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Saunders PA, Ferre-Ortega C, Hill PL, Simakov O, Ezaz T, Burridge CP, Wapstra E. Using a Handful of Transcriptomes to Detect Sex-Linked Markers and Develop Molecular Sexing Assays in a Species with Homomorphic Sex Chromosomes. Genome Biol Evol 2024; 16:evae060. [PMID: 38526014 PMCID: PMC11003529 DOI: 10.1093/gbe/evae060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Revised: 03/12/2024] [Accepted: 03/17/2024] [Indexed: 03/26/2024] Open
Abstract
To understand the biology of a species, it is often crucial to be able to differentiate males and females. However, many species lack easily identifiable sexually dimorphic traits. In those that possess sex chromosomes, molecular sexing offers a good alternative, and molecular sexing assays can be developed through the comparison of male and female genomic sequences. However, in many nonmodel species, sex chromosomes are poorly differentiated, and identifying sex-linked sequences and developing sexing assays can be challenging. In this study, we highlight a simple transcriptome-based procedure for the detection of sex-linked markers suitable for the development of sexing assays that circumvents limitations of more commonly used approaches. We apply it to the spotted snow skink Carinascincus ocellatus, a viviparous lizard with homomorphic XY chromosomes that has environmentally induced sex reversal. With transcriptomes from three males and three females alone, we identify thousands of putative Y-linked sequences. We confirm linkage through alignment of assembled transcripts to a distantly related lizard genome and readily design multiple single locus polymerase chain reaction primers to sex C. ocellatus and related species. Our approach also facilitates valuable comparisons of sex determining systems on a broad taxonomic scale.
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Affiliation(s)
- Paul A Saunders
- Discipline of Biological Sciences, University of Tasmania, Sandy Bay, Tasmania 7000, Australia
| | - Carles Ferre-Ortega
- Discipline of Biological Sciences, University of Tasmania, Sandy Bay, Tasmania 7000, Australia
| | - Peta L Hill
- Institute for Applied Ecology, University of Canberra, Bruce, Australian Capital Territory 2601, Australia
| | - Oleg Simakov
- Department of Molecular Evolution and Development, University of Vienna, Vienna 1010, Austria
| | - Tariq Ezaz
- Institute for Applied Ecology, University of Canberra, Bruce, Australian Capital Territory 2601, Australia
| | - Christopher P Burridge
- Discipline of Biological Sciences, University of Tasmania, Sandy Bay, Tasmania 7000, Australia
| | - Erik Wapstra
- Discipline of Biological Sciences, University of Tasmania, Sandy Bay, Tasmania 7000, Australia
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2
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Beer MA, Proft KM, Veillet A, Kozakiewicz CP, Hamilton DG, Hamede R, McCallum H, Hohenlohe PA, Burridge CP, Margres MJ, Jones ME, Storfer A. Disease-driven top predator decline affects mesopredator population genomic structure. Nat Ecol Evol 2024; 8:293-303. [PMID: 38191839 DOI: 10.1038/s41559-023-02265-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Accepted: 11/02/2023] [Indexed: 01/10/2024]
Abstract
Top predator declines are pervasive and often have dramatic effects on ecological communities via changes in food web dynamics, but their evolutionary consequences are virtually unknown. Tasmania's top terrestrial predator, the Tasmanian devil, is declining due to a lethal transmissible cancer. Spotted-tailed quolls benefit via mesopredator release, and they alter their behaviour and resource use concomitant with devil declines and increased disease duration. Here, using a landscape community genomics framework to identify environmental drivers of population genomic structure and signatures of selection, we show that these biotic factors are consistently among the top variables explaining genomic structure of the quoll. Landscape resistance negatively correlates with devil density, suggesting that devil declines will increase quoll genetic subdivision over time, despite no change in quoll densities detected by camera trap studies. Devil density also contributes to signatures of selection in the quoll genome, including genes associated with muscle development and locomotion. Our results provide some of the first evidence of the evolutionary impacts of competition between a top predator and a mesopredator species in the context of a trophic cascade. As top predator declines are increasing globally, our framework can serve as a model for future studies of evolutionary impacts of altered ecological interactions.
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Affiliation(s)
- Marc A Beer
- School of Biological Sciences, Washington State University, Pullman, WA, USA
| | - Kirstin M Proft
- School of Natural Sciences, University of Tasmania, Hobart, Tasmania, Australia
| | - Anne Veillet
- Hilo Core Genomics Facility, University of Hawaii at Hilo, Hilo, HI, USA
| | - Christopher P Kozakiewicz
- Department of Integrative Biology, Michigan State University, W.K. Kellogg Biological Station, Hickory Corners, MI, USA
| | - David G Hamilton
- School of Natural Sciences, University of Tasmania, Hobart, Tasmania, Australia
| | - Rodrigo Hamede
- School of Natural Sciences, University of Tasmania, Hobart, Tasmania, Australia
- CANECEV, Centre de Recherches Ecologiques et Evolutives sur le Cancer, Montpellier, France
| | - Hamish McCallum
- Environmental Futures Research Institute, Griffith University, Nathan, Queensland, Australia
| | - Paul A Hohenlohe
- Institute for Bioinformatics and Evolutionary Studies, University of Idaho, Moscow, ID, USA
| | | | - Mark J Margres
- Department of Integrative Biology, University of South Florida, Tampa, FL, USA
| | - Menna E Jones
- School of Natural Sciences, University of Tasmania, Hobart, Tasmania, Australia
| | - Andrew Storfer
- School of Biological Sciences, Washington State University, Pullman, WA, USA.
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3
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Devloo‐Delva F, Burridge CP, Kyne PM, Brunnschweiler JM, Chapman DD, Charvet P, Chen X, Cliff G, Daly R, Drymon JM, Espinoza M, Fernando D, Barcia LG, Glaus K, González‐Garza BI, Grant MI, Gunasekera RM, Hernandez S, Hyodo S, Jabado RW, Jaquemet S, Johnson G, Ketchum JT, Magalon H, Marthick JR, Mollen FH, Mona S, Naylor GJP, Nevill JEG, Phillips NM, Pillans RD, Postaire BD, Smoothey AF, Tachihara K, Tillet BJ, Valerio‐Vargas JA, Feutry P. From rivers to ocean basins: The role of ocean barriers and philopatry in the genetic structuring of a cosmopolitan coastal predator. Ecol Evol 2023; 13:e9837. [PMID: 36844667 PMCID: PMC9944188 DOI: 10.1002/ece3.9837] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Revised: 01/31/2023] [Accepted: 01/31/2023] [Indexed: 02/24/2023] Open
Abstract
The Bull Shark (Carcharhinus leucas) faces varying levels of exploitation around the world due to its coastal distribution. Information regarding population connectivity is crucial to evaluate its conservation status and local fishing impacts. In this study, we sampled 922 putative Bull Sharks from 19 locations in the first global assessment of population structure of this cosmopolitan species. Using a recently developed DNA-capture approach (DArTcap), samples were genotyped for 3400 nuclear markers. Additionally, full mitochondrial genomes of 384 Indo-Pacific samples were sequenced. Reproductive isolation was found between and across ocean basins (eastern Pacific, western Atlantic, eastern Atlantic, Indo-West Pacific) with distinct island populations in Japan and Fiji. Bull Sharks appear to maintain gene flow using shallow coastal waters as dispersal corridors, whereas large oceanic distances and historical land-bridges act as barriers. Females tend to return to the same area for reproduction, making them more susceptible to local threats and an important focus for management actions. Given these behaviors, the exploitation of Bull Sharks from insular populations, such as Japan and Fiji, may instigate local decline that cannot readily be replenished by immigration, which can in turn affect ecosystem dynamics and functions. These data also supported the development of a genetic panel to ascertain the population of origin, which will be useful in monitoring the trade of fisheries products and assessing population-level impacts of this harvest.
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Affiliation(s)
- Floriaan Devloo‐Delva
- Oceans and Atmosphere, CSIROHobartTasmaniaAustralia
- Quantitative Marine Science, Institute for Marine and Antarctic Studies, University of TasmaniaHobartTasmaniaAustralia
- Discipline of Biological Sciences, School of Natural SciencesUniversity of TasmaniaHobartTasmaniaAustralia
| | - Christopher P. Burridge
- Discipline of Biological Sciences, School of Natural SciencesUniversity of TasmaniaHobartTasmaniaAustralia
| | - Peter M. Kyne
- Research Institute for the Environment and LivelihoodsCharles Darwin UniversityDarwinNorthern TerritoryAustralia
| | | | - Demian D. Chapman
- Department of Biological SciencesFlorida International UniversityNorth MiamiFloridaUSA
| | - Patricia Charvet
- Programa de Pós‐graduação em Sistemática, Uso e Conservação da BiodiversidadeUniversidade Federal do Ceará (PPGSis ‐ UFC)FortalezaBrazil
| | - Xiao Chen
- College of Veterinary MedicineSouth China Agricultural UniversityGuangzhouChina
| | - Geremy Cliff
- KwaZulu‐Natal Sharks Board, Umhlanga 4320, South Africa and School of Life SciencesUniversity of KwaZulu‐NatalDurbanSouth Africa
| | - Ryan Daly
- Oceanographic Research Institute, South African Association for Marine Biological Research, PointDurbanSouth Africa
- South African Institute for Aquatic BiodiversityMkhandaSouth Africa
| | - J. Marcus Drymon
- Coastal Research and Extension CenterMississippi State UniversityBiloxiMississippiUSA
- Mississippi‐Alabama Sea Grant ConsortiumOcean SpringsMississippiUSA
| | - Mario Espinoza
- Centro de Investigación en Ciencias del Mar y Limnología & Escuela de BiologíaUniversidad de Costa Rica, San Pedro de Montes de OcaSan JoséCosta Rica
| | | | - Laura Garcia Barcia
- Department of Biological SciencesFlorida International UniversityNorth MiamiFloridaUSA
| | - Kerstin Glaus
- Faculty of Science, Technology and Environment, School of Marine StudiesThe University of the South PacificSuvaFiji
| | | | - Michael I. Grant
- College of Science and Engineering, Centre for Sustainable Tropical Fisheries and AquacultureJames Cook UniversityTownsvilleQueenslandAustralia
| | | | - Sebastian Hernandez
- Biomolecular Laboratory, Center for International ProgramsUniversidad VERITASSan JoséCosta Rica
- Sala de Colecciones, Facultad de Ciencias del MarUniversidad Católica del NorteCoquimboChile
| | - Susumu Hyodo
- Laboratory of Physiology, Atmosphere and Ocean Research InstituteUniversity of TokyoKashiwa, ChibaJapan
| | - Rima W. Jabado
- College of Science and Engineering, Centre for Sustainable Tropical Fisheries and AquacultureJames Cook UniversityTownsvilleQueenslandAustralia
- Elasmo ProjectDubaiUnited Arab Emirates
| | - Sébastien Jaquemet
- UMR ENTROPIE (Université de La Réunion, Université de Nouvelle‐Calédonie, IRD, CNRS, IFREMER), Faculté des Sciences et TechnologiesUniversité de La RéunionCedex 09, La RéunionFrance
| | - Grant Johnson
- Department of Industry, Tourism and Trade, Aquatic Resource Research UnitDarwinNorthern TerritoryAustralia
| | | | - Hélène Magalon
- UMR ENTROPIE (Université de La Réunion, Université de Nouvelle‐Calédonie, IRD, CNRS, IFREMER), Faculté des Sciences et TechnologiesUniversité de La RéunionCedex 09, La RéunionFrance
| | - James R. Marthick
- Menzies Institute for Medical ResearchUniversity of TasmaniaHobartTasmaniaAustralia
| | | | - Stefano Mona
- Institut de Systématique, Evolution, Biodiversité, ISYEB (UMR 7205), Muséum National d'Histoire Naturelle, CNRS, Sorbonne Université, EPHEUniversité des AntillesParisFrance
- EPHEPSL Research UniversityParisFrance
| | - Gavin J. P. Naylor
- Florida Museum of Natural HistoryUniversity of FloridaGainesvilleFloridaUSA
| | | | - Nicole M. Phillips
- School of Biological, Environmental and Earth SciencesThe University of Southern MississippiHattiesburgMississippiUSA
| | | | - Bautisse D. Postaire
- UMR ENTROPIE (Université de La Réunion, Université de Nouvelle‐Calédonie, IRD, CNRS, IFREMER), Faculté des Sciences et TechnologiesUniversité de La RéunionCedex 09, La RéunionFrance
| | - Amy F. Smoothey
- NSW Department of Primary Industries, Fisheries ResearchSydney Institute of Marine ScienceMosmanNew South WalesAustralia
| | - Katsunori Tachihara
- Laboratory of Fisheries Biology and Coral Reef Studies, Faculty of ScienceUniversity of Ryukyus, NishiharaOkinawaJapan
| | - Bree J. Tillet
- Translational Research Institute, University of Queensland Diamantina InstituteBrisbaneQueenslandAustralia
| | - Jorge A. Valerio‐Vargas
- Centro de Investigación en Ciencias del Mar y Limnología & Escuela de BiologíaUniversidad de Costa Rica, San Pedro de Montes de OcaSan JoséCosta Rica
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Kozakiewicz CP, Burridge CP, Lee JS, Kraberger SJ, Fountain-Jones NM, Fisher RN, Lyren LM, Jennings MK, Riley SPD, Serieys LEK, Craft ME, Funk WC, Crooks KR, VandeWoude S, Carver S. Habitat connectivity and host relatedness influence virus spread across an urbanising landscape in a fragmentation-sensitive carnivore. Virus Evol 2022; 9:veac122. [PMID: 36694819 PMCID: PMC9865512 DOI: 10.1093/ve/veac122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Revised: 10/22/2022] [Accepted: 12/20/2022] [Indexed: 12/24/2022] Open
Abstract
Spatially heterogeneous landscape factors such as urbanisation can have substantial effects on the severity and spread of wildlife diseases. However, research linking patterns of pathogen transmission to landscape features remains rare. Using a combination of phylogeographic and machine learning approaches, we tested the influence of landscape and host factors on feline immunodeficiency virus (FIVLru) genetic variation and spread among bobcats (Lynx rufus) sampled from coastal southern California. We found evidence for increased rates of FIVLru lineage spread through areas of higher vegetation density. Furthermore, single-nucleotide polymorphism (SNP) variation among FIVLru sequences was associated with host genetic distances and geographic location, with FIVLru genetic discontinuities precisely correlating with known urban barriers to host dispersal. An effect of forest land cover on FIVLru SNP variation was likely attributable to host population structure and differences in forest land cover between different populations. Taken together, these results suggest that the spread of FIVLru is constrained by large-scale urban barriers to host movement. Although urbanisation at fine spatial scales did not appear to directly influence virus transmission or spread, we found evidence that viruses transmit and spread more quickly through areas containing higher proportions of natural habitat. These multiple lines of evidence demonstrate how urbanisation can change patterns of contact-dependent pathogen transmission and provide insights into how continued urban development may influence the incidence and management of wildlife disease.
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Affiliation(s)
| | | | - Justin S Lee
- Genomic Sequencing Laboratory, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA
| | | | | | - Robert N Fisher
- Western Ecological Research Center, U.S. Geological Survey, San Diego, CA 92101, USA
| | - Lisa M Lyren
- Western Ecological Research Center, U.S. Geological Survey, San Diego, CA 92101, USA
| | - Megan K Jennings
- Biology Department, San Diego State University, San Diego, CA 92182, USA
| | - Seth P D Riley
- National Park Service, Santa Monica Mountains National Recreation Area, Thousand Oaks, CA 91360, USA
| | | | - Meggan E Craft
- Department of Ecology, Evolution and Behavior, University of Minnesota, St Paul, MN 55108, USA
| | - W Chris Funk
- Department of Biology, Colorado State University, Fort Collins, CO 80523, USA,Graduate Degree Program in Ecology, Colorado State University, Fort Collins, CO 80523, USA
| | - Kevin R Crooks
- Graduate Degree Program in Ecology, Colorado State University, Fort Collins, CO 80523, USA,Department of Fish, Wildlife, and Conservation Biology, Colorado State University, Fort Collins, CO 80523, USA
| | - Sue VandeWoude
- Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, CO 80523, USA
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5
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von Takach B, Ranjard L, Burridge CP, Cameron SF, Cremona T, Eldridge MDB, Fisher DO, Frankenberg S, Hill BM, Hohnen R, Jolly CJ, Kelly E, MacDonald AJ, Moussalli A, Ottewell K, Phillips BL, Radford IJ, Spencer PBS, Trewella GJ, Umbrello LS, Banks SC. Population genomics of a predatory mammal reveals patterns of decline and impacts of exposure to toxic toads. Mol Ecol 2022; 31:5468-5486. [PMID: 36056907 PMCID: PMC9826391 DOI: 10.1111/mec.16680] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Revised: 08/30/2022] [Accepted: 09/01/2022] [Indexed: 01/11/2023]
Abstract
Mammal declines across northern Australia are one of the major biodiversity loss events occurring globally. There has been no regional assessment of the implications of these species declines for genomic diversity. To address this, we conducted a species-wide assessment of genomic diversity in the northern quoll (Dasyurus hallucatus), an Endangered marsupial carnivore. We used next generation sequencing methods to genotype 10,191 single nucleotide polymorphisms (SNPs) in 352 individuals from across a 3220-km length of the continent, investigating patterns of population genomic structure and diversity, and identifying loci showing signals of putative selection. We found strong heterogeneity in the distribution of genomic diversity across the continent, characterized by (i) biogeographical barriers driving hierarchical population structure through long-term isolation, and (ii) severe reductions in diversity resulting from population declines, exacerbated by the spread of introduced toxic cane toads (Rhinella marina). These results warn of a large ongoing loss of genomic diversity and associated adaptive capacity as mammals decline across northern Australia. Encouragingly, populations of the northern quoll established on toad-free islands by translocations appear to have maintained most of the initial genomic diversity after 16 years. By mapping patterns of genomic diversity within and among populations, and investigating these patterns in the context of population declines, we can provide conservation managers with data critical to informed decision-making. This includes the identification of populations that are candidates for genetic management, the importance of remnant island and insurance/translocated populations for the conservation of genetic diversity, and the characterization of putative evolutionarily significant units.
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Affiliation(s)
- Brenton von Takach
- Research Institute for the Environment and LivelihoodsCharles Darwin UniversityDarwinNorthern TerritoryAustralia,School of Molecular and Life SciencesCurtin UniversityPerthWestern AustraliaAustralia
| | - Louis Ranjard
- The Research School of Biology, Faculty of ScienceThe Australian National UniversityActonAustralian Capital TerritoryAustralia,PlantTech Research InstituteTaurangaNew Zealand
| | | | - Skye F. Cameron
- Australian Wildlife ConservancyKimberleyWestern AustraliaAustralia,School of Biological SciencesUniversity of QueenslandSt LuciaQueenslandAustralia
| | - Teigan Cremona
- Research Institute for the Environment and LivelihoodsCharles Darwin UniversityDarwinNorthern TerritoryAustralia
| | | | - Diana O. Fisher
- School of Biological SciencesUniversity of QueenslandSt LuciaQueenslandAustralia
| | | | - Brydie M. Hill
- Flora and Fauna Division, Department of Environment, Parks and Water SecurityNorthern Territory GovernmentNorthern TerritoryAustralia
| | - Rosemary Hohnen
- Research Institute for the Environment and LivelihoodsCharles Darwin UniversityDarwinNorthern TerritoryAustralia
| | - Chris J. Jolly
- Institute of Land, Water and Society, School of Environmental ScienceCharles Sturt UniversityAlburyNew South WalesAustralia,School of Natural SciencesMacquarie UniversityMacquarie ParkNew South WalesAustralia
| | - Ella Kelly
- School of BioSciencesUniversity of MelbourneParkvilleVictoriaAustralia
| | - Anna J. MacDonald
- The Research School of Biology, Faculty of ScienceThe Australian National UniversityActonAustralian Capital TerritoryAustralia,Australian Antarctic Division, Department of AgricultureWater and the EnvironmentKingstonTasmaniaAustralia
| | - Adnan Moussalli
- School of BioSciencesUniversity of MelbourneParkvilleVictoriaAustralia,Department of ScienceMuseums VictoriaMelbourneVictoriaAustralia
| | - Kym Ottewell
- Department of Biodiversity, Conservation and AttractionsPerthWestern AustraliaAustralia
| | - Ben L. Phillips
- School of BioSciencesUniversity of MelbourneParkvilleVictoriaAustralia
| | - Ian J. Radford
- Department of Biodiversity, Conservation and AttractionsPerthWestern AustraliaAustralia
| | - Peter B. S. Spencer
- Environmental and Conservation Sciences, Murdoch UniversityPerthWestern AustraliaAustralia
| | - Gavin J. Trewella
- Research Institute for the Environment and LivelihoodsCharles Darwin UniversityDarwinNorthern TerritoryAustralia
| | - Linette S. Umbrello
- Department of Biodiversity, Conservation and AttractionsPerthWestern AustraliaAustralia,Collections and Research CentreWestern Australian MuseumWelshpoolWestern AustraliaAustralia
| | - Sam C. Banks
- Research Institute for the Environment and LivelihoodsCharles Darwin UniversityDarwinNorthern TerritoryAustralia
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6
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Næsborg-Nielsen C, Eisenhofer R, Fraser TA, Wilkinson V, Burridge CP, Carver S. Sarcoptic mange changes bacterial and fungal microbiota of bare-nosed wombats (Vombatus ursinus). Parasit Vectors 2022; 15:323. [PMID: 36100860 PMCID: PMC9472346 DOI: 10.1186/s13071-022-05452-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2022] [Accepted: 08/26/2022] [Indexed: 11/25/2022] Open
Abstract
Background Sarcoptes scabiei is globally distributed and one of the most impactful mammalian ectoparasites. Sarcoptic mange, caused by infection with S. scabiei, causes disruption of the epidermis and its bacterial microbiota, but its effects on host fungal microbiota and on the microbiota of marsupials in general have not been studied. Here, we (i) examine bacterial and fungal microbiota changes associated with mange in wild bare-nosed wombats (BNWs) and (ii) evaluate whether opportunistic pathogens are potentiated by S. scabiei infection in this species. Methods Using Amplicon Sequencing of the 16S rRNA and ITS2 rDNA genes, we detected skin microbiota changes of the bare-nosed wombat (Vombatus ursinus). We compared the alpha and beta diversity among healthy, moderate, and severe disease states using ANOVA and PERMANOVA with nesting. Lastly, we identified taxa that differed between disease states using analysis of composition of microbes (ANCOM) testing. Results We detected significant changes in the microbial communities and diversity with mange in BNWs. Severely affected BNWs had lower amplicon sequence variant (ASV) richness compared to that of healthy individuals, and the microbial communities were significantly different between disease states with higher relative abundance of potentially pathogenic microbial taxa in mange-affected BNWs including Staphylococcus sciuri, Corynebacterium spp., Brevibacterium spp., Brachybacterium spp., and Pseudogymnascus spp. and Debaryomyces spp. Conclusion This study represents the first investigation of microbial changes in association with sarcoptic mange in a marsupial host, as well as the first investigation of fungal microbial changes on the skin of any host suffering from sarcoptic mange. Our results are broadly consistent with bacterial microbiota changes observed in humans, pigs, canids, and Iberian ibex, suggesting the epidermal microbial impacts of mange may be generalisable across host species. We recommend that future studies investigating skin microbiota changes include both bacterial and fungal data to gain a more complete picture of the effects of sarcoptic mange. Graphical Abstract ![]()
Supplementary Information The online version contains supplementary material available at 10.1186/s13071-022-05452-y.
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7
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Campbell CSM, Dutoit L, King TM, Craw D, Burridge CP, Wallis GP, Waters JM. Genome‐wide analysis resolves the radiation of New Zealand's freshwater
Galaxias vulgaris
complex and reveals a candidate species obscured by mitochondrial capture. DIVERS DISTRIB 2022. [DOI: 10.1111/ddi.13629] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Affiliation(s)
| | - Ludovic Dutoit
- Department of Zoology University of Otago Dunedin New Zealand
| | - Tania M. King
- Department of Zoology University of Otago Dunedin New Zealand
| | - Dave Craw
- Department of Geology University of Otago Dunedin New Zealand
| | - Christopher P. Burridge
- Discipline of Biological Sciences, School of Natural Sciences University of Tasmania Hobart Australia
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8
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Hill P, While GM, Burridge CP, Ezaz T, Munch KL, McVarish M, Wapstra E. Sex reversal explains some, but not all, climate-mediated sex ratio variation within a viviparous reptile. Proc Biol Sci 2022; 289:20220689. [PMID: 35642367 PMCID: PMC9156933 DOI: 10.1098/rspb.2022.0689] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Evolutionary transitions in sex-determining systems have occurred frequently yet understanding how they occur remains a major challenge. In reptiles, transitions from genetic to temperature-dependent sex determination can occur if the gene products that determine sex evolve thermal sensitivity, resulting in sex-reversed individuals. However, evidence of sex reversal is limited to oviparous reptiles. Here we used thermal experiments to test whether sex reversal is responsible for differences in sex determination in a viviparous reptile, Carinascincus ocellatus, a species with XY sex chromosomes and population-specific sex ratio response to temperature. We show that sex reversal is occurring and that its frequency is related to temperature. Sex reversal was unidirectional (phenotypic males with XX genotype) and observed in both high- and low-elevation populations. We propose that XX-biased genotypic sex ratios could produce either male- or female-biased phenotypic sex ratios as observed in low-elevation C. ocellatus under variable rates of XX sex reversal. We discuss reasons why sex reversal may not influence sex ratios at high elevation. Our results suggest that the mechanism responsible for evolutionary transitions from genotypic to temperature-dependent sex determination is more complex than can be explained by a single process such as sex reversal.
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Affiliation(s)
- Peta Hill
- Discipline of Biological Sciences, University of Tasmania, Private Bag 5, Hobart, Tasmania 7000, Australia
| | - Geoffrey M While
- Discipline of Biological Sciences, University of Tasmania, Private Bag 5, Hobart, Tasmania 7000, Australia
| | - Christopher P Burridge
- Discipline of Biological Sciences, University of Tasmania, Private Bag 5, Hobart, Tasmania 7000, Australia
| | - Tariq Ezaz
- Institute for Applied Ecology, University of Canberra, Bruce, Australian Capital Territory 2601, Australia
| | - Kirke L Munch
- Discipline of Biological Sciences, University of Tasmania, Private Bag 5, Hobart, Tasmania 7000, Australia
| | - Mary McVarish
- Discipline of Biological Sciences, University of Tasmania, Private Bag 5, Hobart, Tasmania 7000, Australia
| | - Erik Wapstra
- Discipline of Biological Sciences, University of Tasmania, Private Bag 5, Hobart, Tasmania 7000, Australia
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9
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Jones ME, Bain GC, Hamer RP, Proft KM, Gardiner RZ, Dixon KJ, Kittipalawattanapol K, Zepeda de Alba AL, Ranyard CE, Munks SA, Barmuta LA, Burridge CP, Johnson CN, Davidson NJ. Research supporting restoration aiming to make a fragmented landscape ‘functional’ for native wildlife. Eco Management Restoration 2021. [DOI: 10.1111/emr.12504] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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10
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Miñano MR, While GM, Yang W, Burridge CP, Sacchi R, Zuffi M, Scali S, Salvi D, Uller T. Climate Shapes the Geographic Distribution and Introgressive Spread of Color Ornamentation in Common Wall Lizards. Am Nat 2021; 198:379-393. [PMID: 34403317 DOI: 10.1086/715186] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
AbstractClimate can exert an effect on the strength of sexual selection, but empirical evidence is limited. Here, we tested whether climate predicts the geographic distribution and introgressive spread of sexually selected male color ornamentation across 114 populations of the common wall lizard, Podarcis muralis. Coloration was highly structured across the landscape and did not reflect genetic differentiation. Instead, color ornamentation was consistently exaggerated in hot and dry environments, suggesting that climate-driven selection maintains geographic variation in spite of gene flow. Introgression of color ornamentation into a distantly related lineage appears to be ongoing and was particularly pronounced in warm climates with wet winters and dry summers. Combined, these results suggest that sexual ornamentation is consistently favored in climates that allow a prolonged reproductive season and high and reliable opportunities for lizard activity. This pattern corroborates theoretical predictions that such climatic conditions reduce the temporal clustering of receptive females and increase male-male competition, resulting in strong sexual selection. In summary, we provide compelling evidence for the importance of climate for the evolution of color ornamentation, and we demonstrate that geographic variation in the strength of sexual selection influences introgression of this phenotype.
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11
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Dominguez JC, Calero-Riestra M, Olea PP, Malo JE, Burridge CP, Proft K, Illanas S, Viñuela J, García JT. Lack of detectable genetic isolation in the cyclic rodent Microtus arvalis despite large landscape fragmentation owing to transportation infrastructures. Sci Rep 2021; 11:12534. [PMID: 34131199 PMCID: PMC8206325 DOI: 10.1038/s41598-021-91824-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Accepted: 05/31/2021] [Indexed: 02/05/2023] Open
Abstract
Although roads are widely seen as dispersal barriers, their genetic consequences for animals that experience large fluctuations in population density are poorly documented. We developed a spatially paired experimental design to assess the genetic impacts of roads on cyclic voles (Microtus arvalis) during a high-density phase in North-Western Spain. We compared genetic patterns from 15 paired plots bisected by three different barrier types, using linear mixed models and computing effect sizes to assess the importance of each type, and the influence of road features like width or the age of the infrastructure. Evidence of effects by roads on genetic diversity and differentiation were lacking. We speculate that the recurrent (each 3-5 generations) episodes of massive dispersal associated with population density peaks can homogenize populations and mitigate the possible genetic impact of landscape fragmentation by roads. This study highlights the importance of developing spatially replicated experimental designs that allow us to consider the large natural spatial variation in genetic parameters. More generally, these results contribute to our understanding of the not well explored effects of habitat fragmentation on dispersal in species showing "boom-bust" dynamics.
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Affiliation(s)
- Julio C Dominguez
- IREC, Instituto de Investigación en Recursos Cinegéticos (CSIC-UCLM-JCCM), Ronda de Toledo, 12, 13071, Ciudad Real, Spain.
| | - María Calero-Riestra
- IREC, Instituto de Investigación en Recursos Cinegéticos (CSIC-UCLM-JCCM), Ronda de Toledo, 12, 13071, Ciudad Real, Spain
| | - Pedro P Olea
- Terrestrial Ecology Group (TEG-UAM), Departamento de Ecología, Facultad de Ciencias, Universidad Autónoma de Madrid, C/Darwin 2, 28049, Madrid, Spain
- Centro de Investigación en Biodiversidad y Cambio Global (CIBC-UAM), Universidad Autónoma de Madrid, C. Darwin 2, 28049, Madrid, Spain
| | - Juan E Malo
- Terrestrial Ecology Group (TEG-UAM), Departamento de Ecología, Facultad de Ciencias, Universidad Autónoma de Madrid, C/Darwin 2, 28049, Madrid, Spain
- Centro de Investigación en Biodiversidad y Cambio Global (CIBC-UAM), Universidad Autónoma de Madrid, C. Darwin 2, 28049, Madrid, Spain
| | - Christopher P Burridge
- Discipline of Biological Sciences, University of Tasmania, Private Bag 55, Hobart, TAS, 7001, Australia
| | - Kirstin Proft
- Discipline of Biological Sciences, University of Tasmania, Private Bag 55, Hobart, TAS, 7001, Australia
| | - Sonia Illanas
- IREC, Instituto de Investigación en Recursos Cinegéticos (CSIC-UCLM-JCCM), Ronda de Toledo, 12, 13071, Ciudad Real, Spain
| | - Javier Viñuela
- IREC, Instituto de Investigación en Recursos Cinegéticos (CSIC-UCLM-JCCM), Ronda de Toledo, 12, 13071, Ciudad Real, Spain
| | - Jesús T García
- IREC, Instituto de Investigación en Recursos Cinegéticos (CSIC-UCLM-JCCM), Ronda de Toledo, 12, 13071, Ciudad Real, Spain
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12
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Tamura J, Ingram J, Martin AM, Burridge CP, Carver S. Contrasting population manipulations reveal resource competition between two large marsupials: bare-nosed wombats and eastern grey kangaroos. Oecologia 2021; 197:313-325. [PMID: 34095983 DOI: 10.1007/s00442-021-04959-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2021] [Accepted: 05/28/2021] [Indexed: 11/27/2022]
Abstract
Resource competition is an important interaction that can structure ecological communities, but is difficult to demonstrate in nature, and rarely demonstrated for large mammals including marsupials. We analysed 10 years of population survey data to investigate resource competition between bare-nosed wombats (Vombatus ursinus) and eastern grey kangaroos (Macropus giganteus) at two sites to assess whether resource competition is occurring. At one site, wombat abundance was reduced by increased mortality from mange disease, whereas at the other site, kangaroo abundance was reduced primarily by culling. We used the modified Lotka-Volterra competition (LVC) models to describe the mechanism of resource competition and fitted those models to the empirical data by maximum likelihood estimation. We found strong negative relationships between the abundance of wombats and kangaroos at each site, and resource competition was also mechanistically supported by the modified LVC models. The estimated competition coefficients indicate that bare-nosed wombats are a slightly superior competitor of eastern grey kangaroos than vice versa, and that intraspecific competition is almost twice as strong as interspecific competition. In addition, this study facilitated the calculation of the transmission rate associated with mange disease at one site (0.011), and the removal rate owing to culling, the introduction of a predator species, and drought at the other site (0.0006). Collectively, this research represents a rare empirical demonstration of resource competition between large mammals and contributes new insight into the ecology of two of Australia's largest grazing marsupials.
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Affiliation(s)
- Julie Tamura
- School of Natural Sciences, University of Tasmania, Sandy Bay, TAS, Australia.
| | - Janeane Ingram
- School of Geography, Planning and Spatial Sciences, University of Tasmania, Sandy Bay, TAS, Australia
| | - Alynn M Martin
- School of Natural Sciences, University of Tasmania, Sandy Bay, TAS, Australia
| | | | - Scott Carver
- School of Natural Sciences, University of Tasmania, Sandy Bay, TAS, Australia
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13
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Hill P, Wapstra E, Ezaz T, Burridge CP. Pleistocene divergence in the absence of gene flow among populations of a viviparous reptile with intraspecific variation in sex determination. Ecol Evol 2021; 11:5575-5583. [PMID: 34026030 PMCID: PMC8131762 DOI: 10.1002/ece3.7458] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Revised: 02/21/2021] [Accepted: 02/25/2021] [Indexed: 12/26/2022] Open
Abstract
Polymorphisms can lead to genetic isolation if there is differential mating success among conspecifics divergent for a trait. Polymorphism for sex-determining system may fall into this category, given strong selection for the production of viable males and females and the low success of heterogametic hybrids when sex chromosomes differ (Haldane's rule). Here we investigated whether populations exhibiting polymorphism for sex determination are genetically isolated, using the viviparous snow skink Carinascincus ocellatus. While a comparatively high elevation population has genotypic sex determination, in a lower elevation population there is an additional temperature component to sex determination. Based on 11,107 SNP markers, these populations appear genetically isolated. "Isolation with Migration" analysis also suggests these populations diverged in the absence of gene flow, across a period encompassing multiple Pleistocene glaciations and likely greater geographic proximity of populations. However, further experiments are required to establish whether genetic isolation may be a cause or consequence of differences in sex determination. Given the influence of temperature on sex in one lineage, we also discuss the implications for the persistence of this polymorphism under climate change.
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Affiliation(s)
- Peta Hill
- Discipline of Biological SciencesUniversity of TasmaniaSandy BayTas.Australia
| | - Erik Wapstra
- Discipline of Biological SciencesUniversity of TasmaniaSandy BayTas.Australia
| | - Tariq Ezaz
- Institute for Applied EcologyUniversity of CanberraBruceACTAustralia
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14
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Proft KM, Bateman BL, Johnson CN, Jones ME, Pauza M, Burridge CP. The effects of weather variability on patterns of genetic diversity in Tasmanian bettongs. Mol Ecol 2021; 30:1777-1790. [PMID: 33590590 DOI: 10.1111/mec.15847] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2020] [Revised: 02/04/2021] [Accepted: 02/11/2021] [Indexed: 12/01/2022]
Abstract
While the effects of climate (long-term, prevailing weather) on species abundance, range and genetic diversity have been widely studied, short-term, localized variations in atmospheric conditions (i.e., weather) can also rapidly alter species' geographical ranges and population sizes, but little is known about how they affect genetic diversity. We investigated the relationship between weather and range-wide genetic diversity in a marsupial, Bettongia gaimardi, using dynamic species distribution models (SDMs). Genetic diversity was lower in parts of the range where the weather-based SDM predicted high variability in probability of B. gaimardi occurrence during 1950-2009. This is probably an effect of lower population sizes and extinction-recolonization cycles in places with highly variable weather. Spatial variation in genetic diversity was also better predicted by mean probabilities of B. gaimardi occurrence from weather- than climate-based SDMs. Our results illustrate the importance of weather in driving population dynamics and species distributions on decadal timescales and thereby in affecting genetic diversity. Modelling the links between changing weather patterns, species distributions and genetic diversity will allow researchers to better forecast biological impacts of climate change.
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Affiliation(s)
- Kirstin M Proft
- School of Natural Sciences, University of Tasmania, Hobart, Tasmania, Australia
| | | | - Christopher N Johnson
- School of Natural Sciences, University of Tasmania, Hobart, Tasmania, Australia.,Australian Research Council Centre of Excellence for Australian Biodiversity and Heritage, University of Tasmania, Hobart, Tasmania, Australia
| | - Menna E Jones
- School of Natural Sciences, University of Tasmania, Hobart, Tasmania, Australia
| | - Matthew Pauza
- Biosecurity Tasmania, Department of Primary Industries, Parks, Water and Environment, Hobart, Tasmania, Australia
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15
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Li Y, Burridge CP, Lv Y, Peng Z. Morphometric and population genomic evidence for species divergence in the Chimarrichthys fish complex of the Tibetan Plateau. Mol Phylogenet Evol 2021; 159:107117. [PMID: 33609705 DOI: 10.1016/j.ympev.2021.107117] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Revised: 01/06/2021] [Accepted: 02/08/2021] [Indexed: 10/22/2022]
Abstract
The uplift of the Tibetan Plateau altered the environmental conditions of the local area substantially. Here, we conducted a comprehensive investigation based on morphometrics, population genomics, and climatic factors to evaluate phenotypic and genome-level variations in a radiation of Chimarrichthys catfish endemic to the Plateau. Discriminant function analysis showed phenotypic differences of Chimarrichthys between rivers with respect to elevation. Genetic structure analysis based on 6606 single nucleotide polymorphisms (SNPs) deduced genetic differences between rivers, and species delimitation indicated that the Chimarrichthys fish complex could be divided into three species. Restriction site-associated DNA tags were mapped to the gene sets of Glyptosternon maculatum, and matches were searched against databases for Gene Ontology annotation. Genomic regions exhibiting marked differences among localities represented a range of biological functions, including growth (gdf11), bone development (bmp8a), cellular response to light stimulus (opn3), regulation of the rhodopsin-mediated signalling pathway (grk1), immune response (rag1 and ung), reproductive process (antxr2), and regulation of intracellular iron levels (ireb2). The tag44126, where gene gdf11 is located, was identified as an outlier exhibiting divergence between rivers with altitude differences, and the SNP is thymine (T) in Dadu and Yalong River (~2700 m), but guanine (G) in Jinsha and Qingyi rivers (~2200 and ~ 684 m), suggesting a possible effect of altitude on its differentiation.
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Affiliation(s)
- Yanping Li
- The Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Southwest University School of Life Sciences, Chongqing 400715, China; Key Laboratory of Sichuan Province for Fishes Conservation and Utilization in the Upper Reaches of the Yangtze River, College of Life Sciences, Neijiang Normal University, Neijiang 641000, China
| | - Christopher P Burridge
- Discipline of Biological Sciences, University of Tasmania, Sandy Bay, Tasmania 7005, Australia
| | - Yunyun Lv
- Key Laboratory of Sichuan Province for Fishes Conservation and Utilization in the Upper Reaches of the Yangtze River, College of Life Sciences, Neijiang Normal University, Neijiang 641000, China
| | - Zuogang Peng
- The Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Southwest University School of Life Sciences, Chongqing 400715, China.
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16
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Hill P, Shams F, Burridge CP, Wapstra E, Ezaz T. Differences in Homomorphic Sex Chromosomes Are Associated with Population Divergence in Sex Determination in Carinascincus ocellatus (Scincidae: Lygosominae). Cells 2021; 10:291. [PMID: 33535518 PMCID: PMC7912723 DOI: 10.3390/cells10020291] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 01/28/2021] [Accepted: 01/28/2021] [Indexed: 01/09/2023] Open
Abstract
Sex determination directs development as male or female in sexually reproducing organisms. Evolutionary transitions in sex determination have occurred frequently, suggesting simple mechanisms behind the transitions, yet their detail remains elusive. Here we explore the links between mechanisms of transitions in sex determination and sex chromosome evolution at both recent and deeper temporal scales (<1 Myr; ~79 Myr). We studied a rare example of a species with intraspecific variation in sex determination, Carinascincus ocellatus, and a relative, Liopholis whitii, using c-banding and mapping of repeat motifs and a custom Y chromosome probe set to identify the sex chromosomes. We identified both unique and conserved regions of the Y chromosome among C. ocellatus populations differing in sex determination. There was no evidence for homology of sex chromosomes between C. ocellatus and L. whitii, suggesting independent evolutionary origins. We discuss sex chromosome homology between members of the subfamily Lygosominae and propose links between sex chromosome evolution, sex determination transitions, and karyotype evolution.
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Affiliation(s)
- Peta Hill
- Discipline of Biological Sciences, University of Tasmania, Private Bag 5, Sandy Bay, TAS 7000, Australia; (C.P.B.); (E.W.)
| | - Foyez Shams
- Institute for Applied Ecology, University of Canberra, Bruce, ACT 2601, Australia; (F.S.); (T.E.)
| | - Christopher P. Burridge
- Discipline of Biological Sciences, University of Tasmania, Private Bag 5, Sandy Bay, TAS 7000, Australia; (C.P.B.); (E.W.)
| | - Erik Wapstra
- Discipline of Biological Sciences, University of Tasmania, Private Bag 5, Sandy Bay, TAS 7000, Australia; (C.P.B.); (E.W.)
| | - Tariq Ezaz
- Institute for Applied Ecology, University of Canberra, Bruce, ACT 2601, Australia; (F.S.); (T.E.)
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17
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Liu M, Baker SC, Burridge CP, Jordan GJ, Clarke LJ. DNA
metabarcoding captures subtle differences in forest beetle communities following disturbance. Restor Ecol 2020. [DOI: 10.1111/rec.13236] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Mingxin Liu
- School of Natural Sciences University of Tasmania Private Bag 55, Hobart Tasmania 7001 Australia
- ARC Centre for Forest Value University of Tasmania Hobart Tasmania 7001 Australia
| | - Susan C. Baker
- School of Natural Sciences University of Tasmania Private Bag 55, Hobart Tasmania 7001 Australia
- ARC Centre for Forest Value University of Tasmania Hobart Tasmania 7001 Australia
| | - Christopher P. Burridge
- School of Natural Sciences University of Tasmania Private Bag 55, Hobart Tasmania 7001 Australia
| | - Gregory J. Jordan
- School of Natural Sciences University of Tasmania Private Bag 55, Hobart Tasmania 7001 Australia
| | - Laurence J. Clarke
- Antarctic Climate and Ecosystems Cooperative Research Centre University of Tasmania Hobart Tasmania 7001 Australia
- Institute for Marine and Antarctic Studies University of Tasmania Hobart Tasmania 7001 Australia
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18
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Kozakiewicz CP, Burridge CP, Funk WC, Craft ME, Crooks KR, Fisher RN, Fountain‐Jones NM, Jennings MK, Kraberger SJ, Lee JS, Lyren LM, Riley SPD, Serieys LEK, VandeWoude S, Carver S. Does the virus cross the road? Viral phylogeographic patterns among bobcat populations reflect a history of urban development. Evol Appl 2020; 13:1806-1817. [PMID: 32908587 PMCID: PMC7463333 DOI: 10.1111/eva.12927] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Revised: 01/03/2020] [Accepted: 01/13/2020] [Indexed: 12/18/2022] Open
Abstract
Urban development has major impacts on connectivity among wildlife populations and is thus likely an important factor shaping pathogen transmission in wildlife. However, most investigations of wildlife diseases in urban areas focus on prevalence and infection risk rather than potential effects of urbanization on transmission itself. Feline immunodeficiency virus (FIV) is a directly transmitted retrovirus that infects many felid species and can be used as a model for studying pathogen transmission at landscape scales. We investigated phylogenetic relationships among FIV isolates sampled from five bobcat (Lynx rufus) populations in coastal southern California that appear isolated due to major highways and dense urban development. Divergence dates among FIV phylogenetic lineages in several cases reflected historical urban growth and construction of major highways. We found strong FIV phylogeographic structure among three host populations north-west of Los Angeles, largely coincident with host genetic structure. In contrast, relatively little FIV phylogeographic structure existed among two genetically distinct host populations south-east of Los Angeles. Rates of FIV transfer among host populations did not vary significantly, with the lack of phylogenetic structure south-east of Los Angeles unlikely to reflect frequent contemporary transmission among populations. Our results indicate that major barriers to host gene flow can also act as barriers to pathogen spread, suggesting potentially reduced susceptibility of fragmented populations to novel directly transmitted pathogens. Infrequent exchange of FIV among host populations suggests that populations would best be managed as distinct units in the event of a severe disease outbreak. Phylogeographic inference of pathogen transmission is useful for estimating the ability of geographic barriers to constrain disease spread and can provide insights into contemporary and historical drivers of host population connectivity.
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Affiliation(s)
| | | | - W. Chris Funk
- Department of BiologyColorado State UniversityFort CollinsCOUSA
- Graduate Degree Program in EcologyColorado State UniversityFort CollinsCOUSA
| | - Meggan E. Craft
- Department of Veterinary Population MedicineUniversity of MinnesotaSt PaulMNUSA
| | - Kevin R. Crooks
- Department of Fish, Wildlife, and Conservation BiologyColorado State UniversityFort CollinsCOUSA
| | - Robert N. Fisher
- Western Ecological Research CenterU.S. Geological SurveySan DiegoCAUSA
| | | | | | - Simona J. Kraberger
- Department of Microbiology, Immunology, and PathologyColorado State UniversityFort CollinsCOUSA
| | - Justin S. Lee
- Department of Microbiology, Immunology, and PathologyColorado State UniversityFort CollinsCOUSA
| | - Lisa M. Lyren
- Western Ecological Research CenterU.S. Geological SurveyThousand OaksCAUSA
| | - Seth P. D. Riley
- National Park ServiceSanta Monica Mountains National Recreation AreaThousand OaksCAUSA
| | - Laurel E. K. Serieys
- Department of Environmental StudiesUniversity of California Santa CruzSanta CruzCAUSA
- Institute for Communities and Wildlife in AfricaBiological SciencesUniversity of Cape TownCape TownSouth Africa
| | - Sue VandeWoude
- Department of Microbiology, Immunology, and PathologyColorado State UniversityFort CollinsCOUSA
| | - Scott Carver
- School of Natural SciencesUniversity of TasmaniaHobartTASAustralia
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19
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Burridge CP, Waters JM. Does migration promote or inhibit diversification? A case study involving the dominant radiation of temperate Southern Hemisphere freshwater fishes. Evolution 2020; 74:1954-1965. [DOI: 10.1111/evo.14066] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Revised: 07/08/2020] [Accepted: 07/20/2020] [Indexed: 12/11/2022]
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20
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Lombal AJ, O'dwyer JE, Friesen V, Woehler EJ, Burridge CP. Identifying mechanisms of genetic differentiation among populations in vagile species: historical factors dominate genetic differentiation in seabirds. Biol Rev Camb Philos Soc 2020; 95:625-651. [PMID: 32022401 DOI: 10.1111/brv.12580] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2019] [Revised: 12/23/2019] [Accepted: 01/08/2020] [Indexed: 01/01/2023]
Abstract
Elucidating the factors underlying the origin and maintenance of genetic variation among populations is crucial for our understanding of their ecology and evolution, and also to help identify conservation priorities. While intrinsic movement has been hypothesized as the major determinant of population genetic structuring in abundant vagile species, growing evidence indicates that vagility does not always predict genetic differentiation. However, identifying the determinants of genetic structuring can be challenging, and these are largely unknown for most vagile species. Although, in principle, levels of gene flow can be inferred from neutral allele frequency divergence among populations, underlying assumptions may be unrealistic. Moreover, molecular studies have suggested that contemporary gene flow has often not overridden historical influences on population genetic structure, which indicates potential inadequacies of any interpretations that fail to consider the influence of history in shaping that structure. This exhaustive review of the theoretical and empirical literature investigates the determinants of population genetic differentiation using seabirds as a model system for vagile taxa. Seabirds provide a tractable group within which to identify the determinants of genetic differentiation, given their widespread distribution in marine habitats and an abundance of ecological and genetic studies conducted on this group. Herein we evaluate mitochondrial DNA (mtDNA) variation in 73 seabird species. Lack of mutation-drift equilibrium observed in 19% of species coincided with lower estimates of genetic differentiation, suggesting that dynamic demographic histories can often lead to erroneous interpretations of contemporary gene flow, even in vagile species. Presence of land across the species sampling range, or sampling of breeding colonies representing ice-free Pleistocene refuge zones, appear to be associated with genetic differentiation in Tropical and Southern Temperate species, respectively, indicating that long-term barriers and persistence of populations are important for their genetic structuring. Conversely, biotic factors commonly considered to influence population genetic structure, such as spatial segregation during foraging, were inconsistently associated with population genetic differentiation. In light of these results, we recommend that genetic studies should consider potential historical events when identifying determinants of genetic differentiation among populations to avoid overestimating the role of contemporary factors, even for highly vagile taxa.
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Affiliation(s)
- Anicee J Lombal
- Discipline of Biological Sciences, University of Tasmania, Private Bag 55, Hobart, TAS, 7001, Australia
| | - James E O'dwyer
- Discipline of Biological Sciences, University of Tasmania, Private Bag 55, Hobart, TAS, 7001, Australia
| | - Vicki Friesen
- Department of Biology, Queen's University, 99 University Avenue, Kingston, OL, K7L 3N6, Canada
| | - Eric J Woehler
- Institute for Marine and Antarctic Studies, University of Tasmania, 20 Castray Esplanade, Hobart, TAS, 7004, Australia
| | - Christopher P Burridge
- Discipline of Biological Sciences, University of Tasmania, Private Bag 55, Hobart, TAS, 7001, Australia
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21
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Van Dyke JU, Thompson MB, Burridge CP, Castelli MA, Clulow S, Dissanayake DSB, Dong CM, Doody JS, Edwards DL, Ezaz T, Friesen CR, Gardner MG, Georges A, Higgie M, Hill PL, Holleley CE, Hoops D, Hoskin CJ, Merry DL, Riley JL, Wapstra E, While GM, Whiteley SL, Whiting MJ, Zozaya SM, Whittington CM. Australian lizards are outstanding models for reproductive biology research. AUST J ZOOL 2020. [DOI: 10.1071/zo21017] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Australian lizards are a diverse group distributed across the continent and inhabiting a wide range of environments. Together, they exhibit a remarkable diversity of reproductive morphologies, physiologies, and behaviours that is broadly representative of vertebrates in general. Many reproductive traits exhibited by Australian lizards have evolved independently in multiple lizard lineages, including sociality, complex signalling and mating systems, viviparity, and temperature-dependent sex determination. Australian lizards are thus outstanding model organisms for testing hypotheses about how reproductive traits function and evolve, and they provide an important basis of comparison with other animals that exhibit similar traits. We review how research on Australian lizard reproduction has contributed to answering broader evolutionary and ecological questions that apply to animals in general. We focus on reproductive traits, processes, and strategies that are important areas of current research, including behaviours and signalling involved in courtship; mechanisms involved in mating, egg production, and sperm competition; nesting and gestation; sex determination; and finally, birth in viviparous species. We use our review to identify important questions that emerge from an understanding of this body of research when considered holistically. Finally, we identify additional research questions within each topic that Australian lizards are well suited for reproductive biologists to address.
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22
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Kozakiewicz CP, Burridge CP, Funk WC, Salerno PE, Trumbo DR, Gagne RB, Boydston EE, Fisher RN, Lyren LM, Jennings MK, Riley SPD, Serieys LEK, VandeWoude S, Crooks KR, Carver S. Urbanization reduces genetic connectivity in bobcats (Lynx rufus) at both intra- and interpopulation spatial scales. Mol Ecol 2019; 28:5068-5085. [PMID: 31613411 DOI: 10.1111/mec.15274] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Revised: 10/07/2019] [Accepted: 10/14/2019] [Indexed: 01/02/2023]
Abstract
Urbanization is a major factor driving habitat fragmentation and connectivity loss in wildlife. However, the impacts of urbanization on connectivity can vary among species and even populations due to differences in local landscape characteristics, and our ability to detect these relationships may depend on the spatial scale at which they are measured. Bobcats (Lynx rufus) are relatively sensitive to urbanization and the status of bobcat populations is an important indicator of connectivity in urban coastal southern California. We genotyped 271 bobcats at 13,520 SNP loci to conduct a replicated landscape resistance analysis in five genetically distinct populations. We tested urban and natural factors potentially influencing individual connectivity in each population separately, as well as study-wide. Overall, landscape genomic effects were most frequently detected at the study-wide spatial scale, with urban land cover (measured as impervious surface) having negative effects and topographic roughness having positive effects on gene flow. The negative effect of urban land cover on connectivity was also evident when populations were analyzed separately despite varying substantially in spatial area and the proportion of urban development, confirming a pervasive impact of urbanization largely independent of spatial scale. The effect of urban development was strongest in one population where stream habitat had been lost to development, suggesting that riparian corridors may help mitigate reduced connectivity in urbanizing areas. Our results demonstrate the importance of replicating landscape genetic analyses across populations and considering how landscape genetic effects may vary with spatial scale and local landscape structure.
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Affiliation(s)
| | | | - W Chris Funk
- Department of Biology, Colorado State University, Fort Collins, CO, USA.,Graduate Degree Program in Ecology, Colorado State University, Fort Collins, CO, USA
| | | | - Daryl R Trumbo
- Department of Biology, Colorado State University, Fort Collins, CO, USA
| | - Roderick B Gagne
- Wildlife Genomics and Disease Ecology Laboratory, Department of Veterinary Sciences, University of Wyoming, Laramie, WY, USA.,Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, CO, USA
| | - Erin E Boydston
- Western Ecological Research Center, U.S. Geological Survey, Thousand Oaks, CA, USA
| | - Robert N Fisher
- Western Ecological Research Center, U.S. Geological Survey, San Diego, CA, USA
| | - Lisa M Lyren
- Western Ecological Research Center, U.S. Geological Survey, Thousand Oaks, CA, USA
| | - Megan K Jennings
- Biology Department, San Diego State University, San Diego, CA, USA
| | - Seth P D Riley
- National Park Service, Santa Monica Mountains National Recreation Area, Thousand Oaks, CA, USA
| | - Laurel E K Serieys
- Department of Environmental Studies, University of California Santa Cruz, Santa Cruz, CA, USA.,Institute for Communities and Wildlife in Africa, Biological Sciences, University of Cape Town, Cape Town, South Africa
| | - Sue VandeWoude
- Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, CO, USA
| | - Kevin R Crooks
- Graduate Degree Program in Ecology, Colorado State University, Fort Collins, CO, USA.,Department of Fish, Wildlife, and Conservation Biology, Colorado State University, Fort Collins, CO, USA
| | - Scott Carver
- School of Natural Sciences, University of Tasmania, Hobart, Tasmania, Australia
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Martin AM, Richards SA, Fraser TA, Polkinghorne A, Burridge CP, Carver S. Population‐scale treatment informs solutions for control of environmentally transmitted wildlife disease. J Appl Ecol 2019. [DOI: 10.1111/1365-2664.13467] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Alynn M. Martin
- School of Natural Sciences University of Tasmania Hobart Australia
| | | | - Tamieka A. Fraser
- School of Natural Sciences University of Tasmania Hobart Australia
- Animal Research Centre University of the Sunshine Coast Sippy Downs Australia
| | - Adam Polkinghorne
- Animal Research Centre University of the Sunshine Coast Sippy Downs Australia
| | | | - Scott Carver
- School of Natural Sciences University of Tasmania Hobart Australia
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24
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Martin A, Carver S, Proft K, Fraser TA, Polkinghorne A, Banks S, Burridge CP. Isolation, marine transgression and translocation of the bare-nosed wombat ( Vombatus ursinus). Evol Appl 2019; 12:1114-1123. [PMID: 31293627 PMCID: PMC6597867 DOI: 10.1111/eva.12785] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Revised: 02/01/2019] [Accepted: 02/14/2019] [Indexed: 11/30/2022] Open
Abstract
Island populations can represent genetically distinct and evolutionarily important lineages relative to mainland conspecifics. However, phenotypic divergence of island populations does not necessarily reflect genetic divergence, particularly for lineages inhabiting islands periodically connected during Pleistocene low sea stands. Marine barriers may also not be solely responsible for any divergence that is observed. Here, we investigated genetic divergence among and within the three phenotypically distinct subspecies of bare-nosed wombats (Vombatus ursinus) in south-east Australia that are presently-but were not historically-isolated by marine barriers. Using genome-wide single nucleotide polymorphisms, we identified three genetically distinct groups (mainland Australia, Bass Strait island, and Tasmania) corresponding to the recognized subspecies. However, isolation by distance was observed in the Tasmanian population, indicating additional constraints on gene flow can contribute to divergence in the absence of marine barriers, and may also explain genetic structuring among fragmented mainland populations. We additionally confirm origins and quantify the genetic divergence of an island population 46 years after the introduction of 21 individuals from the Vulnerable Bass Strait subspecies. In the light of our findings, we make recommendations for the maintenance of genetic variation and fitness across the species range.
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Affiliation(s)
- Alynn Martin
- School of Natural SciencesUniversity of TasmaniaHobartTasmaniaAustralia
| | - Scott Carver
- School of Natural SciencesUniversity of TasmaniaHobartTasmaniaAustralia
| | - Kirstin Proft
- School of Natural SciencesUniversity of TasmaniaHobartTasmaniaAustralia
| | - Tamieka A. Fraser
- School of Natural SciencesUniversity of TasmaniaHobartTasmaniaAustralia
- Animal Research CentreUniversity of the Sunshine CoastSippy DownsQueenslandAustralia
| | - Adam Polkinghorne
- Animal Research CentreUniversity of the Sunshine CoastSippy DownsQueenslandAustralia
| | - Sam Banks
- College of Engineering, IT and EnvironmentCharles Darwin UniversityCasuarinaNorthern TerritoryAustralia
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25
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Peterson AT, Anderson RP, Beger M, Bolliger J, Brotons L, Burridge CP, Cobos ME, Cuervo-Robayo AP, Di Minin E, Diez J, Elith J, Embling CB, Escobar LE, Essl F, Feeley KJ, Hawkes L, Jiménez-García D, Jimenez L, Green DM, Knop E, Kühn I, Lahoz-Monfort JJ, Lira-Noriega A, Lobo JM, Loyola R, Mac Nally R, Machado-Stredel F, Martínez-Meyer E, McCarthy M, Merow C, Nori J, Nuñez-Penichet C, Osorio-Olvera L, Pyšek P, Rejmánek M, Ricciardi A, Robertson M, Rojas Soto O, Romero-Alvarez D, Roura-Pascual N, Santini L, Schoeman DS, Schröder B, Soberon J, Strubbe D, Thuiller W, Traveset A, Treml EA, Václavík T, Varela S, Watson JEM, Wiersma Y, Wintle B, Yanez-Arenas C, Zurell D. Open access solutions for biodiversity journals: Do not replace one problem with another. DIVERS DISTRIB 2019. [DOI: 10.1111/ddi.12885] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Affiliation(s)
- A. Townsend Peterson
- Department of Ecology & Evolutionary Biology and Biodiversity Institute, University of Kansas; Lawrence Kansas
| | - Robert P. Anderson
- City College of New York and Graduate Center; City University of New York; New York New York
| | - Maria Beger
- School of Biology, Faculty of Biological Sciences, University of Leeds; Leeds UK
| | - Janine Bolliger
- Swiss Federal Research Institute WSL; Birmensdorf Switzerland
| | | | | | - Marlon E. Cobos
- Department of Ecology & Evolutionary Biology and Biodiversity Institute, University of Kansas; Lawrence Kansas
| | | | - Enrico Di Minin
- Department of Geosciences and Geography; University of Helsinki; Helsinki Finland
- School of Life Sciences; University of KwaZulu-Natal; Durban South Africa
| | | | - Jane Elith
- University of Melbourne; Parkville Victoria Australia
| | | | - Luis E. Escobar
- Department of Fish and Wildlife Conservation; Virginia Tech Blacksburg Virginia
| | - Franz Essl
- Division of Conservation Biology, Vegetation and Landscape Ecology; University Vienna; Vienna Austria
| | | | - Lucy Hawkes
- College of Life and Environmental Sciences; University of Exeter; Penryn UK
| | - Daniel Jiménez-García
- Centro de Agroecología y Ambiente-ICUAP; Benemérita Universidad Autónoma de Puebla; Puebla Mexico
| | - Laura Jimenez
- Department of Ecology & Evolutionary Biology and Biodiversity Institute, University of Kansas; Lawrence Kansas
| | - David M. Green
- Redpath Museum; McGill University; Montreal Quebec Canada
| | - Eva Knop
- University of Bern; Bern Switzerland
| | - Ingolf Kühn
- Helmholtz Centre for Environmental Research - UFZ; Halle Germany
| | | | | | | | | | - Ralph Mac Nally
- University of Canberra; Bruce Australian Capital Territory Australia
| | - Fernando Machado-Stredel
- Department of Ecology & Evolutionary Biology and Biodiversity Institute, University of Kansas; Lawrence Kansas
| | | | | | | | - Javier Nori
- Universidad Nacional de Córdoba; Córdoba Argentina
| | - Claudia Nuñez-Penichet
- Department of Ecology & Evolutionary Biology and Biodiversity Institute, University of Kansas; Lawrence Kansas
| | - Luis Osorio-Olvera
- Centro del Cambio Global y la Sustentabilidad en el Sureste AC; Tabasco Mexico
| | - Petr Pyšek
- Institute of Botany, Czech Academy of Sciences; Prague Czech Republic
- Faculty of Science; Charles University; Prague Czech Republic
| | | | | | | | | | - Daniel Romero-Alvarez
- Department of Ecology & Evolutionary Biology and Biodiversity Institute, University of Kansas; Lawrence Kansas
| | - Núria Roura-Pascual
- Departament de Ciències Ambientals; Universitat de Girona; Girona Catalonia Spain
| | | | | | - Boris Schröder
- Technische Universität Braunschweig; Braunschweig Germany
| | - Jorge Soberon
- Department of Ecology & Evolutionary Biology and Biodiversity Institute, University of Kansas; Lawrence Kansas
| | | | | | - Anna Traveset
- Mediterranean Institute of Advanced Studies (CSIC-UIB); Mallorca Spain
| | | | | | - Sara Varela
- Université Grenoble Alpes; Grenoble France
- CNRS, Université Savoie Mont Blanc; Chambéry France
- LECA-Laboratoire d’Ecologie Alpes; Gières France
| | - James E. M. Watson
- School of Earth and Environmental Sciences, University of Queensland; Brisbane Queensland Australia
- Wildlife Conservation Society; Bronx New York
| | - Yolanda Wiersma
- Department of Biology; Memorial University; St. John's NL Canada
| | - Brendan Wintle
- University of Melbourne; Parkville Victoria Australia
- University of Queensland; St Lucia Queensland Australia
| | - Carlos Yanez-Arenas
- Laboratorio de Biología de la Conservación, Parque Científico y Tecnológico de Yucatán, Facultad de Ciencias-Universidad Nacional Autónoma de México; Mérida Yucatán México
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Kozakiewicz CP, Burridge CP, Funk WC, VandeWoude S, Craft ME, Crooks KR, Ernest HB, Fountain‐Jones NM, Carver S. Pathogens in space: Advancing understanding of pathogen dynamics and disease ecology through landscape genetics. Evol Appl 2018; 11:1763-1778. [PMID: 30459828 PMCID: PMC6231466 DOI: 10.1111/eva.12678] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Revised: 06/24/2018] [Accepted: 06/28/2018] [Indexed: 12/30/2022] Open
Abstract
Landscape genetics has provided many insights into how heterogeneous landscape features drive processes influencing spatial genetic variation in free-living organisms. This rapidly developing field has focused heavily on vertebrates, and expansion of this scope to the study of infectious diseases holds great potential for landscape geneticists and disease ecologists alike. The potential application of landscape genetics to infectious agents has garnered attention at formative stages in the development of landscape genetics, but systematic examination is lacking. We comprehensively review how landscape genetics is being used to better understand pathogen dynamics. We characterize the field and evaluate the types of questions addressed, approaches used and systems studied. We also review the now established landscape genetic methods and their realized and potential applications to disease ecology. Lastly, we identify emerging frontiers in the landscape genetic study of infectious agents, including recent phylogeographic approaches and frameworks for studying complex multihost and host-vector systems. Our review emphasizes the expanding utility of landscape genetic methods available for elucidating key pathogen dynamics (particularly transmission and spread) and also how landscape genetic studies of pathogens can provide insight into host population dynamics. Through this review, we convey how increasing awareness of the complementarity of landscape genetics and disease ecology among practitioners of each field promises to drive important cross-disciplinary advances.
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Affiliation(s)
| | | | - W. Chris Funk
- Department of BiologyGraduate Degree Program in EcologyColorado State UniversityFort CollinsColorado
| | - Sue VandeWoude
- Department of Microbiology, Immunology, and PathologyColorado State UniversityFort CollinsColorado
| | - Meggan E. Craft
- Department of Veterinary Population MedicineUniversity of MinnesotaSt. PaulMinnesota
| | - Kevin R. Crooks
- Department of Fish, Wildlife, and Conservation BiologyColorado State UniversityFort CollinsColorado
| | - Holly B. Ernest
- Wildlife Genomics and Disease Ecology LaboratoryDepartment of Veterinary SciencesUniversity of WyomingLaramieWyoming
| | | | - Scott Carver
- School of Natural SciencesUniversity of TasmaniaHobartTasmaniaAustralia
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Hill PL, Burridge CP, Ezaz T, Wapstra E. Conservation of Sex-Linked Markers among Conspecific Populations of a Viviparous Skink, Niveoscincus ocellatus, Exhibiting Genetic and Temperature-Dependent Sex Determination. Genome Biol Evol 2018; 10:1079-1087. [PMID: 29659810 PMCID: PMC5905450 DOI: 10.1093/gbe/evy042] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/01/2018] [Indexed: 12/18/2022] Open
Abstract
Sex determination systems are exceptionally diverse and have undergone multiple and independent evolutionary transitions among species, particularly reptiles. However, the mechanisms underlying these transitions have not been established. Here, we tested for differences in sex-linked markers in the only known reptile that is polymorphic for sex determination system, the spotted snow skink, Niveoscincus ocellatus, to quantify the genomic differences that have accompanied this transition. In a highland population, sex is determined genetically, whereas in a lowland population, offspring sex ratio is influenced by temperature. We found a similar number of sex-linked loci in each population, including shared loci, with genotypes consistent with male heterogamety (XY). However, population-specific linkage disequilibrium suggests greater differentiation of sex chromosomes in the highland population. Our results suggest that transitions between sex determination systems can be facilitated by subtle genetic differences.
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Affiliation(s)
- Peta L Hill
- School of Biological Sciences, University of Tasmania, Sandy Bay, Tasmania, Australia
| | | | - Tariq Ezaz
- Institute for Applied Ecology, University of Canberra, Bruce, Australian Capital Territory, Australia
| | - Erik Wapstra
- School of Biological Sciences, University of Tasmania, Sandy Bay, Tasmania, Australia
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28
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Martin AM, Fraser TA, Lesku JA, Simpson K, Roberts GL, Garvey J, Polkinghorne A, Burridge CP, Carver S. The cascading pathogenic consequences of Sarcoptes scabiei infection that manifest in host disease. R Soc Open Sci 2018; 5:180018. [PMID: 29765692 PMCID: PMC5936957 DOI: 10.1098/rsos.180018] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/04/2018] [Accepted: 03/13/2018] [Indexed: 06/08/2023]
Abstract
Sarcoptic mange, caused by the parasitic mite Sarcoptes scabiei, causes a substantive burden of disease to humans, domestic animals and wildlife, globally. There are many effects of S. scabiei infection, culminating in the disease which hosts suffer. However, major knowledge gaps remain on the pathogenic impacts of this infection. Here, we focus on the bare-nosed wombat host (Vombatus ursinus) to investigate the effects of mange on: (i) host heat loss and thermoregulation, (ii) field metabolic rates, (iii) foraging and resting behaviour across full circadian cycles, and (iv) fatty acid composition in host adipose, bone marrow, brain and muscle tissues. Our findings indicate that mange-infected V. ursinus lose more heat to the environment from alopecia-affected body regions than healthy individuals. Additionally, mange-infected individuals have higher metabolic rates in the wild. However, these metabolic demands are difficult to meet, because infected individuals spend less time foraging and more time inactive relative to their healthy counterparts, despite being outside of the burrow for longer. Lastly, mange infection results in altered fatty acid composition in adipose tissue, with increased amounts of omega-6 acids, and decreased amounts of omega-3 acids, a consequence of chronic cutaneous inflammation and inhibition of anti-inflammatory responses. These findings highlight the interactions of mange-induced physiological and behavioural changes, and have implications for the treatment and rehabilitation of infected individuals.
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Affiliation(s)
- Alynn M. Martin
- School of Natural Sciences, University of Tasmania, Sandy Bay, Tasmania 7005Australia
| | - Tamieka A. Fraser
- School of Natural Sciences, University of Tasmania, Sandy Bay, Tasmania 7005Australia
- Animal Research Centre, University of the Sunshine Coast, Sippy Downs, Queensland 4556Australia
| | - John A. Lesku
- School of Life Sciences, La Trobe University, Melbourne, Victoria 3086Australia
| | - Kellie Simpson
- Department of Primary Industries, Parks, Water and Environment, Hobart, Tasmania 7000Australia
| | - Georgia L. Roberts
- School of Humanities and Social Sciences, La Trobe University, Melbourne, Victoria 3086Australia
- School of Science and Engineering, Federation University, Mount Helen, Victoria 3350Australia
| | - Jillian Garvey
- School of Humanities and Social Sciences, La Trobe University, Melbourne, Victoria 3086Australia
| | - Adam Polkinghorne
- Animal Research Centre, University of the Sunshine Coast, Sippy Downs, Queensland 4556Australia
| | | | - Scott Carver
- School of Natural Sciences, University of Tasmania, Sandy Bay, Tasmania 7005Australia
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29
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Proft KM, Jones ME, Johnson CN, Burridge CP. Making the connection: expanding the role of restoration genetics in restoring and evaluating connectivity. Restor Ecol 2018. [DOI: 10.1111/rec.12692] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
- Kirstin M. Proft
- School of Natural Sciences University of Tasmania, Private Bag 55 Hobart Tasmania 7001 Australia
| | - Menna E. Jones
- School of Natural Sciences University of Tasmania, Private Bag 55 Hobart Tasmania 7001 Australia
| | - Christopher N. Johnson
- School of Natural Sciences and Australian Research Council Centre of Excellence for Australian Biodiversity and Heritage University of Tasmania, Private Bag 55 Hobart Tasmania 7001 Australia
| | - Christopher P. Burridge
- School of Natural Sciences University of Tasmania, Private Bag 55 Hobart Tasmania 7001 Australia
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30
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Martin AM, Burridge CP, Ingram J, Fraser TA, Carver S. Invasive pathogen drives host population collapse: Effects of a travelling wave of sarcoptic mange on bare-nosed wombats. J Appl Ecol 2017. [DOI: 10.1111/1365-2664.12968] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
| | | | | | - Tamieka A. Fraser
- University of Tasmania; Hobart Tas. Australia
- University of the Sunshine Coast; Sippy Downs Qld Australia
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31
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Fountain‐Jones NM, Jordan GJ, Burridge CP, Wardlaw TJ, Baker TP, Forster L, Petersfield M, Baker SC. Trophic position determines functional and phylogenetic recovery after disturbance within a community. Funct Ecol 2017. [DOI: 10.1111/1365-2435.12845] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Affiliation(s)
- Nicholas M. Fountain‐Jones
- School of Biological Sciences University of Tasmania Private Bag 55 Hobart Tas.7001 Australia
- Department of Veterinary Population Medicine University of Minnesota 1365 Gortner Avenue St Paul MN55108 USA
| | - Gregory J. Jordan
- School of Biological Sciences University of Tasmania Private Bag 55 Hobart Tas.7001 Australia
| | - Christopher P. Burridge
- School of Biological Sciences University of Tasmania Private Bag 55 Hobart Tas.7001 Australia
| | - Timothy J. Wardlaw
- Forestry Tasmania Hobart Tas.7001 Australia
- ARC Centre for Forest Value University of Tasmania Private Bag 55 Hobart Tas. Australia
| | - Thomas P. Baker
- School of Biological Sciences University of Tasmania Private Bag 55 Hobart Tas.7001 Australia
- ARC Centre for Forest Value University of Tasmania Private Bag 55 Hobart Tas. Australia
| | - Lynette Forster
- School of Land and Food University of Tasmania Hobart Tas.7001 Australia
| | - Morgana Petersfield
- School of Biological Sciences University of Tasmania Private Bag 55 Hobart Tas.7001 Australia
| | - Susan C. Baker
- School of Biological Sciences University of Tasmania Private Bag 55 Hobart Tas.7001 Australia
- ARC Centre for Forest Value University of Tasmania Private Bag 55 Hobart Tas. Australia
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32
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Berman M, Austin CM, Burridge CP, Miller AD. Social structure and landscape genetics of the endemic New Caledonian ant Leptomyrmex pallens Emery, 1883 (Hymenoptera: Formicidae: Dolichoderinae), in the context of fire-induced rainforest fragmentation. CONSERV GENET 2016. [DOI: 10.1007/s10592-016-0833-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Brüniche-Olsen A, Austin JJ, Jones ME, Holland BR, Burridge CP. Detecting Selection on Temporal and Spatial Scales: A Genomic Time-Series Assessment of Selective Responses to Devil Facial Tumor Disease. PLoS One 2016; 11:e0147875. [PMID: 26930198 PMCID: PMC4773136 DOI: 10.1371/journal.pone.0147875] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2015] [Accepted: 11/25/2015] [Indexed: 11/19/2022] Open
Abstract
Detecting loci under selection is an important task in evolutionary biology. In conservation genetics detecting selection is key to investigating adaptation to the spread of infectious disease. Loci under selection can be detected on a spatial scale, accounting for differences in demographic history among populations, or on a temporal scale, tracing changes in allele frequencies over time. Here we use these two approaches to investigate selective responses to the spread of an infectious cancer—devil facial tumor disease (DFTD)—that since 1996 has ravaged the Tasmanian devil (Sarcophilus harrisii). Using time-series ‘restriction site associated DNA’ (RAD) markers from populations pre- and post DFTD arrival, and DFTD free populations, we infer loci under selection due to DFTD and investigate signatures of selection that are incongruent among methods, populations, and times. The lack of congruence among populations influenced by DFTD with respect to inferred loci under selection, and the direction of that selection, fail to implicate a consistent selective role for DFTD. Instead genetic drift is more likely driving the observed allele frequency changes over time. Our study illustrates the importance of applying methods with different performance optima e.g. accounting for population structure and background selection, and assessing congruence of the results.
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Affiliation(s)
- Anna Brüniche-Olsen
- School of Biological Sciences, University of Tasmania, Private Bag 55, Hobart 7001, Tasmania, Australia
- * E-mail:
| | - Jeremy J. Austin
- School of Earth & Environmental Sciences, University of Adelaide, North Terrace Campus, South Australia, 5005, Australia
| | - Menna E. Jones
- School of Biological Sciences, University of Tasmania, Private Bag 55, Hobart 7001, Tasmania, Australia
| | - Barbara R. Holland
- School of Physical Sciences, University of Tasmania, Private Bag 37, Hobart, Tasmania, 7001, Australia
| | - Christopher P. Burridge
- School of Biological Sciences, University of Tasmania, Private Bag 55, Hobart 7001, Tasmania, Australia
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Grosser S, Burridge CP, Peucker AJ, Waters JM. Coalescent Modelling Suggests Recent Secondary-Contact of Cryptic Penguin Species. PLoS One 2015; 10:e0144966. [PMID: 26675310 PMCID: PMC4682933 DOI: 10.1371/journal.pone.0144966] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2015] [Accepted: 11/25/2015] [Indexed: 11/19/2022] Open
Abstract
Molecular genetic analyses present powerful tools for elucidating demographic and biogeographic histories of taxa. Here we present genetic evidence showing a dynamic history for two cryptic lineages within Eudyptula, the world's smallest penguin. Specifically, we use a suite of genetic markers to reveal that two congeneric taxa ('Australia' and 'New Zealand') co-occur in southern New Zealand, with only low levels of hybridization. Coalescent modelling suggests that the Australian little penguin only recently expanded into southern New Zealand. Analyses conducted under time-dependent molecular evolutionary rates lend support to the hypothesis of recent anthropogenic turnover, consistent with shifts detected in several other New Zealand coastal vertebrate taxa. This apparent turnover event highlights the dynamic nature of the region’s coastal ecosystem.
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Affiliation(s)
- Stefanie Grosser
- Allan Wilson Centre, Department of Zoology, University of Otago, Dunedin, New Zealand
- * E-mail:
| | | | - Amanda J. Peucker
- School of Life and Environmental Sciences, Deakin University, Warrnambool, Victoria, Australia
| | - Jonathan M. Waters
- Allan Wilson Centre, Department of Zoology, University of Otago, Dunedin, New Zealand
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35
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Lombal AJ, Wenner TJ, Burridge CP. Assessment of high-resolution melting (HRM) profiles as predictors of microsatellite variation: an example in Providence Petrel (Pterodroma solandri). Genes Genomics 2015. [DOI: 10.1007/s13258-015-0327-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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36
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Brüniche-Olsen A, Jones ME, Austin JJ, Burridge CP, Holland BR. Extensive population decline in the Tasmanian devil predates European settlement and devil facial tumour disease. Biol Lett 2015; 10:20140619. [PMID: 25376800 DOI: 10.1098/rsbl.2014.0619] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The Tasmanian devil (Sarcophilus harrisii) was widespread in Australia during the Late Pleistocene but is now endemic to the island of Tasmania. Low genetic diversity combined with the spread of devil facial tumour disease have raised concerns for the species' long-term survival. Here, we investigate the origin of low genetic diversity by inferring the species' demographic history using temporal sampling with summary statistics, full-likelihood and approximate Bayesian computation methods. Our results show extensive population declines across Tasmania correlating with environmental changes around the last glacial maximum and following unstable climate related to increased 'El Niño-Southern Oscillation' activity.
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Affiliation(s)
- Anna Brüniche-Olsen
- School of Biological Sciences, University of Tasmania, Private Bag 55, Hobart 7001,Tasmania, Australia
| | - Menna E Jones
- School of Biological Sciences, University of Tasmania, Private Bag 55, Hobart 7001,Tasmania, Australia
| | - Jeremy J Austin
- School of Earth and Environmental Sciences, University of Adelaide, North Terrace, South Australia 5005, Australia
| | - Christopher P Burridge
- School of Biological Sciences, University of Tasmania, Private Bag 55, Hobart 7001,Tasmania, Australia
| | - Barbara R Holland
- School of Mathematics and Physics, University of Tasmania, Private Bag 37, Hobart 7001, Tasmania, Australia
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37
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Durrant HMS, Burridge CP, Gardner MG. Isolation via next-generation sequencing of microsatellites from the Tasmanian macroalgae Lessonia corrugata (Lessoniaceae). Appl Plant Sci 2015; 3:apps1500042. [PMID: 26191468 PMCID: PMC4504728 DOI: 10.3732/apps.1500042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 04/14/2015] [Accepted: 05/19/2015] [Indexed: 06/04/2023]
Abstract
PREMISE OF THE STUDY Microsatellite markers for the macroalgae Lessonia corrugata (Lessoniaceae) were developed, for the first time, to enable population genetic assessment of this important foundation species. METHODS AND RESULTS Ion Torrent sequencing identified 16,622 loci, 29 of which were trialed in L. corrugata. Seven loci were found to be polymorphic and screened for variation in 76 individuals from two populations in Tasmania, Australia. Observed heterozygosity ranged from 0.086 to 0.686 (mean 0.386) and the number of alleles per locus ranged from two to five (mean 2.57). Heterozygosity was not significantly different from expected values. CONCLUSIONS These loci can be used to study the population genetics of L. corrugata, a key habitat-forming species in the Tasmanian marine ecosystem, and will help to assess gene flow among spatially discrete populations such as those in marine protected areas.
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Affiliation(s)
- Halley M. S. Durrant
- School of Biological Sciences, University of Tasmania, Private Bag 55, Hobart, Tasmania 7001, Australia
| | - Christopher P. Burridge
- School of Biological Sciences, University of Tasmania, Private Bag 55, Hobart, Tasmania 7001, Australia
| | - Michael G. Gardner
- School of Biological Sciences, Flinders University, GPO Box 2100, Adelaide 5001, South Australia, Australia
- Evolutionary Biology Unit, South Australian Museum, North Terrace, Adelaide 5000, South Australia, Australia
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Cliff HB, Wapstra E, Burridge CP. Persistence and dispersal in a Southern Hemisphere glaciated landscape: the phylogeography of the spotted snow skink (Niveoscincus ocellatus) in Tasmania. BMC Evol Biol 2015; 15:121. [PMID: 26111715 PMCID: PMC4482293 DOI: 10.1186/s12862-015-0397-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2014] [Accepted: 05/29/2015] [Indexed: 11/10/2022] Open
Abstract
Background The aim of this research was to identify the effects of Pleistocene climate change on the distribution of fauna in Tasmania, and contrast this with biotic responses in other temperate regions in the Northern and Southern Hemisphere that experienced glacial activity during this epoch. This was achieved by examining the phylogeographic patterns in a widely distributed Tasmanian endemic reptile, Niveoscincus ocellatus. 204 individuals from 29 populations across the distributional range of N. ocellatus were surveyed for variation at two mitochondrial genes (ND2, ND4), and two nuclear genes (β-globin, RPS8). Phylogenetic relationships were reconstructed using a range of methods (maximum parsimony, Bayesian inference and haplotype networks), and the demographic histories of populations were assessed (AMOVA, Tajima’s D, Fu’s Fs, mismatch distributions, extended Bayesian skyline plots, and relaxed random walk analyses). Results There was a high degree of mitochondrial haplotype diversity (96 unique haplotypes) and phylogeographic structure, where spatially distinct groups were associated with Tasmania’s Northeast and a large area covering Southeast and Central Tasmania. Phylogeographic structure was also present within each major group, but the degree varied regionally, being highest in the Northeast. Only the Southeastern group had a signature of demographic expansion, occurring during the Pleistocene but post-dating the Last Glacial Maximum. In contrast, nuclear DNA had low levels of variation and a lack of phylogeographic structure, and further loci should be surveyed to corroborate the mitochondrial inferences. Conclusions The phylogeographic patterns of N. ocellatus indicate Pleistocene range and demographic expansion in N. ocellatus, particularly in the Southeast and Central areas of Tasmania. Expansion in Central and Southeastern areas appears to have been more recent in both demographic and spatial contexts, than in Northeast Tasmania, which is consistent with inferences for other taxa of greater stability and persistence in Northeast Tasmania during the Last Glacial Maximum. These phylogeographic patterns indicate contrasting demographic histories of populations in close proximity to areas directly affected by glaciers in the Southern Hemisphere during the LGM. Electronic supplementary material The online version of this article (doi:10.1186/s12862-015-0397-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- H B Cliff
- School of Biological Sciences, University of Tasmania, Private Bag 55, Hobart, Tasmania, 7001, Australia.
| | - E Wapstra
- School of Biological Sciences, University of Tasmania, Private Bag 55, Hobart, Tasmania, 7001, Australia.
| | - C P Burridge
- School of Biological Sciences, University of Tasmania, Private Bag 55, Hobart, Tasmania, 7001, Australia.
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Burridge CP, Peucker AJ, Valautham SK, Styan CA, Dann P. Nonequilibrium Conditions Explain Spatial Variability in Genetic Structuring of Little Penguin (Eudyptula minor). J Hered 2015; 106:228-37. [PMID: 25833231 PMCID: PMC4406270 DOI: 10.1093/jhered/esv009] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2014] [Accepted: 02/09/2015] [Indexed: 11/28/2022] Open
Abstract
Factors responsible for spatial structuring of population genetic variation are varied, and in many instances there may be no obvious explanations for genetic structuring observed, or those invoked may reflect spurious correlations. A study of little penguins (Eudyptula minor) in southeast Australia documented low spatial structuring of genetic variation with the exception of colonies at the western limit of sampling, and this distinction was attributed to an intervening oceanographic feature (Bonney Upwelling), differences in breeding phenology, or sea level change. Here, we conducted sampling across the entire Australian range, employing additional markers (12 microsatellites and mitochondrial DNA, 697 individuals, 17 colonies). The zone of elevated genetic structuring previously observed actually represents the eastern half of a genetic cline, within which structuring exists over much shorter spatial scales than elsewhere. Colonies separated by as little as 27 km in the zone are genetically distinguishable, while outside the zone, homogeneity cannot be rejected at scales of up to 1400 km. Given a lack of additional physical or environmental barriers to gene flow, the zone of elevated genetic structuring may reflect secondary contact of lineages (with or without selection against interbreeding), or recent colonization and expansion from this region. This study highlights the importance of sampling scale to reveal the cause of genetic structuring.
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Affiliation(s)
- Christopher P Burridge
- From the School of Biological Sciences, University of Tasmania, Private Bag 55, Hobart, Tasmania 7001, Australia (Burridge and Valautham); the School of Life and Environmental Sciences, Deakin University, Warrnambool, Victoria 3280, Australia (Peucker and Styan); the School of Energy and Resources, UCL Australia, Adelaide, South Australia 5000, Australia (Styan); and the Research Department, Phillip Island Nature Parks, Cowes, Victoria 3922, Australia (Dann).
| | - Amanda J Peucker
- From the School of Biological Sciences, University of Tasmania, Private Bag 55, Hobart, Tasmania 7001, Australia (Burridge and Valautham); the School of Life and Environmental Sciences, Deakin University, Warrnambool, Victoria 3280, Australia (Peucker and Styan); the School of Energy and Resources, UCL Australia, Adelaide, South Australia 5000, Australia (Styan); and the Research Department, Phillip Island Nature Parks, Cowes, Victoria 3922, Australia (Dann)
| | - Sureen K Valautham
- From the School of Biological Sciences, University of Tasmania, Private Bag 55, Hobart, Tasmania 7001, Australia (Burridge and Valautham); the School of Life and Environmental Sciences, Deakin University, Warrnambool, Victoria 3280, Australia (Peucker and Styan); the School of Energy and Resources, UCL Australia, Adelaide, South Australia 5000, Australia (Styan); and the Research Department, Phillip Island Nature Parks, Cowes, Victoria 3922, Australia (Dann)
| | - Craig A Styan
- From the School of Biological Sciences, University of Tasmania, Private Bag 55, Hobart, Tasmania 7001, Australia (Burridge and Valautham); the School of Life and Environmental Sciences, Deakin University, Warrnambool, Victoria 3280, Australia (Peucker and Styan); the School of Energy and Resources, UCL Australia, Adelaide, South Australia 5000, Australia (Styan); and the Research Department, Phillip Island Nature Parks, Cowes, Victoria 3922, Australia (Dann)
| | - Peter Dann
- From the School of Biological Sciences, University of Tasmania, Private Bag 55, Hobart, Tasmania 7001, Australia (Burridge and Valautham); the School of Life and Environmental Sciences, Deakin University, Warrnambool, Victoria 3280, Australia (Peucker and Styan); the School of Energy and Resources, UCL Australia, Adelaide, South Australia 5000, Australia (Styan); and the Research Department, Phillip Island Nature Parks, Cowes, Victoria 3922, Australia (Dann)
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Durrant HMS, Burridge CP, Kelaher BP, Barrett NS, Edgar GJ, Coleman MA. Implications of macroalgal isolation by distance for networks of marine protected areas. Conserv Biol 2014; 28:438-445. [PMID: 24373031 DOI: 10.1111/cobi.12203] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2013] [Accepted: 07/05/2013] [Indexed: 06/03/2023]
Abstract
The global extent of macroalgal forests is declining, greatly affecting marine biodiversity at broad scales through the effects macroalgae have on ecosystem processes, habitat provision, and food web support. Networks of marine protected areas comprise one potential tool that may safeguard gene flow among macroalgal populations in the face of increasing population fragmentation caused by pollution, habitat modification, climate change, algal harvesting, trophic cascades, and other anthropogenic stressors. Optimal design of protected area networks requires knowledge of effective dispersal distances for a range of macroalgae. We conducted a global meta-analysis based on data in the published literature to determine the generality of relation between genetic differentiation and geographic distance among macroalgal populations. We also examined whether spatial genetic variation differed significantly with respect to higher taxon, life history, and habitat characteristics. We found clear evidence of population isolation by distance across a multitude of macroalgal species. Genetic and geographic distance were positively correlated across 49 studies; a modal distance of 50-100 km maintained F(ST) < 0.2. This relation was consistent for all algal divisions, life cycles, habitats, and molecular marker classes investigated. Incorporating knowledge of the spatial scales of gene flow into the design of marine protected area networks will help moderate anthropogenic increases in population isolation and inbreeding and contribute to the resilience of macroalgal forests.
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Affiliation(s)
- Halley M S Durrant
- School of Zoology, University of Tasmania, Private Bag 5, Hobart, Tasmania, 7001, Australia
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Adams M, Raadik TA, Burridge CP, Georges A. Global Biodiversity Assessment and Hyper-Cryptic Species Complexes: More Than One Species of Elephant in the Room? Syst Biol 2014; 63:518-33. [DOI: 10.1093/sysbio/syu017] [Citation(s) in RCA: 113] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Mark Adams
- Evolutionary Biology Unit, South Australian Museum, North Terrace, SA 5000, Australia
- School of Earth and Environmental Sciences, University of Adelaide, Adelaide, SA 5005, Australia
| | - Tarmo A. Raadik
- Aquatic Ecology Section, Arthur Rylah Institute for Environmental Research, Department of Environment and Primary Industries, 123 Brown Street, Heidelberg, VIC 3084, Australia
- Institute for Applied Ecology and Collaborative Research Network for Murray-Darling Futures, University of Canberra, ACT 2601, Australia and
| | - Christopher P. Burridge
- School of Biological Sciences, University of Tasmania, Private Bag 55, Hobart, TAS 7001, Australia
| | - Arthur Georges
- Institute for Applied Ecology and Collaborative Research Network for Murray-Darling Futures, University of Canberra, ACT 2601, Australia and
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Burridge CP, Brown WE, Wadley J, Nankervis DL, Olivier L, Gardner MG, Hull C, Barbour R, Austin JJ. Did postglacial sea-level changes initiate the evolutionary divergence of a Tasmanian endemic raptor from its mainland relative? Proc Biol Sci 2013; 280:20132448. [PMID: 24174114 DOI: 10.1098/rspb.2013.2448] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Populations on continental islands are often distinguishable from mainland conspecifics with respect to body size, appearance, behaviour or life history, and this is often congruent with genetic patterns. It is commonly assumed that such differences developed following the complete isolation of populations by sea-level rise following the Last Glacial Maximum (LGM). However, population divergence may predate the LGM, or marine dispersal and colonization of islands may have occurred more recently; in both cases, populations may have also diverged despite ongoing gene flow. Here, we test these alternative hypotheses for the divergence between wedge-tailed eagles from mainland Australia (Aquila audax audax) and the threatened Tasmanian subspecies (Aquila audax fleayi), based on variation at 20 microsatellite loci and mtDNA. Coalescent analyses indicate that population divergence appreciably postdates the severance of terrestrial habitat continuity and occurred without any subsequent gene flow. We infer a recent colonization of Tasmania by marine dispersal and cannot discount founder effects as the cause of differences in body size and life history. We call into question the general assumption of post-LGM marine transgression as the initiator of divergence of terrestrial lineages on continental islands and adjacent mainland, and highlight the range of alternative scenarios that should be considered.
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Affiliation(s)
- C P Burridge
- School of Zoology, University of Tasmania, , Hobart, Tasmania 7001, Australia, Department of Primary Industry, Parks, Water and Environment, , Hobart, Tasmania 7001, Australia, Australian Centre for Ancient DNA, School of Earth and Environmental Sciences and Environment Institute, University of Adelaide, , North Terrace, Adelaide, South Australia 5005, Australia, School of Biological Sciences, Flinders University, , GPO Box 2100, Adelaide, South Australia 5001, Australia, Evolutionary Biology Unit, South Australian Museum, , North Terrace, Adelaide, South Australia 5001, Australia, Hydro Tasmania, , GPO Box 355, Hobart 7001, Australia, Sciences Department, Museum Victoria, , Carlton Gardens, Melbourne, Victoria 3001, Australia
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Abstract
Shed feathers obtained by noninvasive genetic sampling (NGS) are a valuable source of DNA for genetic studies of birds. They can be collected across a large geographical range and facilitate research on species that would otherwise be extremely difficult to study. A limitation of this approach is uncertainty concerning the quality of the extracted DNA. Here we investigate the relationship between feather type, feather condition and DNA quality (amplification success) in order to provide a simple, cost-effective method for screening samples prior to genetic analysis. We obtained 637 shed feathers of the powerful owl (Ninox strenua) from across its range in southeastern Australia. The extracted DNA was amplified using polymerase chain reaction for a range of markers including mitochondrial DNA, ND3 and nuclear DNA, a simple sequence repeat (Nst02) and a portion of the CHD-1 gene (P2/P8). We found that feather condition significantly influenced the amplification success of all three loci, with feathers characterized as 'good' having greater success. Feather type was found to be of lower importance, with good quality feathers of all types consistently producing high success for all three loci. We also found that the successful amplification of multilocus genotypes was dependant on the condition of the starting material and was highly correlated with successful amplification of the sex-linked CHD-1 locus. Samples with low DNA quality have a higher probability of amplification failure and are more likely to produce incorrect genotypes; therefore, identifying samples with high DNA quality can save substantial time and cost associated with the genetic analysis of NGS. As a result, we propose a method for screening shed feathers in order to provide a subset of samples which will have a greater probability of containing high quality DNA suitable for the amplification of multilocus genotypes.
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Affiliation(s)
- Fiona E Hogan
- School of Life and Environmental Sciences, Deakin University, 221 Burwood Hwy Burwood, Victoria 3125, Australia, Population & Evolutionary Genetics Unit, Sciences Department, Museum Victoria, GPO Box 666, Melbourne, Victoria 3001, Australia, Department of Genetics, University of Melbourne, Victoria 3010, Australia
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Waters JM, Trewick SA, Paterson AM, Spencer HG, Kennedy M, Craw D, Burridge CP, Wallis GP. Biogeography Off the Tracks. Syst Biol 2013; 62:494-8. [DOI: 10.1093/sysbio/syt013] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Berry O, England P, Marriott RJ, Burridge CP, Newman SJ. Understanding age-specific dispersal in fishes through hydrodynamic modelling, genetic simulations and microsatellite DNA analysis. Mol Ecol 2012; 21:2145-59. [PMID: 22417082 DOI: 10.1111/j.1365-294x.2012.05520.x] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Many marine species have vastly different capacities for dispersal during larval, juvenile and adult life stages, and this has the potential to complicate the identification of population boundaries and the implementation of effective management strategies such as marine protected areas. Genetic studies of population structure and dispersal rarely disentangle these differences and usually provide only lifetime-averaged information that can be considered by managers. We address this limitation by combining age-specific autocorrelation analysis of microsatellite genotypes, hydrodynamic modelling and genetic simulations to reveal changes in the extent of dispersal during the lifetime of a marine fish. We focus on an exploited coral reef species, Lethrinus nebulosus, which has a circum-tropical distribution and is a key component of a multispecies fishery in northwestern Australia. Conventional population genetic analyses revealed extensive gene flow in this species over vast distances (up to 1,500 km). Yet, when realistic adult dispersal behaviours were modelled, they could not account for these observations, implying adult dispersal does not dominate gene flow. Instead, hydrodynamic modelling showed that larval L. nebulosus are likely to be transported hundreds of kilometres, easily accounting for the observed gene flow. Despite the vast scale of larval transport, juvenile L. nebulosus exhibited fine-scale genetic autocorrelation, which declined with age. This implies both larval cohesion and extremely limited juvenile dispersal prior to maturity. The multidisciplinary approach adopted in this study provides a uniquely comprehensive insight into spatial processes in this marine fish.
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Affiliation(s)
- Oliver Berry
- CSIRO Wealth From Oceans National Research Flagship, and CSIRO Marine and Atmospheric Research, Private Mail Bag 5, Wembley, WA 6913, Australia.
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Hsu TH, Guillén Madrid AG, Burridge CP, Cheng HY, Gwo JC. Resolution of the Acanthopagrus black seabream complex based on mitochondrial and amplified fragment-length polymorphism analyses. J Fish Biol 2011; 79:1182-1192. [PMID: 22026601 DOI: 10.1111/j.1095-8649.2011.03100.x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
In this study, DNA analyses were employed to verify the identity of six morphologically similar species that occur in the coastal waters of Taiwan: the black seabream complex (Acanthopagrus latus, Acanthopagrus schlegelii, Acanthopagrus sivicolus, Acanthopagrus taiwanensis, Acanthopagrus chinshira and Acanthopagrus pacificus). Amplified fragment-length polymorphism (AFLP) analyses clearly distinguished the same six species that are morphologically diagnosable based on subtle differences in scale counts and anal-fin colouration. In contrast, mitochondrial DNA analyses based on cytochrome b gene sequences did not distinguish individuals of A. schlegelii and A. sivicolus, reflecting either historical introgression or recent speciation and incomplete sorting of their mitochondrial lineages. Phylogenetic relationships among these six north-west Pacific Ocean species of Acanthopagrus analysed using AFLP data were consistent with scale rows above the lateral line (TRac), sperm ultrastructure and geographical distribution. The study provides molecular tools for future research relevant to improved management of these resources, and an increased understanding of the evolutionary history of this radiation.
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Affiliation(s)
- T-H Hsu
- Department of Aquaculture, National Taiwan Ocean University, Keelung 20224, Taiwan
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Shaddick K, Burridge CP, Jerry DR, Schwartz TS, Truong K, Gilligan DM, Beheregaray LB. A hybrid zone and bidirectional introgression between two catadromous species: Australian bass Macquaria novemaculeata and estuary perch Macquaria colonorum. J Fish Biol 2011; 79:1214-1235. [PMID: 22026603 DOI: 10.1111/j.1095-8649.2011.03105.x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
The presence and distribution of hybrid individuals and the existence of a hybrid zone between the catadromous Australian bass Macquaria novemaculeata and estuary perch Macquaria colonorum were investigated throughout the range of both species in Australia. Bayesian analyses and genotypic simulations identified 140 putative hybrids (11·5% of the total sample) with varying levels of introgression. Most hybrids were observed in an area extending from the Snowy River to the Albert River suggesting a hybrid zone in the eastern Bass Strait region. Sixteen hybrids, however, were found outside this zone, possibly reflecting the movement of hybrid offspring between estuaries or their inadvertent release during fish stocking programmes. Biparental backcrossing was found to occur suggesting that hybrids were fertile. These results have implications for the management of the extensive stocking programme in M. novemaculeata and for understanding the potential role of habitat degradation and reduced water flow in facilitating hybridization in species with migratory life histories.
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Affiliation(s)
- K Shaddick
- Molecular Ecology Lab., Department of Biological Sciences, Macquarie University, Sydney, NSW 2109, Australia
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Hsu TH, Adiputra YT, Burridge CP, Gwo JC. Two spinefoot colour morphs: mottled spinefoot Siganus fuscescens and white-spotted spinefoot Siganus canaliculatus are synonyms. J Fish Biol 2011; 79:1350-1355. [PMID: 22026611 DOI: 10.1111/j.1095-8649.2011.03104.x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Mottled spinefoot Siganus fuscescens and white-spotted spinefoot Siganus canaliculatus are two similar species that differ subtly in colouration and morphology. Three major mtDNA clades were identified for these species, but individuals were clustered by amplified fragment length polymorphism (AFLP) according to geography rather than morphology, suggesting that the colour morphs are interbreeding.
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Affiliation(s)
- T-H Hsu
- Department of Aquaculture, National Taiwan Ocean University, Keelung 20224, Taiwan
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McDowall RM, Burridge CP. Erratum: Osteology and relationships of the southern freshwater lower euteleostean fishes. ZOOSYST EVOL 2011. [DOI: 10.1002/zoos.201190000] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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