1
|
Lloyd‐Jones LR, Brien ML, Feutry P, Lawrence E, Beri P, Booth S, Coulson S, Baylis SM, Villiers K, Taplin LE, Westcott DA. Implications of past and present genetic connectivity for management of the saltwater crocodile ( Crocodylus porosus). Evol Appl 2023; 16:911-935. [PMID: 37124084 PMCID: PMC10130557 DOI: 10.1111/eva.13545] [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: 08/17/2022] [Revised: 02/17/2023] [Accepted: 03/16/2023] [Indexed: 04/03/2023] Open
Abstract
Effective management of protected species requires information on appropriate evolutionary and geographic population boundaries and knowledge of how the physical environment and life-history traits combine to shape the population structure and connectivity. Saltwater crocodiles (Crocodylus porosus) are the largest and most widely distributed of living crocodilians, extending from Sri Lanka to Southeast Asia and down to northern Australia. Given the long-distance movement capabilities reported for C. porosus, management units are hypothesised to be highly connected by migration. However, the magnitude, scale, and consistency of connection across managed populations are not fully understood. Here we used an efficient genotyping method that combines DArTseq and sequence capture to survey≈ 3000 high-quality genome-wide single nucleotide polymorphisms from 1176 C. porosus sampled across nearly the entire range of the species in Queensland, Australia. We investigated historical and present-day connectivity patterns using fixation and diversity indices coupled with clustering methods and the spatial distribution of kin pairs. We inferred kinship using forward simulation coupled with a kinship estimation method that is robust to unspecified population structure. The results demonstrated that the C. porosus population has substantial genetic structure with six broad populations correlated with geographical location. The rate of gene flow was highly correlated with spatial distance, with greater differentiation along the east coast compared to the west. Kinship analyses revealed evidence of reproductive philopatry and limited dispersal, with approximately 90% of reported first and second-degree relatives showing a pairwise distance of <50 km between sampling locations. Given the limited dispersal, lack of suitable habitat, low densities of crocodiles and the high proportion of immature animals in the population, future management and conservation interventions should be considered at regional and state-wide scales.
Collapse
Affiliation(s)
- Luke R. Lloyd‐Jones
- Commonwealth Scientific and Industrial Research OrganisationData61BrisbaneQueensland4072Australia
| | - Matthew L. Brien
- Department of Environment and ScienceQueensland GovernmentCairnsQueensland4870Australia
| | - Pierre Feutry
- Commonwealth Scientific and Industrial Research OrganisationOceans and AtmosphereHobartTasmania7000Australia
| | - Emma Lawrence
- Commonwealth Scientific and Industrial Research OrganisationData61BrisbaneQueensland4072Australia
| | - Paul Beri
- Department of Environment and ScienceQueensland GovernmentCairnsQueensland4870Australia
| | - Simon Booth
- Department of Environment and ScienceQueensland GovernmentCairnsQueensland4870Australia
| | - Steven Coulson
- Department of Environment and ScienceQueensland GovernmentCairnsQueensland4870Australia
| | - Shane M. Baylis
- Commonwealth Scientific and Industrial Research OrganisationOceans and AtmosphereHobartTasmania7000Australia
| | - Kira Villiers
- Commonwealth Scientific and Industrial Research OrganisationData61BrisbaneQueensland4072Australia
| | - Laurence E. Taplin
- Department of Environment and ScienceQueensland GovernmentCairnsQueensland4870Australia
| | - David A. Westcott
- Commonwealth Scientific and Industrial Research OrganisationLand and WaterAthertonQueensland4883Australia
| |
Collapse
|
2
|
Nikolic N, Devloo-Delva F, Bailleul D, Noskova E, Rougeux C, Delord C, Borsa P, Liautard-Haag C, Hassan M, Marie AD, Feutry P, Grewe P, Davies C, Farley J, Fernando D, Biton-Porsmoguer S, Poisson F, Parker D, Leone A, Aulich J, Lansdell M, Marsac F, Arnaud-Haond S. Stepping up to genome scan allows stock differentiation in the worldwide distributed blue shark Prionace glauca. Mol Ecol 2023; 32:1000-1019. [PMID: 36511846 DOI: 10.1111/mec.16822] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Revised: 11/29/2022] [Accepted: 12/01/2022] [Indexed: 12/15/2022]
Abstract
The blue shark Prionace glauca is a top predator with one of the widest geographical distributions of any shark species. It is classified as Critically Endangered in the Mediterranean Sea, and Near Threatened globally. Previous genetic studies did not reject the null hypothesis of a single global population. The blue shark was proposed as a possible archetype of the "grey zone of population differentiation," coined to designate cases where population structure may be too recent or too faint to be detected using a limited set of markers. Here, blue shark samples collected throughout its global range were sequenced using a specific RAD method (DArTseq), which recovered 37,655 genome-wide single nucleotide polymorphisms (SNPs). Two main groups emerged, with Mediterranean Sea and northern Atlantic samples (Northern population) differentiated significantly from the Indo-west Pacific samples (Southern population). Significant pairwise FST values indicated further genetic differentiation within the Atlantic Ocean, and between the Atlantic Ocean and the Mediterranean Sea. Reconstruction of recent demographic history suggested divergence between Northern and Southern populations occurred about 500 generations ago and revealed a drastic reduction in effective population size from a large ancestral population. Our results illustrate the power of genome scans to detect population structure and reconstruct demographic history in highly migratory marine species. Given that the management plans of the blue shark (targeted or bycatch) fisheries currently assume panmictic regional stocks, we strongly recommend that the results presented here be considered in future stock assessments and conservation strategies.
Collapse
Affiliation(s)
- Natacha Nikolic
- UMR MARBEC, University of Montpellier, IRD, Ifremer, CNRS, Sète, France.,INRAE, Ecobiop, AQUA, Saint-Pée-sur-Nivelle, France.,ARBRE, Agence de Recherche pour la Biodiversité à la Réunion, Saint-Gilles, France
| | - Floriaan Devloo-Delva
- CSIRO Environment, Hobart, Tasmania, Australia.,School of Natural Sciences-Quantitative Marine Science, University of Tasmania, Hobart, Tasmania, Australia
| | - Diane Bailleul
- UMR MARBEC, University of Montpellier, IRD, Ifremer, CNRS, Sète, France
| | - Ekaterina Noskova
- Computer Technologies Laboratory, ITMO University, St Petersburg, Russia
| | | | - Chrystelle Delord
- UMR MARBEC, University of Montpellier, IRD, Ifremer, CNRS, Sète, France
| | - Philippe Borsa
- Institut de recherche pour le développement, UMR ENTROPIE, Montpellier, France
| | | | - Mohamad Hassan
- UMR MARBEC, University of Montpellier, IRD, Ifremer, CNRS, Sète, France.,Animal Production Department, Tishreen University, Latakia, Syria
| | - Amandine D Marie
- ARBRE, Agence de Recherche pour la Biodiversité à la Réunion, Saint-Gilles, France
| | | | - Peter Grewe
- CSIRO Environment, Hobart, Tasmania, Australia
| | | | | | | | | | - François Poisson
- UMR MARBEC, University of Montpellier, IRD, Ifremer, CNRS, Sète, France
| | - Denham Parker
- Department of Forestry, Fisheries and the Environment, (DFFE), Cape Town, South Africa.,Department of Biological Sciences, University of Cape Town, Rondebosch, South Africa
| | - Agostino Leone
- UMR MARBEC, University of Montpellier, IRD, Ifremer, CNRS, Sète, France
| | | | | | - Francis Marsac
- UMR MARBEC, University of Montpellier, IRD, Ifremer, CNRS, Sète, France
| | | |
Collapse
|
3
|
Foster SD, Feutry P, Grewe P, Davies C. Sample size requirements for genetic studies on yellowfin tuna. PLoS One 2021; 16:e0259113. [PMID: 34735482 PMCID: PMC8568148 DOI: 10.1371/journal.pone.0259113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Accepted: 10/12/2021] [Indexed: 12/02/2022] Open
Abstract
In population genetics, the amount of information for an analytical task is governed by the number of individuals sampled and the amount of genetic information measured on each of those individuals. In this work, we assessed the numbers of individual yellowfin tuna (Thunnus albacares) and genetic markers required for ocean-basin scale inferences. We assessed this for three distinct data analysis tasks that are often employed: testing for differences between genetic profiles; stock delineation, and; assignment of individuals to stocks. For all analytical tasks, we used real (not simulated) data from four sampling locations that span the tropical Pacific Ocean. Whilst spatially separated, the genetic differences between the sampling sites were not substantial, a maximum of approximately Fst = 0.02, which is quite typical of large pelagic fish. We repeatedly sub-sampled the data, mimicking a new survey, and performed the analyses. False positive rates were also assessed by re-sampling and randomly assigning fish to groups. Varying the sample sizes indicated that some analytical tasks, namely profile testing, required relatively few individuals per sampling location (n ≳ 10) and single nucleotide polymorphisms (SNPs, m ≳ 256). Stock delineation required more individuals per sampling location (n ≳ 25). Assignment of fish to sampling locations required substantially more individuals, more in fact than we had available (n > 50), although this sample size could be reduced to n ≳ 30 when individual fish were assumed to belong to one of the groups sampled. With these results, designers of molecular ecological surveys for yellowfin tuna, and users of information from them, can assess whether the information content is adequate for the required inferential task.
Collapse
Affiliation(s)
| | - Pierre Feutry
- CSIRO’s Oceans and Atmospheres, Hobart, Tasmania, Australia
| | - Peter Grewe
- CSIRO’s Oceans and Atmospheres, Hobart, Tasmania, Australia
| | | |
Collapse
|
4
|
Klobucar SL, Rick JA, Mandeville EG, Wagner CE, Budy P. Investigating the morphological and genetic divergence of arctic char ( Salvelinus alpinus) populations in lakes of arctic Alaska. Ecol Evol 2021; 11:3040-3057. [PMID: 33841765 PMCID: PMC8019052 DOI: 10.1002/ece3.7211] [Citation(s) in RCA: 2] [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: 07/26/2019] [Revised: 11/17/2020] [Accepted: 12/08/2020] [Indexed: 12/03/2022] Open
Abstract
Polymorphism facilitates coexistence of divergent morphs (e.g., phenotypes) of the same species by minimizing intraspecific competition, especially when resources are limiting. Arctic char (Salvelinus sp.) are a Holarctic fish often forming morphologically, and sometimes genetically, divergent morphs. In this study, we assessed the morphological and genetic diversity and divergence of 263 individuals from seven populations of arctic char with varying length-frequency distributions across two distinct groups of lakes in northern Alaska. Despite close geographic proximity, each lake group occurs on landscapes with different glacial ages and surface water connectivity, and thus was likely colonized by fishes at different times. Across lakes, a continuum of physical (e.g., lake area, maximum depth) and biological characteristics (e.g., primary productivity, fish density) exists, likely contributing to characteristics of present-day char populations. Although some lakes exhibit bimodal size distributions, using model-based clustering of morphometric traits corrected for allometry, we did not detect morphological differences within and across char populations. Genomic analyses using 15,934 SNPs obtained from genotyping by sequencing demonstrated differences among lake groups related to historical biogeography, but within lake groups and within individual lakes, genetic differentiation was not related to total body length. We used PERMANOVA to identify environmental and biological factors related to observed char size structure. Significant predictors included water transparency (i.e., a primary productivity proxy), char density (fish·ha-1), and lake group. Larger char occurred in lakes with greater primary production and lower char densities, suggesting less intraspecific competition and resource limitation. Thus, char populations in more productive and connected lakes may prove more stable to environmental changes, relative to food-limited and closed lakes, if lake productivity increases concomitantly. Our findings provide some of the first descriptions of genomic characteristics of char populations in arctic Alaska, and offer important consideration for the persistence of these populations for subsistence and conservation.
Collapse
Affiliation(s)
- Stephen L. Klobucar
- Department of Watershed Sciences and the Ecology CenterUtah State UniversityLoganUTUSA
- Present address:
Institute of Arctic BiologyUniversity of Alaska FairbanksFairbanksAKUSA
| | - Jessica A. Rick
- Department of BotanyUniversity of WyomingLaramieWYUSA
- Program in EcologyUniversity of WyomingLaramieWYUSA
| | - Elizabeth G. Mandeville
- Department of BotanyUniversity of WyomingLaramieWYUSA
- Wyoming Cooperative Fish and Wildlife Research UnitDepartment of Zoology and PhysiologyUniversity of WyomingLaramieWYUSA
- Present address:
Department of Integrative BiologyUniversity of GuelphGuelphONCanada
| | - Catherine E. Wagner
- Department of BotanyUniversity of WyomingLaramieWYUSA
- Program in EcologyUniversity of WyomingLaramieWYUSA
| | - Phaedra Budy
- Department of Watershed Sciences and the Ecology CenterUtah State UniversityLoganUTUSA
- U.S. Geological SurveyUtah Cooperative Fish and Wildlife Research UnitLoganUTUSA
| |
Collapse
|
5
|
Feutry P, Devloo-Delva F, Tran Lu Y A, Mona S, Gunasekera RM, Johnson G, Pillans RD, Jaccoud D, Kilian A, Morgan DL, Saunders T, Bax NJ, Kyne PM. One panel to rule them all: DArTcap genotyping for population structure, historical demography, and kinship analyses, and its application to a threatened shark. Mol Ecol Resour 2020; 20:1470-1485. [PMID: 32492756 DOI: 10.1111/1755-0998.13204] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Revised: 05/26/2020] [Accepted: 05/28/2020] [Indexed: 01/25/2023]
Abstract
With recent advances in sequencing technology, genomic data are changing how important conservation management decisions are made. Applications such as Close-Kin Mark-Recapture demand large amounts of data to estimate population size and structure, and their full potential can only be realised through ongoing improvements in genotyping strategies. Here we introduce DArTcap, a cost-efficient method that combines DArTseq and sequence capture, and illustrate its use in a high resolution population analysis of Glyphis garricki, a rare, poorly known and threatened euryhaline shark. Clustering analyses and spatial distribution of kin pairs from four different regions across northern Australia and one in Papua New Guinea, representing its entire known range, revealed that each region hosts at least one distinct population. Further structuring is likely within Van Diemen Gulf, the region that included the most rivers sampled, suggesting additional population structuring would be found if other rivers were sampled. Coalescent analyses and spatially explicit modelling suggest that G. garricki experienced a recent range expansion during the opening of the Gulf of Carpentaria following the conclusion of the Last Glacial Maximum. The low migration rates between neighbouring populations of a species that is found only in restricted coastal and riverine habitats show the importance of managing each population separately, including careful monitoring of local and remote anthropogenic activities that may affect their environments. Overall we demonstrated how a carefully chosen SNP panel combined with DArTcap can provide highly accurate kinship inference and also support population structure and historical demography analyses, therefore maximising cost-effectiveness.
Collapse
Affiliation(s)
| | - Floriaan Devloo-Delva
- CSIRO Oceans and Atmosphere, Hobart, TAS, Australia.,School of Natural Sciences - Quantitative Marine Science, University of Tasmania, Hobart, TAS, Australia
| | - Adrien Tran Lu Y
- Institut de Systématique, Évolution, Biodiversité (ISYEB), UMR 7205, MNHN, CNRS, EPHE, Sorbonne Université, Paris, France.,EPHE, PSL University, Paris, France
| | - Stefano Mona
- Institut de Systématique, Évolution, Biodiversité (ISYEB), UMR 7205, MNHN, CNRS, EPHE, Sorbonne Université, Paris, France.,EPHE, PSL University, Paris, France.,Laboratoire d'Excellence CORAIL, Papetoai, French Polynesia
| | | | - Grant Johnson
- Department of Primary Industry and Fisheries, Aquatic Resource Research Unit, Darwin, NT, Australia
| | | | - Damian Jaccoud
- Diversity Arrays Technology Pty Ltd, University of Canberra, Bruce, ACT, Australia
| | - Andrzej Kilian
- Diversity Arrays Technology Pty Ltd, University of Canberra, Bruce, ACT, Australia
| | - David L Morgan
- Centre for Sustainable Aquatic Ecosystems, Harry Butler Institute, Murdoch University, Murdoch, WA, Australia
| | - Thor Saunders
- Department of Primary Industry and Fisheries, Aquatic Resource Research Unit, Darwin, NT, Australia
| | - Nicholas J Bax
- CSIRO Oceans and Atmosphere, Hobart, TAS, Australia.,Institute for Marine and Antarctic Science, University of Tasmania, Hobart, TAS, Australia
| | - Peter M Kyne
- Research Institute for the Environment and Livelihoods, Charles Darwin University, Darwin, NT, Australia
| |
Collapse
|