1
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Elguweidi A, Crease T. Copy number and sequence variation in rDNA of Daphnia pulex from natural populations: insights from whole-genome sequencing. G3 (BETHESDA, MD.) 2024; 14:jkae105. [PMID: 38771699 PMCID: PMC11228840 DOI: 10.1093/g3journal/jkae105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2024] [Revised: 02/17/2024] [Accepted: 05/10/2024] [Indexed: 05/23/2024]
Abstract
Ribosomal DNA (rDNA) has a vital role in ribosome biogenesis as it contains the genes that encode ribosomal RNA (rRNA) separated by intergenic spacers (IGSs). The rRNA genes occur in hundreds to tens of thousands of copies per haploid genome in eukaryotes and are generally highly conserved with low variation within species. Due to the repetitive nature and large size of rDNA arrays, detecting intraindividual variation can be difficult. In this study, we use whole-genome sequences of 169 Daphnia pulex individuals from 10 natural populations to measure the copy number and sequence variation in rDNA. This revealed that variation in rDNA copy number between individuals spans an order of magnitude. We further observed a substantial level of sequence variation within individual genomes. As expected, single-nucleotide polymorphisms occurred in regions of lower functional constraint such as the IGS and expansion segments of the rRNA genes. The presence of strong linkage disequilibrium among variants facilitated identification of haplotypes within each population. Although there was evidence of recombination among haplotypes from different populations, it is insufficient to eliminate linkage disequilibrium within populations. Estimating copy number and haplotype diversity within individuals revealed that the level of intraindividual sequence variation is not strongly correlated with copy number. The observed patterns of variation highlight a complex evolutionary history of rDNA in D. pulex. Future research should explore the functional implications of rDNA copy number and sequence variation on organismal phenotypes.
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Affiliation(s)
- Abir Elguweidi
- Department of Integrative Biology, University of Guelph, Guelph, ON, N1G2W1, Canada
| | - Teresa Crease
- Department of Integrative Biology, University of Guelph, Guelph, ON, N1G2W1, Canada
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2
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Nadeau CP, Urban MC. Macroecological predictors of evolutionary and plastic potential do not apply at microgeographic scales for a freshwater cladoceran under climate change. Evol Lett 2024; 8:43-55. [PMID: 38370540 PMCID: PMC10872021 DOI: 10.1093/evlett/qrad042] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Revised: 06/28/2023] [Accepted: 09/22/2022] [Indexed: 02/20/2024] Open
Abstract
Rapid evolutionary adaptation could reduce the negative impacts of climate change if sufficient heritability of key traits exists under future climate conditions. Plastic responses to climate change could also reduce negative impacts. Understanding which populations are likely to respond via evolution or plasticity could therefore improve estimates of extinction risk. A large body of research suggests that the evolutionary and plastic potential of a population can be predicted by the degree of spatial and temporal climatic variation it experiences. However, we know little about the scale at which these relationships apply. Here, we test if spatial and temporal variation in temperature affects genetic variation and plasticity of fitness and a key thermal tolerance trait (critical thermal maximum; CTmax) at microgeographic scales using a metapopulation of Daphnia magna in freshwater rock pools. Specifically, we ask if (a) there is a microgeographic adaptation of CTmax and fitness to differences in temperature among the pools, (b) pools with greater temporal temperature variation have more genetic variation or plasticity in CTmax or fitness, and (c) increases in temperature affect the heritability of CTmax and fitness. Although we observed genetic variation and plasticity in CTmax and fitness, and differences in fitness among pools, we did not find support for the predicted relationships between temperature variation and genetic variation or plasticity. Furthermore, the genetic variation and plasticity we observed in CTmax are unlikely sufficient to reduce the impacts of climate change. CTmax plasticity was minimal and heritability was 72% lower when D. magna developed at the higher temperatures predicted under climate change. In contrast, the heritability of fitness increased by 53% under warmer temperatures, suggesting an increase in overall evolutionary potential unrelated to CTmax under climate change. More research is needed to understand the evolutionary and plastic potential under climate change and how that potential will be altered in future climates.
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Affiliation(s)
| | - Mark C Urban
- Ecology and Evolutionary Biology Department, University of Connecticut, Storrs, CT, United States
- Center for Biological Risk, University of Connecticut, Storrs, CT, United States
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3
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Zhang K, Wu J, Deng D, Zhao H, Liu Q, Peng S, Zhang Y, Zhou Z. Population genetic differentiation of Daphnia sinensis in a lasting high-phosphorus Chinese lake, Lake Chaohu. Front Ecol Evol 2023. [DOI: 10.3389/fevo.2022.913738] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
Ecological shifts (e.g., eutrophication) can affect the genetic differentiation of zooplankton populations in lakes. However, the role of environmental change in a lasting high-phosphorus lake driving the genetic differentiation of zooplankton population structure over time is poorly understood. In this paper, the changes of the genetic diversity and differentiation of Daphnia sinensis population were studied by using the mitochondrial COI gene and microsatellite markers on modern groups (from January to June 2016) and historic groups (obtained from resting eggs in the sediments) in Lake Chaohu. Based on the microsatellite markers, six modern groups were clustered into two clusters (the WG cluster and SG cluster) during the seasonal dynamics, whereas the genetic differentiation of the five historic groups showed a wave-like pattern and had evolved into four clusters. Moreover, the haplotype network showed that six modern groups had one origin center whereas five historic groups had two origin centers based on the mitochondrial COI gene marker. Fu’s Fs neutral test and Tajima’s test indicated that the five historic groups deviated from neutral evolution and showed a bottleneck effect in the history process. Water temperature and total dissolved phosphorus were obviously associated with the seasonal genetic differentiation of D. sinensis, whereas nitrogen content of the sediments was significantly related to the long-term microevolution of D. sinensis in the high-phosphorus environment. Therefore, the changing pattern of D. sinensis population genetic structure was one of the environmental selections probably combined with co-evolutionary, where rapid-increasing nitrogen level had a large impact on D. sinensis population genetic structure in lasting high phosphorus environment in Lake Chaohu.
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Huang Q, Xu L, Xie L, Liu P, Rizo EZC, Han BP. Spatial and temporal variation of genetic diversity and genetic differentiation in Daphnia galeata populations in four large reservoirs in southern China. Front Microbiol 2022; 13:1041011. [PMID: 36439856 PMCID: PMC9691881 DOI: 10.3389/fmicb.2022.1041011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2022] [Accepted: 10/24/2022] [Indexed: 03/21/2024] Open
Abstract
Daphnia galeata is a common and dominant species in warmer waters, and has a strong top-down effect on both phytoplankton and bacteria. The knowledge of its temporal and spatial patterns of genetic diversity is fundamental in understanding its population dynamics and potential ecological function in ecosystems. Its population genetics have been investigated at regional scales but few within regions or at smaller spatial scales. Here, we examined the fine-scale spatial genetic variation of D. galeata within four large, deep reservoirs in wet and dry seasons and the six-year variation of genetic diversity in one of the reservoirs by using cytochrome c oxidase subunit I and microsatellites (simple sequence repeat). Our study shows that fine-scale spatial genetic variation commonly occurred within the reservoirs, indicating strong environmental selection at least in the two of reservoirs with strong longitudinal gradients. Since the environmental gradients established in the dry season was largely reduced in the wet season, the fine-scale spatial genetic variation was much higher in the dry season. The dynamics of local genetic diversity did not follow the theoretical pattern of rapid erosion but peaked in mid or mid-late growth season. The local genetic diversity of D. galeata appears to be shaped and maintained not only by recruitment from resting egg banks but also by gene flow within reservoirs. The temporal and fine-scale genetic variation within a water body suggests that it is necessary to pay attention to sampling periods and locations of a given water body in regional studies.
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Affiliation(s)
- Qi Huang
- Department of Ecology and Institute of Hydrobiology, Jinan University, Guangzhou, Guangdong, China
| | - Lei Xu
- South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, Guangdong, China
| | - Lili Xie
- Department of Ecology and Institute of Hydrobiology, Jinan University, Guangzhou, Guangdong, China
| | - Ping Liu
- Department of Ecology and Institute of Hydrobiology, Jinan University, Guangzhou, Guangdong, China
- College of Environmental Science and Engineering, Yangzhou University, Yangzhou, Jiangsu, China
| | - Eric Zeus C. Rizo
- Division of Biological Sciences, College of Arts and Sciences, University of the Philippines-Visayas, Miagao, Iloilo, Philippines
| | - Bo-Ping Han
- Department of Ecology and Institute of Hydrobiology, Jinan University, Guangzhou, Guangdong, China
- Engineering Research Center of Tropical and Subtropical Aquatic Ecological Engineering, Ministry of Education, Guangzhou, China
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5
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Abstract
The ways in which genetic variation is distributed within and among populations is a key determinant of the evolutionary features of a species. However, most comprehensive studies of these features have been restricted to studies of subdivision in settings known to have been driven by local adaptation, leaving our understanding of the natural dispersion of allelic variation less than ideal. Here, we present a geographic population-genomic analysis of 10 populations of the freshwater microcrustacean Daphnia pulex, an emerging model system in evolutionary genomics. These populations exhibit a pattern of moderate isolation-by-distance, with an average migration rate of 0.6 individuals per generation, and average effective population sizes of ∼650,000 individuals. Most populations contain numerous private alleles, and genomic scans highlight the presence of islands of excessively high population subdivision for more common alleles. A large fraction of such islands of population divergence likely reflect historical neutral changes, including rare stochastic migration and hybridization events. The data do point to local adaptive divergence, although the precise nature of the relevant variation is diffuse and cannot be associated with particular loci, despite the very large sample sizes involved in this study. In contrast, an analysis of between-species divergence highlights positive selection operating on a large set of genes with functions nearly nonoverlapping with those involved in local adaptation, in particular ribosome structure, mitochondrial bioenergetics, light reception and response, detoxification, and gene regulation. These results set the stage for using D. pulex as a model for understanding the relationship between molecular and cellular evolution in the context of natural environments.
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Affiliation(s)
- Takahiro Maruki
- Biodesign Center for Mechanisms of Evolution, Arizona State University, Tempe, AZ 85287, USA
| | - Zhiqiang Ye
- Biodesign Center for Mechanisms of Evolution, Arizona State University, Tempe, AZ 85287, USA
| | - Michael Lynch
- Biodesign Center for Mechanisms of Evolution, Arizona State University, Tempe, AZ 85287, USA
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6
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Angst P, Ebert D, Fields PD. Demographic history shapes genomic variation in an intracellular parasite with a wide geographic distribution. Mol Ecol 2022; 31:2528-2544. [DOI: 10.1111/mec.16419] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Revised: 02/14/2022] [Accepted: 02/28/2022] [Indexed: 11/27/2022]
Affiliation(s)
- Pascal Angst
- Department of Environmental Sciences, Zoology University of Basel Vesalgasse 1 4051 Basel Switzerland
| | - Dieter Ebert
- Department of Environmental Sciences, Zoology University of Basel Vesalgasse 1 4051 Basel Switzerland
| | - Peter D. Fields
- Department of Environmental Sciences, Zoology University of Basel Vesalgasse 1 4051 Basel Switzerland
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7
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Llanos‐Garrido A, Pérez‐Tris J, Díaz JA. Low genome-wide divergence between two lizard populations with high adaptive phenotypic differentiation. Ecol Evol 2021; 11:18055-18065. [PMID: 35003657 PMCID: PMC8717303 DOI: 10.1002/ece3.8403] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Revised: 10/14/2021] [Accepted: 11/12/2021] [Indexed: 11/17/2022] Open
Abstract
Usually, adaptive phenotypic differentiation is paralleled by genetic divergence between locally adapted populations. However, adaptation can also happen in a scenario of nonsignificant genetic divergence due to intense gene flow and/or recent differentiation. While this phenomenon is rarely published, findings on incipient ecologically driven divergence or isolation by adaptation are relatively common, which could confound our understanding about the frequency at which they actually occur in nature. Here, we explore genome-wide traces of divergence between two populations of the lacertid lizard Psammodromus algirus separated by a 600 m elevational gradient. These populations seem to be differentially adapted to their environments despite showing low levels of genetic differentiation (according to previously studies of mtDNA and microsatellite data). We performed a search for outliers (i.e., loci subject to selection) trying to identify specific loci with FST statistics significantly higher than those expected on the basis of overall, genome-wide estimates of genetic divergence. We find that local phenotypic adaptation (in terms of a wide diversity of characters) was not accompanied by genome-wide differentiation, even when we maximized the chances of unveiling such differentiation at particular loci with FST-based outlier detection tests. Instead, our analyses confirmed the lack of genome-wide differentiation on the basis of more than 70,000 SNPs, which is concordant with a scenario of local adaptation without isolation by environment. Our results add evidence to previous studies in which local adaptation does not lead to any kind of isolation (or early stages of ecological speciation), but maintains phenotypic divergence despite the lack of a differentiated genomic background.
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Affiliation(s)
- Alejandro Llanos‐Garrido
- Department of Organismic and Evolutionary BiologyHarvard UniversityCambridgeMassachusettsUSA
- Department of Biodiversity, Ecology and EvolutionUCMMadridSpain
| | | | - José A. Díaz
- Department of Biodiversity, Ecology and EvolutionUCMMadridSpain
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8
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de Souza TE, Cruz GADS, de Moura RDC. Impact of Limited Dispersion Capacity and Natural Barriers on the Population Structure of the Grasshopper Ommexecha virens (Orthoptera: Ommexechidae). NEOTROPICAL ENTOMOLOGY 2021; 50:706-715. [PMID: 33978918 DOI: 10.1007/s13744-021-00878-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Accepted: 04/21/2021] [Indexed: 06/12/2023]
Abstract
The grasshopper Ommexecha virens Serville has low dispersion capacity, and it is regarded as a specialist, only being found in sandy, dry environments with high incidence of sunlight. Considering these aspects, we evaluated the diversity and genetic structure of O. virens natural populations using ISSR (Inter Simple Sequence Repeat) markers. The data pointed to low expected heterozygosity for some populations (HE = 0.06-0.09), probably a consequence of positive inbreeding, which is typical of species showing low or null dispersion indices. Moreover, significant genetic differentiation was observed (FST = 0.50 and GST = 0.51), as well as low number of migrants (Nm = 0.47), indicating that the populations are genetically differentiated. This is likely related to the limitation in dispersing and fragmentation of suitable environment localities colonized by O. virens. The populations of O. virens were structured in three genetic groups associated to different landscapes, revealing the presence of a secondary contact zone, possibly arisen from isolation followed by genetic divergence among populations and subsequent gene flow of divergent individuals of O. virens. At last, we found positive isolation by distance (IBD; r: 0.427; P: 0.025) which is an important factor, since it may be adding to the emergence of reproductive barriers among individuals of O. virens that have been experiencing isolation.
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Affiliation(s)
- Tyago Eufrásio de Souza
- Laboratório de Biodiversidade e Genética de Insetos, Universidade de Pernambuco (UPE), Recife, Pernambuco, Brazil
| | - Geyner Alves Dos Santos Cruz
- Laboratório de Biodiversidade e Genética de Insetos, Universidade de Pernambuco (UPE), Recife, Pernambuco, Brazil.
- Laboratório de Biodiversidade e Genética Evolutiva, Universidade de Pernambuco (UPE), Petrolina, Pernambuco, Brazil.
| | - Rita de Cássia de Moura
- Laboratório de Biodiversidade e Genética de Insetos, Universidade de Pernambuco (UPE), Recife, Pernambuco, Brazil.
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9
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Govaert L, De Meester L, Rousseaux S, Declerck SAJ, Pantel JH. Measuring the contribution of evolution to community trait structure in freshwater zooplankton. OIKOS 2021. [DOI: 10.1111/oik.07885] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Affiliation(s)
- Lynn Govaert
- Leibniz Inst. für Gewässerökologie und Binnenfischerei (IGB) Berlin Germany
- Laboratory of Aquatic Ecology, Evolution and Conservation, KU Leuven Leuven Belgium
- Dept of Evolutionary Biology and Environmental Studies, Univ. of Zurich Zurich Switzerland
- Swiss Federal Inst. of Aquatic Science and Technology, Dept of Aquatic Ecology Dübendorf Switzerland
- URPP Global Change and Biodiversity, Univ. of Zurich Zurich Switzerland
| | - Luc De Meester
- Leibniz Inst. für Gewässerökologie und Binnenfischerei (IGB) Berlin Germany
- Laboratory of Aquatic Ecology, Evolution and Conservation, KU Leuven Leuven Belgium
- Inst. of Biology, Freie Univ. Berlin Berlin Germany
| | - Sarah Rousseaux
- Leibniz Inst. für Gewässerökologie und Binnenfischerei (IGB) Berlin Germany
- Laboratory of Aquatic Ecology, Evolution and Conservation, KU Leuven Leuven Belgium
- Natuurinvest, Maatschappelijke zetel Brussel, Herman Teirlinckgebouw Brussel Belgium
| | - Steven A. J. Declerck
- Leibniz Inst. für Gewässerökologie und Binnenfischerei (IGB) Berlin Germany
- Laboratory of Aquatic Ecology, Evolution and Conservation, KU Leuven Leuven Belgium
- Dept of Aquatic Ecology, Netherlands Inst. of Ecology (NIOO‐KNAW) Wageningen the Netherlands
| | - Jelena H. Pantel
- Leibniz Inst. für Gewässerökologie und Binnenfischerei (IGB) Berlin Germany
- Laboratory of Aquatic Ecology, Evolution and Conservation, KU Leuven Leuven Belgium
- Dept of Computer Science, Mathematics and Environmental Science, The American Univ. of Paris Paris France
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10
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Leal BSS, Chaves CJN, Graciano VA, Boury C, Huacre LAP, Heuertz M, Palma-Silva C. Evidence of local adaptation despite strong drift in a Neotropical patchily distributed bromeliad. Heredity (Edinb) 2021; 127:203-218. [PMID: 33953353 PMCID: PMC8322333 DOI: 10.1038/s41437-021-00442-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2020] [Revised: 04/16/2021] [Accepted: 04/17/2021] [Indexed: 02/03/2023] Open
Abstract
Both genetic drift and divergent selection are predicted to be drivers of population differentiation across patchy habitats, but the extent to which these forces act on natural populations to shape traits is strongly affected by species' ecological features. In this study, we infer the genomic structure of Pitcairnia lanuginosa, a widespread herbaceous perennial plant with a patchy distribution. We sampled populations in the Brazilian Cerrado and the Central Andean Yungas and discovered and genotyped SNP markers using double-digest restriction-site associated DNA sequencing. In addition, we analyzed ecophysiological traits obtained from a common garden experiment and compared patterns of phenotypic and genetic divergence (PST-FST comparisons) in a subset of populations from the Cerrado. Our results from molecular analyses pointed to extremely low genetic diversity and a remarkable population differentiation, supporting a major role of genetic drift. Approximately 0.3% of genotyped SNPs were flagged as differentiation outliers by at least two distinct methods, and Bayesian generalized linear mixed models revealed a signature of isolation by environment in addition to isolation by distance for high-differentiation outlier SNPs among the Cerrado populations. PST-FST comparisons suggested divergent selection on two ecophysiological traits linked to drought tolerance. We showed that these traits vary among populations, although without any particular macro-spatial pattern, suggesting local adaptation to differences in micro-habitats. Our study shows that selection might be a relevant force, particularly for traits involved in drought stress, even for populations experiencing strong drift, which improves our knowledge on eco-evolutionary processes acting on non-continuously distributed species.
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Affiliation(s)
- Bárbara Simões Santos Leal
- grid.410543.70000 0001 2188 478XDepartamento de Ecologia, Instituto de Biociências, Universidade Estadual Paulista, Rio Claro, São Paulo Brazil
| | - Cleber Juliano Neves Chaves
- grid.410543.70000 0001 2188 478XDepartamento de Ecologia, Instituto de Biociências, Universidade Estadual Paulista, Rio Claro, São Paulo Brazil
| | - Vanessa Araujo Graciano
- grid.410543.70000 0001 2188 478XDepartamento de Ecologia, Instituto de Biociências, Universidade Estadual Paulista, Rio Claro, São Paulo Brazil
| | - Christophe Boury
- grid.412041.20000 0001 2106 639XINRAE, Univ. Bordeaux, Biogeco, Cestas France
| | - Luis Alberto Pillaca Huacre
- grid.10800.390000 0001 2107 4576Departamento de Ecología, Museo de Historia Natural de la Universidad Nacional Mayor de San Marcos, Lima, Peru
| | - Myriam Heuertz
- grid.412041.20000 0001 2106 639XINRAE, Univ. Bordeaux, Biogeco, Cestas France
| | - Clarisse Palma-Silva
- grid.410543.70000 0001 2188 478XDepartamento de Ecologia, Instituto de Biociências, Universidade Estadual Paulista, Rio Claro, São Paulo Brazil ,grid.411087.b0000 0001 0723 2494Departamento de Biologia Vegetal, Instituto de Biologia, Universidade Estadual de Campinas, Campinas, São Paulo, Brazil
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11
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Ahrens CW, Jordan R, Bragg J, Harrison PA, Hopley T, Bothwell H, Murray K, Steane DA, Whale JW, Byrne M, Andrew R, Rymer PD. Regarding the F-word: The effects of data filtering on inferred genotype-environment associations. Mol Ecol Resour 2021; 21:1460-1474. [PMID: 33565725 DOI: 10.1111/1755-0998.13351] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Revised: 02/01/2021] [Accepted: 02/05/2021] [Indexed: 01/05/2023]
Abstract
Genotype-environment association (GEA) methods have become part of the standard landscape genomics toolkit, yet, we know little about how to best filter genotype-by-sequencing data to provide robust inferences for environmental adaptation. In many cases, default filtering thresholds for minor allele frequency and missing data are applied regardless of sample size, having unknown impacts on the results, negatively affecting management strategies. Here, we investigate the effects of filtering on GEA results and the potential implications for assessment of adaptation to environment. We use empirical and simulated data sets derived from two widespread tree species to assess the effects of filtering on GEA outputs. Critically, we find that the level of filtering of missing data and minor allele frequency affect the identification of true positives. Even slight adjustments to these thresholds can change the rate of true positive detection. Using conservative thresholds for missing data and minor allele frequency substantially reduces the size of the data set, lessening the power to detect adaptive variants (i.e., simulated true positives) with strong and weak strengths of selection. Regardless, strength of selection was a good predictor for GEA detection, but even some SNPs under strong selection went undetected. False positive rates varied depending on the species and GEA method, and filtering significantly impacted the predictions of adaptive capacity in downstream analyses. We make several recommendations regarding filtering for GEA methods. Ultimately, there is no filtering panacea, but some choices are better than others, depending on the study system, availability of genomic resources, and desired objectives.
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Affiliation(s)
- Collin W Ahrens
- Hawkesbury Institute for the Environment, Western Sydney University, Richmond, NSW, Australia
| | | | - Jason Bragg
- Research Centre for Ecosystem Resilience, Australian Institute of Botanical Science, The Royal Botanic Garden, Sydney, NSW, Australia
| | - Peter A Harrison
- School of Natural Sciences and Australian Research Council Training Centre for Forest Value, University of Tasmania, Hobart, Tas., Australia
| | - Tara Hopley
- Department of Biodiversity, Conservation and Attractions, Biodiversity and Conservation Science, Perth, WA, Australia
| | | | - Kevin Murray
- Australian National University, Acton, ACT, Australia
| | - Dorothy A Steane
- CSIRO Land & Water, Hobart, Tas., Australia.,School of Natural Sciences and Australian Research Council Training Centre for Forest Value, University of Tasmania, Hobart, Tas., Australia
| | - John W Whale
- Hawkesbury Institute for the Environment, Western Sydney University, Richmond, NSW, Australia
| | - Margaret Byrne
- Department of Biodiversity, Conservation and Attractions, Biodiversity and Conservation Science, Perth, WA, Australia
| | - Rose Andrew
- School of Environmental and Rural Science, University of New England, Armidale, NSW, Australia
| | - Paul D Rymer
- Hawkesbury Institute for the Environment, Western Sydney University, Richmond, NSW, Australia
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12
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Meng X, Liu T, Zhang L, Jin L, Sun K, Feng J. Effects of Colonization, Geography and Environment on Genetic Divergence in the Intermediate Leaf-Nosed Bat, Hipposideros larvatus. Animals (Basel) 2021; 11:733. [PMID: 33800251 PMCID: PMC7998825 DOI: 10.3390/ani11030733] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Revised: 02/27/2021] [Accepted: 03/03/2021] [Indexed: 11/16/2022] Open
Abstract
Determining the evolutionary history and population drivers, such as past large-scale climatic oscillations, stochastic processes and ecological adaptations, represents one of the aims of evolutionary biology. Hipposideros larvatus is a common bat species in Southern China, including Hainan Island. We examined genetic variation in H. larvatus using mitochondrial DNA and nuclear microsatellites. We found a population structure on both markers with a geographic pattern that corresponds well with the structure on mainland China and Hainan Island. To understand the contributions of geography, the environment and colonization history to the observed population structure, we tested isolation by distance (IBD), isolation by adaptation (IBA) and isolation by colonization (IBC) using serial Mantel tests and RDA analysis. The results showed significant impacts of IBD, IBA and IBC on neutral genetic variation, suggesting that genetic variation in H. larvatus is greatly affected by neutral processes, environmental adaptation and colonization history. This study enriches our understanding of the complex evolutionary forces that shape the distribution of genetic variation in bats.
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Affiliation(s)
- Xiangfeng Meng
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun 130117, China; (X.M.); (T.L.); (L.Z.); (J.F.)
| | - Tong Liu
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun 130117, China; (X.M.); (T.L.); (L.Z.); (J.F.)
| | - Lin Zhang
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun 130117, China; (X.M.); (T.L.); (L.Z.); (J.F.)
| | - Longru Jin
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun 130117, China; (X.M.); (T.L.); (L.Z.); (J.F.)
| | - Keping Sun
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun 130117, China; (X.M.); (T.L.); (L.Z.); (J.F.)
- Key Laboratory of Vegetation Ecology, Ministry of Education, Changchun 130024, China
| | - Jiang Feng
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun 130117, China; (X.M.); (T.L.); (L.Z.); (J.F.)
- School of Life Science, Jilin Agricultural University, Changchun 130118, China
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13
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Tesson SVM, Sha Y. Population connectivity, dispersal, and swimming behavior in Daphnia. Ecol Evol 2021; 11:2873-2885. [PMID: 33767843 PMCID: PMC7981204 DOI: 10.1002/ece3.7246] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 12/30/2020] [Accepted: 01/12/2021] [Indexed: 11/23/2022] Open
Abstract
The water flea Daphnia has the capacity to respond rapidly to environmental stressors, to disperse over large geographical scales, and to preserve its genetic material by forming egg banks in the sediment. Spatial and temporal distributions of D. magna have been extensively studied over the last decades using behavioral or genetic tools, although the correlation between the two has rarely been the focus. In the present study, we therefore investigated the population genetic structure and behavioral response to a lethal threat, ultraviolet radiation (UVR), among individuals from two different water bodies. Our results show two genetic populations with moderate gene flow, highly correlated with geographical location and with inheritable traits through generations. However, despite the strong genetic differences between populations, we show homogeneous refuge demand between populations when exposed to the lethal threat solar UVR.
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Affiliation(s)
- Sylvie V. M. Tesson
- Department of BiologyAarhus UniversityAarhusDenmark
- Department of BiologyLund UniversityLundSweden
| | - Yongcui Sha
- Department of BiologyLund UniversityLundSweden
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14
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Martin GK, Beisner BE, Chain FJJ, Cristescu ME, Del Giorgio PA, Derry AM. Freshwater zooplankton metapopulations and metacommunities respond differently to environmental and spatial variation. Ecology 2020; 102:e03224. [PMID: 33067865 DOI: 10.1002/ecy.3224] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 07/22/2020] [Accepted: 08/17/2020] [Indexed: 11/09/2022]
Abstract
Theory predicts that population genetic structure and metacommunity structure are linked by the common processes of drift and migration, but how population genetic structure and metacommunity structure are related in nature is still unknown. Deeper understanding of the processes influencing both genetic and community diversity is vital for better predicting how environmental change will impact biodiversity patterns. We examined how crustacean zooplankton and rotifer species' metapopulation genetic structure and metacommunities respond to environmental and spatial variation both within and across four regions of boreal Canada. Metapopulation and metacommunity variation partitioning results were compared within and across the four regions. Metapopulations and metacommunities responded differently to environmental variation and spatial structure both within and across regions, as metapopulations were influenced by different environmental variables compared to metacommunities. At larger spatial scales both metapopulations and metacommunities exhibited greater spatial and environmental structuring, again responding to a different subset of environmental variables. Our findings suggest that even though both genetic and species diversity are linked by the same processes, regional variation in environmental characteristics and spatial structure influence resulting biodiversity patterns differently. To date, no other empirical research has explored relationships between entire metapopulation and metacommunity assemblages at large regional spatial scales.
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Affiliation(s)
- Gillian K Martin
- Department of Biological Sciences, Groupe de Recherche Interuniversitaire en Limnologie (GRIL), University of Québec at Montreal, Québec, H2X 3Y7, Canada
| | - Beatrix E Beisner
- Department of Biological Sciences, Groupe de Recherche Interuniversitaire en Limnologie (GRIL), University of Québec at Montreal, Québec, H2X 3Y7, Canada
| | - Frédéric J J Chain
- Department of Biological Science, University of Massachusetts Lowell, Massachusetts, 01854, USA
| | - Melania E Cristescu
- Department of Biology, Groupe de Recherche Interuniversitaire en Limnologie (GRIL), McGill University, Québec, H3A 1B1, Canada
| | - Paul A Del Giorgio
- Department of Biological Sciences, Groupe de Recherche Interuniversitaire en Limnologie (GRIL), University of Québec at Montreal, Québec, H2X 3Y7, Canada
| | - Alison M Derry
- Department of Biological Sciences, Groupe de Recherche Interuniversitaire en Limnologie (GRIL), University of Québec at Montreal, Québec, H2X 3Y7, Canada
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15
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Chan KO, Brown RM. Elucidating the drivers of genetic differentiation in Malaysian torrent frogs (Anura: Ranidae: Amolops): a landscape genomics approach. Zool J Linn Soc 2019. [DOI: 10.1093/zoolinnean/zlz151] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Abstract
The interplay between environmental attributes and evolutionary processes can provide valuable insights into how biodiversity is generated, partitioned and distributed. This study investigates the role of spatial, environmental and historical factors that could potentially drive diversification and shape genetic variation in Malaysian torrent frogs. Torrent frogs are ecologically conserved, and we hypothesize that this could impose tight constraints on dispersal routes, gene flow and consequently genetic structure. Moreover, levels of gene flow were shown to vary among populations from separate mountain ranges, indicating that genetic differentiation could be influenced by landscape features. Using genome-wide single nucleotide polymorphisms, in conjunction with landscape variables derived from Geographic Information Systems, we performed distance-based redundancy analyses and variance partitioning to disentangle the effects of isolation-by-distance (IBD), isolation-by-resistance (IBR) and isolation-by-colonization (IBC). Our results demonstrated that IBR contributed minimally to genetic variation. Intraspecific population structure can be largely attributed to IBD, whereas interspecific diversification was primarily driven by IBC. We also detected two distinct population bottlenecks, indicating that speciation events were likely driven by vicariance or founder events.
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Affiliation(s)
- Kin Onn Chan
- Biodiversity Institute and Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, Kansas, USA
- Lee Kong Chian Natural History Museum, Faculty of Science, National University of Singapore, Singapore, Singapore
| | - Rafe M Brown
- Biodiversity Institute and Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, Kansas, USA
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16
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Lelwala RV, Scott JB, Ades PK, Taylor PWJ. Population Structure of Colletotrichum tanaceti in Australian Pyrethrum Reveals High Evolutionary Potential. PHYTOPATHOLOGY 2019; 109:1779-1792. [PMID: 31179858 DOI: 10.1094/phyto-03-19-0091-r] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Colletotrichum tanaceti, the causal agent of anthracnose, is an emerging pathogen of commercially grown pyrethrum (Tanacetum cinerariifolium) in Australia. A microsatellite marker library was developed to understand the spatio-genetic structure over three sampled years and across two regions where pyrethrum is cultivated in Australia. Results indicated that C. tanaceti was highly diverse with a mixed reproductive mode; comprising both sexual and clonal reproduction. Sexual reproduction of C. tanaceti was more prevalent in Tasmania than in Victoria. Little differentiation was observed among field populations likely due to isolation by colonization but most of the genetic variation was occurring within populations. C. tanaceti was likely to have had a long-distance gene and genotype flow among distant populations within a state and between states. Anthropogenic transmission of propagules and wind dispersal of ascospores are the most probable mechanisms of long-distance dispersal of C. tanaceti. Evaluation of putative population histories suggested that C. tanaceti most likely originated in Tasmania and expanded from an unidentified host onto pyrethrum. Victoria was later invaded by the Tasmanian population. With the mixed mode of reproduction and possible long-distance gene flow, C. tanaceti is likely to have a high evolutionary potential and thereby has ability to adapt to management practices in the future.
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Affiliation(s)
- Ruvini V Lelwala
- School of Agriculture and Food, Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Victoria, Australia 3010
| | - Jason B Scott
- Tasmanian Institute of Agriculture, University of Tasmania, Burnie, Tasmania, Australia 7320
| | - Peter K Ades
- School of Ecosystem and Forest Sciences, University of Melbourne, Victoria, Australia 3010
| | - Paul W J Taylor
- School of Agriculture and Food, Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Victoria, Australia 3010
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17
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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.
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Cornetti L, Fields PD, Van Damme K, Ebert D. A fossil-calibrated phylogenomic analysis of Daphnia and the Daphniidae. Mol Phylogenet Evol 2019; 137:250-262. [DOI: 10.1016/j.ympev.2019.05.018] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Revised: 05/03/2019] [Accepted: 05/20/2019] [Indexed: 11/16/2022]
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19
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Contemporary and historical river connectivity influence population structure in western brook lamprey in the Columbia River Basin. CONSERV GENET 2018. [DOI: 10.1007/s10592-018-1137-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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20
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Montero-Pau J, Gómez A, Serra M. Founder effects drive the genetic structure of passively dispersed aquatic invertebrates. PeerJ 2018; 6:e6094. [PMID: 30581680 PMCID: PMC6294052 DOI: 10.7717/peerj.6094] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Accepted: 11/10/2018] [Indexed: 11/25/2022] Open
Abstract
Populations of passively dispersed organisms in continental aquatic habitats typically show high levels of neutral genetic differentiation despite their high dispersal capabilities. Several evolutionary factors, including founder events, local adaptation, and life cycle features such as high population growth rates and the presence of propagule banks, have been proposed to be responsible for this paradox. Here, we have modeled the colonization process to assess the impact of migration rate, population growth rate, population size, local adaptation and life-cycle features on the population genetic structure in these organisms. Our simulations show that the strongest effect on population structure are persistent founder effects, resulting from the interaction of a few population founders, high population growth rates, large population sizes and the presence of diapausing egg banks. In contrast, the role of local adaptation, genetic hitchhiking and migration is limited to small populations in these organisms. Our results indicate that local adaptation could have different impact on genetic structure in different groups of zooplankters.
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Affiliation(s)
- Javier Montero-Pau
- Department of Biochemistry and Molecular Biology, Universidad de Valencia, Valencia, Spain.,Department of Biological Sciences, University of Hull, Hull, United Kingdom
| | - Africa Gómez
- Department of Biological Sciences, University of Hull, Hull, United Kingdom
| | - Manuel Serra
- Instituto Cavanilles de Biodiversidad y Biología Evolutiva, Universidad de Valencia, Valencia, Spain
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21
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Li JX, Zhu XH, Li Y, Liu Y, Qian ZH, Zhang XX, Sun Y, Ji LY. Adaptive genetic differentiation in Pterocarya stenoptera (Juglandaceae) driven by multiple environmental variables were revealed by landscape genomics. BMC PLANT BIOLOGY 2018; 18:306. [PMID: 30482158 PMCID: PMC6260741 DOI: 10.1186/s12870-018-1524-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Accepted: 11/14/2018] [Indexed: 05/06/2023]
Abstract
BACKGROUND The investigation of the genetic basis of local adaptation in non-model species is an interesting focus of evolutionary biologists and molecular ecologists. Identifying these adaptive genetic variabilities on the genome responsible can provide insight into the genetic mechanism of local adaptation. RESULTS We investigated the spatial distribution of genetic variation in 22 natural populations of Pterocarya stenoptera across its distribution area in China to provide insights into the complex interplay between multiple environmental variables and adaptive genetic differentiation. The Bayesian analysis of population structure showed that the 22 populations of P. stenoptera were subdivided into two groups. Redundancy analysis demonstrated that this genetic differentiation was caused by the divergent selection of environmental difference. A total of 44 outlier loci were mutually identified by Arlequin and BayeScan, 43 of which were environment-associated loci (EAL). The results of latent factor mixed model analysis showed that solar radiation in June (Sr6), minimum temperature of the coldest month (Bio6), temperature seasonality (Bio4), and water vapor pressure in January (Wvp1) were associated with the highest numbers of EAL. Sr6 was associated with the ecological habitat of "prefered light", and Bio6 and Wvp1 were associated with the ecological habitat of "warm and humid environment". CONCLUSIONS Our results provided empirical evidence that environmental variables related to the ecological habitats of species play key roles in driving adaptive differentiation of species genome.
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Affiliation(s)
- Jia-Xin Li
- Innovation Platform of Molecular Biology, College of Forestry, Henan Agricultural University, No.95, Wenhua Road, Zhengzhou, 450002 China
| | - Xiu-Hong Zhu
- Innovation Platform of Molecular Biology, College of Forestry, Henan Agricultural University, No.95, Wenhua Road, Zhengzhou, 450002 China
| | - Yong Li
- Innovation Platform of Molecular Biology, College of Forestry, Henan Agricultural University, No.95, Wenhua Road, Zhengzhou, 450002 China
| | - Ying Liu
- Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, No.135, Xingang Xi Road, Guangzhou, 510275 China
| | - Zhi-Hao Qian
- Innovation Platform of Molecular Biology, College of Forestry, Henan Agricultural University, No.95, Wenhua Road, Zhengzhou, 450002 China
| | - Xue-Xia Zhang
- Innovation Platform of Molecular Biology, College of Forestry, Henan Agricultural University, No.95, Wenhua Road, Zhengzhou, 450002 China
| | - Yue Sun
- Innovation Platform of Molecular Biology, College of Forestry, Henan Agricultural University, No.95, Wenhua Road, Zhengzhou, 450002 China
| | - Liu-Yang Ji
- Innovation Platform of Molecular Biology, College of Forestry, Henan Agricultural University, No.95, Wenhua Road, Zhengzhou, 450002 China
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22
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Isolation and cross-amplification of the first set of polymorphic microsatellite markers of two high-Andean cushion plants. J Genet 2018. [DOI: 10.1007/s12041-018-0999-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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23
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Al-Breiki RD, Kjeldsen SR, Afzal H, Al Hinai MS, Zenger KR, Jerry DR, Al-Abri MA, Delghandi M. Genome-wide SNP analyses reveal high gene flow and signatures of local adaptation among the scalloped spiny lobster (Panulirus homarus) along the Omani coastline. BMC Genomics 2018; 19:690. [PMID: 30231936 PMCID: PMC6146514 DOI: 10.1186/s12864-018-5044-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Accepted: 08/27/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The scalloped spiny lobster (Panulirus homarus) is a popular seafood commodity worldwide and an important export item from Oman. Annual catches in commercial fisheries are in serious decline, which has resulted in calls for the development of an integrated stock management approach. In Oman, the scalloped spiny lobster is currently treated as a single management unit (MU) or stock and there is an absence of information on the genetic population structure of the species that can inform management decisions, particularly at a fine-scale level. This work is the first to identify genome-wide single nucleotide polymorphisms (SNPs) for P. homarus using Diversity Arrays Technology sequencing (DArT-seq) and to elucidate any stock structure in the species. RESULTS After stringent filtering, 7988 high utility SNPs were discovered and used to assess the genetic diversity, connectivity and structure of P. homarus populations from Al Ashkharah, Masirah Island, Duqm, Ras Madrakah, Haitam, Ashuwaymiyah, Mirbat and Dhalkut landing sites. Pairwise FST estimates revealed low differentiation among populations (pairwise FST range = - 0.0008 - 0.0021). Analysis of genetic variation using putatively directional FST outliers (504 SNPs) revealed higher and significant pairwise differentiation (p < 0.01) for all locations, with Ashuwaymiyah being the most diverged population (Ashuwaymiyah pairwise FST range = 0.0288-0.0736). Analysis of population structure using Discriminant Analysis of Principal Components (DAPC) revealed a broad admixture among P. homarus, however, Ashuwaymiyah stock appeared to be potentially under local adaptive pressures. Fine scale analysis using Netview R provided further support for the general admixture of P. homarus. CONCLUSIONS Findings here suggested that stocks of P. homarus along the Omani coastline are admixed. Yet, fishery managers need to treat the lobster stock from Ashuwaymiyah with caution as it might be subject to local adaptive pressures. We emphasize further study with larger number of samples to confirm the genetic status of the Ashuwaymiyah stock. The approach utilised in this study has high transferability in conservation and management of other marine stocks with similar biological and ecological attributes.
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Affiliation(s)
- Rufaida Dhuhai Al-Breiki
- Centre of Excellence in Marine Biotechnology, Sultan Qaboos University, P.O. Box 50, Al-Khoud, 123 Muscat, Sultanate of Oman
- College of Agriculture and Marine Sciences, Department of Marine Sciences and Fisheries, Sultan Qaboos University, P.O. Box 34, Al-Khoud, 123 Muscat, Sultanate of Oman
| | - Shannon R. Kjeldsen
- Centre for Sustainable Tropical Fisheries and Aquaculture and College of Science and Engineering, James Cook University, Townsville, QLD 4810 Australia
| | - Hasifa Afzal
- Centre of Excellence in Marine Biotechnology, Sultan Qaboos University, P.O. Box 50, Al-Khoud, 123 Muscat, Sultanate of Oman
| | - Manal Saif Al Hinai
- Centre of Excellence in Marine Biotechnology, Sultan Qaboos University, P.O. Box 50, Al-Khoud, 123 Muscat, Sultanate of Oman
| | - Kyall R. Zenger
- Centre for Sustainable Tropical Fisheries and Aquaculture and College of Science and Engineering, James Cook University, Townsville, QLD 4810 Australia
| | - Dean R. Jerry
- Centre for Sustainable Tropical Fisheries and Aquaculture and College of Science and Engineering, James Cook University, Townsville, QLD 4810 Australia
| | - Mohammed Ali Al-Abri
- College of Agriculture and Marine Sciences, Department of Animal and Veterinary Sciences and Technology, Sultan Qaboos University, P.O. Box 34, Al-Khoud, 123 Muscat, Sultanate of Oman
| | - Madjid Delghandi
- Centre of Excellence in Marine Biotechnology, Sultan Qaboos University, P.O. Box 50, Al-Khoud, 123 Muscat, Sultanate of Oman
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Nogués-Bravo D, Rodríguez-Sánchez F, Orsini L, de Boer E, Jansson R, Morlon H, Fordham DA, Jackson ST. Cracking the Code of Biodiversity Responses to Past Climate Change. Trends Ecol Evol 2018; 33:765-776. [PMID: 30173951 DOI: 10.1016/j.tree.2018.07.005] [Citation(s) in RCA: 64] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2017] [Revised: 07/16/2018] [Accepted: 07/18/2018] [Indexed: 01/17/2023]
Abstract
How individual species and entire ecosystems will respond to future climate change are among the most pressing questions facing ecologists. Past biodiversity dynamics recorded in the paleoecological archives show a broad array of responses, yet significant knowledge gaps remain. In particular, the relative roles of evolutionary adaptation, phenotypic plasticity, and dispersal in promoting survival during times of climate change have yet to be clarified. Investigating the paleo-archives offers great opportunities to understand biodiversity responses to future climate change. In this review we discuss the mechanisms by which biodiversity responds to environmental change, and identify gaps of knowledge on the role of range shifts and tolerance. We also outline approaches at the intersection of paleoecology, genomics, experiments, and predictive models that will elucidate the processes by which species have survived past climatic changes and enhance predictions of future changes in biological diversity.
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Affiliation(s)
- David Nogués-Bravo
- Center for Macroecology, Evolution and Climate, Natural History Museum of Denmark, University of Copenhagen, Universitetsparken 15, Copenhagen, DK-2100, Denmark.
| | - Francisco Rodríguez-Sánchez
- Departamento de Ecología Integrativa, Estación Biológica de Doñana, Consejo Superior de Investigaciones Científicas, Avda. Américo Vespucio 26, E-41092, Sevilla, Spain
| | - Luisa Orsini
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Erik de Boer
- Institute of Earth Sciences Jaume Almera, Consejo Superior de Investigaciones Científicas, C/Lluís Solé i Sabarís s/n, 08028 Barcelona, Spain
| | - Roland Jansson
- Department of Ecology and Environmental Science, Umeå University, 901 87 Umeå, Sweden
| | - Helene Morlon
- Institut de Biologie, Ecole Normale Supérieure, UMR 8197 CNRS, Paris, France
| | - Damien A Fordham
- Center for Macroecology, Evolution and Climate, Natural History Museum of Denmark, University of Copenhagen, Universitetsparken 15, Copenhagen, DK-2100, Denmark; The Environment Institute, School of Earth and Environmental Sciences, The University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Stephen T Jackson
- Southwest Climate Science Center, US Geological Survey, Tucson, AZ 85719, USA; Department of Geosciences and School of Natural Resources and Environment, University of Arizona, Tucson, AZ 85721, USA
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25
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Subsampling reveals that unbalanced sampling affects STRUCTURE results in a multi-species dataset. Heredity (Edinb) 2018; 122:276-287. [PMID: 30026534 DOI: 10.1038/s41437-018-0124-8] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2018] [Revised: 06/04/2018] [Accepted: 06/06/2018] [Indexed: 11/08/2022] Open
Abstract
Studying the genetic population structure of species can reveal important insights into several key evolutionary, historical, demographic, and anthropogenic processes. One of the most important statistical tools for inferring genetic clusters is the program STRUCTURE. Recently, several papers have pointed out that STRUCTURE may show a bias when the sampling design is unbalanced, resulting in spurious joining of underrepresented populations and spurious separation of overrepresented populations. Suggestions to overcome this bias include subsampling and changing the ancestry model, but the performance of these two methods has not yet been tested on actual data. Here, I use a data set of 12 high-alpine plant species to test whether unbalanced sampling affects the STRUCTURE inference of population differentiation between the European Alps and the Carpathians. For four of the 12 species, subsampling of the Alpine populations-to match the sample size between the Alps and the Carpathians-resulted in a drastically different clustering than the full data set. On the other hand, STRUCTURE results with the alternative ancestry model were indistinguishable from the results with the default model. Based on these results, the subsampling strategy seems a more viable approach to overcome the bias than the alternative ancestry model. However, subsampling is only possible when there is an a priori expectation of what constitute the main clusters. Though these results do not mean that the use of STRUCTURE should be discarded, it does indicate that users of the software should be cautious about the interpretation of the results when sampling is unbalanced.
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Weak population structure and no genetic erosion in Pilosocereus aureispinus: A microendemic and threatened cactus species from eastern Brazil. PLoS One 2018; 13:e0195475. [PMID: 29630653 PMCID: PMC5890996 DOI: 10.1371/journal.pone.0195475] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Accepted: 03/24/2018] [Indexed: 01/23/2023] Open
Abstract
Succulent cacti (Cactaceae) are among the most threatened taxonomic groups assessed to date. Here we evaluated the genetic diversity and population structure of a narrow endemic columnar cactus Pilosocereus aureispinus. This species is only found in a small area of c. 300 km2 of rocky savanna from eastern Brazil and it is currently classified as vulnerable (VU) on the International Union for Conservation of Nature (IUCN) red list. Eight microsatellite loci were genotyped for 91 individuals from four localities of the known P. aureispinus range. In contrast with expectations for narrow endemic species, we found relatively high levels of genetic diversity (e.g., HE = 0.390 to 0.525; HO = 0.394 to 0.572) and very low population structure based on the variation of six loci. All the analyzed individuals were clustered in one unique genetic group in assignment tests. We also generated the sequences of two plastid markers (trnT-trnL and psbD-trnT) and found no variation on a subsample of 39 individuals. We used Landsat 8 images and Normalized Difference Vegetation Index to estimate a potential extent of occurrence of c. 750 km2 for this species. Our results showed that P. aureispinus is not suffering from erosion of nuclear genetic variability due to its narrow distribution. However, we advocate that because of the extremely limited extent of occurrence, the ongoing anthropogenic disturbances in its habitat, and phylogenetic distinctiveness of P. aureispinus, this species should be classified as endangered (EN) on the IUCN Red List.
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Sefbom J, Kremp A, Rengefors K, Jonsson PR, Sjöqvist C, Godhe A. A planktonic diatom displays genetic structure over small spatial scales. Environ Microbiol 2018; 20:2783-2795. [PMID: 29614214 DOI: 10.1111/1462-2920.14117] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2016] [Accepted: 03/22/2018] [Indexed: 11/30/2022]
Abstract
Marine planktonic microalgae have potentially global dispersal, yet reduced gene flow has been confirmed repeatedly for several species. Over larger distances (>200 km) geographic isolation and restricted oceanographic connectivity have been recognized as instrumental in driving population divergence. Here we investigated whether similar patterns, that is, structured populations governed by geographic isolation and/or oceanographic connectivity, can be observed at smaller (6-152 km) geographic scales. To test this we established 425 clonal cultures of the planktonic diatom Skeletonema marinoi collected from 11 locations in the Archipelago Sea (northern Baltic Sea). The region is characterized by a complex topography, entailing several mixing regions of which four were included in the sampling area. Using eight microsatellite markers and conventional F-statistics, significant genetic differentiation was observed between several sites. Moreover, Bayesian cluster analysis revealed the co-occurrence of two genetic groups spread throughout the area. However, geographic isolation and oceanographic connectivity could not explain the genetic patterns observed. Our data reveal hierarchical genetic structuring whereby despite high dispersal potential, significantly diverged populations have developed over small spatial scales. Our results suggest that biological characteristics and historical events may be more important in generating barriers to gene flow than physical barriers at small spatial scales.
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Affiliation(s)
- Josefin Sefbom
- Department of Marine Sciences, University of Gothenburg, Gothenberg, Sweden
| | - Anke Kremp
- Marine Research Centre, Finnish Environment Institute (SYKE), Helsinki, Finland
| | - Karin Rengefors
- Aquatic Ecology, Department of Biology, Lund University, Lund, Sweden
| | - Per R Jonsson
- Department of Marine Sciences-Tjärnö, University of Gothenburg, Gothenberg, Sweden
| | - Conny Sjöqvist
- Marine Research Centre, Finnish Environment Institute (SYKE), Helsinki, Finland.,Environmental and Marine Biology, Åbo Akademi University, Åbo, Finland
| | - Anna Godhe
- Department of Marine Sciences, University of Gothenburg, Gothenberg, Sweden
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Bekker EI, Karabanov DP, Galimov YR, Haag CR, Neretina TV, Kotov AA. Phylogeography of Daphnia magna Straus (Crustacea: Cladocera) in Northern Eurasia: Evidence for a deep longitudinal split between mitochondrial lineages. PLoS One 2018; 13:e0194045. [PMID: 29543844 PMCID: PMC5854346 DOI: 10.1371/journal.pone.0194045] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2017] [Accepted: 02/25/2018] [Indexed: 11/30/2022] Open
Abstract
Species with a large geographic distributions present a challenge for phylogeographic studies due to logistic difficulties of obtaining adequate sampling. For instance, in most species with a Holarctic distribution, the majority of studies has concentrated on the European or North American part of the distribution, with the Eastern Palearctic region being notably understudied. Here, we study the phylogeography of the freshwater cladoceran Daphnia magna Straus, 1820 (Crustacea: Cladocera), based on partial mitochondrial COI sequences and using specimens from populations spread longitudinally from westernmost Europe to easternmost Asia, with many samples from previously strongly understudied regions in Siberia and Eastern Asia. The results confirm the previously suspected deep split between Eastern and Western mitochondrial haplotype super-clades. We find a narrow contact zone between these two super-clades in the eastern part of Western Siberia, with proven co-occurrence in a single lake in the Novosibirsk region. However, at present there is no evidence suggesting that the two mitochondrial super-clades represent cryptic species. Rather, they may be explained by secondary contact after expansion from different refugia. Interestingly, Central Siberia has previously been found to be an important contact zone also in other cladoceran species, and may thus be a crucial area for understanding the Eurasian phylogeography of freshwater invertebrates. Together, our study provides an unprecedented complete, while still not global, picture of the phylogeography of this important model species.
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Affiliation(s)
- Eugeniya I. Bekker
- Laboratory of Aquatic Ecology and Invasions, A. N. Severtsov Institute of Ecology and Evolution of Russian Academy of Sciences, Moscow, Russia
| | - Dmitry P. Karabanov
- Laboratory of Fish Ecology, I. D. Papanin Institute for Biology of Inland Waters of Russian Academy of Sciences, Borok, Yaroslavl Area, Russia
| | - Yan R. Galimov
- Laboratory of Experimental Embryology, Koltzov Institute of Developmental Biology of Russian Academy of Sciences, Moscow, Russia
| | - Christoph R. Haag
- CEFE, CNRS, Univ Montpellier, Univ Paul Valéry Montpellier 3, EPHE, IRD, Montpellier, France
| | - Tatiana V. Neretina
- N.A.Pertsov White Sea Biological Station, Biological Faculty, M.V. Lomonosov Moscow State University, Moscow, 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
- Kazan Federal University, Kazan, Russia
- * E-mail:
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Khan G, Zhang F, Gao Q, Fu P, Zhang Y, Chen S. Spiroides shrubs on Qinghai-Tibetan Plateau: Multilocus phylogeography and palaeodistributional reconstruction of Spiraea alpina and S. Mongolica (Rosaceae). Mol Phylogenet Evol 2018; 123:137-148. [PMID: 29462675 DOI: 10.1016/j.ympev.2018.02.009] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2017] [Revised: 01/31/2018] [Accepted: 02/10/2018] [Indexed: 11/28/2022]
Abstract
A common hypothesis for the rich biodiversity found in mountains is uplift-driven diversification. Using a multilocus approach, here we assessed the influence of Qinghai-Tibetan Plateau (QTP) uplift and fluctuating regional climate on genetic diversity of two sister spiroides shrubs, Spiraea alpina and S. mongolica. Combined with palaeodistributional reconstruction modelling, we investigated the current and past-predicted distribution of these species under different climatic episodes. The study demonstrated that continuous pulses of retreat and expansion during last glacial-interglacial episodes, combined with the uplifting of QTP shaped the current distribution of these species. All the populations showed high level of genetic diversity based on both cpDNA and SSR markers. The average gene diversity within populations based on cpDNA markers was 0.383 ± 0.052 for S. alpina and 0.477 ± 0.048 for S. mongolica. The observed and expected heterozygosities based on SSR for both Spiraea alpina and S. mongolicawere HE(0.72-0.90)/HO(0.35-0.78) and HE(0.77-0.92)/HO(0.47-0.77) respectively. Palaeodistributional reconstruction indicated species' preferences at southeastern edge of the plateau during last glacial maximum, at higher altitude areas of QTP and range expansion to central plateau during the interglacial episodes. Assignment tests in STRUCTURE, discriminant analysis of principal coordinates and Immigrants analysis in GENECLASS based on nuclear SSR markers did not support the hypothesis of gene flow between both the species. However, maximum likelihood approach based on cpDNA showed sharing of haplotypes between both species.
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Affiliation(s)
- Gulzar Khan
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining 810008, China.
| | - Faqi Zhang
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining 810008, China; Qinghai Provincial Key Laboratory of Crop Molecular Breeding, Xining 810008, China.
| | - Qingbo Gao
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining 810008, China.
| | - Pengcheng Fu
- School of Life Sciences, Luoyang Normal University, Luoyang 471022, China.
| | - Yu Zhang
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining 810008, China.
| | - Shilong Chen
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining 810008, China.
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Li Y, Zhang XX, Mao RL, Yang J, Miao CY, Li Z, Qiu YX. Ten Years of Landscape Genomics: Challenges and Opportunities. FRONTIERS IN PLANT SCIENCE 2017; 8:2136. [PMID: 29312391 PMCID: PMC5733015 DOI: 10.3389/fpls.2017.02136] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2017] [Accepted: 12/01/2017] [Indexed: 05/06/2023]
Abstract
Landscape genomics is a relatively new discipline that aims to reveal the relationship between adaptive genetic imprints in genomes and environmental heterogeneity among natural populations. Although the interest in landscape genomics has increased since this term was coined, studies on this topic remain scarce. Landscape genomics has become a powerful method to scan and determine the genes responsible for the complex adaptive evolution of species at population (mostly) and individual (more rarely) level. This review outlines the sampling strategies, molecular marker types and research categories in 37 articles published during the first 10 years of this field (i.e., 2007-2016). We also address major challenges and future directions for landscape genomics. This review aims to promote interest in conducting additional studies in landscape genomics.
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Affiliation(s)
- Yong Li
- College of Forestry, Henan Agricultural University, Zhengzhou, China
| | - Xue-Xia Zhang
- College of Forestry, Henan Agricultural University, Zhengzhou, China
| | - Run-Li Mao
- College of Forestry, Henan Agricultural University, Zhengzhou, China
| | - Jie Yang
- College of Forestry, Henan Agricultural University, Zhengzhou, China
| | - Cai-Yun Miao
- College of Forestry, Henan Agricultural University, Zhengzhou, China
| | - Zhuo Li
- College of Forestry, Henan Agricultural University, Zhengzhou, China
| | - Ying-Xiong Qiu
- Key Laboratory of Conservation Biology for Endangered Wildlife of the Ministry of Education and Laboratory of Systematic and Evolutionary Botany and Biodiversity, College of Life Sciences, Zhejiang University, Hangzhou, China
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Sakaguchi S, Horie K, Ishikawa N, Nagano AJ, Yasugi M, Kudoh H, Ito M. Simultaneous evaluation of the effects of geographic, environmental and temporal isolation in ecotypic populations of Solidago virgaurea. THE NEW PHYTOLOGIST 2017; 216:1268-1280. [PMID: 28833204 DOI: 10.1111/nph.14744] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2017] [Accepted: 07/07/2017] [Indexed: 05/14/2023]
Abstract
Early stages of ecological speciation can create populations with an ecology and reproduction timing distinct from those of related populations. Landscape genetic models incorporating environmental heterogeneity and population-specific reproductive traits enable the processes of population genetic differentiation to be inferred. We investigated genome-wide genetic variation in ecotypic populations of Solidago virgaurea sensu lato, a herbaceous plant inhabiting a wide range of habitats (woodlands, serpentine barrens and alpine grasslands) and displaying remarkable variation in flowering time. Simultaneous evaluation of environmental factors revealed an overwhelming effect of soil type differences on neutral genetic differentiation, compared with elevational differences. This result probably reflects the abrupt environmental changes generated by geological boundaries, whereas mountain slopes exhibit clinal changes, facilitating gene exchange between neighbouring populations. Temporal isolation was positively associated with genetic differentiation, with some early-flowering serpentine populations having allele frequencies distinct from adjacent nonserpentine populations. Overall, this study highlights the importance of ecological processes and of evolution of flowering time to promote genetic differentiation of S. virgaurea populations in a complex landscape.
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Affiliation(s)
- Shota Sakaguchi
- Graduate School of Human and Environmental Studies, Kyoto University, Yoshida-nihonmatsu-cho, Sakyo-ku, Kyoto, 606-8501, Japan
| | - Kenji Horie
- Asahikawa City Northern Wild Plants Garden, Asahikawa, 071-1200, Japan
| | - Naoko Ishikawa
- Graduate School of Arts and Sciences, The University of Tokyo, Tokyo, 153-8902, Japan
| | - Atsushi J Nagano
- Faculty of Agriculture, Ryukoku University, Shiga, 520-2194, Japan
- Center for Ecological Research, Kyoto University, Otsu, Shiga, 520-2113, Japan
- JST CREST, Honcho 4-1-8, Kawaguchi, Saitama, 332-0012, Japan
| | - Masaki Yasugi
- National Institute for Basic Biology, Higashiyama 5-1, Myodaiji, Okazaki, 444-8787, Aichi, Japan
| | - Hiroshi Kudoh
- Center for Ecological Research, Kyoto University, Otsu, Shiga, 520-2113, Japan
| | - Motomi Ito
- Graduate School of Arts and Sciences, The University of Tokyo, Tokyo, 153-8902, Japan
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Evolutionary epidemiology of schistosomiasis: linking parasite genetics with disease phenotype in humans. Int J Parasitol 2017; 48:107-115. [PMID: 29154994 DOI: 10.1016/j.ijpara.2017.07.010] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2017] [Revised: 06/15/2017] [Accepted: 07/05/2017] [Indexed: 12/21/2022]
Abstract
Here we assess the role of parasite genetic variation in host disease phenotype in human schistosomiasis by implementing concepts and techniques from environmental association analysis in evolutionary epidemiology. Schistosomiasis is a tropical disease that affects more than 200 million people worldwide and is caused by parasitic flatworms belonging to the genus Schistosoma. While the role of host genetics has been extensively studied and demonstrated, nothing is yet known on the contribution of parasite genetic variation to host disease phenotype in human schistosomiasis. In this study microsatellite genotypes of 1561 Schistosoma mansoni larvae collected from 44 human hosts in Senegal were linked to host characteristics such as age, gender, infection intensity, liver and bladder morbidity by means of multivariate regression methods (on each parasite locus separately). This revealed a highly significant association between allelic variation at the parasite locus L46951 and host infection intensity and bladder morbidity. Locus L46951 is located in the 3' untranslated region of the cGMP-dependent protein kinase gene that is expressed in reproductive organs of adult schistosome worms and appears to be linked to egg production. This putative link between parasite genetic variation and schistosomiasis disease phenotype sets the stage for further functional research.
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Silva Martins WF, Wilding CS, Steen K, Mawejje H, Antão TR, Donnelly MJ. Local selection in the presence of high levels of gene flow: Evidence of heterogeneous insecticide selection pressure across Ugandan Culex quinquefasciatus populations. PLoS Negl Trop Dis 2017; 11:e0005917. [PMID: 28972985 PMCID: PMC5640252 DOI: 10.1371/journal.pntd.0005917] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2017] [Revised: 10/13/2017] [Accepted: 08/29/2017] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND Culex quinquefasciatus collected in Uganda, where no vector control interventions directly targeting this species have been conducted, was used as a model to determine if it is possible to detect heterogeneities in selection pressure driven by insecticide application targeting other insect species. METHODOLOGY/PRINCIPAL FINDINGS Population genetic structure was assessed through microsatellite analysis, and the impact of insecticide pressure by genotyping two target-site mutations, Vgsc-1014F of the voltage-gated sodium channel target of pyrethroid and DDT insecticides, and Ace1-119S of the acetylcholinesterase gene, target of carbamate and organophosphate insecticides. No significant differences in genetic diversity were observed among populations by microsatellite markers with HE ranging from 0.597 to 0.612 and low, but significant, genetic differentiation among populations (FST = 0.019, P = 0.001). By contrast, the insecticide-resistance markers display heterogeneous allelic distributions with significant differences detected between Central Ugandan (urban) populations relative to Eastern and Southwestern (rural) populations. In the central region, a frequency of 62% for Vgsc-1014F, and 32% for the Ace1-119S resistant allele were observed. Conversely, in both Eastern and Southwestern regions the Vgsc-1014F alleles were close to fixation, whilst Ace1-119S allele frequency was 12% (although frequencies may be underestimated due to copy number variation at both loci). CONCLUSIONS/SIGNIFICANCE Taken together, the microsatellite and both insecticide resistance target-site markers provide evidence that in the face of intense gene flow among populations, disjunction in resistance frequencies arise due to intense local selection pressures despite an absence of insecticidal control interventions targeting Culex.
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Affiliation(s)
- Walter Fabricio Silva Martins
- Department of Vector Biology, Liverpool School of Tropical Medicine, Liverpool, United Kingdom
- Departamento de Biologia, Universidade Estadual da Paraíba, Campina Grande, Brasil
| | - Craig Stephen Wilding
- School of Natural Sciences and Psychology, Liverpool John Moores University, Liverpool, United Kingdom
| | - Keith Steen
- Department of Vector Biology, Liverpool School of Tropical Medicine, Liverpool, United Kingdom
| | | | - Tiago Rodrigues Antão
- Department of Vector Biology, Liverpool School of Tropical Medicine, Liverpool, United Kingdom
- Division of Biological Science, University of Montana, Missoula, United States of America
| | - Martin James Donnelly
- Department of Vector Biology, Liverpool School of Tropical Medicine, Liverpool, United Kingdom
- Malaria Programme, Wellcome Trust Sanger Institute, Cambridge, United Kingdom
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Khan G, Godoy MO, Franco FF, Perez MF, Taylor NP, Zappi DC, Machado MC, Moraes EM. Extreme population subdivision or cryptic speciation in the cactus Pilosocereus jauruensis? A taxonomic challenge posed by a naturally fragmented system. SYST BIODIVERS 2017. [DOI: 10.1080/14772000.2017.1359215] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Gulzar Khan
- Departamento de Biologia, Universidade Federal de São Carlos, Rodovia João Leme dos Santos km 110, 18052780 Sorocaba, São Paulo, Brazil
| | - Mariana O. Godoy
- Departamento de Biologia, Universidade Federal de São Carlos, Rodovia João Leme dos Santos km 110, 18052780 Sorocaba, São Paulo, Brazil
| | - Fernando F. Franco
- Departamento de Biologia, Universidade Federal de São Carlos, Rodovia João Leme dos Santos km 110, 18052780 Sorocaba, São Paulo, Brazil
| | - Manolo F. Perez
- Departamento de Biologia, Universidade Federal de São Carlos, Rodovia João Leme dos Santos km 110, 18052780 Sorocaba, São Paulo, Brazil
| | - Nigel P. Taylor
- Singapore Botanic Gardens, 1 Cluny Road, Singapore 259569, Singapore
| | - Daniela C. Zappi
- Museu Paraense Emílio Goeldi, Av. Perimetral, 1901, Belém, Pará, Brazil
| | - Marlon C. Machado
- Universidade Estadual de Feira de Santana, Rodovia BR 116, km 03, 44031-460 Feira de Santana, Bahia, Brazil
| | - Evandro M. Moraes
- Departamento de Biologia, Universidade Federal de São Carlos, Rodovia João Leme dos Santos km 110, 18052780 Sorocaba, São Paulo, Brazil
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Van Wynsberge S, Andréfouët S, Gaertner-Mazouni N, Tiavouane J, Grulois D, Lefèvre J, Pinsky ML, Fauvelot C. Considering reefscape configuration and composition in biophysical models advance seascape genetics. PLoS One 2017; 12:e0178239. [PMID: 28542261 PMCID: PMC5444781 DOI: 10.1371/journal.pone.0178239] [Citation(s) in RCA: 14] [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: 11/03/2016] [Accepted: 05/10/2017] [Indexed: 01/10/2023] Open
Abstract
Previous seascape genetics studies have emphasized the role of ocean currents and geographic distances to explain the genetic structure of marine species, but the role of benthic habitat has been more rarely considered. Here, we compared the population genetic structure observed in West Pacific giant clam populations against model simulations that accounted habitat composition and configuration, geographical distance, and oceanic currents. Dispersal determined by geographical distance provided a modelled genetic structure in better agreement with the observations than dispersal by oceanic currents, possibly due to insufficient spatial resolution of available oceanographic and coastal circulation models. Considering both habitat composition and configuration significantly improved the match between simulated and observed genetic structures. This study emphasizes the importance of a reefscape genetics approach to population ecology, evolution and conservation in the sea.
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Affiliation(s)
- Simon Van Wynsberge
- UMR-241 EIO, Université de la Polynésie Française, Laboratoire d’Excellence CORAIL, Faa’a, Tahiti, French Polynesia
- UMR-9220 ENTROPIE (Institut de Recherche pour le Développement, Université de La Réunion, CNRS), Laboratoire d’excellence-CORAIL, centre IRD de Nouméa, Nouméa, New Caledonia
- * E-mail:
| | - Serge Andréfouët
- UMR-9220 ENTROPIE (Institut de Recherche pour le Développement, Université de La Réunion, CNRS), Laboratoire d’excellence-CORAIL, centre IRD de Nouméa, Nouméa, New Caledonia
| | - Nabila Gaertner-Mazouni
- UMR-241 EIO, Université de la Polynésie Française, Laboratoire d’Excellence CORAIL, Faa’a, Tahiti, French Polynesia
| | - Josina Tiavouane
- UMR-9220 ENTROPIE (Institut de Recherche pour le Développement, Université de La Réunion, CNRS), Laboratoire d’excellence-CORAIL, centre IRD de Nouméa, Nouméa, New Caledonia
| | - Daphné Grulois
- UMR-9220 ENTROPIE (Institut de Recherche pour le Développement, Université de La Réunion, CNRS), Laboratoire d’excellence-CORAIL, centre IRD de Nouméa, Nouméa, New Caledonia
| | - Jérôme Lefèvre
- UMR-065 LEGOS and UMR-235 MIO, Centre IRD de Nouméa, Nouméa, New Caledonia
| | - Malin L. Pinsky
- Department of Ecology, Evolution, and Natural Resources, Rutgers University, New Brunswick, New Jersey, United States of America
- Institute of Earth, Ocean, and Atmospheric Sciences, Rutgers University, New Brunswick, New Jersey, United States of America
| | - Cécile Fauvelot
- UMR-9220 ENTROPIE (Institut de Recherche pour le Développement, Université de La Réunion, CNRS), Laboratoire d’excellence-CORAIL, centre IRD de Nouméa, Nouméa, New Caledonia
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Isolation mediates persistent founder effects on zooplankton colonisation in new temporary ponds. Sci Rep 2017; 7:43983. [PMID: 28276459 PMCID: PMC5343421 DOI: 10.1038/srep43983] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2014] [Accepted: 02/02/2017] [Indexed: 11/22/2022] Open
Abstract
Understanding the colonisation process in zooplankton is crucial for successful restoration of aquatic ecosystems. Here, we analyzed the clonal and genetic structure of the cyclical parthenogenetic rotifer Brachionus plicatilis by following populations established in new temporary ponds during the first three hydroperiods. Rotifer populations established rapidly after first flooding, although colonisation was ongoing throughout the study. Multilocus genotypes from 7 microsatellite loci suggested that most populations (10 of 14) were founded by few clones. The exception was one of the four populations that persisted throughout the studied hydroperiods, where high genetic diversity in the first hydroperiod suggested colonisation from a historical egg bank, and no increase in allelic diversity was detected with time. In contrast, in another of these four populations, we observed a progressive increase of allelic diversity. This population became less differentiated from the other populations suggesting effective gene flow soon after its foundation. Allelic diversity and richness remained low in the remaining two, more isolated, populations, suggesting little gene flow. Our results highlight the complexity of colonisation dynamics, with evidence for persistent founder effects in some ponds, but not in others, and with early immigration both from external source populations, and from residual, historical diapausing egg banks.
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Jansen M, Geerts AN, Rago A, Spanier KI, Denis C, De Meester L, Orsini L. Thermal tolerance in the keystone species Daphnia magna-a candidate gene and an outlier analysis approach. Mol Ecol 2017; 26:2291-2305. [PMID: 28146303 DOI: 10.1111/mec.14040] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2016] [Revised: 01/16/2017] [Accepted: 01/19/2017] [Indexed: 01/01/2023]
Abstract
Changes in temperature have occurred throughout Earth's history. However, current warming trends exacerbated by human activities impose severe and rapid loss of biodiversity. Although understanding the mechanisms orchestrating organismal response to climate change is important, remarkably few studies document their role in nature. This is because only few systems enable the combined analysis of genetic and plastic responses to environmental change over long time spans. Here, we characterize genetic and plastic responses to temperature increase in the aquatic keystone grazer Daphnia magna combining a candidate gene and an outlier analysis approach. We capitalize on the short generation time of our species, facilitating experimental evolution, and the production of dormant eggs enabling the analysis of long-term response to environmental change through a resurrection ecology approach. We quantify plasticity in the expression of 35 candidate genes in D. magna populations resurrected from a lake that experienced changes in average temperature over the past century and from experimental populations differing in thermal tolerance isolated from a selection experiment. By measuring expression in multiple genotypes from each of these populations in control and heat treatments, we assess plastic responses to extreme temperature events. By measuring evolutionary changes in gene expression between warm- and cold-adapted populations, we assess evolutionary response to temperature changes. Evolutionary response to temperature increase is also assessed via an outlier analysis using EST-linked microsatellite loci. This study provides the first insights into the role of plasticity and genetic adaptation in orchestrating adaptive responses to environmental change in D. magna.
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Affiliation(s)
- M Jansen
- Laboratory of Aquatic Ecology, Evolution and Conservation, University of Leuven, Ch. Deberiotstraat 32, 3000 Leuven, Belgium
| | - A N Geerts
- Laboratory of Aquatic Ecology, Evolution and Conservation, University of Leuven, Ch. Deberiotstraat 32, 3000 Leuven, Belgium
| | - A Rago
- Environmental Genomics Group, School of Biosciences, University of Birmingham, Birmingham, B15 2TT, United Kingdom
| | - K I Spanier
- Laboratory of Aquatic Ecology, Evolution and Conservation, University of Leuven, Ch. Deberiotstraat 32, 3000 Leuven, Belgium
| | - C Denis
- Laboratory of Aquatic Ecology, Evolution and Conservation, University of Leuven, Ch. Deberiotstraat 32, 3000 Leuven, Belgium
| | - L De Meester
- Laboratory of Aquatic Ecology, Evolution and Conservation, University of Leuven, Ch. Deberiotstraat 32, 3000 Leuven, Belgium
| | - L Orsini
- Environmental Genomics Group, School of Biosciences, University of Birmingham, Birmingham, B15 2TT, United Kingdom
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Wagner HH, Chávez-Pesqueira M, Forester BR. Spatial detection of outlier loci with Moran eigenvector maps. Mol Ecol Resour 2017; 17:1122-1135. [DOI: 10.1111/1755-0998.12653] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2016] [Revised: 12/01/2016] [Accepted: 12/06/2016] [Indexed: 11/30/2022]
Affiliation(s)
- Helene H. Wagner
- Department of Biology; University of Toronto Mississauga; 3359 Mississauga Road Mississauga ON L5L 1C6 Canada
| | - Mariana Chávez-Pesqueira
- Department of Biology; University of Toronto Mississauga; 3359 Mississauga Road Mississauga ON L5L 1C6 Canada
- Unidad de Recursos Naturales; Centro de Investigación Científica de Yucatán; Calle 43 No. 130, Col. Chuburná de Hidalgo CP 97205 Mérida, Yucatán México
| | - Brenna R. Forester
- Nicholas School of the Environment; University Program in Ecology; Duke University; Durham NC 27708 USA
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Frisch D, Morton PK, Culver BW, Edlund MB, Jeyasingh PD, Weider LJ. Paleogenetic records of Daphnia pulicaria in two North American lakes reveal the impact of cultural eutrophication. GLOBAL CHANGE BIOLOGY 2017; 23:708-718. [PMID: 27474788 DOI: 10.1111/gcb.13445] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2015] [Accepted: 07/04/2016] [Indexed: 06/06/2023]
Abstract
Understanding the evolutionary consequences of the green revolution, particularly in wild populations, is an important frontier in contemporary biology. Because human impacts have occurred at varying magnitudes or time periods depending on the study ecosystem, evolutionary histories may vary considerably among populations. Paleogenetics in conjunction with paleolimnology enable us to associate microevolutionary dynamics with detailed information on environmental change. We used this approach to reconstruct changes in the temporal population genetic structure of the keystone zooplankton grazer, Daphnia pulicaria, using dormant eggs extracted from sediments in two Minnesota lakes (South Center, Hill). The extent of agriculture and human population density in the catchment of these lakes has differed markedly since European settlement in the late 19th century and is reflected in their environmental histories reconstructed here. The reconstructed environments of these two lakes differed strongly in terms of environmental stability and their associated patterns of Daphnia population structure. We detected long periods of stability in population structure and environmental conditions in South Center Lake that were followed by a dramatic temporal shift in population genetic structure after the onset of European settlement and industrialized agriculture in its watershed. In particular, we noted a 24.3-fold increase in phosphorus (P) flux between pre-European and modern sediment P accumulation rates (AR) in this lake. In contrast, no such shifts were detected in Hill Lake, where the watershed was not as impacted by European settlement and rates of change were less directional with a much smaller increase in sediment P AR (2.3-fold). We identify direct and indirect effects of eutrophication proxies on genetic structure in these lake populations and demonstrate the power of using this approach in understanding the consequences of anthropogenic environmental change on natural populations throughout historic time periods.
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Affiliation(s)
- Dagmar Frisch
- Program in Ecology and Evolutionary Biology, Department of Biology, University of Oklahoma, Norman, OK, 73071, USA
- School of Biosciences, University of Birmingham, Birmingham, B15 2TT, UK
| | - Philip K Morton
- Program in Ecology and Evolutionary Biology, Department of Biology, University of Oklahoma, Norman, OK, 73071, USA
- Division of Science, Murray State College, Tishomingo, OK, 73460, USA
| | - Billy W Culver
- Program in Ecology and Evolutionary Biology, Department of Biology, University of Oklahoma, Norman, OK, 73071, USA
| | - Mark B Edlund
- St. Croix Watershed Research Station, Science Museum of Minnesota, Marine on St. Croix, MN, 55047, USA
| | - Punidan D Jeyasingh
- Oklahoma State University, Department of Integrative Biology, Stillwater, OK, 74078, USA
| | - Lawrence J Weider
- Program in Ecology and Evolutionary Biology, Department of Biology, University of Oklahoma, Norman, OK, 73071, USA
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40
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Orsini L, Marshall H, Cuenca Cambronero M, Chaturvedi A, Thomas KW, Pfrender ME, Spanier KI, De Meester L. Temporal genetic stability in natural populations of the waterflea Daphnia magna in response to strong selection pressure. Mol Ecol 2016; 25:6024-6038. [PMID: 27862502 DOI: 10.1111/mec.13907] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2016] [Revised: 09/22/2016] [Accepted: 10/27/2016] [Indexed: 01/08/2023]
Abstract
Studies monitoring changes in genetic diversity and composition through time allow a unique understanding of evolutionary dynamics and persistence of natural populations. However, such studies are often limited to species with short generation times that can be propagated in the laboratory or few exceptional cases in the wild. Species that produce dormant stages provide powerful models for the reconstruction of evolutionary dynamics in the natural environment. A remaining open question is to what extent dormant egg banks are an unbiased representation of populations and hence of the species' evolutionary potential, especially in the presence of strong environmental selection. We address this key question using the water flea Daphnia magna, which produces dormant stages that accumulate in biological archives over time. We assess temporal genetic stability in three biological archives, previously used in resurrection ecology studies showing adaptive evolutionary responses to rapid environmental change. We show that neutral genetic diversity does not decline with the age of the population and it is maintained in the presence of strong selection. In addition, by comparing temporal genetic stability in hatched and unhatched populations from the same biological archive, we show that dormant egg banks can be consulted to obtain a reliable measure of genetic diversity over time, at least in the multidecadal time frame studied here. The stability of neutral genetic diversity through time is likely mediated by the buffering effect of the resting egg bank.
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Affiliation(s)
- Luisa Orsini
- Environmental Genomics Group, School of Biosciences, the University of Birmingham, Birmingham, B15 2TT, UK
| | - Hollie Marshall
- Environmental Genomics Group, School of Biosciences, the University of Birmingham, Birmingham, B15 2TT, UK
| | - Maria Cuenca Cambronero
- Environmental Genomics Group, School of Biosciences, the University of Birmingham, Birmingham, B15 2TT, UK
| | - Anurag Chaturvedi
- Laboratory of Aquatic Ecology, Evolution and Conservation, KU Leuven - University of Leuven, Ch. Deberiotstraat 32, 3000, Leuven, Belgium
| | - Kelley W Thomas
- Hubbard Center for Genome Studies, University of New Hampshire, Durham, NH, 03824, USA
| | - Michael E Pfrender
- Department of Biological Sciences, Eck Institute for Global Health & Environmental Change Initiative, Galvin Life Science Center, Notre Dame, IN, 46556, USA
| | - Katina I Spanier
- Laboratory of Aquatic Ecology, Evolution and Conservation, KU Leuven - University of Leuven, Ch. Deberiotstraat 32, 3000, Leuven, Belgium
| | - Luc De Meester
- Laboratory of Aquatic Ecology, Evolution and Conservation, KU Leuven - University of Leuven, Ch. Deberiotstraat 32, 3000, Leuven, Belgium
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41
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Wood CW, Brodie ED. Evolutionary response when selection and genetic variation covary across environments. Ecol Lett 2016; 19:1189-200. [DOI: 10.1111/ele.12662] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2016] [Revised: 06/27/2016] [Accepted: 07/13/2016] [Indexed: 12/30/2022]
Affiliation(s)
- Corlett W. Wood
- Mountain Lake Biological Station and Department of Biology University of Virginia Charlottesville VA22904 USA
| | - Edmund D. Brodie
- Mountain Lake Biological Station and Department of Biology University of Virginia Charlottesville VA22904 USA
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42
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Salisbury SJ, McCracken GR, Keefe D, Perry R, Ruzzante DE. A portrait of a sucker using landscape genetics: how colonization and life history undermine the idealized dendritic metapopulation. Mol Ecol 2016; 25:4126-45. [PMID: 27393723 DOI: 10.1111/mec.13757] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2016] [Revised: 06/28/2016] [Accepted: 06/28/2016] [Indexed: 01/19/2023]
Abstract
Dendritic metapopulations have been attributed unique properties by in silico studies, including an elevated genetic diversity relative to a panmictic population of equal total size. These predictions have not been rigorously tested in nature, nor has there been full consideration of the interacting effects among contemporary landscape features, colonization history and life history traits of the target species. We tested for the effects of dendritic structure as well as the relative importance of life history, environmental barriers and historical colonization on the neutral genetic structure of a longnose sucker (Catostomus catostomus) metapopulation in the Kogaluk watershed of northern Labrador, Canada. Samples were collected from eight lakes, genotyped with 17 microsatellites, and aged using opercula. Lakes varied in differentiation, historical and contemporary connectivity, and life history traits. Isolation by distance was detected only by removing two highly genetically differentiated lakes, suggesting a lack of migration-drift equilibrium and the lingering influence of historical factors on genetic structure. Bayesian analyses supported colonization via the Kogaluk's headwaters. The historical concentration of genetic diversity in headwaters inferred by this result was supported by high historical and contemporary effective sizes of the headwater lake, T-Bone. Alternatively, reduced allelic richness in headwaters confirmed the dendritic structure's influence on gene flow, but this did not translate to an elevated metapopulation effective size. A lack of equilibrium and upstream migration may have dampened the effects of dendritic structure. We suggest that interacting historical and contemporary factors prevent the achievement of the idealized traits of a dendritic metapopulation in nature.
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Affiliation(s)
- Sarah J Salisbury
- Department of Biology, Dalhousie University, Halifax, NS, B3H4R2, Canada
| | | | - Donald Keefe
- Department of Environment and Conservation, Newfoundland and Labrador, Corner Brook, NL, Canada
| | - Robert Perry
- Department of Environment and Conservation, Newfoundland and Labrador, Corner Brook, NL, Canada
| | - Daniel E Ruzzante
- Department of Biology, Dalhousie University, Halifax, NS, B3H4R2, Canada
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43
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Dudaniec RY, Tesson SVM. Applying landscape genetics to the microbial world. Mol Ecol 2016; 25:3266-75. [PMID: 27146426 DOI: 10.1111/mec.13691] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2015] [Revised: 04/07/2016] [Accepted: 05/03/2016] [Indexed: 12/31/2022]
Abstract
Landscape genetics, which explicitly quantifies landscape effects on gene flow and adaptation, has largely focused on macroorganisms, with little attention given to microorganisms. This is despite overwhelming evidence that microorganisms exhibit spatial genetic structuring in relation to environmental variables. The increasing accessibility of genomic data has opened up the opportunity for landscape genetics to embrace the world of microorganisms, which may be thought of as 'the invisible regulators' of the macroecological world. Recent developments in bioinformatics and increased data accessibility have accelerated our ability to identify microbial taxa and characterize their genetic diversity. However, the influence of the landscape matrix and dynamic environmental factors on microorganism genetic dispersal and adaptation has been little explored. Also, because many microorganisms coinhabit or codisperse with macroorganisms, landscape genomic approaches may improve insights into how micro- and macroorganisms reciprocally interact to create spatial genetic structure. Conducting landscape genetic analyses on microorganisms requires that we accommodate shifts in spatial and temporal scales, presenting new conceptual and methodological challenges not yet explored in 'macro'-landscape genetics. We argue that there is much value to be gained for microbial ecologists from embracing landscape genetic approaches. We provide a case for integrating landscape genetic methods into microecological studies and discuss specific considerations associated with the novel challenges this brings. We anticipate that microorganism landscape genetic studies will provide new insights into both micro- and macroecological processes and expand our knowledge of species' distributions, adaptive mechanisms and species' interactions in changing environments.
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Affiliation(s)
- Rachael Y Dudaniec
- Department of Biological Sciences, Macquarie University, Sydney, NSW, 2109, Australia
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44
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Strobel HM, Alda F, Sprehn CG, Blum MJ, Heins DC. Geographic and host-mediated population genetic structure in a cestode parasite of the three-spined stickleback. Biol J Linn Soc Lond 2016. [DOI: 10.1111/bij.12826] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Hannah M. Strobel
- Department of Ecology and Evolutionary Biology; Tulane University; New Orleans LA 70118 USA
| | - Fernando Alda
- Department of Ecology and Evolutionary Biology; Tulane University; New Orleans LA 70118 USA
- Tulane-Xavier Center for Bioenvironmental Research; Tulane University; New Orleans LA 70118 USA
| | - C. Grace Sprehn
- Department of Ecology and Evolutionary Biology; Tulane University; New Orleans LA 70118 USA
| | - Michael J. Blum
- Department of Ecology and Evolutionary Biology; Tulane University; New Orleans LA 70118 USA
- Tulane-Xavier Center for Bioenvironmental Research; Tulane University; New Orleans LA 70118 USA
| | - David C. Heins
- Department of Ecology and Evolutionary Biology; Tulane University; New Orleans LA 70118 USA
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45
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Haileselasie TH, Mergeay J, Weider LJ, Jeppesen E, De Meester L. Colonization history and clonal richness of asexual Daphnia in periglacial habitats of contrasting age in West Greenland. J Anim Ecol 2016; 85:1108-17. [PMID: 27279332 DOI: 10.1111/1365-2656.12513] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2015] [Accepted: 02/25/2016] [Indexed: 12/01/2022]
Abstract
Due to climate change, Arctic ice sheets are retreating. This leads to the formation of numerous new periglacial ponds and lakes, which are being colonized by planktonic organisms such as the water flea Daphnia. This system provides unique opportunities to test genotype colonization dynamics and the genetic assemblage of populations. Here, we studied clonal richness of the Daphnia pulex species complex in novel periglacial habitats created by glacial retreat in the Jakobshavn Isbrae area of western Greenland. Along a 10 km transect, we surveyed 73 periglacial habitats out of which 61 were colonized by Daphnia pulex. Hence, for our analysis, we used 21 ponds and 40 lakes in two clusters of habitats differing in age (estimated <50 years vs. >150 years). We tested the expectation that genetic diversity would be low in recently formed (i.e. young), small habitats, but would increase with increasing age and size. We identified a total of 42 genetically distinct clones belonging to two obligately asexual species of the D. pulex species complex: D. middendorffiana and the much more abundant D. pulicaria. While regional clonal richness was high, most clones were rare: 16 clones were restricted to a single habitat and the five most widespread clones accounted for 68% of all individuals sampled. On average, 3·2 clones (range: 1-12) coexisted in a given pond or lake. There was no relationship between clonal richness and habitat size when we controlled for habitat age. Whereas clonal richness was statistically higher in the cluster of older habitats when compared with the cluster of younger ponds and lakes, most young habitats were colonized by multiple genotypes. Our data suggest that newly formed (periglacial) ponds and lakes are colonized within decades by multiple genotypes via multiple colonization events, even in the smallest of our study systems (4 m(2) ).
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Affiliation(s)
| | - Joachim Mergeay
- Laboratory of Aquatic Ecology, Evolution and Conservation, KU Leuven, Leuven, Belgium.,Research Institute for Nature and Forest, Gaverstraat 4, 9500, Geraardsbergen, Belgium
| | - Lawrence J Weider
- Department of Biology, Program in Ecology and Evolutionary Biology, University of Oklahoma, Norman, OK, 73071, USA
| | - Erik Jeppesen
- Department of Bioscience and Arctic Research Centre, Aarhus University, Silkeborg, Denmark.,Sino-Danish Centre for Education and Research (SDC), UCAS, Beijing, China
| | - Luc De Meester
- Laboratory of Aquatic Ecology, Evolution and Conservation, KU Leuven, Leuven, Belgium
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46
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De Meester L, Vanoverbeke J, Kilsdonk LJ, Urban MC. Evolving Perspectives on Monopolization and Priority Effects. Trends Ecol Evol 2016; 31:136-146. [DOI: 10.1016/j.tree.2015.12.009] [Citation(s) in RCA: 170] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2015] [Revised: 12/03/2015] [Accepted: 12/04/2015] [Indexed: 11/30/2022]
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47
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Özdemir E, Altındağ A, Kandemir İ. Molecular diversity of some species belonging to the genus Daphnia O. F. Müller, 1785 (Crustacea: Cladocera) in Turkey. Mitochondrial DNA A DNA Mapp Seq Anal 2016; 28:424-433. [PMID: 27159716 DOI: 10.3109/19401736.2015.1136303] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Daphnia is a freshwater zooplankton species with controversial taxonomy due to its high morphological variation linked to environmental factors and inter-specific hybridization and polyploidy in some groups. The aim of the present study is to examine molecular diversity of some Daphnia species in Turkey and to establish DNA barcodes of Turkish Daphnia species. Sequence analysis was performed using 540 bp region of cytochrome oxidase subunit I gene of mitochondrial DNA. A total of 34 haplotypes have been identified for Turkey. Daphnia pulex complex was divided into two clades with 16.1% sequence divergence according to molecular taxonomy based on Kimura 2-parameter. The clade which was molecularly diverged from Daphnia pulex with 16.1% sequence divergence was found to show 99% similarity with Daphnia cf. pulicaria (sensu Alonso 1996) instead of Daphnia pulicaria Forbes, 1893. Furthermore, this study has contributed to Turkish zoogeography by demonstrating the distribution of Daphnia species in Turkey.
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Affiliation(s)
- Ebru Özdemir
- a Department of Molecular Biology and Genetics, Faculty of Science and Letters , University of Kafkas , Kars , Turkey.,b Department of Biology, Faculty of Science , University of Ankara , Ankara , Turkey
| | - Ahmet Altındağ
- b Department of Biology, Faculty of Science , University of Ankara , Ankara , Turkey
| | - İrfan Kandemir
- b Department of Biology, Faculty of Science , University of Ankara , Ankara , Turkey
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48
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Wenzel MA, Douglas A, James MC, Redpath SM, Piertney SB. The role of parasite-driven selection in shaping landscape genomic structure in red grouse (Lagopus lagopus scotica). Mol Ecol 2015; 25:324-41. [PMID: 26578090 DOI: 10.1111/mec.13473] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2015] [Revised: 11/09/2015] [Accepted: 11/10/2015] [Indexed: 12/25/2022]
Abstract
Landscape genomics promises to provide novel insights into how neutral and adaptive processes shape genome-wide variation within and among populations. However, there has been little emphasis on examining whether individual-based phenotype-genotype relationships derived from approaches such as genome-wide association (GWAS) manifest themselves as a population-level signature of selection in a landscape context. The two may prove irreconcilable as individual-level patterns become diluted by high levels of gene flow and complex phenotypic or environmental heterogeneity. We illustrate this issue with a case study that examines the role of the highly prevalent gastrointestinal nematode Trichostrongylus tenuis in shaping genomic signatures of selection in red grouse (Lagopus lagopus scotica). Individual-level GWAS involving 384 SNPs has previously identified five SNPs that explain variation in T. tenuis burden. Here, we examine whether these same SNPs display population-level relationships between T. tenuis burden and genetic structure across a small-scale landscape of 21 sites with heterogeneous parasite pressure. Moreover, we identify adaptive SNPs showing signatures of directional selection using F(ST) outlier analysis and relate population- and individual-level patterns of multilocus neutral and adaptive genetic structure to T. tenuis burden. The five candidate SNPs for parasite-driven selection were neither associated with T. tenuis burden on a population level, nor under directional selection. Similarly, there was no evidence of parasite-driven selection in SNPs identified as candidates for directional selection. We discuss these results in the context of red grouse ecology and highlight the broader consequences for the utility of landscape genomics approaches for identifying signatures of selection.
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Affiliation(s)
- Marius A Wenzel
- Institute of Biological and Environmental Sciences, University of Aberdeen, Tillydrone Avenue, Aberdeen, AB24 2TZ, UK
| | - Alex Douglas
- Institute of Biological and Environmental Sciences, University of Aberdeen, Tillydrone Avenue, Aberdeen, AB24 2TZ, UK
| | - Marianne C James
- Institute of Biological and Environmental Sciences, University of Aberdeen, Tillydrone Avenue, Aberdeen, AB24 2TZ, UK
| | - Steve M Redpath
- Institute of Biological and Environmental Sciences, University of Aberdeen, Tillydrone Avenue, Aberdeen, AB24 2TZ, UK
| | - Stuart B Piertney
- Institute of Biological and Environmental Sciences, University of Aberdeen, Tillydrone Avenue, Aberdeen, AB24 2TZ, UK
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49
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Fields PD, Reisser C, Dukić M, Haag CR, Ebert D. Genes mirror geography inDaphnia magna. Mol Ecol 2015; 24:4521-36. [DOI: 10.1111/mec.13324] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2015] [Revised: 07/13/2015] [Accepted: 07/14/2015] [Indexed: 02/06/2023]
Affiliation(s)
- Peter D. Fields
- Zoological Institute; University of Basel; Vesalgasse 1 Basel CH-4051 Switzerland
| | - Céline Reisser
- Centre d'Ecologie Fonctionnelle et Evolutive - UMR 5175; campus CNRS 1919 route de Mende 34293 Montpellier Cedex 5 France
- Department of Biology; Ecology and Evolution; University of Fribourg; Chemin du Muśee 10 1700 Fribourg Switzerland
| | - Marinela Dukić
- Zoological Institute; University of Basel; Vesalgasse 1 Basel CH-4051 Switzerland
| | - Christoph R. Haag
- Centre d'Ecologie Fonctionnelle et Evolutive - UMR 5175; campus CNRS 1919 route de Mende 34293 Montpellier Cedex 5 France
- Department of Biology; Ecology and Evolution; University of Fribourg; Chemin du Muśee 10 1700 Fribourg Switzerland
| | - Dieter Ebert
- Zoological Institute; University of Basel; Vesalgasse 1 Basel CH-4051 Switzerland
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50
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Hochmuth JD, De Meester L, Pereira CMS, Janssen CR, De Schamphelaere KAC. Rapid Adaptation of a Daphnia magna Population to Metal Stress Is Associated with Heterozygote Excess. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2015; 49:9298-9307. [PMID: 26130190 DOI: 10.1021/acs.est.5b00724] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Although natural populations can harbor evolutionary potential to adapt genetically to chemical stress, it is often thought that natural selection leads to a general reduction of genetic diversity and involves costs. Here, a 10 week microevolution experiment was conducted with a genetically diverse and representative sample of one natural Daphnia magna population that was exposed to copper and zinc. Both Cu- and Zn-selected populations developed a significantly higher metal tolerance (i.e., genetic adaptation), indicated by higher reproduction probabilities of clonal lines in Cu and Zn exposures than observed for the original and control populations. The complete recovery of the population densities after 10 weeks of Zn selection (following an initial decrease of 74%) illustrates an example of evolutionary rescue. Microsatellite genotyping revealed a decrease in clonal diversity but no change in allelic richness, and showed an excess in heterozygosity in the Cu- and Zn-selected populations compared to the control and original populations. The excess heterozygosity in metal-selected populations that we observed has important consequences for risk assessment, as it contributes to the maintenance of a higher allelic diversity under multigenerational chemical exposure. This study is, to our knowledge, the first report of an increase in heterozygosity following multigenerational exposure to metal stress, despite a decline in clonal diversity. In a follow-up study with the Zn-selected populations, we observed no effect of Zn selection on the tolerance to heat and cyanobacteria. However, we observed higher tolerance to Cd in the Zn-selected than in the original and control populations if the 20% effective concentration of Cd was considered (cross-tolerance). Our results suggest only limited costs of adaptation but future research is needed to evaluate the adaptive potential of metal-selected populations to novel stressors and to determine to what extent increased heterozygosity is preserved after genetic recombination following periods of sexual reproduction.
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Affiliation(s)
- Jennifer D Hochmuth
- †Laboratory of Environmental Toxicology and Aquatic Ecology, Environmental Toxicology Unit (GhEnToxLab), Ghent University (UGent), Jozef Plateaustraat 22, B-9000 Gent, Belgium
| | - Luc De Meester
- ‡Laboratory of Aquatic Ecology, Evolution and Conservation, University of Leuven (KU Leuven), Deberiotstraat 32, B-3000 Leuven, Belgium
| | - Cecília M S Pereira
- †Laboratory of Environmental Toxicology and Aquatic Ecology, Environmental Toxicology Unit (GhEnToxLab), Ghent University (UGent), Jozef Plateaustraat 22, B-9000 Gent, Belgium
| | - Colin R Janssen
- †Laboratory of Environmental Toxicology and Aquatic Ecology, Environmental Toxicology Unit (GhEnToxLab), Ghent University (UGent), Jozef Plateaustraat 22, B-9000 Gent, Belgium
| | - Karel A C De Schamphelaere
- †Laboratory of Environmental Toxicology and Aquatic Ecology, Environmental Toxicology Unit (GhEnToxLab), Ghent University (UGent), Jozef Plateaustraat 22, B-9000 Gent, Belgium
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