1
|
Van Der Wal C, Ahyong ST, Adams MWD, Ewart KM, Ho SYW, Lo N. Genomic analysis reveals strong population structure in the Giant Sydney Crayfish (Euastacus spinifer (Heller, 1865)). Mol Phylogenet Evol 2023; 178:107629. [PMID: 36191898 DOI: 10.1016/j.ympev.2022.107629] [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: 03/24/2022] [Revised: 09/14/2022] [Accepted: 09/19/2022] [Indexed: 12/14/2022]
Abstract
Australia is home to over 140 species of freshwater crayfish (Decapoda: Parastacidae), representing a centre of diversity for this group in the Southern Hemisphere. Species delimitation in freshwater crayfish is difficult because many species show significant variation in colouration and morphology. This is particularly evident in the genus Euastacus, which exhibits large variations in colour and spination throughout its putative range. To understand this variation, we investigated the genetic diversity, population structure, phylogeny, and evolutionary timescale of the Giant Sydney Crayfish (Euastacus spinifer (Heller, 1865)). Our data set is sampled from over 70 individuals from across the ∼600 km range of the species, and includes a combination of two mitochondrial markers and more than 7000 single-nucleotide polymorphisms (SNPs) from the nuclear genome. Data were also obtained for representatives of the close relative, Euastacus vesper McCormack and Ahyong, 2017. Genomic SNP analyses revealed strong population structure, with multiple distinct populations showing little evidence of gene flow or migration. Phylogenetic analyses of mitochondrial data revealed similar structure between populations. Taken together, our analyses suggest that E. spinifer, as currently understood, represents a species complex, of which E. vesper is a member. Molecular clock estimates place the divergences within this group during the Pleistocene. The isolated and highly fragmented populations identified in our analyses probably represent relict populations of a previously widespread ancestral species. Periodic flooding events during the Pleistocene are likely to have facilitated the movement of these otherwise restricted freshwater crayfish within and between drainage basins, including the Murray-Darling and South East Coast Drainages. We present evidence supporting the recognition of populations in the southern parts of the range of E. spinifer as one or two separate species, which would raise the number of species within the E. spinifer complex to at least three. Our results add to the growing body of evidence that many freshwater crayfish exhibit highly fragmented, range-restricted distributions. In combination with the life-history traits of these species, the restricted distributions exacerbate the threats already placed on freshwater crayfish, which are among the five most endangered animal groups globally.
Collapse
Affiliation(s)
- Cara Van Der Wal
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW 2006, Australia; Australian Museum Research Institute, Australian Museum, 1 William Street, Sydney, NSW 2010, Australia.
| | - Shane T Ahyong
- Australian Museum Research Institute, Australian Museum, 1 William Street, Sydney, NSW 2010, Australia; School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, NSW 2052, Australia
| | - Maxim W D Adams
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW 2006, Australia
| | - Kyle M Ewart
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW 2006, Australia
| | - Simon Y W Ho
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW 2006, Australia
| | - Nathan Lo
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW 2006, Australia.
| |
Collapse
|
2
|
Stronen AV, Norman AJ, Vander Wal E, Paquet PC. The relevance of genetic structure in ecotype designation and conservation management. Evol Appl 2022; 15:185-202. [PMID: 35233242 PMCID: PMC8867706 DOI: 10.1111/eva.13339] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 12/02/2021] [Accepted: 12/20/2021] [Indexed: 11/28/2022] Open
Abstract
The concept of ecotypes is complex, partly because of its interdisciplinary nature, but the idea is intrinsically valuable for evolutionary biology and applied conservation. The complex nature of ecotypes has spurred some confusion and inconsistencies in the literature, thereby limiting broader theoretical development and practical application. We provide suggestions for how incorporating genetic analyses can ease confusion and help define ecotypes. We approach this by systematically reviewing 112 publications across taxa that simultaneously mention the terms ecotype, conservation and management, to examine the current use of the term in the context of conservation and management. We found that most ecotype studies involve fish, mammals and plants with a focus on habitat use, which at 60% was the most common criterion used for categorization of ecotypes. Only 53% of the studies incorporated genetic analyses, and major discrepancies in available genomic resources among taxa could have contributed to confusion about the role of genetic structure in delineating ecotypes. Our results show that the rapid advances in genetic methods, also for nonmodel organisms, can help clarify the spatiotemporal distribution of adaptive and neutral genetic variation and their relevance to ecotype designations. Genetic analyses can offer empirical support for the ecotype concept and provide a timely measure of evolutionary potential, especially in changing environmental conditions. Genetic variation that is often difficult to detect, including polygenic traits influenced by small contributions from several genes, can be vital for adaptation to rapidly changing environments. Emerging ecotypes may signal speciation in progress, and findings from genome-enabled organisms can help clarify important selective factors driving ecotype development and persistence, and thereby improve preservation of interspecific genetic diversity. Incorporation of genetic analyses in ecotype studies will help connect evolutionary biology and applied conservation, including that of problematic groups such as natural hybrid organisms and urban or anthropogenic ecotypes.
Collapse
Affiliation(s)
- Astrid V. Stronen
- Department of BiologyBiotechnical FacultyUniversity of LjubljanaLjubljanaSlovenia
- Department of Biotechnology and Life SciencesInsubria UniversityVareseItaly
- Department of Chemistry and BioscienceAalborg UniversityAalborgDenmark
| | - Anita J. Norman
- Department of Fish, Wildlife and Environmental StudiesSwedish University of Agricultural SciencesUmeåSweden
| | - Eric Vander Wal
- Department of BiologyMemorial University of NewfoundlandSt. John’sNLCanada
| | - Paul C. Paquet
- Department of GeographyUniversity of VictoriaVictoriaBCCanada
- Raincoast Conservation FoundationSidneyBCCanada
| |
Collapse
|
3
|
Combining herbarium databases and genetic methods to evaluate the invasion of a popular horticultural species, baby’s breath (Gypsophila paniculata), in the United States. Biol Invasions 2021. [DOI: 10.1007/s10530-020-02354-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
|
4
|
Mintram KS, van Oosterhout C, Lighten J. Genetic variation in resistance and high fecundity impede viral biocontrol of invasive fish. J Appl Ecol 2021. [DOI: 10.1111/1365-2664.13762] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Kate S. Mintram
- Biosciences College of Life and Environmental Sciences University of Exeter Exeter UK
| | - Cock van Oosterhout
- School of Environmental Sciences University of East AngliaNorwich Research Park Norwich UK
| | - Jackie Lighten
- Biosciences College of Life and Environmental Sciences University of Exeter Exeter UK
| |
Collapse
|
5
|
Biocontrol of the Common Carp (Cyprinus carpio) in Australia: A Review and Future Directions. FISHES 2020. [DOI: 10.3390/fishes5020017] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Invasive pest species are recognized as one of the important drivers of reduced global biodiversity. In Australia, the 267 invasive plant, animal and microbial species, established since European colonization in the 1770s, have been unequivocally declared the most important threat to species diversity in this country. One invasive pest, the common carp (Cyprinus carpio), has been targeted in an integrated pest management plan that might include cyprinid herpesvirus 3 (CyHV-3) as a potential biocontrol agent. The species-specificity of the released virus (and of field variants that will inevitably arise) has been assessed, and the virus judged to be safe. It has also been hypothesised that, because the virulence of the CyHV-3 will likely decline following release, the virus should be used strategically: initially, the aim would be to markedly reduce numbers of carp in naive populations, and then some other, as yet uncertain, complementary broad-scale control measure would knock-down carp numbers even further. Brief results are included from recent studies on the modelling of release and spread of the virus, the ecological and social concerns associated with virus release, and the restoration benefits that might be expected following carp control. We conclude that, while further work is required (on the virus, the target species, environmental issues, and especially the identification of a suitable broad-scale complementary control measure), optimism must prevail in order to ensure an eventual solution to this important environmental problem.
Collapse
|
6
|
Silcock JL, Fensham RJ. Degraded or Just Dusty? Examining Ecological Change in Arid Lands. Bioscience 2019. [DOI: 10.1093/biosci/biz054] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
AbstractThe ecological history of rangelands is often presented as a tale of devastation, where fragile drylands are irreversibly degraded through inappropriate land use. However, there is confusion about how to recognize and measure degradation, especially in low-productivity environments characterized by extreme natural variability and where abrupt and comprehensive management upheavals preclude benchmarks. These issues have important consequences for rangeland management programs, which are typically founded on presumptions of substantial and ongoing degradation from former “natural” states. We explore complementary approaches to critically assess degradation: the historical record, long-term grazing exclosures, surveys for potentially rare and sensitive plant species, and assessment of water-remote areas in relation to rare plant occurrence. Employing these approaches in inland Australia, we show that prevailing paradigms have become entrenched despite being inconsistent with empirical evidence. Our methodology can be applied to drylands with abrupt changes in management and contentious ecological narratives.
Collapse
Affiliation(s)
- Jennifer L Silcock
- Centre for Biodiversity and Conservation Science, National Environmental Science Program, Threatened Species Recovery Hub, University of Queensland, Saint Lucia, Australia
- Sustainable Agriculture Flagship, CSIRO Ecosystem Sciences, Dutton Park, Queensland, Australia
| | - Rod J Fensham
- Centre for Biodiversity and Conservation Science, National Environmental Science Program, Threatened Species Recovery Hub, University of Queensland, Saint Lucia, Australia
- Queensland Herbarium, Department of Environment and Science, Brisbane Botanic Gardens, Toowong, Queensland, Australia
| |
Collapse
|
7
|
Kopf RK, Boutier M, Finlayson CM, Hodges K, Humphries P, King A, Kingsford RT, Marshall J, McGinness HM, Thresher R, Vanderplasschen A. Biocontrol in Australia: Can a carp herpesvirus (CyHV-3) deliver safe and effective ecological restoration? Biol Invasions 2019. [DOI: 10.1007/s10530-019-01967-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
|
8
|
Díez-Del-Molino D, García-Berthou E, Araguas RM, Alcaraz C, Vidal O, Sanz N, García-Marín JL. Effects of water pollution and river fragmentation on population genetic structure of invasive mosquitofish. THE SCIENCE OF THE TOTAL ENVIRONMENT 2018; 637-638:1372-1382. [PMID: 29801230 DOI: 10.1016/j.scitotenv.2018.05.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2018] [Revised: 04/13/2018] [Accepted: 05/01/2018] [Indexed: 06/08/2023]
Abstract
We analyzed variation at the GPI-2 locus and eleven microsatellite loci of eastern mosquitofish Gambusia holbrooki populations introduced to the Ebro River (Spain), sampling above and below a dam (Flix Reservoir) where severe chronic pollution has been well documented. Allele frequency changes at the GPI-2 locus in the sites nearest to the polluted sediments agree with previous results from studies in mercury-exposed populations of this highly invasive fish. Genetic distinction of the mosquitofish collected close to the polluted sediments was detected at the GPI locus but also at the presumptive neutral microsatellite loci. Recent migration rates estimated from microsatellites indicated that around 30% of fish collected in a specific location were immigrants from upstream and downstream sources. Such high migration rates probably contribute to the mosquitofish's invasive success and suggest that the consequences on the mosquitofish regional genetic structured of high levels of water toxicants could be mediated by immigration from other sites, but the effect of pollutants on local diversity might be higher than observed here.
Collapse
Affiliation(s)
- David Díez-Del-Molino
- Laboratori d'Ictiologia Genètica (LIG), University of Girona, Edifici AC-LEAR, Carrer M. Aurèlia Capmany, 40, 17003 Girona, Spain; Dept. of Bioinformatics and Genetics, Swedish Museum of Natural History, Box 50007, 104 05 Stockholm, Sweden.
| | | | - Rosa-Maria Araguas
- Laboratori d'Ictiologia Genètica (LIG), University of Girona, Edifici AC-LEAR, Carrer M. Aurèlia Capmany, 40, 17003 Girona, Spain.
| | - Carles Alcaraz
- IRTA Marine and Continental Waters, Carretera Poble Nou, km 5.5, 43540 Sant Carles de la Ràpita, Spain.
| | - Oriol Vidal
- Laboratori d'Ictiologia Genètica (LIG), University of Girona, Edifici AC-LEAR, Carrer M. Aurèlia Capmany, 40, 17003 Girona, Spain.
| | - Nuria Sanz
- Laboratori d'Ictiologia Genètica (LIG), University of Girona, Edifici AC-LEAR, Carrer M. Aurèlia Capmany, 40, 17003 Girona, Spain.
| | - Jose-Luis García-Marín
- Laboratori d'Ictiologia Genètica (LIG), University of Girona, Edifici AC-LEAR, Carrer M. Aurèlia Capmany, 40, 17003 Girona, Spain.
| |
Collapse
|
9
|
Population dynamics of invading freshwater fish: common carp (Cyprinus carpio) in the Murray-Darling Basin, Australia. Biol Invasions 2012. [DOI: 10.1007/s10530-012-0290-1] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
|
10
|
Haynes GD, Gongora J, Gilligan DM, Grewe P, Moran C, Nicholas FW. Cryptic hybridization and introgression between invasive Cyprinid species Cyprinus carpio and Carassius auratus in Australia: implications for invasive species management. Anim Conserv 2011. [DOI: 10.1111/j.1469-1795.2011.00490.x] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- G. D. Haynes
- Faculty of Veterinary Science; University of Sydney; Camperdown; NSW; Australia
| | - J. Gongora
- Faculty of Veterinary Science; University of Sydney; Camperdown; NSW; Australia
| | - D. M. Gilligan
- Department of Primary Industries; Batemans Bay Fisheries Centre; Batemans Bay; NSW; Australia
| | - P. Grewe
- CSIRO Division of Marine and Atmospheric Research; Castray Esplanade; Hobart; TAS; Australia
| | - C. Moran
- Faculty of Veterinary Science; University of Sydney; Camperdown; NSW; Australia
| | - F. W. Nicholas
- Faculty of Veterinary Science; University of Sydney; Camperdown; NSW; Australia
| |
Collapse
|
11
|
Simon A, Britton R, Gozlan R, van Oosterhout C, Volckaert FAM, Hänfling B. Invasive cyprinid fish in Europe originate from the single introduction of an admixed source population followed by a complex pattern of spread. PLoS One 2011; 6:e18560. [PMID: 21674031 PMCID: PMC3108587 DOI: 10.1371/journal.pone.0018560] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2010] [Accepted: 03/11/2011] [Indexed: 11/19/2022] Open
Abstract
The Asian cyprinid fish, the topmouth gudgeon (Pseudorasbora parva), was introduced into Europe in the 1960s. A highly invasive freshwater fish, it is currently found in at least 32 countries outside its native range. Here we analyse a 700 base pair fragment of the mitochondrial cytochrome b gene to examine different models of colonisation and spread within the invasive range, and to investigate the factors that may have contributed to their invasion success. Haplotype and nucleotide diversity of the introduced populations from continental Europe was higher than that of the native populations, although two recently introduced populations from the British Isles showed low levels of variability. Based on coalescent theory, all introduced and some native populations showed a relative excess of nucleotide diversity compared to haplotype diversity. This suggests that these populations are not in mutation-drift equilibrium, but rather that the relative inflated level of nucleotide diversity is consistent with recent admixture. This study elucidates the colonisation patterns of P. parva in Europe and provides an evolutionary framework of their invasion. It supports the hypothesis that their European colonisation was initiated by their introduction to a single location or small geographic area with subsequent complex pattern of spread including both long distance and stepping-stone dispersal. Furthermore, it was preceded by, or associated with, the admixture of genetically diverse source populations that may have augmented its invasive-potential.
Collapse
Affiliation(s)
- Andrea Simon
- Evolutionary Biology Group, Department of Biological Sciences, University of Hull, Hull, United Kingdom.
| | | | | | | | | | | |
Collapse
|
12
|
Haynes GD, Gilligan DM, Grewe P, Moran C, Nicholas FW. Population genetics of invasive common carp Cyprinus carpio L. in coastal drainages in eastern Australia. JOURNAL OF FISH BIOLOGY 2010; 77:1150-1157. [PMID: 21039496 DOI: 10.1111/j.1095-8649.2010.02742.x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
The common carp Cyprinus carpio introduced in two drainages in eastern Australia are largely descended from European common carp, and in a third drainage they descend largely from East Asian common carp. The partial genetic differentiation among the species in those drainages is consistent with their origins.
Collapse
Affiliation(s)
- G D Haynes
- Faculty of Veterinary Science, University of Sydney, NSW 2006, Australia. gwilym
| | | | | | | | | |
Collapse
|
13
|
Faulks LK, Gilligan DM, Beheregaray LB. Islands of water in a sea of dry land: hydrological regime predicts genetic diversity and dispersal in a widespread fish from Australia's arid zone, the golden perch (Macquaria ambigua). Mol Ecol 2010; 19:4723-37. [PMID: 20887362 DOI: 10.1111/j.1365-294x.2010.04848.x] [Citation(s) in RCA: 65] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Rivers provide an excellent system to study interactions between patterns of biodiversity structure and ecological processes. In these environments, gene flow is restricted by the spatial hierarchy and temporal variation of connectivity within the drainage network. In the Australian arid zone, this variability is high and rivers often exist as isolated waterholes connected during unpredictable floods. These conditions cause boom/bust cycles in the population dynamics of taxa, but their influence on spatial genetic diversity is largely unknown. We used a landscape genetics approach to assess the effect of hydrological variability on gene flow, spatial population structure and genetic diversity in an Australian freshwater fish, Macquaria ambigua. Our analysis is based on microsatellite data of 590 samples from 26 locations across the species range. Despite temporal isolation of populations, the species showed surprisingly high rates of dispersal, with population genetic structure only evident among major drainage basins. Within drainages, hydrological variability was a strong predictor of genetic diversity, being positively correlated with spring-time flow volume. We propose that increases in flow volume during spring stimulate recruitment booms and dispersal, boosting population size and genetic diversity. Although it is uncertain how the hydrological regime in arid Australia may change under future climate scenarios, management strategies for arid-zone fishes should mitigate barriers to dispersal and alterations to the natural flow regime to maintain connectivity and the species' evolutionary potential. This study contributes to our understanding of the influence of spatial and temporal heterogeneity on population and landscape processes.
Collapse
Affiliation(s)
- Leanne K Faulks
- Molecular Ecology Laboratory, Macquarie University, Department of Biological Sciences Macquarie University, Sydney, NSW 2109, Australia.
| | | | | |
Collapse
|
14
|
Low diversity and high levels of population genetic structuring in introduced eastern mosquitofish (Gambusia holbrooki) in the greater Melbourne area, Australia. Biol Invasions 2010. [DOI: 10.1007/s10530-010-9766-z] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
|