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Sudasinghe H, Ranasinghe T, Wijesooriya K, Rüber L, Meegaskumbura M. Phylogenetic and phylogeographic insights into Sri Lankan killifishes (Teleostei: Aplocheilidae). JOURNAL OF FISH BIOLOGY 2024; 105:340-357. [PMID: 38769734 DOI: 10.1111/jfb.15792] [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: 10/22/2023] [Revised: 04/14/2024] [Accepted: 05/03/2024] [Indexed: 05/22/2024]
Abstract
Three nominal species of the killifish genus Aplocheilus are reported from the lowlands of Sri Lanka. Two of these, Aplocheilus dayi and Aplocheilus werneri, are considered endemic to the island, whereas Aplocheilus parvus is reported from both Sri Lanka and Peninsular India. Here, based on a collection from 28 locations in Sri Lanka, also including a dataset of Asian Aplocheilus downloaded from GenBank, we present a phylogeny constructed from the mitochondrial cytochrome b (cytb), mitochondrial cytochrome c oxidase subunit 1 (cox1), and nuclear recombination activating protein 1 (rag1), and investigate the interrelationships of the species of Aplocheilus in Sri Lanka. The endemic Sri Lankan aplocheilid clade comprising A. dayi and A. werneri is recovered as the sister group to the clade comprising A. parvus from Sri Lanka and Aplocheilus blockii from Peninsular India. The reciprocal monophyly of A. dayi and A. werneri is not supported in our molecular phylogeny. A. dayi and A. werneri display strong sexual dimorphism, but species-level differences are subtle, explained mostly by pigmentation patterns. Their phenotypes exhibit a parapatric distribution and may represent locally adapted forms of a single species. Alternatively, the present study does not rule out the possibility that A. dayi and A. werneri may represent an incipient species pair or that they have undergone introgression or hybridization in their contact zones. We provide evidence that the Nilwala-Gin region of southwestern Sri Lanka may have acted as a drought refugium for these fishes.
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Affiliation(s)
- Hiranya Sudasinghe
- Evolutionary Ecology and Systematics Laboratory, Department of Molecular Biology and Biotechnology, University of Peradeniya, Peradeniya, Sri Lanka
- Postgraduate Institute of Science, University of Peradeniya, Peradeniya, Sri Lanka
- Division of Evolutionary Ecology, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
- Naturhistorisches Museum Bern, Bern, Switzerland
| | | | - Kumudu Wijesooriya
- Department of Zoology, Faculty of Science, University of Peradeniya, Peradeniya, Sri Lanka
| | - Lukas Rüber
- Naturhistorisches Museum Bern, Bern, Switzerland
- Division of Aquatic Ecology and Evolution, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
| | - Madhava Meegaskumbura
- Guangxi Key Laboratory for Forest Ecology and Conservation, College of Forestry, Guangxi University, Nanning, People's Republic of China
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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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Norambuena HV, Els P, Victoriano PF, Knowles L. Genome‐wide DNA and phenotypic information supports recent colonization of South American grasslands by Correndera Pipit (Aves, Motacillidae). ZOOL SCR 2021. [DOI: 10.1111/zsc.12485] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
| | - Paul Els
- Department of Biological Sciences and Museum of Natural Science Louisiana State University Baton Rouge LA USA
- Groningen Institute for Evolutionary Life Sciences University of Groningen Groningen The Netherlands
| | - Pedro F. Victoriano
- Departamento de Zoología Facultad de Ciencias Naturales y Oceanográficas Universidad de Concepción Concepción Chile
| | - Lacey Knowles
- Department of Ecology and Evolutionary Biology Museum of Zoology University of Michigan Ann Arbor MI USA
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Liu Q, Lu Z, He W, Li F, Chen W, Li C, Chao Z, Tian E. Development and characterization of 16 novel microsatellite markers by Transcriptome sequencing for Angelica dahurica and test for cross-species amplification. BMC PLANT BIOLOGY 2020; 20:152. [PMID: 32268882 PMCID: PMC7140362 DOI: 10.1186/s12870-020-02374-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Accepted: 03/31/2020] [Indexed: 05/31/2023]
Abstract
BACKGROUND Angelica dahurica (Apiaceae) is an important herb in traditional Chinese medicine. Because of its important medicinal and economic values, its wild resources were over-exploited and increasingly reduced. Meanwhile, the diversity of cultivars of A. dahurica has decreased as a result of long-term artificial cultivation. However, there are no population genetics studies of natural A. dahurica reported yet, especially for using microsatellite markers (SSRs) to investigate population genetics of the species. RESULTS Sixteen polymorphic EST-SSR loci were isolated from A. dahurica with transcriptome sequencing technology (RNA-Seq). The number of alleles varied from 2 to 15 per polymorphic locus over populations with the observed and expected heterozygosities ranging from 0.000 to 1.000 and from 0.000 to 0.829, respectively. Significant deviations from Hardy-Weinberg equilibrium were observed at 8 loci. Tests of linkage disequilibrium showed 11 informative locus pairs were significant across all populations. Cross-species amplification showed that 14 out of 16 SSR loci have the transferability in cultivar-A. dahurica cv. 'Hangbaizhi' and A. decursiva. CONCLUSIONS The 16 newly developed loci microsatellite primers with RNA-Seq will be useful for further investigating population genetics of A. dahurica, cultivars and other members of this genus.
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Affiliation(s)
- Qianqian Liu
- Affiliated Cancer Hospital & Institute of Guangzhou Medical University, Guangzhou, 510095, China
| | - Zuyu Lu
- School of Traditional Chinese Medicine, Southern Medical University, Guangzhou, 515005, China
| | - Wei He
- School of Traditional Chinese Medicine, Southern Medical University, Guangzhou, 515005, China
| | - Fang Li
- School of Traditional Chinese Medicine, Southern Medical University, Guangzhou, 515005, China
| | - Wenna Chen
- College of Landscape and Ecological Engineering, Hebei University of Engineering, Handan, 056038, China
| | - Chan Li
- School of Traditional Chinese Medicine, Southern Medical University, Guangzhou, 515005, China
| | - Zhi Chao
- School of Traditional Chinese Medicine, Southern Medical University, Guangzhou, 515005, China.
| | - Enwei Tian
- School of Traditional Chinese Medicine, Southern Medical University, Guangzhou, 515005, China.
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Crawford DL, Schulte PM, Whitehead A, Oleksiak MF. Evolutionary Physiology and Genomics in the Highly Adaptable Killifish (
Fundulus heteroclitus
). Compr Physiol 2020; 10:637-671. [DOI: 10.1002/cphy.c190004] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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Bartáková V, Nagy B, Polačik M, Blažek R, Lamtane H, Reichard M. Genetic diversity of a widespread annual killifish from coastal Tanzania. BMC Evol Biol 2020; 20:1. [PMID: 31906845 PMCID: PMC6943906 DOI: 10.1186/s12862-019-1549-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Accepted: 11/27/2019] [Indexed: 02/07/2023] Open
Abstract
Background African annual killifishes (Nothobranchius spp.) are adapted to seasonally desiccating habitats (ephemeral pools), surviving dry periods as dormant eggs. Given their peculiar life history, geographic aspects of their diversity uniquely combine patterns typical for freshwater taxa (river basin structure and elevation gradient) and terrestrial animals (rivers acting as major dispersal barriers). However, our current knowledge on fine-scale inter-specific and intra-specific genetic diversity of African annual fish is limited to a single, particularly dry region of their distribution (subtropical Mozambique). Using a widespread annual killifish from coastal Tanzania and Kenya, we tested whether the same pattern of genetic divergence pertains to a wet equatorial region in the centre of Nothobranchius distribution. Results In populations of Nothobranchius melanospilus species group across its range, we genotyped a part of mitochondrial cytochrome oxidase subunit 1 (COI) gene (83 individuals from 22 populations) and 10 nuclear microsatellite markers (251 individuals from 16 populations). We found five lineages with a clear phylogeographic structure but frequent secondary contact. Mitochondrial lineages were largely congruent with main population genetic clusters identified on microsatellite markers. In the upper Wami basin, populations are isolated as a putative Nothobranchius prognathus, but include also a population from a periphery of the middle Ruvu basin. Other four lineages (including putative Nothobranchius kwalensis) coexisted in secondary contact zones, but possessed clear spatial pattern. Main river channels did not form apparent barriers to dispersal. The most widespread lineage had strong signal of recent population expansion. Conclusions We conclude that dispersal of a Nothobranchius species from a wet part of the genus distribution (tropical lowland) is not constrained by main river channels and closely related lineages frequently coexist in secondary contact zones. We also demonstrate contemporary connection between the Ruvu and Rufiji river basins. Our data do not provide genetic support for existence of recently described cryptic species from N. melanospilus complex, but cannot resolve this issue.
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Affiliation(s)
- Veronika Bartáková
- Czech Academy of Sciences, Institute of Vertebrate Biology, Květná 8, 603 65, Brno, Czech Republic
| | | | - Matej Polačik
- Czech Academy of Sciences, Institute of Vertebrate Biology, Květná 8, 603 65, Brno, Czech Republic
| | - Radim Blažek
- Czech Academy of Sciences, Institute of Vertebrate Biology, Květná 8, 603 65, Brno, Czech Republic
| | - Hieromin Lamtane
- Department of Animal, Aquaculture and Range Sciences, Sokoine University of Agriculture, P.O. Box 3004, Morogoro, Tanzania
| | - Martin Reichard
- Czech Academy of Sciences, Institute of Vertebrate Biology, Květná 8, 603 65, Brno, Czech Republic.
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McKenzie JL, Chung DJ, Healy TM, Brennan RS, Bryant HJ, Whitehead A, Schulte PM. Mitochondrial Ecophysiology: Assessing the Evolutionary Forces That Shape Mitochondrial Variation. Integr Comp Biol 2019; 59:925-937. [PMID: 31282925 DOI: 10.1093/icb/icz124] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
The mitonuclear species concept hypothesizes that incompatibilities between interacting gene products of the nuclear and mitochondrial genomes are a major factor establishing and maintaining species boundaries. However, most of the data available to test this concept come from studies of genetic variation in mitochondrial DNA, and clines in the mitochondrial genome across contact zones can be produced by a variety of forces. Here, we show that using a combination of population genomic analyses of the nuclear and mitochondrial genomes and studies of mitochondrial function can provide insight into the relative roles of neutral processes, adaptive evolution, and mitonuclear incompatibility in establishing and maintaining mitochondrial clines, using Atlantic killifish (Fundulus heteroclitus) as a case study. There is strong evidence for a role of secondary contact following the last glaciation in shaping a steep mitochondrial cline across a contact zone between northern and southern subspecies of killifish, but there is also evidence for a role of adaptive evolution in driving differentiation between the subspecies in a variety of traits from the level of the whole organism to the level of mitochondrial function. In addition, studies are beginning to address the potential for mitonuclear incompatibilities in admixed populations. However, population genomic studies have failed to detect evidence for a strong and pervasive influence of mitonuclear incompatibilities, and we suggest that polygenic selection may be responsible for the complex patterns observed. This case study demonstrates that multiple forces can act together in shaping mitochondrial clines, and illustrates the challenge of disentangling their relative roles.
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Affiliation(s)
- Jessica L McKenzie
- Department of Zoology and Biodiversity Research Centre, The University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Dillon J Chung
- Department of Zoology and Biodiversity Research Centre, The University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Timothy M Healy
- Department of Zoology and Biodiversity Research Centre, The University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Reid S Brennan
- Department of Environmental Toxicology, University of California-Davis, 4138 Meyer Hall, 1 Shields Avenue, Davis, CA 95616, USA
| | - Heather J Bryant
- Department of Zoology and Biodiversity Research Centre, The University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Andrew Whitehead
- Department of Environmental Toxicology, University of California-Davis, 4138 Meyer Hall, 1 Shields Avenue, Davis, CA 95616, USA
| | - Patricia M Schulte
- Department of Zoology and Biodiversity Research Centre, The University of British Columbia, Vancouver, BC V6T 1Z4, Canada
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Takahashi D, Teramine T, Sakaguchi S, Setoguchi H. Genetic data reveals a complex history of multiple admixture events in presently allopatric wild gingers (Asarum spp.) showing intertaxonomic clinal variation in calyx lobe length. Mol Phylogenet Evol 2019; 137:146-155. [PMID: 31075504 DOI: 10.1016/j.ympev.2019.05.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Revised: 05/06/2019] [Accepted: 05/06/2019] [Indexed: 10/26/2022]
Abstract
Clinal variation is a major pattern of observed phenotypic diversity and identifying underlying demographic processes is a necessary step to understand the establishment of clinal variation. The wild ginger series Sakawanum (genus Asarum) comprises four taxa, which exhibit intertaxonomic clinal variation in calyx lobe length across two continental islands isolated by a sea strait. To test alternative hypotheses of the evolutionary history and to determine the implications for the formation of clinal variation, we conducted approximate Bayesian computation (ABC) analysis and ecological niche modeling (ENM). ABC analysis indicated that the scenario assuming multiple admixture events was strongly supported. This scenario assumed two admixture events occurred between morphologically distinct taxa, likely leading to the generation of intermediate taxa. One of the admixture events was estimated to have occurred during the last glacial maximum (LGM), during which the taxa were estimated to have formed a common refugia in southern areas by ENM analysis. Although four taxa are currently distributed allopatrically on different islands and trans-oceanic dispersal appears unlikely, the formation of a land bridge and the geographic range shift to refugia would have allowed secondary contact between previously isolated taxa. This study suggests that clinal variation can be shaped by demographic history including multiple admixtures due to climatic oscillations.
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Affiliation(s)
- Daiki Takahashi
- Graduate School of Human and Environmental Studies, Kyoto University, Yoshida-Nihonmatsu, Sakyo-ku, Kyoto 606-8501, Japan.
| | | | - Shota Sakaguchi
- Graduate School of Human and Environmental Studies, Kyoto University, Yoshida-Nihonmatsu, Sakyo-ku, Kyoto 606-8501, Japan
| | - Hiroaki Setoguchi
- Graduate School of Human and Environmental Studies, Kyoto University, Yoshida-Nihonmatsu, Sakyo-ku, Kyoto 606-8501, Japan
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9
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Dayan DI, Du X, Baris TZ, Wagner DN, Crawford DL, Oleksiak MF. Population genomics of rapid evolution in natural populations: polygenic selection in response to power station thermal effluents. BMC Evol Biol 2019; 19:61. [PMID: 30808292 PMCID: PMC6390305 DOI: 10.1186/s12862-019-1392-5] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Accepted: 02/14/2019] [Indexed: 01/09/2023] Open
Abstract
BACKGROUND Examples of rapid evolution are common in nature but difficult to account for with the standard population genetic model of adaptation. Instead, selection from the standing genetic variation permits rapid adaptation via soft sweeps or polygenic adaptation. Empirical evidence of this process in nature is currently limited but accumulating. RESULTS We provide genome-wide analyses of rapid evolution in Fundulus heteroclitus populations subjected to recently elevated temperatures due to coastal power station thermal effluents using 5449 SNPs across two effluent-affected and four reference populations. Bayesian and multivariate analyses of population genomic structure reveal a substantial portion of genetic variation that is most parsimoniously explained by selection at the site of thermal effluents. An FST outlier approach in conjunction with additional conservative requirements identify significant allele frequency differentiation that exceeds neutral expectations among exposed and closely related reference populations. Genomic variation patterns near these candidate loci reveal that individuals living near thermal effluents have rapidly evolved from the standing genetic variation through small allele frequency changes at many loci in a pattern consistent with polygenic selection on the standing genetic variation. CONCLUSIONS While the ultimate trajectory of selection in these populations is unknown and we survey only a minority of genomic loci, our findings suggest that polygenic models of adaptation may play important roles in large, natural populations experiencing recent selection due to environmental changes that cause broad physiological impacts.
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Affiliation(s)
- David I. Dayan
- Rosenstiel School of Marine and Atmospheric Science, University of Miami, 4600 Rickenbacker Causeway, Miami, FL 33149 USA
| | - Xiao Du
- Rosenstiel School of Marine and Atmospheric Science, University of Miami, 4600 Rickenbacker Causeway, Miami, FL 33149 USA
| | - Tara Z. Baris
- Rosenstiel School of Marine and Atmospheric Science, University of Miami, 4600 Rickenbacker Causeway, Miami, FL 33149 USA
| | - Dominique N. Wagner
- Rosenstiel School of Marine and Atmospheric Science, University of Miami, 4600 Rickenbacker Causeway, Miami, FL 33149 USA
| | - Douglas L. Crawford
- Rosenstiel School of Marine and Atmospheric Science, University of Miami, 4600 Rickenbacker Causeway, Miami, FL 33149 USA
| | - Marjorie F. Oleksiak
- Rosenstiel School of Marine and Atmospheric Science, University of Miami, 4600 Rickenbacker Causeway, Miami, FL 33149 USA
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Hurt C, Ellis N, Harman A, Savage C. Genetic Structure at the Major Histocompatibility Complex in the Endangered Barrens Topminnow (Fundulus julisia). SOUTHEAST NAT 2019. [DOI: 10.1656/058.018.0102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Affiliation(s)
- Carla Hurt
- Department of Biology, Tennessee Technological University, Cookeville, TN 38505
| | - Natalie Ellis
- Department of Biology, Tennessee Technological University, Cookeville, TN 38505
| | - Alexis Harman
- Department of Biology, Tennessee Technological University, Cookeville, TN 38505
| | - Courtney Savage
- Department of Biology, Tennessee Technological University, Cookeville, TN 38505
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Morim T, Bigg GR, Madeira PM, Palma J, Duvernell DD, Gisbert E, Cunha RL, Castilho R. Invasion genetics of the mummichog ( Fundulus heteroclitus): recent anthropogenic introduction in Iberia. PeerJ 2019; 7:e6155. [PMID: 30775165 PMCID: PMC6369826 DOI: 10.7717/peerj.6155] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Accepted: 11/25/2018] [Indexed: 11/29/2022] Open
Abstract
Human activities such as trade and transport have increased considerably in the last decades, greatly facilitating the introduction and spread of non-native species at a global level. In the Iberian Peninsula, Fundulus heteroclitus, a small euryhaline coastal fish with short dispersal, was found for the first time in the mid-1970s. Since then, F. heteroclitus has undergone range expansions, colonizing the southern region of Portugal, southwestern coast of Spain and the Ebro Delta in the Mediterranean Sea. Cytochrome b sequences were used to elucidate the species invasion pathway in Iberia. Three Iberian locations (Faro, Cádiz and Ebro Delta) and 13 other locations along the native range of F. heteroclitus in North America were sampled. Results revealed a single haplotype, common to all invasive populations, which can be traced to the northern region of the species’ native range. We posit that the origin of the founder individuals is between New York and Nova Scotia. Additionally, the lack of genetic structure within Iberia is consistent with a recent invasion scenario and a strong founder effect. We suggest the most probable introduction vector is associated with the aquarium trade. We further discuss the hypothesis of a second human-mediated introduction responsible for the establishment of individuals in the Ebro Delta supported by the absence of adequate muddy habitats linking Cádiz and the Ebro Delta. Although the species has a high tolerance to salinity and temperature, ecological niche modelling indicates that benthic habitat constraints prevent along-shore colonisation suggesting that such expansions would need to be aided by human release.
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Affiliation(s)
- Teófilo Morim
- Centre for Marine Sciences (CCMAR), University of Algarve, Faro, Portugal
| | - Grant R Bigg
- Department of Geography, University of Sheffield, Sheffield, United Kingdom
| | - Pedro M Madeira
- Centre for Marine Sciences (CCMAR), University of Algarve, Faro, Portugal
| | - Jorge Palma
- Centre for Marine Sciences (CCMAR), University of Algarve, Faro, Portugal
| | - David D Duvernell
- Department of Biological Sciences, Missouri University of Science and Technology, Rolla, MO, United States of America
| | - Enric Gisbert
- IRTA, Aquaculture Program, Centre de Sant Carles de la Ràpita, Sant Carles de la Ràpita, Spain
| | - Regina L Cunha
- Centre for Marine Sciences (CCMAR), University of Algarve, Faro, Portugal
| | - Rita Castilho
- Centre for Marine Sciences (CCMAR), University of Algarve, Faro, Portugal
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12
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Bertl J, Ringbauer H, Blum MG. Can secondary contact following range expansion be distinguished from barriers to gene flow? PeerJ 2018; 6:e5325. [PMID: 30294507 PMCID: PMC6171497 DOI: 10.7717/peerj.5325] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2016] [Accepted: 07/01/2018] [Indexed: 11/20/2022] Open
Abstract
Secondary contact is the reestablishment of gene flow between sister populations that have diverged. For instance, at the end of the Quaternary glaciations in Europe, secondary contact occurred during the northward expansion of the populations which had found refugia in the southern peninsulas. With the advent of multi-locus markers, secondary contact can be investigated using various molecular signatures including gradients of allele frequency, admixture clines, and local increase of genetic differentiation. We use coalescent simulations to investigate if molecular data provide enough information to distinguish between secondary contact following range expansion and an alternative evolutionary scenario consisting of a barrier to gene flow in an isolation-by-distance model. We find that an excess of linkage disequilibrium and of genetic diversity at the suture zone is a unique signature of secondary contact. We also find that the directionality index ψ, which was proposed to study range expansion, is informative to distinguish between the two hypotheses. However, although evidence for secondary contact is usually conveyed by statistics related to admixture coefficients, we find that they can be confounded by isolation-by-distance. We recommend to account for the spatial repartition of individuals when investigating secondary contact in order to better reflect the complex spatio-temporal evolution of populations and species.
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Affiliation(s)
- Johanna Bertl
- Department of Molecular Medicine, Aarhus University, Aarhus, Denmark
- Vienna Graduate School of Population Genetics, Vetmeduni Vienna, Vienna, Austria
| | - Harald Ringbauer
- Department of Human Genetics, University of Chicago, Chicago, IL, USA
- Institute of Science and Technology Austria, Klosterneuburg, Austria
| | - Michael G.B. Blum
- Laboratoire TIMC-IMAG, UMR 5525, Université Grenoble Alpes, CNRS, Grenoble, France
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Dolby GA, Hechinger R, Ellingson RA, Findley LT, Lorda J, Jacobs DK. Sea-level driven glacial-age refugia and post-glacial mixing on subtropical coasts, a palaeohabitat and genetic study. Proc Biol Sci 2017; 283:rspb.2016.1571. [PMID: 27903870 DOI: 10.1098/rspb.2016.1571] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2016] [Accepted: 10/31/2016] [Indexed: 11/12/2022] Open
Abstract
Using a novel combination of palaeohabitat modelling and genetic mixture analyses, we identify and assess a sea-level-driven recolonization process following the Last Glacial Maximum (LGM). Our palaeohabitat modelling reveals dramatic changes in estuarine habitat distribution along the coast of California (USA) and Baja California (Mexico). At the LGM (approx. 20 kya), when sea level was approximately 130 m lower, the palaeo-shoreline was too steep for tidal estuarine habitat formation, eliminating this habitat type from regions where it is currently most abundant, and limiting such estuaries to a northern and a southern refugium separated by 1000 km. We assess the recolonization of estuaries formed during post-LGM sea-level rise through examination of refugium-associated alleles and approximate Bayesian computation in three species of estuarine fishes. Results reveal sourcing of modern populations from both refugia, which admix in the newly formed habitat between the refuges. We infer a dramatic peak in habitat area between 15 and 10 kya with subsequent decline. Overall, this approach revealed a previously undocumented dynamic and integrated relationship between sea-level change, coastal processes and population genetics. These results extend glacial refugial dynamics to unglaciated subtropical coasts and have significant implications for biotic response to predicted sea-level rise.
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Affiliation(s)
- Greer A Dolby
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Ryan Hechinger
- Scripps Institution of Oceanography-Marine Biology Research Division, UC San Diego, La Jolla, CA 92093-0218, USA
| | - Ryan A Ellingson
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Lloyd T Findley
- Centro de Investigación en Alimentación y Desarrollo, A.C.-Unidad Guaymas, Carretera al Varadero Nacional km. 6.6, Colonia Las Playitas, Guaymas, Sonora 85480, México
| | - Julio Lorda
- Facultad de Ciencias, Universidad Autónoma de Baja California. Carretera Transpeninsular Ensenada - Tijuana No. 3917, Colonia Playitas, C.P. 22860, Ensenada, Baja California, México
| | - David K Jacobs
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, CA 90095, USA
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Kim JK, Bae SE, Lee SJ, Yoon MG. New insight into hybridization and unidirectional introgression between Ammodytes japonicus and Ammodytes heian (Trachiniformes, Ammodytidae). PLoS One 2017; 12:e0178001. [PMID: 28582394 PMCID: PMC5459329 DOI: 10.1371/journal.pone.0178001] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2017] [Accepted: 05/05/2017] [Indexed: 11/19/2022] Open
Abstract
Based on northern (NOL) and southern (SOL) mitochondrial lineages, recently, it proposed the new species Ammodytes heian and revived the species name Ammodytes japonicus to describe sand lances from the northwestern Pacific Ocean. This study used molecular methods to investigate genetic relationships between the two sand lance species in Korea and Japan. In total, 154 specimens were collected from four locations in Korea (Baengnyeongdo in the Yellow Sea, Tongyeong in the Korean Strait, and Jumunjin and Gijang in the East Sea), and 50 specimens were collected from a single location in Japan (Wakkanai in the Okhotsk Sea). Mitochondrial DNA analysis demonstrated that the individuals from Baengnyeongdo and Tongyeong all belonged to the SOL, whereas those from Gijang, Jumunjin, and Wakkanai included individuals from both the NOL and SOL (over 75% NOL). Population structure analyses were performed on the same individuals using seven microsatellite DNA markers. The population structure analysis based on 201 specimens identified two clusters (named as northern group and southern group), with the admixture proportion (q) of < 0.1 for the northern group in the Backyeongdo and Tongyeong sand lances and < 0.1 for the southern group in the Wakkanai sand lances. The high heterogeneity indicated that the former was probably A. japonicus and the latter probably A. heian. However, the admixture proportion in the Jumunjin and Gijang sand lances was 0.71–0.75 for the southern group, indicating that hybridization and unidirectional introgression from SOL to NOL occurs in southwestern margin of the East Sea. Our findings illustrate the speciation process based on different patterns of gene flow between Korean and Japanese sand lance, which is strongly influenced by both the paleo-climatic change and the contemporary local oceanic current pattern.
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Affiliation(s)
- Jin-Koo Kim
- Department of Marine Biology, Pukyong National University, Busan, Korea
- * E-mail:
| | - Seung Eun Bae
- Department of Marine Biology, Pukyong National University, Busan, Korea
| | - Soo Jeong Lee
- Department of Marine Biology, Pukyong National University, Busan, Korea
- Fisheries Resources and Environment Division, East Sea Fisheries Research Institute, National Institute of Fisheries Science, Gangnung, Korea
| | - Moon Geun Yoon
- Marine Biodiversity Institute of Korea, Seocheon-gun, Chungcheongnam-do, Korea
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15
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Hurt C, Kuhajda B, Harman A, Ellis N, Nalan M. Genetic diversity and population structure in the Barrens Topminnow (Fundulus julisia): implications for conservation and management of a critically endangered species. CONSERV GENET 2017. [DOI: 10.1007/s10592-017-0984-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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16
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Baris TZ, Wagner DN, Dayan DI, Du X, Blier PU, Pichaud N, Oleksiak MF, Crawford DL. Evolved genetic and phenotypic differences due to mitochondrial-nuclear interactions. PLoS Genet 2017; 13:e1006517. [PMID: 28362806 PMCID: PMC5375140 DOI: 10.1371/journal.pgen.1006517] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2016] [Accepted: 12/01/2016] [Indexed: 02/05/2023] Open
Abstract
The oxidative phosphorylation (OxPhos) pathway is responsible for most aerobic ATP production and is the only pathway with both nuclear and mitochondrial encoded proteins. The importance of the interactions between these two genomes has recently received more attention because of their potential evolutionary effects and how they may affect human health and disease. In many different organisms, healthy nuclear and mitochondrial genome hybrids between species or among distant populations within a species affect fitness and OxPhos functions. However, what is less understood is whether these interactions impact individuals within a single natural population. The significance of this impact depends on the strength of selection for mito-nuclear interactions. We examined whether mito-nuclear interactions alter allele frequencies for ~11,000 nuclear SNPs within a single, natural Fundulus heteroclitus population containing two divergent mitochondrial haplotypes (mt-haplotypes). Between the two mt-haplotypes, there are significant nuclear allele frequency differences for 349 SNPs with a p-value of 1% (236 with 10% FDR). Unlike the rest of the genome, these 349 outlier SNPs form two groups associated with each mt-haplotype, with a minority of individuals having mixed ancestry. We use this mixed ancestry in combination with mt-haplotype as a polygenic factor to explain a significant fraction of the individual OxPhos variation. These data suggest that mito-nuclear interactions affect cardiac OxPhos function. The 349 outlier SNPs occur in genes involved in regulating metabolic processes but are not directly associated with the 79 nuclear OxPhos proteins. Therefore, we postulate that the evolution of mito-nuclear interactions affects OxPhos function by acting upstream of OxPhos.
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Affiliation(s)
- Tara Z. Baris
- Marine Biology and Ecology, Rosenstiel School of Marine and Atmospheric Sciences, University of Miami, Rickenbacker Causeway, Miami, FL, United States of America
- * E-mail:
| | - Dominique N. Wagner
- Marine Biology and Ecology, Rosenstiel School of Marine and Atmospheric Sciences, University of Miami, Rickenbacker Causeway, Miami, FL, United States of America
| | - David I. Dayan
- Marine Biology and Ecology, Rosenstiel School of Marine and Atmospheric Sciences, University of Miami, Rickenbacker Causeway, Miami, FL, United States of America
| | - Xiao Du
- Marine Biology and Ecology, Rosenstiel School of Marine and Atmospheric Sciences, University of Miami, Rickenbacker Causeway, Miami, FL, United States of America
| | - Pierre U. Blier
- Dept de Biologie, Université du Québec à Rimouski, 300 Allée des Ursulines, Rimouski, Quebec, Canada
| | - Nicolas Pichaud
- Dept de Biologie, Université du Québec à Rimouski, 300 Allée des Ursulines, Rimouski, Quebec, Canada
| | - Marjorie F. Oleksiak
- Marine Biology and Ecology, Rosenstiel School of Marine and Atmospheric Sciences, University of Miami, Rickenbacker Causeway, Miami, FL, United States of America
| | - Douglas L. Crawford
- Marine Biology and Ecology, Rosenstiel School of Marine and Atmospheric Sciences, University of Miami, Rickenbacker Causeway, Miami, FL, United States of America
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17
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Fine-scale genetic structure due to adaptive divergence among microhabitats. Heredity (Edinb) 2017; 118:594-604. [PMID: 28295034 DOI: 10.1038/hdy.2017.6] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2016] [Revised: 01/20/2016] [Accepted: 01/22/2017] [Indexed: 02/03/2023] Open
Abstract
It has been suggested that adaptive evolution on ecological timescales shapes communities. However, adaptation among environments relies on isolation or large selection coefficients that exceed migration effects. This reliance is tempered if adaptation is polygenic-does not depend on one allele completely replacing another but instead requires small allele frequency changes at many loci. Thus, whether individuals can evolve adaptation to fine-scale habitat variation (for example, microhabitats) is not resolved. Here we analyze the genetic divergence of the teleost fish, Fundulus heteroclitus, among microhabitats that are <200 m apart in three separate saltmarshes using 4741 single-nucleotide polymorphisms (SNPs). Among these SNPs, 1.3-2.3% have large and highly significant differences among microhabitats (mean FST=0.15; false discovery rate ⩽1%). The divergence among microhabitats for these outlier SNPs is larger than that among populations, exceeds neutral expectation and indicates surprising population structure among microhabitats. Thus, we suggest that polygenic selection is surprisingly effective in altering allele frequencies among many different SNPs that share similar biological functions in response to environmental and ecological differences over very small geographic distances. We acknowledge the evolutionary difficulty of large genetic divergence among well-connected habitats. Therefore, these studies are only the first step to discern whether natural selection is responsible and capable of effecting genetic divergence on such a fine scale.
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18
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Nacci D, Proestou D, Champlin D, Martinson J, Waits ER. Genetic basis for rapidly evolved tolerance in the wild: adaptation to toxic pollutants by an estuarine fish species. Mol Ecol 2016; 25:5467-5482. [DOI: 10.1111/mec.13848] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2016] [Revised: 08/22/2016] [Accepted: 08/30/2016] [Indexed: 01/28/2023]
Affiliation(s)
- Diane Nacci
- U.S. Environmental Protection Agency Office of Research and Development National Health and Environmental Effects Research Laboratory Atlantic Ecology Division 27 Tarzwell Dr. Narragansett RI 02882 USA
| | - Dina Proestou
- U.S. Environmental Protection Agency Office of Research and Development National Health and Environmental Effects Research Laboratory Atlantic Ecology Division 27 Tarzwell Dr. Narragansett RI 02882 USA
| | - Denise Champlin
- U.S. Environmental Protection Agency Office of Research and Development National Health and Environmental Effects Research Laboratory Atlantic Ecology Division 27 Tarzwell Dr. Narragansett RI 02882 USA
| | - John Martinson
- U.S. Environmental Protection Agency Office of Research and Development National Exposure Research Laboratory Ecological Exposure Research Division 26 W. Martin Luther King Dr. Cincinnati OH 45268 USA
| | - Eric R. Waits
- U.S. Environmental Protection Agency Office of Research and Development National Exposure Research Laboratory Ecological Exposure Research Division 26 W. Martin Luther King Dr. Cincinnati OH 45268 USA
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McKenzie JL, Dhillon RS, Schulte PM. Steep, coincident, and concordant clines in mitochondrial and nuclear-encoded genes in a hybrid zone between subspecies of Atlantic killifish, Fundulus heteroclitus. Ecol Evol 2016; 6:5771-87. [PMID: 27547353 PMCID: PMC4983590 DOI: 10.1002/ece3.2324] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2016] [Revised: 06/23/2016] [Accepted: 06/27/2016] [Indexed: 01/15/2023] Open
Abstract
Steep genetic clines resulting from recent secondary contact between previously isolated taxa can either gradually erode over time or be stabilized by factors such as ecological selection or selection against hybrids. We used patterns of variation in 30 nuclear and two mitochondrial SNPs to examine the factors that could be involved in stabilizing clines across a hybrid zone between two subspecies of the Atlantic killifish, Fundulus heteroclitus. Increased heterozygote deficit and cytonuclear disequilibrium in populations near the center of the mtDNA cline suggest that some form of reproductive isolation such as assortative mating or selection against hybrids may be acting in this hybrid zone. However, only a small number of loci exhibited these signatures, suggesting locus-specific, rather than genomewide, factors. Fourteen of the 32 loci surveyed had cline widths inconsistent with neutral expectations, with two SNPs in the mitochondrial genome exhibiting the steepest clines. Seven of the 12 putatively non-neutral nuclear clines were for SNPs in genes related to oxidative metabolism. Among these putatively non-neutral nuclear clines, SNPs in two nuclear-encoded mitochondrial genes (SLC25A3 and HDDC2), as well as SNPs in the myoglobin, 40S ribosomal protein S17, and actin-binding LIM protein genes, had clines that were coincident and concordant with the mitochondrial clines. When hybrid index was calculated using this subset of loci, the frequency distribution of hybrid indices for a population located at the mtDNA cline center was non-unimodal, suggesting selection against advanced-generation hybrids, possibly due to effects on processes involved in oxidative metabolism.
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Affiliation(s)
- Jessica L. McKenzie
- Department of ZoologyUniversity of British ColumbiaVancouverBritish ColumbiaCanada
- Centre for Aquaculture and Environmental ResearchFisheries and Oceans CanadaWest VancouverBritish ColumbiaCanada
| | - Rashpal S. Dhillon
- Department of ZoologyUniversity of British ColumbiaVancouverBritish ColumbiaCanada
- Present address: Department of Biomolecular ChemistryEpigenetics ThemeWisconsin Institute for DiscoveryUniversity of WisconsinMadisonWisconsin
| | - Patricia M. Schulte
- Department of ZoologyUniversity of British ColumbiaVancouverBritish ColumbiaCanada
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20
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Brennan RS, Hwang R, Tse M, Fangue NA, Whitehead A. Local adaptation to osmotic environment in killifish, Fundulus heteroclitus, is supported by divergence in swimming performance but not by differences in excess post-exercise oxygen consumption or aerobic scope. Comp Biochem Physiol A Mol Integr Physiol 2016; 196:11-19. [DOI: 10.1016/j.cbpa.2016.02.006] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2015] [Revised: 02/08/2016] [Accepted: 02/10/2016] [Indexed: 11/25/2022]
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21
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Bergland AO, Tobler R, González J, Schmidt P, Petrov D. Secondary contact and local adaptation contribute to genome-wide patterns of clinal variation in Drosophila melanogaster. Mol Ecol 2016; 25:1157-74. [PMID: 26547394 DOI: 10.1111/mec.13455] [Citation(s) in RCA: 93] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2014] [Revised: 10/29/2015] [Accepted: 11/02/2015] [Indexed: 12/12/2022]
Abstract
Populations arrayed along broad latitudinal gradients often show patterns of clinal variation in phenotype and genotype. Such population differentiation can be generated and maintained by both historical demographic events and local adaptation. These evolutionary forces are not mutually exclusive and can in some cases produce nearly identical patterns of genetic differentiation among populations. Here, we investigate the evolutionary forces that generated and maintain clinal variation genome-wide among populations of Drosophila melanogaster sampled in North America and Australia. We contrast patterns of clinal variation in these continents with patterns of differentiation among ancestral European and African populations. Using established and novel methods we derive here, we show that recently derived North America and Australia populations were likely founded by both European and African lineages and that this hybridization event likely contributed to genome-wide patterns of parallel clinal variation between continents. The pervasive effects of admixture mean that differentiation at only several hundred loci can be attributed to the operation of spatially varying selection using an FST outlier approach. Our results provide novel insight into the well-studied system of clinal differentiation in D. melanogaster and provide a context for future studies seeking to identify loci contributing to local adaptation in a wide variety of organisms, including other invasive species as well as temperate endemics.
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Affiliation(s)
- Alan O Bergland
- Department of Biology, Stanford University, Stanford, CA, 94305-5020, USA
| | - Ray Tobler
- Department of Biology, Stanford University, Stanford, CA, 94305-5020, USA.,Institut für Populationsgenetik, Vetmeduni Vienna, Veterinärplatz 1, Vienna, A-1210, Austria
| | - Josefa González
- Department of Biology, Stanford University, Stanford, CA, 94305-5020, USA.,Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Passeig Maritim de la Barceloneta 37-49, 0800, 3 Barcelona, Spain
| | - Paul Schmidt
- Department of Biology, The University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Dmitri Petrov
- Department of Biology, Stanford University, Stanford, CA, 94305-5020, USA
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22
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McKenzie JL, Dhillon RS, Schulte PM. Evidence for a bimodal distribution of hybrid indices in a hybrid zone with high admixture. ROYAL SOCIETY OPEN SCIENCE 2015; 2:150285. [PMID: 27019720 PMCID: PMC4807441 DOI: 10.1098/rsos.150285] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2015] [Accepted: 11/09/2015] [Indexed: 05/30/2023]
Abstract
The genetic structure of a hybrid zone can provide insights into the relative roles of the various factors that maintain the zone. Here, we use a multilocus approach to characterize a hybrid zone between two subspecies of killifish (Fundulus heteroclitus, Walbaum 1792) found along the Atlantic coast of North America. We first analysed clinal variation along the Atlantic coast using a single-nucleotide polymorphism in the mitochondrial DNA (mtDNA) displacement loop (D-loop) and a panel of nine nuclear microsatellite markers. A model constraining all clines to the same width and centre was not significantly different from a model in which the clines were allowed to vary independently. Locus-by-locus analysis indicated that the majority of nuclear clines shared the same centre as the mtDNA cline, and the widths of these clines were also narrower than that predicted by a neutral model, suggesting that selection is operating to maintain the hybrid zone. However, two of the nuclear clines had widths greater than the neutral prediction and had centres that were displaced relative to the mtDNA cline centre. We also found that a marsh located near the centre of the mtDNA cline demonstrated a bimodal distribution of nuclear hybrid index values, suggesting a deficit of first-generation hybrids and backcrossed genotypes. Thus, selection against hybrid genotypes may be playing a role in maintaining this hybrid zone and the associated steep nuclear and mtDNA clines.
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Affiliation(s)
- Jessica L. McKenzie
- Department of Zoology, University of British Columbia, Vancouver, British Columbia, Canada
- Centre for Aquaculture and Environmental Research, Fisheries and Oceans Canada, West Vancouver, British Columbia, Canada
| | - Rashpal S. Dhillon
- Department of Zoology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Patricia M. Schulte
- Department of Zoology, University of British Columbia, Vancouver, British Columbia, Canada
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23
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Pappalardo AM, Gonzalez EG, Tigano C, Doadrio I, Ferrito V. Comparative pattern of genetic structure in two Mediterranean killifishes Aphanius fasciatus and Aphanius iberus inferred from both mitochondrial and nuclear data. JOURNAL OF FISH BIOLOGY 2015; 87:69-87. [PMID: 26010329 DOI: 10.1111/jfb.12693] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2014] [Accepted: 03/08/2015] [Indexed: 06/04/2023]
Abstract
In this study, genetic variation was assessed in Aphanius fasciatus and Aphanius iberus characterized by similar ecological traits but with very different distribution ranges in the Mediterranean area. Five populations of A. iberus and five of A. fasciatus were analysed using five polymorphic microsatellite loci and partial mitochondrial control region (D-loop) sequences. Congruent results were found with both nuclear and mitochondrial molecular markers. The results showed that similar levels of genetic divergence, based on mitochondrial control region sequences, are present among populations of A. iberus and among populations of A. fasciatus despite the very different geographic distance existing among the examined populations of the two species (low geographic distance in A. iberus and high in A. fasciatus). A possible explanation could be that the populations of A. iberus were isolated for a longer time than the populations of A. fasciatus supporting the hypothesis that the split in the lineage leading to A. iberus is older than the split in the lineage leading to A. fasciatus. The possibility that the wide circum-Mediterranean distribution of A. fasciatus ensures the high connectivity of its populations, preventing, in some cases, local differentiation, however, cannot be ruled out.
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Affiliation(s)
- A M Pappalardo
- Department of Biological, Geological and Environmental Sciences, University of Catania, Via Androne 81, I-95124 Catania, Italy
| | - E G Gonzalez
- Departmento de Biodiversidad y Biología Evolutiva, Museo Nacional de Ciencias Naturales, MNCN-CSIC, José Gutierrez Abascal, 2, 28006, Madrid, Spain
| | - C Tigano
- Department of Biological, Geological and Environmental Sciences, University of Catania, Via Androne 81, I-95124 Catania, Italy
| | - I Doadrio
- Departmento de Biodiversidad y Biología Evolutiva, Museo Nacional de Ciencias Naturales, MNCN-CSIC, José Gutierrez Abascal, 2, 28006, Madrid, Spain
| | - V Ferrito
- Department of Biological, Geological and Environmental Sciences, University of Catania, Via Androne 81, I-95124 Catania, Italy
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Dayan DI, Crawford DL, Oleksiak MF. Phenotypic plasticity in gene expression contributes to divergence of locally adapted populations ofFundulus heteroclitus. Mol Ecol 2015; 24:3345-59. [DOI: 10.1111/mec.13188] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2014] [Revised: 03/13/2015] [Accepted: 03/19/2015] [Indexed: 01/08/2023]
Affiliation(s)
- David I. Dayan
- Marine Biology and Fisheries; Rosenstiel School of Marine and Atmospheric Sciences; University of Miami; 4600 Rickenbacker Causeway Miami FL 33149 USA
| | - Douglas L. Crawford
- Marine Biology and Fisheries; Rosenstiel School of Marine and Atmospheric Sciences; University of Miami; 4600 Rickenbacker Causeway Miami FL 33149 USA
| | - Marjorie F. Oleksiak
- Marine Biology and Fisheries; Rosenstiel School of Marine and Atmospheric Sciences; University of Miami; 4600 Rickenbacker Causeway Miami FL 33149 USA
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25
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Xiao Y, Li J, Ren G, Ma D, Wang Y, Xiao Z, Xu S. Pronounced population genetic differentiation in the rock bream Oplegnathus fasciatus inferred from mitochondrial DNA sequences. Mitochondrial DNA A DNA Mapp Seq Anal 2014; 27:2045-52. [PMID: 25427804 DOI: 10.3109/19401736.2014.982553] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The population genetic structure of the rock bream (Oplegnathus fasciatus) along the coastal waters of China was estimated based on three mtDNA fragments (D-loop, COI, and Cytb). A total of 112 polymorphic sites were checked, which defined 63 haplotypes. A pattern with high levels of haplotype diversity (hCOI = 0.886 ± 0.034, hCytb = 0.874 ± 0.023) and low levels of nucleotide diversity (лCOI = 0.009 ± 0.005, лCytb = 0.006 ± 0.003) was detected based on the COI and Cytb fragments, and high levels of genetic diversity (hD-loop = 0.995 ± 0.007, лD-loop = 0.021 ± 0.011) were detected from the mtDNA D-loop. The population genetic diversity of O. fasciatus in south China was significantly higher than those of north China. Three genealogical clades were checked in the O. fasciatus populations based on the NJ and MST analyses of mtDNA COI gene sequence, and the genetic distances among the clades ranged from 0.018 to 0.025. Significant population genetic differentiation was also checked based on the Fst (0.331, p = 0.000) and exact p (0.000) test analyses. No significant population differentiations were checked based on mtDNA D-loop and Cytb fragments. Using a variety of phylogenetic methods, coalescent reasoning, and molecular dating interpreted in conjunction with paleoclimatic and physiographic evidences, we inferred that the genetic make-up of extant populations of O. fasciatus was shaped by Pleistocene environmental impacts on the historical demography of this species. Coalescent analyses (neutrality tests, mismatch distribution analysis, and Bayesian skyline analyses) showed that the species along coastline of China has experienced population expansions originated in its most recent history at about 169-175 kya before present.
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Affiliation(s)
- Yongshuang Xiao
- a Institute of Oceanology, Chinese Academy of Sciences , Qingdao , China and
| | - Jun Li
- a Institute of Oceanology, Chinese Academy of Sciences , Qingdao , China and
| | - Guijing Ren
- b East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences , Shanghai , China
| | - Daoyuan Ma
- a Institute of Oceanology, Chinese Academy of Sciences , Qingdao , China and
| | - Yanfeng Wang
- a Institute of Oceanology, Chinese Academy of Sciences , Qingdao , China and
| | - ZhiZhong Xiao
- a Institute of Oceanology, Chinese Academy of Sciences , Qingdao , China and
| | - Shihong Xu
- a Institute of Oceanology, Chinese Academy of Sciences , Qingdao , China and
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26
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Schulte PM. What is environmental stress? Insights from fish living in a variable environment. ACTA ACUST UNITED AC 2014; 217:23-34. [PMID: 24353201 DOI: 10.1242/jeb.089722] [Citation(s) in RCA: 166] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Although the term environmental stress is used across multiple fields in biology, the inherent ambiguity associated with its definition has caused confusion when attempting to understand organismal responses to environmental change. Here I provide a brief summary of existing definitions of the term stress, and the related concepts of homeostasis and allostasis, and attempt to unify them to develop a general framework for understanding how organisms respond to environmental stressors. I suggest that viewing stressors as environmental changes that cause reductions in performance or fitness provides the broadest and most useful conception of the phenomenon of stress. I examine this framework in the context of animals that have evolved in highly variable environments, using the Atlantic killifish, Fundulus heteroclitus, as a case study. Consistent with the extreme environmental variation that they experience in their salt marsh habitats, killifish have substantial capacity for both short-term resistance and long-term plasticity in the face of changing temperature, salinity and oxygenation. There is inter-population variation in the sensitivity of killifish to environmental stressors, and in their ability to acclimate, suggesting that local adaptation can shape the stress response even in organisms that are broadly tolerant and highly plastic. Whole-organism differences between populations in stressor sensitivity and phenotypic plasticity are reflected at the biochemical and molecular levels in killifish, emphasizing the integrative nature of the response to environmental stressors. Examination of this empirical example highlights the utility of using an evolutionary perspective on stressors, stress and stress responses.
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Affiliation(s)
- Patricia M Schulte
- Department of Zoology, 6270 University Blvd, University of British Columbia, Vancouver, BC, V6T 1Z4 Canada
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27
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Zhang H, Geller JB, Vrijenhoek RC. Genetic diversity in native and introduced populations of the amethyst gem clam Gemma gemma (Totten, 1834) from the U.S. east and west coasts. Biol Invasions 2014. [DOI: 10.1007/s10530-014-0699-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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28
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Yuan N, Sun Y, Comes HP, Fu CX, Qiu YX. Understanding population structure and historical demography in a conservation context: population genetics of the endangered Kirengeshoma palmata (Hydrangeaceae). AMERICAN JOURNAL OF BOTANY 2014; 101:521-529. [PMID: 24650862 DOI: 10.3732/ajb.1400043] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
PREMISE OF THE STUDY Both historical and contemporary microevolutionary processes greatly influence the genetic patterns of East Asian plant endemics, but the spatial and temporal contexts of these processes remain poorly understood. Here, we investigate the relative influences of historical and contemporary gene flow and drift on the population genetic structure of Kirengeshoma palmata, a perennial herb from East China and South Japan. METHODS We used data from nine polymorphic microsatellite loci to assess the levels of genetic diversity, effective population size, and contemporary and historical gene flow for six of the seven known populations. KEY RESULTS We found high levels of inbreeding and allelic diversity within populations. Both contemporary and historical migration rates among populations were low, and a test of alternate models of population history strongly favored a model of long-term drift-migration equilibrium. We inferred declines in population size ca. 10,000-100,000 yr ago, but failed to detect recent declines. Bayesian clustering divided K. palmata populations into three genetic clusters, two of which were consistent with a glacial refugium hypothesis for two mountain ranges in East China. CONCLUSIONS These results suggest that anthropogenic fragmentation has had little effect on the genetic characteristics of Chinese K. palmata. Rather, past decline in population size due to Late Pleistocene climate change as well as restricted pollen and seed dispersal may have contributed to low levels of both historical and contemporary gene flow, resulting in high genetic differentiation between adjacent mountain ranges due to genetic drift and inbreeding.
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Affiliation(s)
- Na Yuan
- Key Laboratory of Conservation Biology for Endangered Wildlife of the Ministry of Education, and College of Life Sciences, Zhejiang University, Hangzhou 310058, China
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29
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Olafsson K, Pampoulie C, Hjorleifsdottir S, Gudjonsson S, Hreggvidsson GO. Present-day genetic structure of Atlantic salmon (Salmo salar) in Icelandic rivers and ice-cap retreat models. PLoS One 2014; 9:e86809. [PMID: 24498283 PMCID: PMC3911922 DOI: 10.1371/journal.pone.0086809] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2013] [Accepted: 12/18/2013] [Indexed: 12/04/2022] Open
Abstract
Due to an improved understanding of past climatological conditions, it has now become possible to study the potential concordance between former climatological models and present-day genetic structure. Genetic variability was assessed in 26 samples from different rivers of Atlantic salmon in Iceland (total of 2,352 individuals), using 15 microsatellite loci. F-statistics revealed significant differences between the majority of the populations that were sampled. Bayesian cluster analyses using both prior information and no prior information on sampling location revealed the presence of two distinguishable genetic pools - namely, the Northern (Group 1) and Southern (Group 2) regions of Iceland. Furthermore, the random permutation of different allele sizes among allelic states revealed a significant mutational component to the genetic differentiation at four microsatellite loci (SsaD144, Ssa171, SSsp2201 and SsaF3), and supported the proposition of a historical origin behind the observed variation. The estimated time of divergence, using two different ABC methods, suggested that the observed genetic pattern originated from between the Last Glacial Maximum to the Younger Dryas, which serves as additional evidence of the relative immaturity of Icelandic fish populations, on account of the re-colonisation of this young environment following the Last Glacial Maximum. Additional analyses suggested the presence of several genetic entities which were likely to originate from the original groups detected.
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Affiliation(s)
- Kristinn Olafsson
- Faculty of Life and Environmental Sciences, University of Iceland, Reykjavik, Iceland
- Genetics, Matis Ltd., Reykjavík, Iceland
- * E-mail:
| | | | | | | | - Gudmundur O. Hreggvidsson
- Faculty of Life and Environmental Sciences, University of Iceland, Reykjavik, Iceland
- Genetics, Matis Ltd., Reykjavík, Iceland
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Reitzel AM, Karchner SI, Franks DG, Evans BR, Nacci D, Champlin D, Vieira VM, Hahn ME. Genetic variation at aryl hydrocarbon receptor (AHR) loci in populations of Atlantic killifish (Fundulus heteroclitus) inhabiting polluted and reference habitats. BMC Evol Biol 2014; 14:6. [PMID: 24422594 PMCID: PMC3899389 DOI: 10.1186/1471-2148-14-6] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2013] [Accepted: 12/18/2013] [Indexed: 11/27/2022] Open
Abstract
Background The non-migratory killifish Fundulus heteroclitus inhabits clean and polluted environments interspersed throughout its range along the Atlantic coast of North America. Several populations of this species have successfully adapted to environments contaminated with toxic aromatic hydrocarbon pollutants such as polychlorinated biphenyls (PCBs). Previous studies suggest that the mechanism of resistance to these and other “dioxin-like compounds” (DLCs) may involve reduced signaling through the aryl hydrocarbon receptor (AHR) pathway. Here we investigated gene diversity and evidence for positive selection at three AHR-related loci (AHR1, AHR2, AHRR) in F. heteroclitus by comparing alleles from seven locations ranging over 600 km along the northeastern US, including extremely polluted and reference estuaries, with a focus on New Bedford Harbor (MA, USA), a PCB Superfund site, and nearby reference sites. Results We identified 98 single nucleotide polymorphisms within three AHR-related loci among all populations, including synonymous and nonsynonymous substitutions. Haplotype distributions were spatially segregated and F-statistics suggested strong population genetic structure at these loci, consistent with previous studies showing strong population genetic structure at other F. heteroclitus loci. Genetic diversity at these three loci was not significantly different in contaminated sites as compared to reference sites. However, for AHR2 the New Bedford Harbor population had significant FST values in comparison to the nearest reference populations. Tests for positive selection revealed ten nonsynonymous polymorphisms in AHR1 and four in AHR2. Four nonsynonymous SNPs in AHR1 and three in AHR2 showed large differences in base frequency between New Bedford Harbor and its reference site. Tests for isolation-by-distance revealed evidence for non-neutral change at the AHR2 locus. Conclusion Together, these data suggest that F. heteroclitus populations in reference and polluted sites have similar genetic diversity, providing no evidence for strong genetic bottlenecks for populations in polluted locations. However, the data provide evidence for genetic differentiation among sites, selection at specific nucleotides in AHR1 and AHR2, and specific AHR2 SNPs and haplotypes that are associated with the PCB-resistant phenotype in the New Bedford Harbor population. The results suggest that AHRs, and especially AHR2, may be important, recurring targets for selection in local adaptation to dioxin-like aromatic hydrocarbon contaminants.
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Affiliation(s)
| | | | | | | | | | | | | | - Mark E Hahn
- Biology Department, Woods Hole Oceanographic Institution, 45 Water Street, Woods Hole, MA 02568, USA.
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Proestou DA, Flight P, Champlin D, Nacci D. Targeted approach to identify genetic loci associated with evolved dioxin tolerance in Atlantic killifish (Fundulus heteroclitus). BMC Evol Biol 2014; 14:7. [PMID: 24422627 PMCID: PMC4029433 DOI: 10.1186/1471-2148-14-7] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2013] [Accepted: 12/30/2013] [Indexed: 11/10/2022] Open
Abstract
Background The most toxic aromatic hydrocarbon pollutants are categorized as dioxin-like compounds (DLCs) to which extreme tolerance has evolved independently and contemporaneously in (at least) four populations of Atlantic killifish (Fundulus heteroclitus). Surprisingly, the magnitude and phenotype of DLC tolerance is similar among these killifish populations that have adapted to varied, but highly aromatic hydrocarbon-contaminated urban/industrialized estuaries of the US Atlantic coast. Multiple tolerant and neighboring sensitive killifish populations were compared with the expectation that genetic loci associated with DLC tolerance would be revealed. Results Since the aryl hydrocarbon receptor (AHR) pathway partly or fully mediates DLC toxicity in vertebrates, single nucleotide polymorphisms (SNPs) from 42 genes associated with the AHR pathway were identified to serve as targeted markers. Wild fish (N = 36/37) from four highly tolerant killifish populations and four nearby sensitive populations were genotyped using 59 SNP markers. Similar to other killifish population genetic analyses, strong genetic differentiation among populations was detected, consistent with isolation by distance models. When DLC-sensitive populations were pooled and compared to pooled DLC-tolerant populations, multi-locus analyses did not distinguish the two groups. However, pairwise comparisons of nearby tolerant and sensitive populations revealed high differentiation among sensitive and tolerant populations at these specific loci: AHR 1 and 2, cathepsin Z, the cytochrome P450s (CYP1A and 3A30), and the NADH dehydrogenase subunits. In addition, significant shifts in minor allele frequency were observed at AHR2 and CYP1A loci across most sensitive/tolerant pairs, but only AHR2 exhibited shifts in the same direction across all pairs. Conclusions The observed differences in allelic composition at the AHR2 and CYP1A SNP loci were identified as significant among paired sensitive/tolerant populations of Atlantic killifish with multiple statistical tests. The genetic patterns reported here lend support to the argument that AHR2 and CYP1A play a role in the adaptive response to extreme DLC contamination. Additional functional assays are required to isolate the exact mechanism of DLC tolerance.
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Affiliation(s)
- Dina A Proestou
- US Environmental Protection Agency, Office of Research and Development, National Health and Environmental Effects Research Laboratory, Atlantic Ecology Division, 27 Tarzwell Drive, Narragansett, RI 02882, USA.
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32
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Xiao Y, Song N, Li J, Xiao Z, Gao T. Significant population genetic structure detected in the small yellow croaker Larimichthys polyactis inferred from mitochondrial control region. MITOCHONDRIAL DNA 2013; 26:409-19. [PMID: 24228686 DOI: 10.3109/19401736.2013.843076] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The population genetic structure of the small yellow croaker (Larimichthys polyactis) between China and Korea was further estimated by broad-scale sampling locations (Gulf of Bohai, Yellow Sea including Korea). One hundred and seventeen individuals from eight localities from coastal waters of China and Korea were analyzed based on mtDNA control region sequences (5' mtDNA CR). A total of 97 polymorphic sites were checked, which defined 136 haplotypes. A pattern with high levels of haplotype diversity (h=0.994 ± 0.002) and nucleotide diversity (л=0.020 ± 0.010) was detected in the examined range, and the genetic diversity of Korea populations was higher than that of China populations. Population genetic structure analyses (MDS, AMOVA, Fst, Barrier) showed that significant genetic differentiation existed between China and Korea populations. The migration analysis indicated asymmetry migration also existed among populations, which was consistent with the result of population genetic structure. Using a variety of phylogenetic methods, coalescent reasoning, and molecular dating interpreted in conjunction with paleoclimateic and physiographic evidence, we inferred that the genetic make-up of extant populations of L. polyactis was shaped by Pleistocene environmental impacts on the historical demography of this species. Coalescent analyses (Neutrality tests, Mismatch distribution analysis, Bayesian skyline analyses) showed that the species along coastline of China and Korea has experienced population expansions originated in its most recent history at about 32-196 kya and 166-662 kya before present, respectively.
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Affiliation(s)
- Yongshuang Xiao
- Institute of Evolution & Marine Biodiversity, Ocean University of China , Qingdao , China and
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Bosker T, Munkittrick KR, Nacci DE, MacLatchy DL. Laboratory Spawning Patterns of Mummichogs,Fundulus heteroclitus(Cyprinodontiformes: Fundulidae). COPEIA 2013. [DOI: 10.1643/ci-11-175] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Ren G, Liu Q, Gao T, Yanagimoto T. Population demography and genetic structure of the fat greenling (Hexagrammos otakii) inferred from mtDNA control region sequence analyses. BIOCHEM SYST ECOL 2013. [DOI: 10.1016/j.bse.2012.09.026] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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Reitzel AM, Herrera S, Layden MJ, Martindale MQ, Shank TM. Going where traditional markers have not gone before: utility of and promise for RAD sequencing in marine invertebrate phylogeography and population genomics. Mol Ecol 2013; 22:2953-70. [PMID: 23473066 DOI: 10.1111/mec.12228] [Citation(s) in RCA: 117] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2012] [Accepted: 12/11/2012] [Indexed: 12/20/2022]
Abstract
Characterization of large numbers of single-nucleotide polymorphisms (SNPs) throughout a genome has the power to refine the understanding of population demographic history and to identify genomic regions under selection in natural populations. To this end, population genomic approaches that harness the power of next-generation sequencing to understand the ecology and evolution of marine invertebrates represent a boon to test long-standing questions in marine biology and conservation. We employed restriction-site-associated DNA sequencing (RAD-seq) to identify SNPs in natural populations of the sea anemone Nematostella vectensis, an emerging cnidarian model with a broad geographic range in estuarine habitats in North and South America, and portions of England. We identified hundreds of SNP-containing tags in thousands of RAD loci from 30 barcoded individuals inhabiting four locations from Nova Scotia to South Carolina. Population genomic analyses using high-confidence SNPs resulted in a highly-resolved phylogeography, a result not achieved in previous studies using traditional markers. Plots of locus-specific FST against heterozygosity suggest that a majority of polymorphic sites are neutral, with a smaller proportion suggesting evidence for balancing selection. Loci inferred to be under balancing selection were mapped to the genome, where 90% were located in gene bodies, indicating potential targets of selection. The results from analyses with and without a reference genome supported similar conclusions, further highlighting RAD-seq as a method that can be efficiently applied to species lacking existing genomic resources. We discuss the utility of RAD-seq approaches in burgeoning Nematostella research as well as in other cnidarian species, particularly corals and jellyfishes, to determine phylogeographic relationships of populations and identify regions of the genome undergoing selection.
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Affiliation(s)
- A M Reitzel
- Biology Department, Woods Hole Oceanographic Institution, Woods Hole, MA 02543, USA.
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36
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Lougheed SC, Campagna L, Dávila JA, Tubaro PL, Lijtmaer DA, Handford P. Continental phylogeography of an ecologically and morphologically diverse Neotropical songbird, Zonotrichia capensis. BMC Evol Biol 2013; 13:58. [PMID: 23452908 PMCID: PMC3632491 DOI: 10.1186/1471-2148-13-58] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2012] [Accepted: 02/26/2013] [Indexed: 11/12/2022] Open
Abstract
BACKGROUND The Neotropics are exceptionally diverse, containing roughly one third of all extant bird species on Earth. This remarkable species richness is thought to be a consequence of processes associated with both Andean orogenesis throughout the Tertiary, and climatic fluctuations during the Quaternary. Phylogeographic studies allow insights into how such events might have influenced evolutionary trajectories of species and ultimately contribute to a better understanding of speciation. Studies on continentally distributed species are of particular interest because different populations of such taxa may show genetic signatures of events that impacted the continent-wide biota. Here we evaluate the genealogical history of one of the world's most broadly-distributed and polytypic passerines, the rufous-collared sparrow (Zonotrichia capensis). RESULTS We obtained control region DNA sequences from 92 Zonotrichia capensis individuals sampled across the species' range (Central and South America). Six additional molecular markers, both nuclear and mitochondrial, were sequenced for a subset of individuals with divergent control region haplotypes. Median-joining network analysis, and Bayesian and maximum parsimony phylogenetic analyses all recovered three lineages: one spanning Middle America, the Dominican Republic, and north-western South America; one encompassing the Dominican Republic, Roraima (Venezuela) and La Paz (Bolivia) south to Tierra del Fuego, Argentina; and a third, including eastern Argentina and Brazil. Phylogenetic analyses suggest that the Middle American/north-western South American clade is sister to the remaining two. Bayesian and maximum likelihood coalescent simulations used to study lineage demographic history, diversification times, migration rates and population expansion together suggested that diversification of the three lineages occurred rapidly during the Pleistocene, with negligible gene flow, leaving genetic signatures of population expansions. CONCLUSIONS The Pleistocene history of the rufous-collared sparrow involved extensive range expansion from a probable Central American origin. Its remarkable morphological and behavioral diversity probably represents recent responses to local conditions overlying deeper patterns of lineage diversity, which are themselves produced by isolation and the history of colonization of South America.
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Affiliation(s)
- Stephen C Lougheed
- Department of Biology, Queen’s University, Kingston, ON, K7L 3N6, Canada
| | - Leonardo Campagna
- Department of Biology, Queen’s University, Kingston, ON, K7L 3N6, Canada
- División de Ornitología, Museo Argentino de Ciencias Naturales “Bernardino Rivadavia”, Avenida Ángel Gallardo 470, Ciudad de Buenos Aires, Buenos Aires, C1405DJR, Argentina
| | - José A Dávila
- Instituto de Investigación en Recursos Cinegéticos, Ronda de Toledo s/n, Cuidad Real, 13005, Spain
| | - Pablo L Tubaro
- División de Ornitología, Museo Argentino de Ciencias Naturales “Bernardino Rivadavia”, Avenida Ángel Gallardo 470, Ciudad de Buenos Aires, Buenos Aires, C1405DJR, Argentina
| | - Darío A Lijtmaer
- División de Ornitología, Museo Argentino de Ciencias Naturales “Bernardino Rivadavia”, Avenida Ángel Gallardo 470, Ciudad de Buenos Aires, Buenos Aires, C1405DJR, Argentina
| | - Paul Handford
- Department of Biology, University of Western Ontario, London, ON, N6A 5B7, Canada
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Ghedotti MJ, Davis MP. Phylogeny, Classification, and Evolution of Salinity Tolerance of the North American Topminnows and Killifishes, Family Fundulidae (Teleostei: Cyprinodontiformes). ACTA ACUST UNITED AC 2013. [DOI: 10.3158/2158-5520-12.7.1] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Hasselman DJ, Ricard D, Bentzen P. Genetic diversity and differentiation in a wide ranging anadromous fish, American shad (Alosa sapidissima), is correlated with latitude. Mol Ecol 2013; 22:1558-73. [PMID: 23379260 DOI: 10.1111/mec.12197] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2012] [Revised: 11/16/2012] [Accepted: 12/05/2012] [Indexed: 11/27/2022]
Affiliation(s)
- Daniel J. Hasselman
- Marine Gene Probe Laboratory; Biology Department; Dalhousie University; Halifax Nova Scotia B3H 4R2 Canada
| | - Daniel Ricard
- Biology Department; Dalhousie University; Halifax Nova Scotia B3H 4R2 Canada
- Institute of Hydrobiology; Fish Ecology Unit; Biology Centre of the Academy of Sciences of the Czech Republic; Na Sádkách 7 České Budějovice 370 05 Czech Republic
| | - Paul Bentzen
- Marine Gene Probe Laboratory; Biology Department; Dalhousie University; Halifax Nova Scotia B3H 4R2 Canada
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Loftus SJ, Crawford DL. Interindividual variation in Complex I activity in Fundulus heteroclitus along a steep thermocline. Physiol Biochem Zool 2012; 86:82-91. [PMID: 23303323 DOI: 10.1086/668850] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
The first enzyme in the oxidative phosphorylation pathway is Complex I (EC 1.6.5.3). Complex I is a large heteromeric enzyme complex with 45 protein subunits that translocates H(+) ions across the mitochondrial inner membrane. Among northern and southern populations of the teleost fish Fundulus heteroclitus, Complex I subunits have fixed amino acid substitutions. Additionally, there are differences in oxidative phosphorylation activity among populations of F. heteroclitus. To investigate whether these differences are related to Complex I, enzyme activity was measured in 121 individuals from five populations of F. heteroclitus and its sister species Fundulus grandis acclimated to a constant 20°C temperature. Within each population, Complex I activity is highly variable among individuals of F. heteroclitus (coefficient of variation percentage among individuals has a mean of 90% in the five F. heteroclitus populations), and the mean Complex I activity among populations is significantly different at the latitudinal extremes of the range. Importantly, Complex I activity is more similar between F. heteroclitus from the southernmost population and its sister species F. grandis than to the northern populations of F. heteroclitus, suggesting important evolutionary differences. Unexpectedly, the activity is nearly fourfold higher in southern populations than northern populations. Mitochondrial density appears to compensate partially for decreased activity in northern individuals; activity per wet weight is only twofold higher in southern populations. We suggest that some of the variation in Complex I activity is genetically based and thus is being influenced by directional selection. However, this conclusion presents a conundrum: there should not be so much variation in Complex I activity within a population if this variation is biologically important.
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Affiliation(s)
- Samuel J Loftus
- Rosenstiel School of Marine and Atmospheric Science, University of Miami, 4600 Rickenbacker Causeway, Miami, FL 33149, USA
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40
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Strand AE, Williams LM, Oleksiak MF, Sotka EE. Can diversifying selection be distinguished from history in geographic clines? A population genomic study of killifish (Fundulus heteroclitus). PLoS One 2012; 7:e45138. [PMID: 23049770 PMCID: PMC3458873 DOI: 10.1371/journal.pone.0045138] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2012] [Accepted: 08/14/2012] [Indexed: 02/03/2023] Open
Abstract
A common geographical pattern of genetic variation is the one-dimensional cline. Clines may be maintained by diversifying selection across a geographical gradient but can also reflect historical processes such as allopatry followed by secondary contact. To identify loci that may be undergoing diversifying selection, we examined the distribution of geographical variation patterns across the range of the killifish (Fundulus heteroclitus) in 310 loci, including microsatellites, allozymes, and single nucleotide polymorphisms. We employed two approaches to detect loci under strong diversifying selection. First, we developed an automated method to identify clinal variation on a per-locus basis and examined the distribution of clines to detect those that exhibited signifcantly steeper slopes. Second, we employed a classic [Formula: see text]-outlier method as a complementary approach. We also assessed performance of these techniques using simulations. Overall, latitudinal clines were detected in nearly half of all loci genotyped (i.e., all eight microsatellite loci, 12 of 16 allozyme loci and 44% of the 285 SNPs). With the exception of few outlier loci (notably mtDNA and malate dehydrogenase), the positions and slopes of Fundulus clines were statistically indistinguishable. The high frequency of latitudinal clines across the genome indicates that secondary contact plays a central role in the historical demography of this species. Our simulation results indicate that accurately detecting diversifying selection using genome scans is extremely difficult in species with a strong signal of secondary contact; neutral evolution under this history produces clines as steep as those expected under selection. Based on these results, we propose that demographic history can explain all clinal patterns observed in F. heteroclitus without invoking natural selection to either establish or maintain the pattern we observe today.
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Affiliation(s)
- Allan E Strand
- College of Charleston, Department of Biology, Grice Marine Laboratory, Charleston, South Carolina, USA. strandacofc.edu
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Harris LN, Howland KL, Kowalchuk MW, Bajno R, Lindsay MM, Taylor EB. Microsatellite and mtDNA analysis of lake trout, Salvelinus namaycush, from Great Bear Lake, Northwest Territories: impacts of historical and contemporary evolutionary forces on Arctic ecosystems. Ecol Evol 2012; 3:145-61. [PMID: 23404390 PMCID: PMC3568850 DOI: 10.1002/ece3.439] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2012] [Revised: 10/22/2012] [Accepted: 10/29/2012] [Indexed: 11/17/2022] Open
Abstract
Resolving the genetic population structure of species inhabiting pristine, high latitude ecosystems can provide novel insights into the post-glacial, evolutionary processes shaping the distribution of contemporary genetic variation. In this study, we assayed genetic variation in lake trout (Salvelinus namaycush) from Great Bear Lake (GBL), NT and one population outside of this lake (Sandy Lake, NT) at 11 microsatellite loci and the mtDNA control region (d-loop). Overall, population subdivision was low, but significant (global F(ST) θ = 0.025), and pairwise comparisons indicated that significance was heavily influenced by comparisons between GBL localities and Sandy Lake. Our data indicate that there is no obvious genetic structure among the various basins within GBL (global F(ST) = 0.002) despite the large geographic distances between sampling areas. We found evidence of low levels of contemporary gene flow among arms within GBL, but not between Sandy Lake and GBL. Coalescent analyses suggested that some historical gene flow occurred among arms within GBL and between GBL and Sandy Lake. It appears, therefore, that contemporary (ongoing dispersal and gene flow) and historical (historical gene flow and large founding and present-day effective population sizes) factors contribute to the lack of neutral genetic structure in GBL. Overall, our results illustrate the importance of history (e.g., post-glacial colonization) and contemporary dispersal ecology in shaping genetic population structure of Arctic faunas and provide a better understanding of the evolutionary ecology of long-lived salmonids in pristine, interconnected habitats.
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Affiliation(s)
- Les N Harris
- Fisheries and Oceans Canada 501 University Crescent, Winnipeg, MB, Canada, R3T 2N6
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Williams LM, Oleksiak MF. Evolutionary and functional analyses of cytochrome P4501A promoter polymorphisms in natural populations. Mol Ecol 2011; 20:5236-47. [PMID: 22093087 DOI: 10.1111/j.1365-294x.2011.05360.x] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The functional importance of variable, transcriptional regulatory sequences within and among natural populations is largely unexplored. We analysed the cytochrome P4501A (CYP1A) promoter in three populations of the minnow, Fundulus heteroclitus, because two SNPs in the promoter and first intron of CYP1A are under selection in populations adapted to pollutants. To define the importance of these SNPs, 1630 bp of the CYP1A promoter and first intron and exon were sequenced in eight individuals from three populations: a population from a polluted environment resistant to some aromatic pollutants and two flanking reference populations. CYP1A is induced by many aromatic pollutants, but in populations adapted to pollutants, CYP1A has been shown to be refractory to induction. We were interested in understanding whether variation in the CYP1A promoter explains mechanism(s) of adaptation to these aromatic pollutants. The CYP1A promoter was extremely variable (an average of 9.3% of the promoter nucleotides varied among all populations) and exhibited no fixed differences between populations. As CYP1A is poorly inducible in adapted fish, we hypothesized that CYP1A promoter regions might vary functionally between populations. Unexpectedly, in vitro analysis showed significantly greater transcription from CYP1A promoters found in the population from the polluted environment relative to promoters found in both reference populations. Thus, despite extensive variation among populations and lack of fixed differences between populations, individuals from a polluted environment have significantly enhanced promoter activity. These data demonstrate that intraspecific variation, which provides the raw material for natural selection to act on, can occur while maintaining promoter function.
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Affiliation(s)
- Larissa M Williams
- Department of Environmental and Molecular Toxicology, PO Box 7633, North Carolina State University, Raleigh, NC 27695-7633, USA
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Flight PA, Nacci D, Champlin D, Whitehead A, Rand DM. The effects of mitochondrial genotype on hypoxic survival and gene expression in a hybrid population of the killifish, Fundulus heteroclitus. Mol Ecol 2011; 20:4503-20. [PMID: 21980951 DOI: 10.1111/j.1365-294x.2011.05290.x] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The physiological link between oxygen availability and mitochondrial function is well established. However, whether or not fitness variation is associated with mitochondrial genotypes in the field remains a contested topic in evolutionary biology. In this study, we draw on a population of the teleost fish, Fundulus heteroclitus, where functionally distinct subspecies hybridize, likely as a result of past glacial events. We had two specific aims: (i) to determine the effect of mtDNA genotype on survivorship of male and female fish under hypoxic stress and (ii) to determine the effect of hypoxic stress, sex and mtDNA genotype on gene expression. We found an unexpected and highly significant effect of sex on survivorship under hypoxic conditions, but no significant effect of mtDNA genotype. Gene expression analyses revealed hundreds of transcripts differentially regulated by sex and hypoxia. Mitochondrial transcripts and other predicted pathways were among those influenced by hypoxic stress, and a transcript corresponding to the mtDNA control region was the most highly suppressed transcript under the conditions of hypoxia. An RT-PCR experiment on the control region was consistent with microarray results. Effects of mtDNA sequence variation on genome expression were limited; however, a potentially important epistasis between mtDNA sequence and expression of a nuclear-encoded mitochondrial translation protein was discovered. Overall, these results confirm that mitochondrial regulation is a major component of hypoxia tolerance and further suggest that purifying selection has been the predominant selective force on mitochondrial genomes in these two subspecies.
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Affiliation(s)
- Patrick A Flight
- Department of Ecology and Evolutionary Biology, Brown University, 80 Waterman St., Box G-W, Providence, RI 02912, USA.
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Whitehead A, Pilcher W, Champlin D, Nacci D. Common mechanism underlies repeated evolution of extreme pollution tolerance. Proc Biol Sci 2011; 279:427-33. [PMID: 21733895 DOI: 10.1098/rspb.2011.0847] [Citation(s) in RCA: 81] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Human alterations to the environment can exert strong evolutionary pressures, yet contemporary adaptation to human-mediated stressors is rarely documented in wildlife populations. A common-garden experimental design was coupled with comparative transcriptomics to discover evolved mechanisms enabling three populations of killifish resident in urban estuaries to survive normally lethal pollution exposure during development, and to test whether mechanisms are unique or common across populations. We show that killifish populations from these polluted sites have independently converged on a common adaptive mechanism, despite variation in contaminant profiles among sites. These populations are united by a similarly profound desensitization of aryl-hydrocarbon receptor-mediated transcriptional activation, which is associated with extreme tolerance to the lethal effects of toxic dioxin-like pollutants. The rapid, repeated, heritable and convergent nature of evolved tolerance suggests that ancestral killifish populations harboured genotypes that enabled adaptation to twentieth-century industrial pollutants.
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Affiliation(s)
- Andrew Whitehead
- Department of Biological Sciences, Louisiana State University, 202 Life Sciences Building, Baton Rouge, LA 70803, USA.
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Drees C, Hüfner S, Matern A, Nève G, Assmann T. Repeated sampling detects gene flow in a flightless ground beetle in a fragmented landscape. Hereditas 2011; 148:36-45. [PMID: 21410469 DOI: 10.1111/j.1601-5223.2010.02212.x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Abstract
Secondary clines level down in the course of time if the gene flow is not interrupted. Temporally repeated sampling of populations in a cline allows the investigation not only of its occurrence but also of the estimation of the amount of ongoing gene flow. We reinvestigated an allozyme gradient in Carabus auronitens populations in the Westphalian Lowlands (northwestern Germany) 15 to 20 years after it had originally been recorded. A total of 977 individuals of this flightless woodland species from 29 sample sites were genotyped at the diallelic Est-1 locus in 2005-2006 and compared to former findings, collected in 1985-1994 from the same populations. Both data sets showed clinal variation. Pairwise differences between the samples of both data sets indicated significant decrease in the steepness of the cline during the past 15 to 20 years. The estimated average gene flow per generation is 0.6% of each beetle population. Ongoing gene flow in the flightless ground beetle C. auronitens led to a less pronounced cline despite a stable degree of fragmentation (and connectivity) of the landscape. Migration and gene flow were obviously enabled by the numerous hedgerows. The corridors are seen to be a prerequisite for migration between populations and for possible future range shifts of forest insect species.
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Affiliation(s)
- Claudia Drees
- Institute of Ecology, Leuphana University Lüneburg, Lüneburg, Germany.
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Williams LM, Oleksiak MF. Ecologically and evolutionarily important SNPs identified in natural populations. Mol Biol Evol 2011; 28:1817-26. [PMID: 21220761 DOI: 10.1093/molbev/msr004] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Evolution by natural selection acts on natural populations amidst migration, gene-by-environmental interactions, constraints, and tradeoffs, which affect the rate and frequency of adaptive change. We asked how many and how rapidly loci change in populations subject to severe, recent environmental changes. To address these questions, we used genomic approaches to identify randomly selected single nucleotide polymorphisms (SNPs) with evolutionarily significant patterns in three natural populations of Fundulus heteroclitus that inhabit and have adapted to highly polluted Superfund sites. Three statistical tests identified 1.4-2.5% of SNPs that were significantly different from the neutral model in each polluted population. These nonneutral patterns in populations adapted to highly polluted environments suggest that these loci or closely linked loci are evolving by natural selection. One SNP identified in all polluted populations using all tests is in the gene for the xenobiotic metabolizing enzyme, cytochrome P4501A (CYP1A), which has been identified previously as being refractory to induction in the three highly polluted populations. Extrapolating across the genome, these data suggest that rapid evolutionary change in natural populations can involve hundreds of loci, a few of which will be shared in independent events.
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Affiliation(s)
- Larissa M Williams
- Department of Environmental and Molecular Toxicology, North Carolina State University, NC, USA
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Pörtner HO, Schulte PM, Wood CM, Schiemer F. Niche dimensions in fishes: an integrative view. Physiol Biochem Zool 2010; 83:808-26. [PMID: 20704490 DOI: 10.1086/655977] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Current shifts in ecosystem composition and function emphasize the need for an understanding of the links between environmental factors and organism fitness and tolerance. The examples discussed here illustrate how recent progress in the field of comparative physiology may provide a better mechanistic understanding of the ecological concepts of the fundamental and realized niches and thus provide insights into the impacts of anthropogenic disturbance. Here we argue that, as a link between physiological and ecological indicators of organismal performance, the mechanisms shaping aerobic scope and passive tolerance set the dimensions of an animal's niche, here defined as its capacity to survive, grow, behave, and interact with other species. We demonstrate how comparative studies of cod or killifish populations in a latitudinal cline have unraveled mitochondrial mechanisms involved in establishing a species' niche, performance, and energy budget. Riverine fish exemplify how the performance windows of various developmental stages follow the dynamic regimes of both seasonal temperatures and river hydrodynamics, as synergistic challenges. Finally, studies of species in extreme environments, such as the tilapia of Lake Magadi, illustrate how on evolutionary timescales functional and morphological shifts can occur, associated with new specializations. We conclude that research on the processes and time course of adaptations suitable to overcome current niche limits is urgently needed to assess the resilience of species and ecosystems to human impact, including the challenges of global climate change.
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Affiliation(s)
- H O Pörtner
- Alfred-Wegener-Institute for Polar and Marine Research, Bremerhaven D-27515, Germany.
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Mach ME, Sbrocco EJ, Hice LA, Duffy TA, Conover DO, Barber PH. Regional differentiation and post-glacial expansion of the Atlantic silverside, Menidia menidia, an annual fish with high dispersal potential. MARINE BIOLOGY 2010; 158:515-530. [PMID: 24391257 PMCID: PMC3873031 DOI: 10.1007/s00227-010-1577-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/07/2010] [Accepted: 11/02/2010] [Indexed: 06/03/2023]
Abstract
The coastal marine environment of the Northwest Atlantic contains strong environmental gradients that create distinct marine biogeographic provinces by limiting dispersal, recruitment, and survival. This region has also been subjected to numerous Pleistocene glacial cycles, resulting in repeated extirpations and recolonizations in northern populations of marine organisms. In this study, we examined patterns of genetic structure and historical demography in the Atlantic silverside, Menidia menidia, an annual marine fish with high dispersal potential but with well-documented patterns of clinal phenotypic adaptation along the environmental gradients of the Northwest Atlantic. Contrary to previous studies indicating genetic homogeneity that should preclude regional adaptation, results demonstrate subtle but significant (FST = 0.07; P < 0.0001) genetic structure among three phylogeographic regions that partially correspond with biogeographic provinces, suggesting regional limits to gene flow. Tests for non-equilibrium population dynamics and latitudinal patterns in genetic diversity indicate northward population expansion from a single southern refugium following the last glacial maximum, suggesting that phylogeographic and phenotypic patterns have relatively recent origins. The recovery of phylogeographic structure and the partial correspondence of these regions to recognized biogeographic provinces suggest that the environmental gradients that shape biogeographic patterns in the Northwest Atlantic may also limit gene flow in M. menidia, creating phylogeographic structure and contributing to the creation of latitudinal phenotypic clines in this species.
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Affiliation(s)
- Megan E. Mach
- Institute for Resource, Environment and Sustainability, Aquatic Ecosystem Research Laboratories, University of British Columbia, 429-2202 Main Mall, Vancouver, BC V6T 1Z4 Canada
| | - Elizabeth J. Sbrocco
- Department of Biology, Boston University, 5 Cummington Street, Boston, MA 02215 USA
| | - Lyndie A. Hice
- School of Marine and Atmospheric Sciences, Stony Brook University, Stony Brook, NY 11794-5000 USA
| | - Tara A. Duffy
- School of Marine and Atmospheric Sciences, Stony Brook University, Stony Brook, NY 11794-5000 USA
| | - David O. Conover
- School of Marine and Atmospheric Sciences, Stony Brook University, Stony Brook, NY 11794-5000 USA
| | - Paul H. Barber
- Department of Ecology and Evolutionary Biology, University of California Los Angeles, 621 Charles E. Young Drive South, Los Angeles, CA 90045 USA
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The influence of glacial epochs and habitat dependence on the diversity and phylogeography of a coastal dolphin species: Lagenorhynchus albirostris. CONSERV GENET 2010. [DOI: 10.1007/s10592-010-0075-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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Bozinovic G, Oleksiak MF. Embryonic gene expression among pollutant resistant and sensitive Fundulus heteroclitus populations. AQUATIC TOXICOLOGY (AMSTERDAM, NETHERLANDS) 2010; 98:221-229. [PMID: 20363516 PMCID: PMC3225961 DOI: 10.1016/j.aquatox.2010.02.022] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2009] [Revised: 02/08/2010] [Accepted: 02/16/2010] [Indexed: 05/22/2023]
Abstract
Changes in gene expression, coupled with biochemical, physiological, and behavioral alterations, play a critical role in adaptation to environmental stress. Our goal was to explore ways natural populations may have adapted to local, polluted environments. We took advantage of natural populations of Fundulus heteroclitus, one of the few studied fish species in North America that has established resistant populations in highly contaminated urban estuaries. We analyzed morphology, physiology, and gene expression of developing F. heteroclitus embryos during late organogenesis (stage 31); these embryos were from both resistant and sensitive populations and were raised in a common, unpolluted environment. While cardiac heart rates show significant differences between embryos of parents from clean and heavily contaminated Superfund sites, time-to-stage, embryo morphology, and gene expression profile analyses do not differ significantly between untreated embryos from resistant and sensitive populations. Further evaluation that includes tissue-specific approaches in gene expression analysis and larger sample sizes may be necessary to highlight important phenotypes associated with mechanisms of sensitivity and resistance among natural F. heteroclitus embryo populations. Alternatively, population differences may be masked by developmental canalization, and biologically important differences between sensitive and resistant embryos may only manifest with exposure (e.g., be dependent on gene by environment interactions).
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Affiliation(s)
- Goran Bozinovic
- Department of Environmental and Molecular Toxicology, Box 7633, North, Carolina State University, Raleigh, NC 27695-7633, United States.
| | - Marjorie F Oleksiak
- Rosenstiel School of Marine and Atmospheric Sciences, University of Miami, 4600 Rickenbacker Causeway, Miami, FL 33149, United States.
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