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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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Snyman M, Xu S. Transcriptomics and the origin of obligate parthenogenesis. Heredity (Edinb) 2023; 131:119-129. [PMID: 37280308 PMCID: PMC10382572 DOI: 10.1038/s41437-023-00628-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Revised: 05/18/2023] [Accepted: 05/18/2023] [Indexed: 06/08/2023] Open
Abstract
Despite the presence of obligately parthenogenetic (OP) lineages derived from sexual ancestors in diverse phylogenetic groups, the genetic mechanisms giving rise to the OP lineages remain poorly understood. The freshwater microcrustacean Daphnia pulex typically reproduces via cyclical parthenogenesis. However, some populations of OP D. pulex have emerged due to ancestral hybridization and introgression events between two cyclically parthenogenetic (CP) species D. pulex and D. pulicaria. These OP hybrids produce both subitaneous and resting eggs parthenogenetically, deviating from CP isolates where resting eggs are produced via conventional meiosis and mating. This study examines the genome-wide expression and alternative splicing patterns of early subitaneous versus early resting egg production in OP D. pulex isolates to gain insight into the genes and mechanisms underlying this transition to obligate parthenogenesis. Our differential expression and functional enrichment analyses revealed a downregulation of meiosis and cell cycle genes during early resting egg production, as well as divergent expression patterns of metabolism, biosynthesis, and signaling pathways between the two reproductive modes. These results provide important gene candidates for future experimental verification, including the CDC20 gene that activates the anaphase-promoting complex in meiosis.
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Affiliation(s)
- Marelize Snyman
- Department of Biology, University of Texas at Arlington, Arlington, TX, 76019, USA
- Department of Dermatology, University of Texas Southwestern Medical Center, Dallas, TX, 75235, USA
| | - Sen Xu
- Department of Biology, University of Texas at Arlington, Arlington, TX, 76019, USA.
- Division of Biological Sciences, University of Missouri, Columbia, MO, 65211, USA.
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3
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Huynh TV, Hall AS, Xu S. The Transcriptomic Signature of Cyclical Parthenogenesis. Genome Biol Evol 2023; 15:evad122. [PMID: 37392457 PMCID: PMC10340444 DOI: 10.1093/gbe/evad122] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 06/13/2023] [Accepted: 06/28/2023] [Indexed: 07/03/2023] Open
Abstract
Cyclical parthenogenesis, where females can engage in sexual or asexual reproduction depending on environmental conditions, represents a novel reproductive phenotype that emerged during eukaryotic evolution. The fact that environmental conditions can trigger cyclical parthenogens to engage in distinct reproductive modes strongly suggests that gene expression plays a key role in the origin of cyclical parthenogenesis. However, the genetic basis underlying cyclical parthenogenesis remains understudied. In this study, we characterize the female transcriptomic signature of sexual versus asexual reproduction in the cyclically parthenogenetic microcrustacean Daphnia pulex and Daphnia pulicaria. Our analyses of differentially expressed genes (DEGs), pathway enrichment, and gene ontology (GO) term enrichment clearly show that compared with sexual reproduction, the asexual reproductive stage is characterized by both the underregulation of meiosis and cell cycle genes and the upregulation of metabolic genes. The consensus set of DEGs that this study identifies within the meiotic, cell cycle, and metabolic pathways serves as candidate genes for future studies investigating how the two reproductive cycles in cyclical parthenogenesis are mediated at a molecular level. Furthermore, our analyses identify some cases of divergent expression among gene family members (e.g., doublesex and NOTCH2) associated with asexual or sexual reproductive stage, suggesting potential functional divergence among gene family members.
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Affiliation(s)
- Trung Viet Huynh
- Department of Biology, University of Texas at Arlington, Arlington, Texas, USA
| | - Alexander S Hall
- Department of Biology, University of Texas at Arlington, Arlington, Texas, USA
| | - Sen Xu
- Department of Biology, University of Texas at Arlington, Arlington, Texas, USA
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4
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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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5
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Xu S, Huynh TV, Snyman M. The transcriptomic signature of obligate parthenogenesis. Heredity (Edinb) 2022; 128:132-138. [PMID: 35039663 PMCID: PMC8814003 DOI: 10.1038/s41437-022-00498-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 01/04/2022] [Accepted: 01/04/2022] [Indexed: 02/03/2023] Open
Abstract
Investigating the origin of parthenogenesis through interspecific hybridization can provide insight into how meiosis may be altered by genetic incompatibilities, which is fundamental for our understanding of the formation of reproductive barriers. Yet the genetic mechanisms giving rise to obligate parthenogenesis in eukaryotes remain understudied. In the microcrustacean Daphnia pulex species complex, obligately parthenogenetic (OP) isolates emerged as backcrosses of two cyclically parthenogenetic (CP) parental species, D. pulex and D. pulicaria, two closely related but ecologically distinct species. We examine the genome-wide expression in OP females at the early resting egg production stage, a life-history stage distinguishing OP and CP reproductive strategies, in comparison to CP females of the same stage from the two parental species. Our analyses of the expression data reveal that underdominant and overdominant genes are abundant in OP isolates, suggesting widespread regulatory incompatibilities between the parental species. More importantly, underdominant genes (i.e., genes with expression lower than both parentals) in the OP isolates are enriched in meiosis and cell-cycle pathways, indicating an important role of underdominance in the origin of obligate parthenogenesis. Furthermore, metabolic and biosynthesis pathways enriched with overdominant genes (i.e., expression higher than both parentals) are another genomic signature of OP isolates.
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Affiliation(s)
- Sen Xu
- Department of Biology, University of Texas at Arlington, Arlington, TX, 76019, USA.
| | - Trung V Huynh
- Department of Biology, University of Texas at Arlington, Arlington, TX, 76019, USA
| | - Marelize Snyman
- Department of Biology, University of Texas at Arlington, Arlington, TX, 76019, USA
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6
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Neupane S, Xu S. Adaptive Divergence of Meiotic Recombination Rate in Ecological Speciation. Genome Biol Evol 2021; 12:1869-1881. [PMID: 32857858 PMCID: PMC7594247 DOI: 10.1093/gbe/evaa182] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/24/2020] [Indexed: 02/06/2023] Open
Abstract
Theories predict that directional selection during adaptation to a novel habitat results in elevated meiotic recombination rate. Yet the lack of population-level recombination rate data leaves this hypothesis untested in natural populations. Here, we examine the population-level recombination rate variation in two incipient ecological species, the microcrustacean Daphnia pulex (an ephemeral-pond species) and Daphnia pulicaria (a permanent-lake species). The divergence of D. pulicaria from D. pulex involved habitat shifts from pond to lake habitats as well as strong local adaptation due to directional selection. Using a novel single-sperm genotyping approach, we estimated the male-specific recombination rate of two linkage groups in multiple populations of each species in common garden experiments and identified a significantly elevated recombination rate in D. pulicaria. Most importantly, population genetic analyses show that the divergence in recombination rate between these two species is most likely due to divergent selection in distinct ecological habitats rather than neutral evolution.
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Affiliation(s)
| | - Sen Xu
- Department of Biology, University of Texas at Arlington
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7
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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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8
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Moy I, Green M, Pham TP, Luu D, Xu S. The life-history fitness of F 1 hybrids of the microcrustacean Daphnia pulex and D. pulicaria (Crustacea, Anomopoda). INVERTEBRATE BIOLOGY : A QUARTERLY JOURNAL OF THE AMERICAN MICROSCOPICAL SOCIETY AND THE DIVISION OF INVERTEBRATE ZOOLOGY/ASZ 2021; 140:e12333. [PMID: 34366655 PMCID: PMC8341403 DOI: 10.1111/ivb.12333] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Negative interaction between alleles that arise independently in diverging populations (i.e., Dobzhansky-Muller incompatibilities) can cause reduction of fitness in their hybrids. However, heterosis in hybrids can emerge if hybridization breaks down detrimental epistatic interaction within parental lineages. In this study, we examined the life-history fitness of the inter-specific F1s of two recently diverged microcrustacean species Daphnia pulex and D. pulicaria as well as intra-specific crosses of D. pulex. We identified heterosis in two out of five life-history traits in the inter-specific F1s. According to theories that heterosis can transiently emerge in early speciation, the observation of heterosis in these life-history traits suggests that there are no major genetic incompatibilities between these two species affecting these traits and that D. pulex and D. pulicaria are at an early stage of speciation.
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Affiliation(s)
| | | | | | | | - Sen Xu
- Correspondence: 501 S. Nedderman Dr, Arlington, TX, 76019.
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9
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Chin TA, Cáceres CE, Cristescu ME. The evolution of reproductive isolation in Daphnia. BMC Evol Biol 2019; 19:216. [PMID: 31775606 PMCID: PMC6880586 DOI: 10.1186/s12862-019-1542-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Accepted: 11/15/2019] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The process by which populations evolve to become new species involves the emergence of various reproductive isolating barriers (RIB). Despite major advancements in understanding this complex process, very little is known about the order in which RIBs evolve or their relative contribution to the total restriction of gene flow during various stages of speciation. This is mainly due to the difficulties of studying reproductive isolation during the early stages of species formation. This study examines ecological and non-ecological RIB within and between Daphnia pulex and Daphnia pulicaria, two recently diverged species that inhabit distinct habitats and exhibit an unusual level of intraspecific genetic subdivision. RESULTS We find that while ecological prezygotic barriers are close to completion, none of the non-ecological barriers can restrict gene flow between D. pulex and D. pulicaria completely when acting alone. Surprisingly, we also identified high levels of postzygotic reproductive isolation in 'conspecific' interpopulation crosses of D. pulex. CONCLUSIONS While the ecological prezygotic barriers are prevalent during the mature stages of speciation, non-ecological barriers likely dominated the early stages of speciation. This finding indicates the importance of studying the very early stages of speciation and suggests the contribution of postzygotic isolation in initiating the process of speciation.
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Affiliation(s)
- Tiffany A Chin
- Department of Biology, McGill University, 1205 ave Docteur Penfield, Montreal, Quebec, H3A 1B1, Canada.
| | - Carla E Cáceres
- School of Integrative Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Melania E Cristescu
- Department of Biology, McGill University, 1205 ave Docteur Penfield, Montreal, Quebec, H3A 1B1, Canada
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10
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Abstract
Daphnia normally reproduce by cyclical parthenogenesis, with offspring sex being determined by environmental cues. However, some females have lost the ability to produce males. Our results demonstrate that this loss of male-producing ability is controlled by a dominant allele at a single locus. We identified the locus by comparing whole-genome sequences of 67 nonmale-producing (NMP) and 100 male-producing (MP) clones from 5 Daphnia pulex populations, revealing 132 NMP-linked SNPs and 59 NMP-linked indels within a single 1.1-Mb nonrecombining region on chromosome I. These markers include 7 nonsynonymous mutations, all of which are located within one unannotated protein-coding gene (gene 8960). Within this single gene, all of the marker-linked NMP haplotypes from different populations form a monophyletic clade, suggesting a single origin of the NMP phenotype, with the NMP haplotype originating by introgression from a sister species, Daphnia pulicaria Methyl farnesoate (MF) is the innate juvenile hormone in daphnids, which induces the production of males and whose inhibition results in female-only production. Gene 8960 is sensitive to treatment by MF in MP clones, but such responsiveness is greatly reduced in NMP clones. Thus, we hypothesize that gene 8960 is located downstream of the MF-signaling pathway in D. pulex, with the NMP phenotype being caused by expression change of gene 8960.
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11
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Abstract
Comparing genomes of closely related genotypes from populations with distinct demographic histories can help reveal the impact of effective population size on genome evolution. For this purpose, we present a high quality genome assembly of Daphnia pulex (PA42), and compare this with the first sequenced genome of this species (TCO), which was derived from an isolate from a population with >90% reduction in nucleotide diversity. PA42 has numerous similarities to TCO at the gene level, with an average amino acid sequence identity of 98.8 and >60% of orthologous proteins identical. Nonetheless, there is a highly elevated number of genes in the TCO genome annotation, with ∼7000 excess genes appearing to be false positives. This view is supported by the high GC content, lack of introns, and short length of these suspicious gene annotations. Consistent with the view that reduced effective population size can facilitate the accumulation of slightly deleterious genomic features, we observe more proliferation of transposable elements (TEs) and a higher frequency of gained introns in the TCO genome.
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12
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Abstract
The ability to appropriately respond to proteotoxic stimuli is a major determinant of longevity and involves induction of various heat shock response (HSR) genes, which are essential to cope with cellular and organismal insults throughout lifespan. The activity of NAD+-dependent deacetylase Sir2, originally discovered in yeast, is known to be essential for effective HSR and longevity. Our previous work on HSR inDaphnia pulicaria indicated a drastic reduction of the HSR in older organisms. In this report we investigate the role of Sir2 in regulating HSR during the lifespan of D. pulicaria. We cloned Daphnia Sir2 open reading frame (ORF) to characterize the enzyme activity and confirmed that the overall function of Sir2 was conserved in Daphnia. The Sir2 mRNA levels increased while the enzyme activity declined with age and considering that Sir2 activity regulates HSR, this explains the previously observed age-dependent decline in HSR. Finally, we tested the effect of Sir2 knockdown throughout adult life by using our new RNA interference (RNAi) method by feeding. Sir2 knockdown severely reduced both the median lifespan as well as significantly increased mortality following heat shock. Our study provides the first characterization and functional study of Daphnia Sir2.
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13
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Eagle SHC, Crease TJ. Distribution of the DNA transposon family, Pokey in the Daphnia pulex species complex. Mob DNA 2016; 7:11. [PMID: 27330569 PMCID: PMC4912750 DOI: 10.1186/s13100-016-0067-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2016] [Accepted: 06/13/2016] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND The Pokey family of DNA transposons consists of two putatively autonomous groups, PokeyA and PokeyB, and two groups of Miniature Inverted-repeat Transposable Elements (MITEs), mPok1 and mPok2. This TE family is unusual as it inserts into a specific site in ribosomal (r)DNA, as well as other locations in Daphnia genomes. The goals of this study were to determine the distribution of the Pokey family in lineages of the Daphnia pulex species complex, and to test the hypothesis that unusally high PokeyA number in some isolates of Daphnia pulicaria is the result of recent transposition. To do this, we estimated the haploid number of Pokey, mPok, and rRNA genes in 45 isolates from five Daphnia lineages using quantitative PCR. We also cloned and sequenced partial copies of PokeyA from four isolates of D. pulicaria. RESULTS Haploid PokeyA and PokeyB number is generally less than 20 and tends to be higher outside rDNA in four lineages. Conversely, the number of both groups is much higher outside rDNA (~120) in D. arenata, and PokeyB is also somewhat higher inside rDNA. mPok1 was only detected in D. arenata. mPok2 occurs both outside (~30) and inside rDNA (~6) in D. arenata, but was rare (≤2) outside rDNA in the other four lineages. There is no correlation between Pokey and rRNA gene number (mean = 240 across lineages) in any lineage. Variation among cloned partial PokeyA sequences is significantly higher in isolates with high number compared to isolates with an average number. CONCLUSIONS The high Pokey number outside rDNA in D. arenata and inside rDNA in some D. pulicaria isolates is consistent with a recent increase in transposition rate. The D. pulicaria increase may have been triggered by insertion of PokeyA into a region of transcriptionally active rDNA. The expansion in D. arenata (thought to be of hybrid origin) may be a consequence of release from epigenetic repression following hybridization. Previous work found D. obtusa to be very different from the D. pulex complex; mean PokeyA is higher in rDNA (~75), rDNA array size is nearly twice as large (415), and the two are positively correlated. The predominance of Pokey in only one location could be explained by purifying selection against ectopic recombination between elements inside and outside rDNA.
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Affiliation(s)
- Shannon H C Eagle
- Department of Integrative Biology, University of Guelph, Guelph, ON N1G 2 W1 Canada
| | - Teresa J Crease
- Department of Integrative Biology, University of Guelph, Guelph, ON N1G 2 W1 Canada
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14
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Athanasio CG, Chipman JK, Viant MR, Mirbahai L. Optimisation of DNA extraction from the crustacean Daphnia. PeerJ 2016; 4:e2004. [PMID: 27190714 PMCID: PMC4867708 DOI: 10.7717/peerj.2004] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2016] [Accepted: 04/12/2016] [Indexed: 11/20/2022] Open
Abstract
Daphnia are key model organisms for mechanistic studies of phenotypic plasticity, adaptation and microevolution, which have led to an increasing demand for genomics resources. A key step in any genomics analysis, such as high-throughput sequencing, is the availability of sufficient and high quality DNA. Although commercial kits exist to extract genomic DNA from several species, preparation of high quality DNA from Daphnia spp. and other chitinous species can be challenging. Here, we optimise methods for tissue homogenisation, DNA extraction and quantification customised for different downstream analyses (e.g., LC-MS/MS, Hiseq, mate pair sequencing or Nanopore). We demonstrate that if Daphnia magna are homogenised as whole animals (including the carapace), absorbance-based DNA quantification methods significantly over-estimate the amount of DNA, resulting in using insufficient starting material for experiments, such as preparation of sequencing libraries. This is attributed to the high refractive index of chitin in Daphnia's carapace at 260 nm. Therefore, unless the carapace is removed by overnight proteinase digestion, the extracted DNA should be quantified with fluorescence-based methods. However, overnight proteinase digestion will result in partial fragmentation of DNA therefore the prepared DNA is not suitable for downstream methods that require high molecular weight DNA, such as PacBio, mate pair sequencing and Nanopore. In conclusion, we found that the MasterPure DNA purification kit, coupled with grinding of frozen tissue, is the best method for extraction of high molecular weight DNA as long as the extracted DNA is quantified with fluorescence-based methods. This method generated high yield and high molecular weight DNA (3.10 ± 0.63 ng/µg dry mass, fragments >60 kb), free of organic contaminants (phenol, chloroform) and is suitable for large number of downstream analyses.
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Affiliation(s)
| | - James K Chipman
- School of Biosciences, University of Birmingham , Birmingham , United Kingdom
| | - Mark R Viant
- School of Biosciences, University of Birmingham , Birmingham , United Kingdom
| | - Leda Mirbahai
- School of Biosciences, University of Birmingham , Birmingham , United Kingdom
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15
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A Male-Specific Genetic Map of the Microcrustacean Daphnia pulex Based on Single-Sperm Whole-Genome Sequencing. Genetics 2015; 201:31-8. [PMID: 26116153 DOI: 10.1534/genetics.115.179028] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2015] [Accepted: 06/24/2015] [Indexed: 12/12/2022] Open
Abstract
Genetic linkage maps are critical for assembling draft genomes to a meaningful chromosome level and for deciphering the genomic underpinnings of biological traits. The estimates of recombination rates derived from genetic maps also play an important role in understanding multiple aspects of genomic evolution such as nucleotide substitution patterns and accumulation of deleterious mutations. In this study, we developed a high-throughput experimental approach that combines fluorescence-activated cell sorting, whole-genome amplification, and short-read sequencing to construct a genetic map using single-sperm cells. Furthermore, a computational algorithm was developed to analyze single-sperm whole-genome sequencing data for map construction. These methods allowed us to rapidly build a male-specific genetic map for the freshwater microcrustacean Daphnia pulex, which shows significant improvements compared to a previous map. With a total of mapped 1672 haplotype blocks and an average intermarker distance of 0.87 cM, this map spans a total genetic distance of 1451 Kosambi cM and comprises 90% of the resolved regions in the current Daphnia reference assembly. The map also reveals the mistaken mapping of seven scaffolds in the reference assembly onto chromosome II by a previous microsatellite map based on F2 crosses. Our approach can be easily applied to many other organisms and holds great promise for unveiling the intragenomic and intraspecific variation in the recombination rates.
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16
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Settepani V, Bechsgaard J, Bilde T. Low genetic diversity and strong but shallow population differentiation suggests genetic homogenization by metapopulation dynamics in a social spider. J Evol Biol 2014; 27:2850-5. [DOI: 10.1111/jeb.12520] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2014] [Revised: 09/26/2014] [Accepted: 09/27/2014] [Indexed: 01/10/2023]
Affiliation(s)
- V. Settepani
- Department of Bioscience; Aarhus University; Aarhus C Denmark
| | - J. Bechsgaard
- Department of Bioscience; Aarhus University; Aarhus C Denmark
| | - T. Bilde
- Department of Bioscience; Aarhus University; Aarhus C Denmark
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Schumpert C, Handy I, Dudycha JL, Patel RC. Relationship between heat shock protein 70 expression and life span in Daphnia. Mech Ageing Dev 2014; 139:1-10. [PMID: 24814302 DOI: 10.1016/j.mad.2014.04.001] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2013] [Revised: 04/23/2014] [Accepted: 04/29/2014] [Indexed: 10/25/2022]
Abstract
The longevity of an organism is directly related to its ability to effectively cope with cellular stress. Heat shock response (HSR) protects the cells against accumulation of damaged proteins after exposure to elevated temperatures and also in aging cells. To understand the role of Hsp70 in regulating life span of Daphnia, we examined the expression of Hsp70 in two ecotypes that exhibit strikingly different life spans. Daphnia pulicaria, the long lived ecotype, showed a robust Hsp70 induction as compared to the shorter lived Daphnia pulex. Interestingly, the short-lived D. pulex isolates showed no induction of Hsp70 at the mid point in their life span. In contrast to this, the long-lived D. pulicaria continued to induce Hsp70 expression at an equivalent age. We further show that the Hsp70 expression was induced at transcriptional level in response to heat shock. The transcription factor responsible for Hsp70 induction, heat shock factor-1 (HSF-1), although present in aged organisms did not exhibit DNA-binding capability. Thus, the decline of Hsp70 induction in old organisms could be attributed to a decline in HSF-1's DNA-binding activity. These results for the first time, present a molecular analysis of the relationship between HSR and life span in Daphnia.
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Affiliation(s)
- Charles Schumpert
- Department of Biological Sciences, University of South Carolina, Columbia, SC 29208, United States
| | - Indhira Handy
- Department of Biological Sciences, University of South Carolina, Columbia, SC 29208, United States
| | - Jeffry L Dudycha
- Department of Biological Sciences, University of South Carolina, Columbia, SC 29208, United States
| | - Rekha C Patel
- Department of Biological Sciences, University of South Carolina, Columbia, SC 29208, United States.
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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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19
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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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20
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Eagle SH, Crease TJ. Copy number variation of ribosomal DNA and Pokey transposons in natural populations of Daphnia. Mob DNA 2012; 3:4. [PMID: 22390386 PMCID: PMC3315735 DOI: 10.1186/1759-8753-3-4] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2011] [Accepted: 03/05/2012] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Despite their ubiquity and high diversity in eukaryotic genomes, DNA transposons are rarely encountered in ribosomal DNA (rDNA). In contrast, R-elements, a diverse group of non-LTR retrotransposons, specifically target rDNA. Pokey is a DNA transposon that targets a specific rDNA site, but also occurs in many other genomic locations, unlike R-elements. However, unlike most DNA transposons, Pokey has been a stable component of Daphnia genomes for over 100 million years. Here we use qPCR to estimate the number of 18S and 28S ribosomal RNA genes and Pokey elements in rDNA (rPokey), as well as other genomic locations (gPokey) in two species of Daphnia. Our goals are to estimate the correlation between (1) the number of 18S and 28S rRNA genes, (2) the number of 28S genes and rPokey, and (3) the number of rPokey and gPokey. In addition, we ask whether Pokey number and distribution in both genomic compartments are affected by differences in life history between D. pulex and D. pulicaria. RESULTS We found differences in 18S and 28S gene number within isolates that are too large to be explained by experimental variation. In general, Pokey number within isolates is modest (< 20), and most are gPokey. There is no correlation between the number of rRNA genes and rPokey, or between rPokey and gPokey. However, we identified three isolates with unusually high numbers of both rPokey and gPokey, which we infer is a consequence of recent transposition. We also detected other rDNA insertions (rInserts) that could be degraded Pokey elements, R- elements or the divergent PokeyB lineage recently detected in the Daphnia genome sequence. Unlike rPokey, rInserts are positively correlated with rRNA genes, suggesting that they are amplified by the same mechanisms that amplify rDNA units even though rPokey is not. Overall, Pokey frequency and distribution are similar in D. pulex and D. pulicaria suggesting that differences in life history have no impact on Pokey. CONCLUSIONS The possibility that many rDNA units do not contain a copy of both 18S and 28S genes suggests that rDNA is much more complicated than once thought, and warrants further study. In addition, the lack of correlation between rPokey, gPokey and rDNA unit numbers suggests that Pokey transposition rate is generally very low, and that recombination, in combination with natural selection, eliminates rPokey much faster than gPokey. Our results suggest that further research to determine the mechanisms by which Pokey has escaped complete inactivation by its host (the usual fate of DNA transposons), would provide important insights into transposon biology.
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Affiliation(s)
- Shannon Hc Eagle
- Department of Integrative Biology, University of Guelph, Guelph, ON N1G 2W1, Canada.
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Cristescu ME, Constantin A, Bock DG, Cáceres CE, Crease TJ. Speciation with gene flow and the genetics of habitat transitions. Mol Ecol 2012; 21:1411-22. [PMID: 22269101 DOI: 10.1111/j.1365-294x.2011.05465.x] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Whether speciation can advance to completion in the face of initially high levels of gene flow is a very controversial topic in evolutionary biology. Extensive gene exchange is generally considered to homogenize populations and counteract divergence. Moreover, the role of introgressive hybridization in evolution remains largely unexplored in animals, particularly in freshwater zooplankton in which allopatric speciation is considered to be the norm. Our work investigates the genetic structure of two young ecological species: the pond species, Daphnia pulex and the lake species, Daphnia pulicaria. Phylogenetic and population genetics analyses were conducted on mitochondrial NADH dehydrogenase 5 (ND5) gene, the nuclear Lactate dehydrogenase (Ldh) gene and 21 nuclear microsatellite markers in 416 individuals from habitats with various degrees of permanence. The strong and consistent phylogenetic discordance between nuclear and mitochondrial markers suggests a complex evolutionary history of multiple independent habitat transition events that involved hybridization and introgression between lake and pond Daphnia. On the other hand, the low level of contemporary gene flow between adjacent populations indicates the presence of effective habitat isolating barriers. The Daphnia system provides strong evidence for a divergence-with-gene flow speciation model that involves multiple habitat transition events.
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Affiliation(s)
- Melania E Cristescu
- Great Lakes Institute for Environmental Research, University of Windsor, Windsor, ON, Canada.
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22
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WALSER B, HAAG CR. Strong intraspecific variation in genetic diversity and genetic differentiation inDaphnia magna: the effects of population turnover and population size. Mol Ecol 2012; 21:851-61. [DOI: 10.1111/j.1365-294x.2011.05416.x] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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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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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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Costanzo KS, Taylor DJ. Rapid ecological isolation and intermediate genetic divergence in lacustrine cyclic parthenogens. BMC Evol Biol 2010; 10:166. [PMID: 20525388 PMCID: PMC2895610 DOI: 10.1186/1471-2148-10-166] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2009] [Accepted: 06/05/2010] [Indexed: 11/18/2022] Open
Abstract
Background Ecological shifts can promote rapid divergence and speciation. However, the role of ecological speciation in animals that reproduce predominantly asexually with periodic sex and strong dispersal, such as lacustrine cladocerans, is poorly understood. These life history traits may slow or prevent ecological lineage formation among populations. Proponents of the postglacial ecological isolation hypothesis for Daphnia suggest that some species have formed postglacially in adjacent, but ecologically different habitats. We tested this hypothesis with ecological, morphological, and multilocus coalescence analyses in the putative lacustrine sister species, Daphnia parvula and Daphnia retrocurva. Results Daphnia parvula and D. retrocurva showed strong habitat separation with rare co-occurrence. Lakes inhabited by D. parvula were smaller in size and contained lower densities of invertebrate predators compared to lakes containing D. retrocurva. In the laboratory, D. retrocurva was less vulnerable to invertebrate predation, whereas D. parvula was less vulnerable to vertebrate predation and was smaller and more transparent than D. retrocurva. The species are significantly differentiated at mitochondrial and nuclear loci and form an intermediate genetic divergence pattern between panmixia and reciprocal monophyly. Coalescence and population genetic modelling indicate a Late or Post Glacial time of divergence with a demographic expansion. Conclusions Despite their young age and mixed breeding system, D. parvula and D. retrocurva exhibit significant ecological and genetic divergence that is coincident with the formation of deep temperate glacial lakes. We propose that predation may have facilitated the rapid divergence between D. parvula and D. retrocurva and that intermediate divergence of aquatic cyclic parthenogens is likely more common than previously thought.
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Affiliation(s)
- Katie S Costanzo
- Department of Biological Sciences, The State University of New York at Buffalo, Buffalo, NY 14260, USA.
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