1
|
Choi TJ, Malik A, Han SM, Kim CB. Differences in alternative splicing events in the adaptive strategies of two Daphnia galeata genotypes induced by fish kairomones. BMC Genomics 2024; 25:725. [PMID: 39060996 PMCID: PMC11282837 DOI: 10.1186/s12864-024-10643-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2024] [Accepted: 07/19/2024] [Indexed: 07/28/2024] Open
Abstract
BACKGROUND Daphnia galeata is a suitable model organism for investigating predator-induced defense. Genes and pathways exhibiting differential expression between fish kairomone-treated and untreated groups in D. galeata have been identified. However, understanding of the significance of alternative splicing, a crucial process of the regulation of gene expression in eukaryotes, to this mechanism remains limited. This study measured life-history traits and conducted short-read RNA sequencing and long-read isoform sequencing of two Korean D. galeata genotypes (KB1 and KE2) to uncover the genetic mechanism underlying their phenotypic plasticity under predation stress. RESULTS KB1 exhibited strategies to enhance fertility and decrease body length when exposed to fish kairomones, while KE2 deployed an adaptive strategy to increase body length. Full-length transcriptomes from KB1 and KE2 yielded 65,736 and 57,437 transcripts, respectively, of which 32 differentially expressed transcripts (DETs) were shared under predation stress across both genotypes. Prominent DETs common to both genotypes were related to energy metabolism and the immune system. Additionally, differential alternative splicing (DAS) events were detected in both genotypes in response to fish kairomones. DAS genes shared between both genotypes may indicate their significant role in the post-transcriptional stress response to fish predation. Calpain-3, involved in digestion and nutrient absorption, was identified as a DAS gene in both genotypes when exposed to fish kairomones. In addition, the gene encoding thymosin beta, which is related to growth, was found to be a statistically significant DAS only in KB1, while that encoding ultraspiracle protein, also associated with growth, was only identified in KE2. Moreover, transcripts encoding proteins such as EGF-like domain-containing protein, vitellogenin fused with superoxide dismutase, and others were identified overlapping between DAS events and DETs and potentially elucidating their association with the observed phenotypic variation in each genotype. CONCLUSIONS Our findings highlight the crucial role of alternative splicing in modulating transcriptome landscape under predation stress in D. galeata, emphasizing the requirement for integrating gene expression and splicing analyses in evolutionary adaptation studies.
Collapse
Affiliation(s)
- Tae-June Choi
- Department of Biotechnology, Sangmyung University, Seoul, 03016, Korea
| | - Adeel Malik
- Institute of Intelligence Informatics Technology, Sangmyung University, Seoul, 03016, Korea
| | - Seung-Min Han
- Department of Biotechnology, Sangmyung University, Seoul, 03016, Korea
| | - Chang-Bae Kim
- Department of Biotechnology, Sangmyung University, Seoul, 03016, Korea.
| |
Collapse
|
2
|
Goodman J, Brand J, Laptev G, Auld SKJR. Radiation‐mediated supply of genetic variation outweighs the effects of selection and drift in Chernobyl
Daphnia
populations. J Evol Biol 2022; 35:413-422. [PMID: 35048452 PMCID: PMC9303301 DOI: 10.1111/jeb.13983] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Revised: 12/20/2021] [Accepted: 12/21/2021] [Indexed: 11/27/2022]
Affiliation(s)
- Jessica Goodman
- Biological & Environmental Sciences University of Stirling Stirling United Kingdom
| | - June Brand
- Biological & Environmental Sciences University of Stirling Stirling United Kingdom
| | | | - Stuart K. J. R. Auld
- Biological & Environmental Sciences University of Stirling Stirling United Kingdom
| |
Collapse
|
3
|
Loria A, Cristescu ME, Gonzalez A. Genotype diversity promotes the persistence of Daphnia populations exposed to severe copper stress. J Evol Biol 2022; 35:265-277. [PMID: 35000231 DOI: 10.1111/jeb.13979] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2021] [Revised: 12/15/2021] [Accepted: 12/20/2021] [Indexed: 11/29/2022]
Abstract
When environmental stressors of high intensity are sustained for long periods of time, populations face high probabilities of being extirpated. However, depending on the intensity of the stressor, large populations with sufficient genetic diversity may persist. We report the results of an experiment that tracked the persistence of Daphnia populations exposed to copper contamination. We assessed whether genotypic diversity reduced the risk of extinction. We created monoclonal and multiclonal populations and monitored their population sizes during a 32-week experiment. Cu was applied at a sub-lethal concentration and then increased every week until the population sizes dropped to about 10% of the carrying capacity (Cu at 180 μg/L). The concentration was then increased up to 186 μg/L and held stable until the end of the experiment. A survival analysis showed that clonal diversity extended the persistence of Daphnia populations, but copper contamination caused a substantial genetic erosion followed by population extirpation. However, some Cu-treated populations, mostly multiclonal, showed U-shaped patterns of growth consistent with evolutionary rescue but these did not lead to lasting population recovery. These results highlight the importance of genetic variation for population persistence, but they also show how quickly it can be lost in contaminated environments.
Collapse
Affiliation(s)
| | | | - Andrew Gonzalez
- Department of Biology, McGill University, Montreal, QC, Canada
| |
Collapse
|
4
|
Nickel J, Schell T, Holtzem T, Thielsch A, Dennis SR, Schlick-Steiner BC, Steiner FM, Möst M, Pfenninger M, Schwenk K, Cordellier M. Hybridization Dynamics and Extensive Introgression in the Daphnia longispina Species Complex: New Insights from a High-Quality Daphnia galeata Reference Genome. Genome Biol Evol 2021; 13:6448229. [PMID: 34865004 PMCID: PMC8695838 DOI: 10.1093/gbe/evab267] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/24/2021] [Indexed: 01/02/2023] Open
Abstract
Hybridization and introgression are recognized as an important source of variation that influence adaptive processes; both phenomena are frequent in the genus Daphnia, a keystone zooplankton taxon in freshwater ecosystems that comprises several species complexes. To investigate genome-wide consequences of introgression between species, we provide here the first high-quality genome assembly for a member of the Daphnia longispina species complex, Daphnia galeata. We further resequenced 49 whole genomes of three species of the complex and their interspecific hybrids both from genotypes sampled in the water column and from single resting eggs extracted from sediment cores. Populations from habitats with diverse ecological conditions offered an opportunity to study the dynamics of hybridization linked to ecological changes and revealed a high prevalence of hybrids. Using phylogenetic and population genomic approaches, we provide first insights into the intra- and interspecific genome-wide variability in this species complex and identify regions of high divergence. Finally, we assess the length of ancestry tracts in hybrids to characterize introgression patterns across the genome. Our analyses uncover a complex history of hybridization and introgression reflecting multiple generations of hybridization and backcrossing in the Daphnia longispina species complex. Overall, this study and the new resources presented here pave the way for a better understanding of ancient and contemporary gene flow in the species complex and facilitate future studies on resting egg banks accumulating in lake sediment.
Collapse
Affiliation(s)
- Jana Nickel
- Institute of Zoology, Universität Hamburg, Germany
| | - Tilman Schell
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Frankfurt am Main, Germany
| | - Tania Holtzem
- Department of Ecology, University of Innsbruck, Austria
| | - Anne Thielsch
- Molecular Ecology, Institute for Environmental Sciences, University Koblenz-Landau, Landau in der Pfalz, Germany
| | - Stuart R Dennis
- Department of Aquatic Ecology, EAWAG, Dübendorf, Switzerland
| | | | | | - Markus Möst
- Department of Ecology, University of Innsbruck, Austria
| | - Markus Pfenninger
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Frankfurt am Main, Germany.,Molecular Ecology, Senckenberg Biodiversity and Climate Research Centre, Frankfurt, Germany.,IoME, Gutenberg University, Mainz, Germany
| | - Klaus Schwenk
- Molecular Ecology, Institute for Environmental Sciences, University Koblenz-Landau, Landau in der Pfalz, Germany
| | | |
Collapse
|
5
|
Zuykova EI, Bochkarev NA, Kotov AA. Specific and Genetic Structure of the Daphnia longispina s. l. Complex (Cladocera, Daphniidae) in Water Bodies of Southern Siberia. BIOL BULL+ 2021. [DOI: 10.1134/s1062359021070323] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
|
6
|
Abstract
Desert aquatic systems are widely separated, lack hydrologic connections, and are subject to drought. However, they provide unique settings to investigate distributional patterns of micrometazoans, including rotifers. Thus, to understand rotifer biodiversity we sampled 236 sites across an array of habitats including rock pools, springs, tanks, flowing waters, playas, lakes, and reservoirs in the Chihuahuan Desert of the USA (n = 202) and Mexico (n = 34) over a period of >20 years. This allowed us to calculate diversity indices and examine geographic patterns in rotifer community composition. Of ~1850 recognized rotifer species, we recorded 246 taxa (~13%), with greatest diversity in springs (n = 175), lakes (n = 112), and rock pools (n = 72). Sampling effort was positively related to observed richness in springs, lakes, rivers, and tanks. Nestedness analyses indicated that rotifers in these sites, and most subsets thereof, were highly nested (support from 4 null models). Distance was positively correlated with species composition dissimilarity on small spatial scales. We predicted species richness for unsampled locations using empirical Bayesian kriging. These findings provide a better understanding of regional rotifer diversity in aridlands and provide information on potential biodiversity hotspots for aquatic scientists and resource managers.
Collapse
|
7
|
Unexpected endemism in the Daphnia longispina complex (Crustacea: Cladocera) in Southern Siberia. PLoS One 2019; 14:e0221527. [PMID: 31479467 PMCID: PMC6719860 DOI: 10.1371/journal.pone.0221527] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Accepted: 08/09/2019] [Indexed: 02/01/2023] Open
Abstract
The biological significance of regional cladoceran morphotypes in the montane regions of the central Palearctic remains poorly understood. In the Holarctic Daphnia longispina complex (Cladocera: Daphniidae), several variants, lineages and species have been proposed as endemic for Southern Siberia. Daphnia turbinata Sars, for example, named after its unusual head shape, is known only from Southern Siberia. Here we sequence DNA of Daphnia from three mitochondrial genes (12S rRNA, 16S rRNA, and NADH dehydrogenase subunit 2, ND2) from 57 localities in Russia and Mongolia (the majority being from Southern Siberia) and place them in evolutionary context with existing data. Our aim was to examine regional endemism of the Daphnia longispina complex in Southern Siberian; to improve the phylogenetic understanding with improved taxonomic and regional sampling, and to better understand the influence of Pleistocene glaciation on the biogeography of these lineages. At least three lineages showed genetic evidence for endemism in Southern Siberia. There was strong support for D. turbinata as a sister lineage to to D. longispina/D. dentifera. Another endemic, Siberian D. cf. longispina, is a sister group to the longispina group in general. Within D. longispina s. str. there was an endemic Siberian clade with a western range boundary near the Yenisei River Basin. Gene flow estimates among populations (based on FST values) were very low for clades of D. longispina on a regional (the original 12S dataset), and on a pan-Eurasian (the extended 12S dataset) scale. Negative values of Fu’s FS and Tajima’s D tests prevailed for the species examined with significant values found for two D. longispina clades, D. dentifera, D. galeata and D. cristata. Our results support the notion that Southern Siberia is an important biogeographic region for cladocerans as it contained unexpected diversity of endemics (such as D. turbinata, D. cf. longispina and lineages of D. umbra and D. longsipina s.str.) and from being the geographic meeting place of expanding postglacial lineages from eastern and western refugia.
Collapse
|
8
|
Ravindran SP, Herrmann M, Cordellier M. Contrasting patterns of divergence at the regulatory and sequence level in European Daphnia galeata natural populations. Ecol Evol 2019; 9:2487-2504. [PMID: 30891195 PMCID: PMC6405927 DOI: 10.1002/ece3.4894] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2018] [Revised: 12/05/2018] [Accepted: 12/13/2018] [Indexed: 12/30/2022] Open
Abstract
Understanding the genetic basis of local adaptation has long been a focus of evolutionary biology. Recently, there has been increased interest in deciphering the evolutionary role of Daphnia's plasticity and the molecular mechanisms of local adaptation. Using transcriptome data, we assessed the differences in gene expression profiles and sequences in four European Daphnia galeata populations. In total, ~33% of 32,903 transcripts were differentially expressed between populations. Among 10,280 differentially expressed transcripts, 5,209 transcripts deviated from neutral expectations and their population-specific expression pattern is likely the result of local adaptation processes. Furthermore, a SNP analysis allowed inferring population structure and distribution of genetic variation. The population divergence at the sequence level was comparatively higher than the gene expression level by several orders of magnitude consistent with strong founder effects and lack of gene flow between populations. Using sequence homology, the candidate transcripts were annotated using a comparative genomics approach. Additionally, we also performed a weighted gene co-expression analysis to identify population-specific regulatory patterns of transcripts in D. galeata. Thus, we identified candidate transcriptomic regions for local adaptation in this key species of aquatic ecosystems in the absence of any laboratory-induced stressor.
Collapse
Affiliation(s)
| | - Maike Herrmann
- Department of Veterinary MedicinePaul‐Ehrlich‐InstitutLangenGermany
| | | |
Collapse
|
9
|
Ma X, Hu W, Smilauer P, Yin M, Wolinska J. Daphnia galeata
and D. dentifera
are geographically and ecologically separated whereas their hybrids occur in intermediate habitats: A survey of 44 Chinese lakes. Mol Ecol 2019; 28:785-802. [DOI: 10.1111/mec.14991] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2017] [Revised: 11/21/2018] [Accepted: 12/14/2018] [Indexed: 12/25/2022]
Affiliation(s)
- Xiaolin Ma
- MOE Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Science; Fudan University; Shanghai China
| | - Wei Hu
- MOE Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Science; Fudan University; Shanghai China
| | - Petr Smilauer
- Department of Ecosystem Biology, Faculty of Science; University of South Bohemia; Ceske Budejovice Czech Republic
| | - Mingbo Yin
- MOE Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Science; Fudan University; Shanghai China
| | - Justyna Wolinska
- Department of Ecosystem Research; Leibniz-Institute of Freshwater Ecology and Inland Fisheries; Berlin Germany
- Department of Biology, Chemistry, Institute of Biology; Freie Universität Berlin; Berlin Germany
| |
Collapse
|
10
|
Zuykova EI, Simonov EP, Bochkarev NA, Abramov SA, Sheveleva NG, Kotov AA. Contrasting phylogeographic patterns and demographic history in closely related species of Daphnia longispina group (Crustacea: Cladocera) with focus on North-Eastern Eurasia. PLoS One 2018; 13:e0207347. [PMID: 30427905 PMCID: PMC6235318 DOI: 10.1371/journal.pone.0207347] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2018] [Accepted: 10/30/2018] [Indexed: 12/11/2022] Open
Abstract
Species with large geographic distributions present a challenge for phylogeographic studies due to the logistic difficulties of obtaining adequate samples. Daphnia O.F. Müller (Anomopoda: Daphniidae) is a model genus for evolutionary biology and ecology, but many regions such as the remote areas of Siberia, remain poorly studied. Here we examined genetic polymorphism in the ribosomal 12S and the protein-coding ND2 mitochondrial genes of three closely related taxa of the Daphnia (Daphnia) longispina complex, namely D. galeata Sars, D. longispina O.F. Müller and D. dentifera Forbes. We estimated the phylogenetic relationships among these taxa based on a concatenated alignment of these two genes. Using sequences from the present study and those available in GenBank, we investigated the geographic distributions of the mitochondrial haplotypes of these species and proposed an evolutionary scenario for each taxon. Network structures, haplotype distribution patterns, and FST values indicated significant differences in the evolutionary history of the examined species. Our analysis of D. galeata populations confirmed its recent and fast expansion, without a previous phase of a strong population disconnection. In contrast, the high haplotype diversity in D. dentifera and D. longispina could be explained by the survival of different phylogroups in several glacial refugia located in different geographic regions. For all studied species, maximum haplotype diversity was recorded in the remote regions of Siberia-lakes of the Yenisei River and Transbaikalia. Our study is an important step in our understanding of the evolutionary history of the Daphnia longispina group and provides further evidence of the biogeographic significance of Siberia for freshwater taxa.
Collapse
Affiliation(s)
- Elena I. Zuykova
- Laboratory for Ecology of Vertebrate Communities, Institute of Systematics and Ecology of Animals of Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Evgeniy P. Simonov
- Laboratory for Ecology of Vertebrate Communities, Institute of Systematics and Ecology of Animals of Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Nickolai A. Bochkarev
- Laboratory for Ecology of Vertebrate Communities, Institute of Systematics and Ecology of Animals of Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Sergey A. Abramov
- Laboratory for Ecology of Vertebrate Communities, Institute of Systematics and Ecology of Animals of Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Natalia G. Sheveleva
- Laboratory of Biology of Aquatic Invertebrates, Limnological Institute of Siberian Branch of the Russian Academy of Sciences, Irkutsk, Russia
| | - Alexey A. Kotov
- Laboratory of Aquatic Ecology and Invasions, A.N. Severtsov Institute of Ecology and Evolution of Russian Academy of Sciences, Moscow, Russia
| |
Collapse
|
11
|
Yin M, Wang X, Ma X, Gießler S, Petrusek A, Griebel J, Hu W, Wolinska J. Cytonuclear diversity and shared mitochondrial haplotypes among Daphnia galeata populations separated by seven thousand kilometres. BMC Evol Biol 2018; 18:130. [PMID: 30176793 PMCID: PMC6122193 DOI: 10.1186/s12862-018-1256-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2017] [Accepted: 08/27/2018] [Indexed: 01/16/2023] Open
Abstract
BACKGROUND The zooplanktonic cladocerans Daphnia, present in a wide range of water bodies, are an important component of freshwater ecosystems. In contrast to their high dispersal capacity through diapausing eggs carried by waterfowl, Daphnia often exhibit strong population genetic differentiation. Here, to test for common patterns in the population genetic structure of a widespread Holarctic species, D. galeata, we genotyped two sets of populations collected from geographically distant areas: across 13 lakes in Eastern China and 14 lakes in Central Europe. The majority of these populations were genotyped at two types of markers: a mitochondrial gene (for 12S rRNA) and 15 nuclear microsatellite loci. RESULTS Mitochondrial DNA demonstrated relatively shallow divergence within D. galeata, with distinct haplotype compositions in the two study regions but one widely distributed haplotype shared between several of the Chinese as well as European populations. At microsatellite markers, clear separation was observed at both large (between China and Europe) and small (within Europe) geographical scales, as demonstrated by Factorial Correspondence Analyses, Bayesian assignment and a clustering method based on genetic distances. Genetic diversity was comparable between the sets of Chinese and European D. galeata populations for both types of markers. Interestingly, we observed a significant association between genetic distance and geographical distance for D. galeata populations in China but not in Europe. CONCLUSIONS Our results indicate relatively recent spread of D. galeata across wide expanses of the Palaearctic, with one mtDNA lineage of D. galeata successfully establishing over large distances. Despite a clear differentiation of Chinese and European D. galeata at a nuclear level, the pattern of genetic variation is nevertheless similar between both regions. Overall, our findings provide insights into the genetic population structure of a cladoceran species with extremely wide geographical range.
Collapse
Affiliation(s)
- Mingbo Yin
- MOE Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Science, Fudan University, Songhu Road, Shanghai, 2005, China.
| | - Xiaoyu Wang
- MOE Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Science, Fudan University, Songhu Road, Shanghai, 2005, China
| | - Xiaolin Ma
- MOE Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Science, Fudan University, Songhu Road, Shanghai, 2005, China
| | - Sabine Gießler
- Department Biologie II, Aquatic Evolutionary Ecology, Ludwig-Maximilians-Universität, Großhaderner Str. 2, 82152 Planegg-, Martinsried, Germany
| | - Adam Petrusek
- Faculty of Science, Department of Ecology, Charles University, Viničná 7, 12844, Prague, Czechia
| | - Johanna Griebel
- Leibniz-Institute of Freshwater Ecology and Inland Fisheries, Department of Ecosystem Research, Mueggelseedamm 301, 12587, Berlin, Germany
| | - Wei Hu
- MOE Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Science, Fudan University, Songhu Road, Shanghai, 2005, China
| | - Justyna Wolinska
- Leibniz-Institute of Freshwater Ecology and Inland Fisheries, Department of Ecosystem Research, Mueggelseedamm 301, 12587, Berlin, Germany.,Department of Biology, Chemistry, Pharmacy, Institute of Biology, Freie Universität Berlin, Konigin-Luise-Str. 1-3, 14195, Berlin, Germany
| |
Collapse
|
12
|
Zuykova EI, Simonov EP, Bochkarev NA, Taylor DJ, Kotov AA. Resolution of the Daphnia umbra problem (Crustacea: Cladocera) using an integrated taxonomic approach. Zool J Linn Soc 2018. [DOI: 10.1093/zoolinnean/zly015] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Affiliation(s)
- Elena I Zuykova
- Institute of Systematics and Ecology of Animals, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Evgeniy P Simonov
- Institute of Systematics and Ecology of Animals, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
- Siberian Federal University, Svobodny pr., Krasnoyarsk, Russia
| | - Nikolay A Bochkarev
- Institute of Systematics and Ecology of Animals, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Derek J Taylor
- Department of Biological Sciences, The State University of New York at Buffalo, Buffalo, NY, USA
| | - Alexey A Kotov
- A. N. Severtsov Institute of Ecology and Evolution, Leninsky Prospect, Moscow, Russia
- Kazan Federal University, Kazan, Russia
| |
Collapse
|
13
|
Xu L, Lin Q, Xu S, Gu Y, Hou J, Liu Y, Dumont HJ, Han B. Daphnia diversity on the Tibetan Plateau measured by DNA taxonomy. Ecol Evol 2018; 8:5069-5078. [PMID: 29876082 PMCID: PMC5980554 DOI: 10.1002/ece3.4071] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2017] [Revised: 03/25/2018] [Accepted: 03/26/2018] [Indexed: 02/04/2023] Open
Abstract
Daphnia on the Tibetan Plateau has been little studied, and information on species diversity and biogeography is lacking. Here, we conducted a 4-year survey using the barcoding fragment of the mitochondrial COI gene to determine the distribution and diversity of Daphnia species found across the Plateau. Our results show that species richness is higher than previously thought, with total described and provisional species number doubling from 5 to 10. Six of the taxonomic units recovered by DNA taxonomy agreed well with morphology, but DNA barcoding distinguished three clades each for the D. longispina (D. galeata, D. dentifera, and D. longispina) and D. pulex (D. pulex, D. cf. tenebrosa, and D. pulicaria) complexes. The sequence divergence between congeneric species varied within a large range, from 9.25% to 30.71%. The endemic D. tibetana was the most common and widespread species, occurring in 12 hyposaline to mesosaline lakes. The lineage of D. longispina is the first confirmed occurrence in west Tibet.
Collapse
Affiliation(s)
- Lei Xu
- South China Sea Fisheries Research InstituteChinese Academy of Fishery SciencesGuangzhouChina
- Institute of HydrobiologyJinan UniversityGuangzhouChina
- Guangdong Provincial Key Laboratory of Fishery Ecology and EnvironmentGuangzhouChina
- Key Laboratory of South China Sea Fishery ResourcesDevelopment and UtilizationMinistry of AgricultureGuangzhouChina
| | - Qiuqi Lin
- Institute of HydrobiologyJinan UniversityGuangzhouChina
| | - Shaolin Xu
- Institute of HydrobiologyJinan UniversityGuangzhouChina
| | - Yangliang Gu
- Institute of HydrobiologyJinan UniversityGuangzhouChina
| | - Juzhi Hou
- Institute of Tibetan Plateau ResearchChinese Academy of SciencesBeijingChina
| | - Yongqin Liu
- Institute of Tibetan Plateau ResearchChinese Academy of SciencesBeijingChina
| | | | - Bo‐Ping Han
- Institute of HydrobiologyJinan UniversityGuangzhouChina
| |
Collapse
|
14
|
Burns M, Hedin M, Tsurusaki N. Population genomics and geographical parthenogenesis in Japanese harvestmen (Opiliones, Sclerosomatidae, Leiobunum). Ecol Evol 2018; 8:36-52. [PMID: 29321849 PMCID: PMC5756897 DOI: 10.1002/ece3.3605] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Revised: 10/09/2017] [Accepted: 10/11/2017] [Indexed: 01/03/2023] Open
Abstract
Naturally occurring population variation in reproductive mode presents an opportunity for researchers to test hypotheses regarding the evolution of sex. Asexual reproduction frequently assumes a geographical pattern, in which parthenogenesis-dominated populations are more broadly dispersed than their sexual conspecifics. We evaluate the geographical distribution of genomic signatures associated with parthenogenesis using nuclear and mitochondrial DNA sequence data from two Japanese harvestman sister taxa, Leiobunum manubriatum and Leiobunum globosum. Asexual reproduction is putatively facultative in these species, and female-biased localities are common in habitat margins. Past karyotypic and current cytometric work indicates L. globosum is entirely tetraploid, while L. manubriatum may be either diploid or tetraploid. We estimated species phylogeny, genetic differentiation, diversity, and mitonuclear discordance in females collected across the species range in order to identify range expansion toward marginal habitat, potential for hybrid origin, and persistence of asexual lineages. Our results point to northward expansion of a tetraploid ancestor of L. manubriatum and L. globosum, coupled with support for greater male gene flow in southern L. manubriatum localities. Specimens from localities in the Tohoku and Hokkaido regions were indistinct, particularly those of L. globosum, potentially due to little mitochondrial differentiation or haplotypic variation. Although L. manubriatum overlaps with L. globosum across its entire range, L. globosum was reconstructed as monophyletic with strong support using mtDNA, and marginal support with nuclear loci. Ultimately, we find evidence for continued sexual reproduction in both species and describe opportunities to clarify the rate and mechanism of parthenogenesis.
Collapse
Affiliation(s)
- Mercedes Burns
- Department of BiologySan Diego State UniversitySan DiegoCAUSA
- Department of Biological SciencesUniversity of MarylandBaltimore County, BaltimoreMDUSA
| | - Marshal Hedin
- Department of BiologySan Diego State UniversitySan DiegoCAUSA
| | | |
Collapse
|
15
|
Herrmann M, Henning-Lucass N, Cordellier M, Schwenk K. A genotype-phenotype association approach to reveal thermal adaptation inDaphnia galeata. JOURNAL OF EXPERIMENTAL ZOOLOGY PART 2017; 327:53-65. [DOI: 10.1002/jez.2070] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2016] [Revised: 03/15/2017] [Accepted: 03/16/2017] [Indexed: 12/22/2022]
Affiliation(s)
- Maike Herrmann
- Institute for Environmental Sciences; University Koblenz-Landau; Fortstraße 7 76829 Landau in der Pfalz Germany
- Biodiversity and Climate Research Centre; Georg-Voigt-Straße 14-16 60325 Frankfurt/Main Germany
| | - Nicole Henning-Lucass
- Institute for Environmental Sciences; University Koblenz-Landau; Fortstraße 7 76829 Landau in der Pfalz Germany
- Biodiversity and Climate Research Centre; Georg-Voigt-Straße 14-16 60325 Frankfurt/Main Germany
| | - Mathilde Cordellier
- Universität Hamburg; Biozentrum Grindel, Martin-Luther-King Platz 3 20146 Hamburg Germany
| | - Klaus Schwenk
- Institute for Environmental Sciences; University Koblenz-Landau; Fortstraße 7 76829 Landau in der Pfalz Germany
- Biodiversity and Climate Research Centre; Georg-Voigt-Straße 14-16 60325 Frankfurt/Main Germany
| |
Collapse
|
16
|
Riparbelli MG, Gottardo M, Callaini G. Parthenogenesis in Insects: The Centriole Renaissance. Results Probl Cell Differ 2017; 63:435-479. [PMID: 28779329 DOI: 10.1007/978-3-319-60855-6_19] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Building a new organism usually requires the contribution of two differently shaped haploid cells, the male and female gametes, each providing its genetic material to restore diploidy of the new born zygote. The successful execution of this process requires defined sequential steps that must be completed in space and time. Otherwise, development fails. Relevant among the earlier steps are pronuclear migration and formation of the first mitotic spindle that promote the mixing of parental chromosomes and the formation of the zygotic nucleus. A complex microtubule network ensures the proper execution of these processes. Instrumental to microtubule organization and bipolar spindle assembly is a distinct non-membranous organelle, the centrosome. Centrosome inheritance during fertilization is biparental, since both gametes provide essential components to build a functional centrosome. This model does not explain, however, centrosome formation during parthenogenetic development, a special mode of sexual reproduction in which the unfertilized egg develops without the contribution of the male gamete. Moreover, whereas fertilization is a relevant example in which the cells actively check the presence of only one centrosome, to avoid multipolar spindle formation, the development of parthenogenetic eggs is ensured, at least in insects, by the de novo assembly of multiple centrosomes.Here, we will focus our attention on the assembly of functional centrosomes following fertilization and during parthenogenetic development in insects. Parthenogenetic development in which unfertilized eggs are naturally depleted of centrosomes would provide a useful experimental system to investigate centriole assembly and duplication together with centrosome formation and maturation.
Collapse
Affiliation(s)
| | - Marco Gottardo
- Department of Life Sciences, University of Siena, Via A. Moro 2, 53100, Siena, Italy
| | - Giuliano Callaini
- Department of Life Sciences, University of Siena, Via A. Moro 2, 53100, Siena, Italy.
| |
Collapse
|
17
|
Fadda A, Palmas F, Camin F, Ziller L, Padedda BM, Luglié A, Manca M, Sabatini A. Analysis of δ13C and δ15N isotopic signatures to shed light on the hydrological cycle’s influence on the trophic behavior of fish in a Mediterranean reservoir. Biologia (Bratisl) 2016. [DOI: 10.1515/biolog-2016-0160] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
|
18
|
Holmes CJ, Figary S, Schulz KL, Cáceres CE. Effects of diversity on community assembly in newly formed pond communities. Ecosphere 2016. [DOI: 10.1002/ecs2.1377] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Affiliation(s)
- Christopher J. Holmes
- Department of Animal Biology School of Integrative Biology University of Illinois at Urbana‐Champaign 515 Morrill Hall 505 S. Goodwin Avenue Urbana Illinois 61801 USA
| | - Stephanie Figary
- Department of Environmental and Forest Biology College of Environmental Science and Forestry State University of New York 1 Forestry Drive Syracuse New York 13210 USA
| | - Kimberly L. Schulz
- Department of Environmental and Forest Biology College of Environmental Science and Forestry State University of New York 1 Forestry Drive Syracuse New York 13210 USA
| | - Carla E. Cáceres
- Department of Animal Biology School of Integrative Biology University of Illinois at Urbana‐Champaign 515 Morrill Hall 505 S. Goodwin Avenue Urbana Illinois 61801 USA
| |
Collapse
|
19
|
Holmes CJ, Pantel JH, Schulz KL, Cáceres CE. Initial genetic diversity enhances population establishment and alters genetic structuring of a newly establishedDaphniametapopulation. Mol Ecol 2016; 25:3299-308. [DOI: 10.1111/mec.13672] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2015] [Revised: 03/12/2016] [Accepted: 04/06/2016] [Indexed: 11/29/2022]
Affiliation(s)
- Christopher J. Holmes
- Department of Animal Biology; School of Integrative Biology; University of Illinois at Urbana-Champaign; 515 Morrill Hall 505 S. Goodwin Ave Urbana IL 61801 USA
| | - Jelena H. Pantel
- Centre d'Ecologie fonctionnelle et Evolutive; UMR 5175 CNRS - Université de Montpellier -EPHE; Campus CNRS; 1919 route de Mende 34293 Montpellier Cedex 05 France
| | - Kimberly L. Schulz
- Department of Environmental and Forest Biology; State University of New York; College of Environmental Science and Forestry; 1 Forestry Drive Syracuse NY 13210 USA
| | - Carla E. Cáceres
- Department of Animal Biology; School of Integrative Biology; University of Illinois at Urbana-Champaign; 515 Morrill Hall 505 S. Goodwin Ave Urbana IL 61801 USA
| |
Collapse
|
20
|
Henning-Lucass N, Cordellier M, Streit B, Schwenk K. Phenotypic plasticity in life-history traits of Daphnia galeata in response to temperature - a comparison across clonal lineages separated in time. Ecol Evol 2016; 6:881-91. [PMID: 26941934 PMCID: PMC4761779 DOI: 10.1002/ece3.1924] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2015] [Revised: 12/05/2015] [Accepted: 12/09/2015] [Indexed: 11/26/2022] Open
Abstract
Climatic changes are projected to result in rapid adaptive events with considerable phenotypic shifts. In order to reconstruct the impact of increased mean water temperatures during past decades and to reveal possible thermal micro‐evolution, we applied a resurrection ecology approach using dormant eggs of the freshwater keystone species Daphnia galeata. To this end, we compared the adaptive response of D. galeata clones from Lake Constance of two different time periods, 1965–1974 (“historical”) versus 2000–2009 (“recent”), to experimentally increased temperature regimes. In order to distinguish between genetic versus environmentally induced effects, we performed a common garden experiment in a flow‐through system and measured variation in life‐history traits. Experimental thermal regimes were chosen according to natural temperature conditions during the reproductive period of D. galeata in Central European lakes, with one additional temperature regime exceeding the currently observable maximum (+2°C). Increased water temperatures were shown to significantly affect measured life‐history traits, and significant “temperature × clonal age” interactions were revealed. Compared to historical clones, recent clonal lineages exhibited a shorter time to first reproduction and a higher survival rate, which may suggest temperature‐driven micro‐evolution over time but does not allow an explicit conclusion on the adaptive nature of such responses.
Collapse
Affiliation(s)
- Nicole Henning-Lucass
- Biodiversity and Climate Research Centre Georg-Voigt-Straße 14-1660325 Frankfurt/Main Germany; Institute for Environmental Sciences University Koblenz-Landau Fortstraße 776829 Landau in der Pfalz Germany
| | - Mathilde Cordellier
- University of Hamburg, Biozentrum Grindel Martin-Luther-King Platz 3 20146 Hamburg Germany
| | - Bruno Streit
- Biodiversity and Climate Research Centre Georg-Voigt-Straße 14-1660325 Frankfurt/Main Germany; Department of Ecology and Evolution Frankfurt University Max-von-Laue-Straße 1360438 Frankfurt am Main Germany
| | - Klaus Schwenk
- Biodiversity and Climate Research Centre Georg-Voigt-Straße 14-1660325 Frankfurt/Main Germany; Institute for Environmental Sciences University Koblenz-Landau Fortstraße 776829 Landau in der Pfalz Germany
| |
Collapse
|
21
|
Griebel J, Gießler S, Yin M, Wolinska J. Parental and hybrid Daphnia
from the D. longispina
complex: long-term dynamics in genetic structure and significance of overwintering modes. J Evol Biol 2016; 29:810-23. [DOI: 10.1111/jeb.12828] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2015] [Revised: 12/18/2015] [Accepted: 01/10/2016] [Indexed: 12/22/2022]
Affiliation(s)
- J. Griebel
- Department of Ecosystem Research; Leibniz-Institute of Freshwater Ecology and Inland Fisheries; Berlin Germany
- Department of Biology II; Ludwig Maximilian University Munich; Munich Germany
| | - S. Gießler
- Department of Biology II; Ludwig Maximilian University Munich; Munich Germany
| | - M. Yin
- MOE Key Laboratory of Biodiversity Science and Ecological Engineering; School of Life Science; Fudan University; Shanghai China
| | - J. Wolinska
- Department of Ecosystem Research; Leibniz-Institute of Freshwater Ecology and Inland Fisheries; Berlin Germany
- Department of Biology, Chemistry and Pharmacy; Institute of Biology; Freie Universität Berlin; Berlin Germany
| |
Collapse
|
22
|
Alric B, Möst M, Domaizon I, Pignol C, Spaak P, Perga ME. Local human pressures influence gene flow in a hybridizing Daphnia
species complex. J Evol Biol 2016; 29:720-35. [DOI: 10.1111/jeb.12820] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2014] [Revised: 12/22/2015] [Accepted: 12/22/2015] [Indexed: 11/28/2022]
Affiliation(s)
- B. Alric
- INRA; UMR 0042 CARRTEL; Thonon-les-Bains France
- University of Savoie; Le Bourget du Lac France
- CNRS; UMR 5558; Laboratory of Biometry and Evolutionary Biology; University of Lyon; University Lyon 1; Villeurbanne France
| | - M. Möst
- Eawag; Swiss Federal Institute of Aquatic Science and Technology; Dübendorf Switzerland
- Institute of Integrative Biology; ETH Zurich; Zurich Switzerland
- Department of Zoology; University of Cambridge; Cambridge UK
| | - I. Domaizon
- INRA; UMR 0042 CARRTEL; Thonon-les-Bains France
- University of Savoie; Le Bourget du Lac France
| | - C. Pignol
- UMR 5204 EDYTEM; University of Savoie; Le Bourget du Lac France
| | - P. Spaak
- Eawag; Swiss Federal Institute of Aquatic Science and Technology; Dübendorf Switzerland
- Institute of Integrative Biology; ETH Zurich; Zurich Switzerland
| | - M.-E. Perga
- INRA; UMR 0042 CARRTEL; Thonon-les-Bains France
- University of Savoie; Le Bourget du Lac France
| |
Collapse
|
23
|
Lange B, Kaufmann AP, Ebert D. Genetic, ecological and geographic covariables explaining host range and specificity of a microsporidian parasite. J Anim Ecol 2015; 84:1711-9. [DOI: 10.1111/1365-2656.12421] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2015] [Accepted: 05/24/2015] [Indexed: 11/30/2022]
Affiliation(s)
- Benjamin Lange
- Zoological Institute; Basel University; Vesalgasse 1 4051 Basel Switzerland
| | - Andrea Patricia Kaufmann
- Zoological Institute; Basel University; Vesalgasse 1 4051 Basel Switzerland
- Tvärminne Zoological Station; Hanko FI-10900 Finland
| | - Dieter Ebert
- Zoological Institute; Basel University; Vesalgasse 1 4051 Basel Switzerland
- Tvärminne Zoological Station; Hanko FI-10900 Finland
| |
Collapse
|
24
|
Wei W, Gießler S, Wolinska J, Ma X, Yang Z, Hu W, Yin M. Genetic structure of Daphnia galeata populations in Eastern China. PLoS One 2015; 10:e0120168. [PMID: 25768727 PMCID: PMC4358959 DOI: 10.1371/journal.pone.0120168] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2014] [Accepted: 01/26/2015] [Indexed: 11/18/2022] Open
Abstract
This study presents the first examination of the genetic structure of Daphnia longispina complex populations in Eastern China. Only one species, D. galeata, was present across the eight investigated lakes; as identified by taxon assignment using allelic variation at 15 microsatellite loci. Three genetically differentiated D. galeata subgroups emerged independent of the type of statistical analysis applied. Thus, Bayesian clustering, discriminant analysis based on results from factorial correspondence analysis, and UPGMA clustering consistently showed that populations from two neighbouring lakes were genetically separated from a mixture of genotypes found in other lakes, which formed another two subgroups. Clonal diversity was high in all D. galeata populations, and most samples showed no deviation from Hardy-Weinberg equilibrium, indicating that clonal selection had little effect on the genetic diversity. Overall, populations did not cluster by geographical origin. Further studies will show if the observed pattern can be explained by natural colonization processes or by recent anthropogenic impact on predominantly artificial lakes.
Collapse
Affiliation(s)
- Wenzhi Wei
- Yangzhou University, College of Animal Science and Technology, Yangzhou, China
| | - Sabine Gießler
- Ludwig-Maximilians-Universität, Department Biologie II, Evolutionsökologie, Planegg-Martinsried, Germany
| | - Justyna Wolinska
- Leibniz-Institute of Freshwater Ecology and Inland Fisheries, Department of Ecosystem Research, Berlin, Germany
| | - Xiaolin Ma
- Fudan University, School of Life Science, MOE Key Laboratory for Biodiversity Science and Ecological Engineering, Shanghai, China
| | - Zhong Yang
- Fudan University, School of Life Science, MOE Key Laboratory for Biodiversity Science and Ecological Engineering, Shanghai, China
| | - Wei Hu
- Fudan University, School of Life Science, MOE Key Laboratory for Biodiversity Science and Ecological Engineering, Shanghai, China
| | - Mingbo Yin
- Fudan University, School of Life Science, MOE Key Laboratory for Biodiversity Science and Ecological Engineering, Shanghai, China
| |
Collapse
|
25
|
Thielsch A, Glass N, Streit B, Meester LD, Ortells R, Schwenk K. Fitness differences and persistent founder effects determine the clonal composition during population build-up inDaphnia. OIKOS 2014. [DOI: 10.1111/oik.01575] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Anne Thielsch
- Inst. for Environmental Science, Molecular Ecology, Univ. of Koblenz-Landau; Fortstraße 7 DE-76829 Landau Germany
| | - Nicole Glass
- Dept of Ecology and Evolution; Goethe-Univ. - Biologicum; Max-von-Laue-Straße 13 DE-60438 Frankfurt am Main Germany
| | - Bruno Streit
- Dept of Ecology and Evolution; Goethe-Univ. - Biologicum; Max-von-Laue-Straße 13 DE-60438 Frankfurt am Main Germany
| | - Luc De Meester
- Laboratory Aquatic Ecology, Evolution and Conservation, KU Leuven - Univ. of Leuven; Charles Deberiotstraat 32 BE-3000 Leuven Belgium
| | - Raquel Ortells
- Inst. Cavanilles de Biodiversitat i Biologia Evolutiva, Univ. of Valencia; C/Catedrático José Beltrán, 2 ES-46980 Paterna Spain
| | - Klaus Schwenk
- Inst. for Environmental Science, Molecular Ecology, Univ. of Koblenz-Landau; Fortstraße 7 DE-76829 Landau Germany
| |
Collapse
|
26
|
Yin M, Gießler S, Griebel J, Wolinska J. Hybridizing Daphnia communities from ten neighbouring lakes: spatio-temporal dynamics, local processes, gene flow and invasiveness. BMC Evol Biol 2014; 14:80. [PMID: 24725969 PMCID: PMC4101843 DOI: 10.1186/1471-2148-14-80] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2013] [Accepted: 04/04/2014] [Indexed: 05/28/2023] Open
Abstract
BACKGROUND In natural communities of cyclical parthenogens, rapid response to environmental change is enabled by switching between two reproduction modes. While long periods of asexual reproduction allow some clones to outcompete others, and may result in "clonal erosion", sexual reproduction restores genetic variation in such systems. Moreover, sexual reproduction may result in the formation of interspecific hybrids. These hybrids can then reach high abundances, through asexual clonal reproduction. In the present study, we explored genetic variation in water fleas of the genus Daphnia. The focus was on the short-term dynamics within several clonal assemblages from the hybridizing Daphnia longispina complex and the impact of gene flow at small spatial scales. RESULTS Daphnia individuals belonged either to the parental species D. galeata and D. longispina, or to different hybrid classes, as identified by 15 microsatellite markers. The distribution and genotypic structure of parental species, but not hybrids, corresponded well with the geographical positions of the lakes. Within parental species, the genetic distance among populations of D. galeata was lower than among populations of D. longispina. Moreover, D. galeata dominance was associated with higher phosphorous load. Finally, there was no evidence for clonal erosion. CONCLUSIONS Our results suggest that the contemporary structure of hybridizing Daphnia communities from ten nearby lakes is influenced by colonization events from neighbouring habitats as well as by environmental factors. Unlike the parental species, however, there was little evidence for successful dispersal of hybrids, which seem to be produced locally. Finally, in contrast to temporary Daphnia populations, in which a decrease in clonal diversity was sometimes detectable over a single growing season, the high clonal diversity and lack of clonal erosion observed here might result from repeated hatching of sexually produced offspring. Overall, our study provides insights into spatio-temporal dynamics in a hybridizing Daphnia species complex in a recently established lake system, and relates genetic similarities of populations to a scenario of secondary invasion enhanced by environmental factors.
Collapse
Affiliation(s)
| | - Sabine Gießler
- Department Biologie II, Evolutionsökologie, Ludwig-Maximilians-Universität, Großhaderner Str, 2, 82152 Planegg-Martinsried, Germany.
| | | | | |
Collapse
|
27
|
Ventura M, Petrusek A, Miró A, Hamrová E, Buñay D, De Meester L, Mergeay J. Local and regional founder effects in lake zooplankton persist after thousands of years despite high dispersal potential. Mol Ecol 2014; 23:1014-27. [DOI: 10.1111/mec.12656] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2013] [Revised: 12/22/2013] [Accepted: 12/30/2013] [Indexed: 02/02/2023]
Affiliation(s)
- M. Ventura
- Center for Advanced Studies of Blanes; Spanish Research Council (CEAB-CSIC); Biodiversity and Biogeodynamics Group; Blanes 17300 Catalonia Girona Spain
- Institut de Recerca de l'Aigua; Universitat de Barcelona; Av. Diagonal 684 08034 Barcelona Catalonia Spain
| | - A. Petrusek
- Department of Ecology; Faculty of Science; Charles University in Prague; Viničná 7 CZ-12844 Prague 2 Czech Republic
| | - A. Miró
- Center for Advanced Studies of Blanes; Spanish Research Council (CEAB-CSIC); Biodiversity and Biogeodynamics Group; Blanes 17300 Catalonia Girona Spain
| | - E. Hamrová
- Department of Ecology; Faculty of Science; Charles University in Prague; Viničná 7 CZ-12844 Prague 2 Czech Republic
| | - D. Buñay
- Center for Advanced Studies of Blanes; Spanish Research Council (CEAB-CSIC); Biodiversity and Biogeodynamics Group; Blanes 17300 Catalonia Girona Spain
| | - L. De Meester
- Laboratory of Aquatic Ecology, Evolution and Conservation; KU Leuven; University of Leuven; Deberiotstraat 32 B-3000 Leuven Belgium
| | - J. Mergeay
- Laboratory of Aquatic Ecology, Evolution and Conservation; KU Leuven; University of Leuven; Deberiotstraat 32 B-3000 Leuven Belgium
- Research Institute for Nature and Forest; Gaverstraat 4 B-9500 Geraardsbergen Belgium
| |
Collapse
|
28
|
Zuykova EI, Bochkarev NA, Katokhin AV. Molecular genetic identification and phylogeny of Daphnia species (Crustacea, Cladocera) from water bodies of the Lake Chany basin. RUSS J GENET+ 2013. [DOI: 10.1134/s1022795412120186] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
|
29
|
HAMROVÁ EVA, KRAJICEK MARTIN, KARANOVIC TOMISLAV, ČERNÝ MARTIN, PETRUSEK ADAM. Congruent patterns of lineage diversity in two species complexes of planktonic crustaceans,Daphnia longispina(Cladocera) andEucyclops serrulatus(Copepoda), in East European mountain lakes. Zool J Linn Soc 2012. [DOI: 10.1111/j.1096-3642.2012.00864.x] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
|
30
|
Schwentner M, Timms BV, Richter S. Flying with the birds? Recent large-area dispersal of four Australian Limnadopsis species (Crustacea: Branchiopoda: Spinicaudata). Ecol Evol 2012; 2:1605-26. [PMID: 22957166 PMCID: PMC3434933 DOI: 10.1002/ece3.265] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2012] [Accepted: 03/26/2012] [Indexed: 11/05/2022] Open
Abstract
Temporary water bodies are important freshwater habitats in the arid zone of Australia. They harbor a distinct fauna and provide important feeding and breeding grounds for water birds. This paper assesses, on the basis of haplotype networks, analyses of molecular variation and relaxed molecular clock divergence time estimates, the phylogeographic history, and population structure of four common temporary water species of the Australian endemic clam shrimp taxon Limnadopsis in eastern and central Australia (an area of >1,350,000 km(2)). Mitochondrial cytochrome c oxidase subunit I sequences of 413 individuals and a subset of 63 nuclear internal transcribed spacer 2 sequences were analyzed. Genetic differentiation was observed between populations inhabiting southeastern and central Australia and those inhabiting the northern Lake Eyre Basin and Western Australia. However, over large parts of the study area and across river drainage systems in southeastern and central Australia (the Murray-Darling Basin, Bulloo River, and southern Lake Eyre Basin), no evidence of population subdivision was observed in any of the four Limnadopsis species. This indicates recent gene flow across an area of ∼800,000 km(2). This finding contrasts with patterns observed in other Australian arid zone taxa, particularly freshwater species, whose populations are often structured according to drainage systems. The lack of genetic differentiation within the area in question may be linked to the huge number of highly nomadic water birds that potentially disperse the resting eggs of Limnadopsis among temporary water bodies. Genetically undifferentiated populations on a large geographic scale contrast starkly with findings for many other large branchiopods in other parts of the world, where pronounced genetic structure is often observed even in populations inhabiting pools separated by a few kilometers. Due to its divergent genetic lineages (up to 5.6% uncorrected p-distance) and the relaxed molecular clock divergence time estimates obtained, Limnadopsis parvispinus is assumed to have inhabited the Murray-Darling Basin continuously since the mid-Pliocene (∼4 million years ago). This means that suitable temporary water bodies would have existed in this area throughout the wet-dry cycles of the Pleistocene.
Collapse
Affiliation(s)
- Martin Schwentner
- Universität Rostock, Allgemeine und Spezielle Zoologie, Institut für Biowissenschaften, Universitätsplatz 218055 Rostock, Germany
| | - Brian V Timms
- Australian MuseumSydney, NSW 2000, Australia
- Australian Wetland and Rivers Centre, University of NSWSydney, NSW 2052, Australia
| | - Stefan Richter
- Universität Rostock, Allgemeine und Spezielle Zoologie, Institut für Biowissenschaften, Universitätsplatz 218055 Rostock, Germany
| |
Collapse
|
31
|
Thielsch A, Völker E, Kraus RHS, Schwenk K. Discrimination of hybrid classes using cross-species amplification of microsatellite loci: methodological challenges and solutions in Daphnia. Mol Ecol Resour 2012; 12:697-705. [PMID: 22487563 DOI: 10.1111/j.1755-0998.2012.03142.x] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
Microsatellite markers are important tools in population, conservation and forensic studies and are frequently used for species delineation, the detection of hybridization and introgression. Therefore, marker sets that amplify variable DNA regions in two species are required; however, cross-species amplification is often difficult, as genotyping errors such as null alleles may occur. To estimate the level of potential misidentifications based on genotyping errors, we compared the occurrence of parental alleles in laboratory and natural Daphnia hybrids (Daphnia longispina group). We tested a set of 12 microsatellite loci with regard to their suitability for unambiguous species and hybrid class identification using F(1) hybrids bred in the laboratory. Further, a large set of 44 natural populations of D. cucullata, D. galeata and D. longispina (1715 individuals) as well as their interspecific hybrids were genotyped to validate the discriminatory power of different marker combinations. Species delineation using microsatellite multilocus genotypes produced reliable results for all three studied species using assignment tests. Daphnia galeata × cucullata hybrid detection was limited due to three loci exhibiting D. cucullata-specific null alleles, which most likely are caused by differences in primer-binding sites of parental species. Overall, discriminatory power in hybrid detection was improved when a subset of markers was identified that amplifies equally well in both species.
Collapse
Affiliation(s)
- A Thielsch
- Molecular Ecology, Institute for Environmental Sciences, University Koblenz-Landau, Fortstr. 7, 76829 Landau, Germany.
| | | | | | | |
Collapse
|
32
|
Allen DE, Lynch M. The effect of variable frequency of sexual reproduction on the genetic structure of natural populations of a cyclical parthenogen. Evolution 2012; 66:919-926. [PMID: 22380451 PMCID: PMC4521562 DOI: 10.1111/j.1558-5646.2011.01488.x] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Cyclical parthenogens are a valuable system in which to empirically test theoretical predictions as to the genetic consequences of sexual reproduction in natural populations, particularly if the frequency of sexual relative to asexual reproduction can be quantified. In this study, we used a series of lake populations of the cyclical parthenogen, Daphnia pulicaria, that vary consistently in their investment in sexual reproduction, to address the questions of whether the ecological variation in investment in sex is detectable at the genetic level, and if so, whether the genetic patterns seen are consistent with theoretical predictions. We show that there is variation in the genetic structure of these populations in a manner consistent with their investment in sexual reproduction. Populations engaging in a high frequency of sex were in Hardy-Weinberg and gametic phase equilibrium, and showed little genotypic differentiation across sampled years. In contrast, populations with a lower frequency of sex deviated widely from equilibrium, had reduced multilocus clonal diversity, and showed significant temporal genotypic deviation.
Collapse
Affiliation(s)
- Desiree E Allen
- Department of Biology, Indiana University, Bloomington, Indiana 47405 E-mail:
| | - Michael Lynch
- Department of Biology, Indiana University, Bloomington, Indiana 47405 E-mail:
| |
Collapse
|
33
|
Fine-scale temporal and spatial variation of taxon and clonal structure in the Daphnia longispina hybrid complex in heterogeneous environments. BMC Evol Biol 2012; 12:12. [PMID: 22280487 PMCID: PMC3305588 DOI: 10.1186/1471-2148-12-12] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2011] [Accepted: 01/27/2012] [Indexed: 11/16/2022] Open
Abstract
Background Cyclical parthenogenetic water fleas of the genus Daphnia have become a prominent model organism in ecology and evolution. In the past, analyses of their population structure have been limited by the prevailing use of allozyme markers, which in general do not allow for the distinction of individual clones. In this study, we used 10 microsatellite markers to track changes in the taxonomic and clonal composition of Daphnia populations, and traced the abundance of the most common clones in two European reservoirs. One of the localities was inhabited by a single species of the Daphnia longispina complex (D. galeata), the other by two parental species (D. galeata and D. longispina) and their interspecific hybrids. The study took place during the transition from summer stratification to autumn mixing, representing a period of major environmental change within lake habitats. Results In both reservoirs, we observed temporal (generation-to-generation) and spatial (along the heterogeneous reservoir environment) changes in Daphnia community structure. In the single-species reservoir, the clonal diversity of D. galeata increased with time, as a few dominant clones were replaced by a higher number of less common clones. A loss in selective advantage for the dominant clones may have been due to gradual changes in the environment, or due to selection acting in a negative frequency-dependent manner. In the multispecies reservoir, there were no apparent temporal trends in clonal diversity but we observed significantly lower clonal diversity in the interspecific hybrids than in the coexisting parental species, supporting the existence of reproductive barriers between the parental genomes. Conclusions Our study, tracing clonal lineages of Daphnia in time and space by the fine-resolution markers, contributes to the understanding of how clonal reproduction impacts community structure in cyclically parthenogenetic organisms.
Collapse
|
34
|
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]
|
35
|
Yin M, Petrusek A, Seda J, Wolinska J. Fine-scale genetic analysis of Daphnia host populations infected by two virulent parasites – strong fluctuations in clonal structure at small temporal and spatial scales. Int J Parasitol 2012; 42:115-21. [DOI: 10.1016/j.ijpara.2011.11.004] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2011] [Revised: 11/04/2011] [Accepted: 11/06/2011] [Indexed: 10/15/2022]
|
36
|
|
37
|
Hamrová E, Mergeay J, Petrusek A. Strong differences in the clonal variation of two Daphnia species from mountain lakes affected by overwintering strategy. BMC Evol Biol 2011; 11:231. [PMID: 21824417 PMCID: PMC3161014 DOI: 10.1186/1471-2148-11-231] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2011] [Accepted: 08/08/2011] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The population structure of cyclical parthenogens such as water fleas is strongly influenced by the frequency of alternations between sexual and asexual (parthenogenetic) reproduction, which may differ among populations and species. We studied genetic variation within six populations of two closely related species of water fleas of the genus Daphnia (Crustacea, Cladocera). D. galeata and D. longispina both occur in lakes in the Tatra Mountains (Central Europe), but their populations show distinct life history strategies in that region. In three studied lakes inhabited by D. galeata, daphnids overwinter under the ice as adult females. In contrast, in lakes inhabited by D. longispina, populations apparently disappear from the water column and overwinter as dormant eggs in lake sediments. We investigated to what extent these different strategies lead to differences in the clonal composition of late summer populations. RESULTS Analysis of genetic variation at nine microsatellite loci revealed that clonal richness (expressed as the proportion of different multilocus genotypes, MLGs, in the whole analysed sample) consistently differed between the two studied species. In the three D. longispina populations, very high clonal richness was found (MLG/N ranging from 0.97 to 1.00), whereas in D. galeata it was much lower (0.05 to 0.50). The dominant MLGs in all D. galeata populations were heterozygous at five or more loci, suggesting that such individuals all represented the same clonal lineages rather than insufficiently resolved groups of different clones. CONCLUSIONS The low clonal diversities and significant deviations from Hardy-Weinberg equilibrium in D. galeata populations were likely a consequence of strong clonal erosion over extended periods of time (several years or even decades) and the limited influence of sexual reproduction. Our data reveal that populations of closely related Daphnia species living in relatively similar habitats (permanent, oligotrophic mountain lakes) within the same region may show strikingly different genetic structures, which most likely depend on their reproductive strategy during unfavourable periods. We assume that similar impacts of life history on population structures are also relevant for other cyclical parthenogen groups. In extreme cases, prolonged clonal erosion may result in the dominance of a single clone within a population, which might limit its microevolutionary potential if selection pressures suddenly change.
Collapse
Affiliation(s)
- Eva Hamrová
- Department of Ecology, Faculty of Science, Charles University in Prague, Prague, Czech Republic
| | | | | |
Collapse
|
38
|
|
39
|
YIN MINGBO, WOLINSKA JUSTYNA, GIEßLER SABINE. Clonal diversity, clonal persistence and rapid taxon replacement in natural populations of species and hybrids of the Daphnia longispina complex. Mol Ecol 2010; 19:4168-78. [DOI: 10.1111/j.1365-294x.2010.04807.x] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
|
40
|
ALLEN MICHAELR, THUM RYANA, CÁCERES CARLAE. Does local adaptation to resources explain genetic differentiation among Daphnia populations? Mol Ecol 2010; 19:3076-87. [DOI: 10.1111/j.1365-294x.2010.04728.x] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
|
41
|
Bláha M, Hulák M, Slouková J, Těšitel J. Molecular and morphological patterns acrossAcanthocyclops vernalis-robustusspecies complex (Copepoda, Cyclopoida). ZOOL SCR 2010. [DOI: 10.1111/j.1463-6409.2010.00422.x] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
|