J Crease
- Department of Integrative Biology, University of Guelph, Guelph, Ontario N1G 2W1, Canada
| | - Robin Floyd
- Department of Integrative Biology, University of Guelph, Guelph, Ontario N1G 2W1, Canada
- School of Clinical Sciences, Southmead Hospital, University of Bristol, Bristol BS105NB, UK
| | - Melania E Cristescu
- Great Lakes Institute for Environmental Research, University of Windsor, Windsor, Ontario N9B 3P4, Canada
| | - David Innes
- Department of Biology, Memorial University of Newfoundland, St. John's, Newfoundland and Labrador A1B 3X9, Canada
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Mable BK, Alexandrou MA, Taylor MI. Genome duplication in amphibians and fish: an extended synthesis. J Zool (1987) 2011. [DOI: 10.1111/j.1469-7998.2011.00829.x] [Citation(s) in RCA: 173] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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Dufresne F, Marková S, Vergilino R, Ventura M, Kotlík P. Diversity in the reproductive modes of European Daphnia pulicaria deviates from the geographical parthenogenesis. PLoS One 2011; 6:e20049. [PMID: 21655327 PMCID: PMC3104988 DOI: 10.1371/journal.pone.0020049] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2011] [Accepted: 04/23/2011] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Multiple transitions to obligate parthenogenesis have occurred in the Daphnia pulex complex in North America. These newly formed asexual lineages are differentially distributed being found predominantly at high latitudes. This conforms to the rule of geographical parthenogenesis postulating prevalence of asexuals at high latitudes and altitudes. While the reproductive mode of high-latitude populations is relatively well studied, little is known about the reproduction mode in high altitudes. This study aimed to assess the reproductive mode of Daphnia pulicaria, a species of the D. pulex complex, from high altitude lakes in Europe. METHODOLOGY/PRINCIPAL FINDINGS Variation at eight microsatellite loci revealed that D. pulicaria from the High Tatra Mountains (HTM) had low genotype richness and showed excess of heterozygotes and significant deviations from Hardy-Weinberg expectations, and was thus congruent with reproduction by obligate parthenogenesis. By contrast, populations from the Pyrenees (Pyr) were generally in Hardy-Weinberg equilibrium and had higher genotypic richness, suggesting that they are cyclic parthenogens. Four lakes from lowland areas (LLaP) had populations with an uncertain or mixed breeding mode. All D. pulicaria had mtDNA ND5 haplotypes of the European D. pulicaria lineage. Pyr were distinct from LLaP and HTM at the ND5 gene. By contrast, HTM shared two haplotypes with LLaP and one with Pyr. Principal Coordinate Analysis of the microsatellite data revealed clear genetic differentiation into three groups. HTM isolates were intermediate to Pyr and LLaP, congruent with a hybrid origin. CONCLUSION/SIGNIFICANCE Inferred transitions to obligate parthenogenesis have occurred only in HTM, most likely as a result of hybridizations. In contrast to North American populations, these transitions do not appear to involve meiosis suppressor genes and have not been accompanied by polyploidy. The absence of obligate parthenogenesis in Pyr, an environment highly similar to the HTM, may be due to the lack of opportunities for hybridization.
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Affiliation(s)
- France Dufresne
- Département de Biologie, Centre d'Études Nordiques, Université du Québec à Rimouski, Rimouski, Québec, Canada.
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Vergilino R, Markova S, Ventura M, Manca M, Dufresne F. Reticulate evolution of the Daphnia pulex complex as revealed by nuclear markers. Mol Ecol 2011; 20:1191-207. [PMID: 21294799 DOI: 10.1111/j.1365-294x.2011.05004.x] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The study of species complexes is of particular interest to understand how evolutionary young species maintain genomic integrity. The Daphnia pulex complex has been intensively studied as it includes species that dominate freshwater environments in the Northern hemisphere and as it is the sole North American complex that shows transitions to obligate parthenogenesis. Past studies using mitochondrial markers have revealed the presence of 10 distinct lineages in the complex. This study is the first to examine genetic relationships among seven species of the complex at nuclear markers (nine microsatellite loci and one protein-coding gene). Clones belonging to the seven species of the Daphnia pulex complex were characterized at the mitochondrial NADH dehydrogenase (ND5) gene and at the Lactate dehydrogenase (LDH) locus. K-means, principal coordinate analyses and phylogenetic network analyses on the microsatellite data all separated European D. pulicaria, D. tenebrosa, North American D. pulex, D. pulicaria and their hybrids into distinct clusters. The hybrid cluster was composed of diploid and polyploid hybrids with D. pulex mitochondria and some clones with D. pulicaria mitochondria. By contrast, the phylogeny of the D. pulex complex using Rab4 was not well resolved but still showed clusters consisting mostly of D. pulex alleles and others of D. pulicaria alleles. Incomplete lineage sorting and hybridization may obscure genetic relationships at this locus. This study shows that hybridization and introgression have played an important role in the evolution of this complex.
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Affiliation(s)
- Roland Vergilino
- Département de Biologie, Centre d'Études Nordiques, Université du Québec à Rimouski, Québec, Canada
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19
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SHAFER AARONBA, CULLINGHAM CATHERINEI, CÔTÉ STEEVED, COLTMAN DAVIDW. Of glaciers and refugia: a decade of study sheds new light on the phylogeography of northwestern North America. Mol Ecol 2010; 19:4589-621. [PMID: 20849561 DOI: 10.1111/j.1365-294x.2010.04828.x] [Citation(s) in RCA: 261] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- AARON B. A. SHAFER
- Department of Biological Sciences, CW 405 Biological Sciences Building, University of Alberta, Edmonton, Alberta T6G 2E9, Canada
| | - CATHERINE I. CULLINGHAM
- Department of Biological Sciences, CW 405 Biological Sciences Building, University of Alberta, Edmonton, Alberta T6G 2E9, Canada
| | - STEEVE D. CÔTÉ
- Département de Biologie and Centre for Northern Studies, Université Laval, Québec, Québec G1V 0A6, Canada
| | - DAVID W. COLTMAN
- Department of Biological Sciences, CW 405 Biological Sciences Building, University of Alberta, Edmonton, Alberta T6G 2E9, Canada
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20
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VERGILINO ROLAND, BELZILE CLAUDE, DUFRESNE FRANCE. Genome size evolution and polyploidy in the Daphnia pulex complex (Cladocera: Daphniidae). Biol J Linn Soc Lond 2009. [DOI: 10.1111/j.1095-8312.2008.01185.x] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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21
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Adamowicz SJ, Petrusek A, Colbourne JK, Hebert PD, Witt JD. The scale of divergence: A phylogenetic appraisal of intercontinental allopatric speciation in a passively dispersed freshwater zooplankton genus. Mol Phylogenet Evol 2009; 50:423-36. [DOI: 10.1016/j.ympev.2008.11.026] [Citation(s) in RCA: 108] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2007] [Revised: 11/24/2008] [Accepted: 11/26/2008] [Indexed: 11/16/2022]
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22
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MERGEAY JOACHIM, AGUILERA XIMENA, DECLERCK STEVEN, PETRUSEK ADAM, HUYSE TINE, DE MEESTER LUC. The genetic legacy of polyploid BolivianDaphnia: the tropical Andes as a source for the North and South AmericanD. pulicariacomplex. Mol Ecol 2008; 17:1789-800. [DOI: 10.1111/j.1365-294x.2007.03679.x] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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23
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Colbourne JK, Crease TJ, Weider LJ, Hebert PDN, Duferesne F, Hobaek A. Phylogenetics and evolution of a circumarctic species complex (Cladocera: Daphnia pulex). Biol J Linn Soc Lond 2008. [DOI: 10.1111/j.1095-8312.1998.tb01146.x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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24
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Cryptic intercontinental colonization in water fleas Daphnia pulicaria inferred from phylogenetic analysis of mitochondrial DNA variation. Mol Phylogenet Evol 2007; 44:42-52. [DOI: 10.1016/j.ympev.2006.12.025] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2006] [Revised: 12/18/2006] [Accepted: 12/20/2006] [Indexed: 11/17/2022]
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25
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26
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Gómez-Zurita J, Funk DJ, Vogler AP. THE EVOLUTION OF UNISEXUALITY IN CALLIGRAPHA LEAF BEETLES: MOLECULAR AND ECOLOGICAL INSIGHTS ON MULTIPLE ORIGINS VIA INTERSPECIFIC HYBRIDIZATION. Evolution 2006. [DOI: 10.1111/j.0014-3820.2006.tb01110.x] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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27
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Gómez-Zurita J, Funk DJ, Vogler AP. THE EVOLUTION OF UNISEXUALITY IN CALLIGRAPHA LEAF BEETLES: MOLECULAR AND ECOLOGICAL INSIGHTS ON MULTIPLE ORIGINS VIA INTERSPECIFIC HYBRIDIZATION. Evolution 2006. [DOI: 10.1554/05-452.1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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28
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Penton EH, Hebert PDN, Crease TJ. Mitochondrial DNA variation in North American populations of Daphnia obtusa: continentalism or cryptic endemism? Mol Ecol 2004; 13:97-107. [PMID: 14653792 DOI: 10.1046/j.1365-294x.2003.02024.x] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The morphological stasis of many freshwater crustaceans has resulted in the prior delineation of cosmopolitan species and has been explained by their capacity for long-distance dispersal. This study examines the phylogeography of Daphnia obtusa, a cladoceran thought to be widespread in North America. However, sequence variation of the mitochondrial cytochrome c oxidase subunit I gene indicates that this taxon is composed of two morphologically cryptic species, designated D. obtusa NA1 and NA2. NA2 is restricted to the east, whereas NA1 is broadly distributed across the United States, and is subdivided into four phylogroups that show weak genetic differentiation over broad geographical areas, which likely reflects recent long-distance dispersal. The current distributions of the four phylogroups in NA1 can be explained by recent range expansion from different refugia following the last Pleistocene glacial advance. Interestingly, the mitochondrial phylogroups identified in this study do not correspond to lineages detected in a previous allozyme analysis. However, the latter groups are associated with a habitat shift suggesting that natural selection may have played a role in their divergence. The results of this and previous studies illustrate the complicated biogeographical history of freshwater cladocerans.
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Affiliation(s)
- E H Penton
- Department of Zoology, University of Guelph, Guelph, Ontario, N1G 2W1, Canada
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29
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ADAMOWICZ SARAHJ, HEBERT PAULDN, MARINONE MARÍACRISTINA. Species diversity and endemism in the Daphnia of Argentina: a genetic investigation. Zool J Linn Soc 2004. [DOI: 10.1111/j.1096-3642.2003.00089.x] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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30
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Weider LJ, Hobaek A. Glacial refugia, haplotype distributions, and clonal richness of the Daphnia pulex complex in arctic Canada. Mol Ecol 2003; 12:463-73. [PMID: 12535096 DOI: 10.1046/j.1365-294x.2003.01746.x] [Citation(s) in RCA: 56] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
As part of a large international Arctic biodiversity expedition (Tundra Northwest '99), we examined the distribution of members of the arctic Daphnia pulex complex (Cladocera, Anomopoda) from 121 tundra ponds, spread across 16 sites spanning a large portion of arctic Canada (i.e. from 62 degrees 22' N to 79 degrees 01' N; 66 degrees 45' W to 139 degrees 37' W). Using allozyme electrophoresis and mitochondrial (mt)DNA analyses, we examined the population genetic (clonal) structure of these populations. The following taxa were detected in this complex: Daphnia pulicaria, D. middendorffiana and D. tenebrosa. Clear geographical differences in mean clonal richness and diversity were observed, with most western sites exhibiting higher clonal richness and diversity, than sites in the eastern Canadian Arctic. For both the pulicaria group (i.e. D. pulicaria and D. middendorffiana) and D. tenebrosa, the highest mean regional clonal richness was detected from the southern section of Banks Island, an unglaciated site situated on the edge or directly in the eastern fringe of the Beringian glacial refuge. A significant negative correlation was found between geographical distance from the Beringian edge, and overall regional clonal richness (i.e. sites closer to the edge harboured greater clonal richness). These results clearly indicate that more recently deglaciated regions (i.e. eastern Canadian Arctic) harbour lower levels of clonal richness than western regions nearer Beringia. We discuss the role that glacial refugia have played in influencing both biotic and genetic diversity in arctic taxa.
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Affiliation(s)
- L J Weider
- University of Oklahoma Biological Station, HC-71, Box 205 Kingston, OK 73439, US, Norwegian Institute for Water Research, Bergen, Norway.
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31
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Jansson R, Dynesius M. The Fate of Clades in a World of Recurrent Climatic Change: Milankovitch Oscillations and Evolution. ACTA ACUST UNITED AC 2002. [DOI: 10.1146/annurev.ecolsys.33.010802.150520] [Citation(s) in RCA: 271] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Roland Jansson
- Landscape Ecology Group, Department of Ecology and Environmental Science, Umeå University, SE-901 87 Umeå, Sweden;
| | - Mats Dynesius
- Landscape Ecology Group, Department of Ecology and Environmental Science, Umeå University, SE-901 87 Umeå, Sweden;
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32
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Abstract
Determining the evolutionary age of asexual lineages should help in inferring the temporal scale under which asexuality and sex evolve and assessing selective factors involved in the evolution of asexuality. We used 416 bp of the mitochondrial COI gene to infer phylogenetic relationships of virtually all known Timema walkingstick species, including extensive intraspecific sampling for all five of the asexuals and their close sexual relatives. The asexuals T. douglasi and T. shepardii were very closely related to each other and evolutionarily young (less than 0.5 million years old). For the asexuals T. monikensis and T. tahoe, evidence for antiquity was weak since only one population of each was sampled, intraspecific divergences were low, and genetic distances to related sexuals were high: maximum-likelihood molecular-clock age estimates ranged from 0.26 to 2.39 million years in T. monikensis and from 0.29-1.06 million years in T. tahoe. By contrast, T. genevieve was inferred to be an ancient asexual, with an age of 0.81 to 1.42 million years. The main correlate of the age of asexual lineages was their geographic position, with younger asexuals being found further north.
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Affiliation(s)
- Jennifer H Law
- Department of Biosciences, Simon Fraser University, Burnaby, British Columbia, Canada.
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33
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Adamowicz SJ, Gregory TR, Marinone MC, Hebert PDN. New insights into the distribution of polyploid Daphnia: the Holarctic revisited and Argentina explored. Mol Ecol 2002; 11:1209-17. [PMID: 12074728 DOI: 10.1046/j.1365-294x.2002.01517.x] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
It has long been known that polyploid organisms are more prevalent in arctic than in temperate environments. Past explanations for this geographical trend have focused on the role of glacial cycles in generating polyploids and the influence of abiotic factors in favouring polyploidy in the north. In combination, these mechanisms probably suffice to explain the observed geographical cline in ploidy levels in members of the Daphnia pulex complex in the Holarctic. While only diploid members of the D. pulex complex are found in the temperate regions of North America and Europe, allozyme and DNA quantification analyses indicate that the southern Argentine pulex-complex fauna is dominated by polyploids. Indeed, the present study is the first to document the presence of polyploid members of the D. pulex complex in any temperate climate. The results of phylogeographic analyses suggest that this difference in polyploid distribution between the northern and southern hemispheres is based more on ecological and historical contingencies than direct selection for polyploidy. Specifically, competition with diploid relatives probably limits the lower latitudinal range of polyploids in the north, but appears not to have occurred in Argentina. Because of these differences, the present study provides important insights into the diverse factors that determine the distributions and evolutionary fates of polyploid organisms.
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Affiliation(s)
- Sarah J Adamowicz
- Department of Zoology, University of Guelph, Guelph, ON, Canada, N1G 2W1.
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35
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Hebert PD, Finston TL. Macrogeographic patterns of breeding system diversity in the Daphnia pulex group from the United States and Mexico. Heredity (Edinb) 2001; 87:153-61. [PMID: 11703505 DOI: 10.1046/j.1365-2540.2001.00885.x] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Studies on the biogeographical patterning of reproductive systems promise to extend understanding of the factors which modulate breeding system transitions. Two closely allied cladoceran crustaceans, Daphnia pulex and D. pulicaria, show varied modes of reproduction, with populations reproducing by either cyclic or obligate parthenogenesis. Prior studies have provided a detailed understanding of their breeding system diversity in the polar and cold temperate regions of North America. The present investigation extends this analysis, characterizing breeding systems and clonal diversity at sites throughout the United States and Mexico. Genotypic diversity in these southern areas was high, but only diploids were detected, indicating that polyploids are restricted to the north. F(1) hybrids and their two parental species were present in most areas, although their frequencies varied geographically. Hybrids invariably reproduced by obligate asexuality, but both parental taxa showed regional shifts in their breeding system. The complexity of these latter patterns suggests that they reflect the interplay of historical factors and selection.
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Affiliation(s)
- P D Hebert
- Department of Zoology, University of Guelph, Guelph, Ontario, Canada N1G 2 W1.
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36
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Johnson, Leefe. Clonal diversity and polyphyletic origins of hybrid and spontaneous parthenogenetic Campeloma (Gastropoda: Viviparidae) from the south-eastern United States. J Evol Biol 1999. [DOI: 10.1046/j.1420-9101.1999.00099.x] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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37
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Little TJ, Demelo R, Taylor DJ, Hebert PDN. Genetic characterization of an arctic
zooplankter
: insights into geographic polyploidy. Proc Biol Sci 1997. [DOI: 10.1098/rspb.1997.0189] [Citation(s) in RCA: 25] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- Tom J. Little
- Department of Zoology, University of Guelph, Ontario N1G 2W1, Canada
| | - Rita Demelo
- Department of Zoology, University of Guelph, Ontario N1G 2W1, Canada
| | - Derek J. Taylor
- Department of Zoology, University of Guelph, Ontario N1G 2W1, Canada
| | - Paul D. N. Hebert
- Department of Zoology, University of Guelph, Ontario N1G 2W1, Canada
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