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Mills KK, Hildebrandt KPB, Everson KM, Horstmann L, Misarti N, Olson LE. Ancient DNA indicates a century of overhunting did not reduce genetic diversity in Pacific Walruses (Odobenus rosmarus divergens). Sci Rep 2024; 14:8257. [PMID: 38589385 PMCID: PMC11001934 DOI: 10.1038/s41598-024-57414-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2023] [Accepted: 03/18/2024] [Indexed: 04/10/2024] Open
Abstract
Pacific Walruses (Odobenus rosmarus divergens [Illiger 1815]) are gregarious marine mammals considered to be sentinels of the Arctic because of their dependence on sea ice for feeding, molting, and parturition. Like many other marine mammal species, their population sizes were decimated by historical overhunting in the nineteenth and twentieth centuries. Although they have since been protected from nearly all commercial hunting pressure, they now face rapidly accelerating habitat loss as global warming reduces the extent of summer sea ice in the Arctic. To investigate how genetic variation was impacted by overhunting, we obtained mitochondrial DNA sequences from historic Pacific Walrus samples in Alaska that predate the period of overhunting, as well as from extant populations. We found that genetic variation was unchanged over this period, suggesting Pacific Walruses are resilient to genetic attrition in response to reduced population size, and that this may be related to their high vagility and lack of population structure. Although Pacific Walruses will almost certainly continue to decline in number as the planet warms and summer sea ice is further reduced, they may be less susceptible to the ratcheting effects of inbreeding that typically accompany shrinking populations.
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Affiliation(s)
- Kendall K Mills
- Department of Mammalogy, University of Alaska Museum, 1962 Yukon Drive, Fairbanks, AK, 99775, USA.
- Department of Biology and Wildlife, University of Alaska Fairbanks, Fairbanks, AK, 99775, USA.
| | - Kyndall P B Hildebrandt
- Department of Mammalogy, University of Alaska Museum, 1962 Yukon Drive, Fairbanks, AK, 99775, USA
| | - Kathryn M Everson
- Department of Mammalogy, University of Alaska Museum, 1962 Yukon Drive, Fairbanks, AK, 99775, USA
- Department of Integrative Biology, Oregon State University, 2701 SW Campus Way, Corvallis, OR, 97331, USA
| | - Lara Horstmann
- College of Fisheries and Ocean Sciences, University of Alaska Fairbanks, Fairbanks, AK, 99775, USA
| | - Nicole Misarti
- Water and Environmental Research Center, University of Alaska Fairbanks, Fairbanks, AK, 99775, USA
| | - Link E Olson
- Department of Mammalogy, University of Alaska Museum, 1962 Yukon Drive, Fairbanks, AK, 99775, USA
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Bender AN, Krause DJ, Goebel ME, Hoffman JI, Lewallen EA, Bonin CA. Genetic diversity and demographic history of the leopard seal: A Southern Ocean top predator. PLoS One 2023; 18:e0284640. [PMID: 37566609 PMCID: PMC10420386 DOI: 10.1371/journal.pone.0284640] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Accepted: 06/14/2023] [Indexed: 08/13/2023] Open
Abstract
Leopard seals (Hydrurga leptonyx) are top predators that can exert substantial top-down control of their Antarctic prey species. However, population trends and genetic diversity of leopard seals remain understudied, limiting our understanding of their ecological role. We investigated the genetic diversity, effective population size and demographic history of leopard seals to provide fundamental data that contextualizes their predatory influence on Antarctic ecosystems. Ninety leopard seals were sampled from the northern Antarctic Peninsula during the austral summers of 2008-2019 and a 405bp segment of the mitochondrial control region was sequenced for each individual. We uncovered moderate levels of nucleotide (π = 0.013) and haplotype (Hd = 0.96) diversity, and the effective population size was estimated at around 24,000 individuals (NE = 24,376; 95% CI: 16,876-33,126). Consistent with findings from other ice-breeding pinnipeds, Bayesian skyline analysis also revealed evidence for population expansion during the last glacial maximum, suggesting that historical population growth may have been boosted by an increase in the abundance of sea ice. Although leopard seals can be found in warmer, sub-Antarctic locations, the species' core habitat is centered on the Antarctic, making it inherently vulnerable to the loss of sea ice habitat due to climate change. Therefore, detailed assessments of past and present leopard seal population trends are needed to inform policies for Antarctic ecosystems.
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Affiliation(s)
- Arona N. Bender
- Marine and Environmental Sciences Department, Hampton University, Hampton, VA, United States of America
| | - Douglas J. Krause
- Antarctic Ecosystem Research Division, Southwest Fisheries Science Center, NOAA Fisheries, La Jolla, CA, United States of America
| | - Michael E. Goebel
- Ecology and Evolutionary Biology Department, University of California, Santa Cruz, Santa Cruz, CA, United States of America
| | - Joseph I. Hoffman
- Department of Animal Behaviour, University of Bielefeld, Bielefeld, Germany
- British Antarctic Survey, Cambridge, United Kingdom
| | - Eric A. Lewallen
- Department of Biological Sciences, Hampton University, Hampton, VA, United States of America
| | - Carolina A. Bonin
- Marine and Environmental Sciences Department, Hampton University, Hampton, VA, United States of America
- Department of Biological Sciences, Hampton University, Hampton, VA, United States of America
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Phylogeography of the Atlantic Blue Crab Callinectes sapidus (Brachyura: Portunidae) in the Americas versus the Mediterranean Sea: Determining Origins and Genetic Connectivity of a Large-Scale Invasion. BIOLOGY 2022; 12:biology12010035. [PMID: 36671728 PMCID: PMC9854962 DOI: 10.3390/biology12010035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Revised: 12/14/2022] [Accepted: 12/20/2022] [Indexed: 12/28/2022]
Abstract
The American blue crab Callinectes sapidus is a particularly successful invader in estuarine ecosystems worldwide. Despite increasing awareness of its potential harm, the invasion history and underlying genetic diversity of this species within the Mediterranean Sea remain unknown. This study constitutes the first large-scale approach to study phylogeographic patterns of C. sapidus in Europe, facilitated by the first comparison of all currently available COI sequence data. For this investigation, 71 individuals of C. sapidus were newly analyzed and the entire COI gene was sequenced and used for a comparative phylogeographic analyses. For the first time, two separately used adjacent regions of this gene were combined in a single dataset. This allowed emphasizing the prevalence of three geographically defined lineages within the native range: (1) eastern North America, including the Gulf of Mexico, (2) the Caribbean, and (3) Brazil. New data from the Mediterranean reveal that non-native populations of C. sapidus are characterized by a conspicuously low genetic diversity (except for Turkey, where stocking took place), and that there is surprisingly low connectivity among established populations. The occurrence of strong genetic bottlenecks suggests few founder individuals. This confirms that, even under a scenario of restricted large-scale gene flow, a very limited number of invasive individuals is sufficient for a massive impact.
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Intronic primers reveal unexpectedly high major histocompatibility complex diversity in Antarctic fur seals. Sci Rep 2022; 12:17933. [PMID: 36289307 PMCID: PMC9606363 DOI: 10.1038/s41598-022-21658-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Accepted: 09/29/2022] [Indexed: 01/20/2023] Open
Abstract
The major histocompatibility complex (MHC) is a group of genes comprising one of the most important components of the vertebrate immune system. Consequently, there has been much interest in characterising MHC variation and its relationship with fitness in a variety of species. Due to the exceptional polymorphism of MHC genes, careful PCR primer design is crucial for capturing all of the allelic variation present in a given species. We therefore developed intronic primers to amplify the full-length 267 bp protein-coding sequence of the MHC class II DQB exon 2 in the Antarctic fur seal. We then characterised patterns of MHC variation among mother-offspring pairs from two breeding colonies and detected 19 alleles among 771 clone sequences from 56 individuals. The distribution of alleles within and among individuals was consistent with a single-copy, classical DQB locus showing Mendelian inheritance. Amino acid similarity at the MHC was significantly associated with genome-wide relatedness, but no relationship was found between MHC heterozygosity and genome-wide heterozygosity. Finally, allelic diversity was several times higher than reported by a previous study based on partial exon sequences. This difference appears to be related to allele-specific amplification bias, implying that primer design can strongly impact the inference of MHC diversity.
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Hoffman JI, Chen RS, Vendrami DLJ, Paijmans AJ, Dasmahapatra KK, Forcada J. Demographic Reconstruction of Antarctic Fur Seals Supports the Krill Surplus Hypothesis. Genes (Basel) 2022; 13:541. [PMID: 35328094 PMCID: PMC8954904 DOI: 10.3390/genes13030541] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Accepted: 03/10/2022] [Indexed: 11/16/2022] Open
Abstract
Much debate surrounds the importance of top-down and bottom-up effects in the Southern Ocean, where the harvesting of over two million whales in the mid twentieth century is thought to have produced a massive surplus of Antarctic krill. This excess of krill may have allowed populations of other predators, such as seals and penguins, to increase, a top-down hypothesis known as the 'krill surplus hypothesis'. However, a lack of pre-whaling population baselines has made it challenging to investigate historical changes in the abundance of the major krill predators in relation to whaling. Therefore, we used reduced representation sequencing and a coalescent-based maximum composite likelihood approach to reconstruct the recent demographic history of the Antarctic fur seal, a pinniped that was hunted to the brink of extinction by 18th and 19th century sealers. In line with the known history of this species, we found support for a demographic model that included a substantial reduction in population size around the time period of sealing. Furthermore, maximum likelihood estimates from this model suggest that the recovered, post-sealing population at South Georgia may have been around two times larger than the pre-sealing population. Our findings lend support to the krill surplus hypothesis and illustrate the potential of genomic approaches to shed light on long-standing questions in population biology.
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Affiliation(s)
- Joseph I. Hoffman
- Department of Animal Behavior, University of Bielefeld, P.O. BOX 100131, 33615 Bielefeld, Germany; (R.S.C.); (D.L.J.V.); (A.J.P.)
- British Antarctic Survey, High Cross, Madingley Road, Cambridge CB3 OET, UK;
| | - Rebecca S. Chen
- Department of Animal Behavior, University of Bielefeld, P.O. BOX 100131, 33615 Bielefeld, Germany; (R.S.C.); (D.L.J.V.); (A.J.P.)
| | - David L. J. Vendrami
- Department of Animal Behavior, University of Bielefeld, P.O. BOX 100131, 33615 Bielefeld, Germany; (R.S.C.); (D.L.J.V.); (A.J.P.)
| | - Anna J. Paijmans
- Department of Animal Behavior, University of Bielefeld, P.O. BOX 100131, 33615 Bielefeld, Germany; (R.S.C.); (D.L.J.V.); (A.J.P.)
| | | | - Jaume Forcada
- British Antarctic Survey, High Cross, Madingley Road, Cambridge CB3 OET, UK;
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Weinberger CS, Vianna JA, Faugeron S, Marquet PA. Inferring the impact of past climate changes and hunting on the South American sea lion. DIVERS DISTRIB 2021. [DOI: 10.1111/ddi.13421] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Affiliation(s)
- Constanza S. Weinberger
- Departamento de Ecología Facultad de Ciencias Biológicas Pontificia Universidad Católica de Chile Santiago Chile
| | - Juliana A. Vianna
- Departamento de Ecosistemas y Medio Ambiente Facultad de Agronomía e Ingeniería Forestal Pontifícia Universidad Católica de Chile Santiago Chile
- Centro Cambio Global UC Pontificia Universidad Católica de Chile Santiago Chile
| | - Sylvain Faugeron
- Departamento de Ecología Facultad de Ciencias Biológicas Pontificia Universidad Católica de Chile Santiago Chile
- IRL3614 Evolutionary Biology and Ecology of Algae CNRS Sorbonne Université Pontificia Universidad Católica de ChileUniversidad Austral de ChileStation Biologique Roscoff France
| | - Pablo A. Marquet
- Departamento de Ecología Facultad de Ciencias Biológicas Pontificia Universidad Católica de Chile Santiago Chile
- Centro Cambio Global UC Pontificia Universidad Católica de Chile Santiago Chile
- Instituto de Ecología y Biodiversidad (IEB) Santiago Chile
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Peralta DM, Cappozzo HL, Ibañez EA, Lucero S, Failla M, Túnez JI. Phylogeography of Otaria flavescens (Carnivora: Pinnipedia): unravelling genetic connectivity at the southernmost limit of its distribution. Biol J Linn Soc Lond 2021. [DOI: 10.1093/biolinnean/blab053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Abstract
The Pleistocene glacial period shaped the current genetic structure of numerous species. The last glacial dynamics has been proposed to have split the South American sea lion, Otaria flavescens, into two Evolutionarily Significant Units (ESUs), one on each side of the continent. However, previous studies have not provided genetic information on colonies found along 3000 km of coastline of the southernmost limit of the species distribution, where gene flow could occur. We conducted an exhaustive phylogeographical analysis of O. flavescens using a mtDNA marker, including, for the first time, data from colonies living south of latitude 45° S, in the Argentinian provinces of Santa Cruz and Tierra del Fuego. Our results indicated the presence of five Conservation Units across the distribution range of O. flavescens and suggest that the Patagonian population must have expanded about 150 000 BP. We found evidence for gene flow across the entire species range, supporting a scenario of secondary contact in Tierra del Fuego where representatives of the oldest lineages coexist. The presence of gene flow between oceans leads us to reject the assumption of complete reciprocal monophyly for mtDNA between the presumed ESUs, suggesting that the species constitutes a single Evolutionarily Significant Unit.
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Affiliation(s)
- Diego M Peralta
- Grupo de Investigación en Ecología Molecular, Instituto de Ecología y Desarrollo Sustentable (INEDES-CONICET-CIC-UNLu), Luján, Buenos Aires, Argentina
- Laboratorio de Ecología, Comportamiento y Mamíferos Marinos, Museo Argentino de Ciencias Naturales “Bernardino Rivadavia” (MACN-CONICET), CABA, Buenos Aires, Argentina
| | - Humberto L Cappozzo
- Laboratorio de Ecología, Comportamiento y Mamíferos Marinos, Museo Argentino de Ciencias Naturales “Bernardino Rivadavia” (MACN-CONICET), CABA, Buenos Aires, Argentina
| | - Ezequiel A Ibañez
- Grupo de Investigación en Ecología Molecular, Instituto de Ecología y Desarrollo Sustentable (INEDES-CONICET-CIC-UNLu), Luján, Buenos Aires, Argentina
- Departamento de Ciencias Básicas, Universidad Nacional de Luján, Luján, Buenos Aires, Argentina
| | - Sergio Lucero
- División Mastozoología, Museo Argentino de Ciencias Naturales “Bernardino Rivadavia” (MACN-CONICET), CABA, Buenos Aires, Argentina
| | | | - Juan I Túnez
- Grupo de Investigación en Ecología Molecular, Instituto de Ecología y Desarrollo Sustentable (INEDES-CONICET-CIC-UNLu), Luján, Buenos Aires, Argentina
- Departamento de Ciencias Básicas, Universidad Nacional de Luján, Luján, Buenos Aires, Argentina
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Grant SM, Waller CL, Morley SA, Barnes DKA, Brasier MJ, Double MC, Griffiths HJ, Hughes KA, Jackson JA, Waluda CM, Constable AJ. Local Drivers of Change in Southern Ocean Ecosystems: Human Activities and Policy Implications. Front Ecol Evol 2021. [DOI: 10.3389/fevo.2021.624518] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Local drivers are human activities or processes that occur in specific locations, and cause physical or ecological change at the local or regional scale. Here, we consider marine and land-derived pollution, non-indigenous species, tourism and other human visits, exploitation of marine resources, recovery of marine mammals, and coastal change as a result of ice loss, in terms of their historic and current extent, and their interactions with the Southern Ocean environment. We summarise projected increases or decreases in the influence of local drivers, and projected changes to their geographic range, concluding that the influence of non-indigenous species, fishing, and the recovery of marine mammals are predicted to increase in the future across the Southern Ocean. Local drivers can be managed regionally, and we identify existing governance frameworks as part of the Antarctic Treaty System and other instruments which may be employed to mitigate or limit their impacts on Southern Ocean ecosystems.
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Taboun ZS, Walter RP, Ovenden JR, Heath DD. Spatial and temporal genetic variation in an exploited reef fish: The effects of exploitation on cohort genetic structure. Evol Appl 2021; 14:1286-1300. [PMID: 34025768 PMCID: PMC8127707 DOI: 10.1111/eva.13198] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2020] [Revised: 01/05/2021] [Accepted: 01/06/2021] [Indexed: 12/01/2022] Open
Abstract
Many coral reef fishes are fished, often resulting in detrimental genetic effects; however, reef fishes often show unpredictable patterns of genetic variation, which potentially mask the effects of fishing. Our goals were to characterize spatial and temporal genetic variation and determine the effects of fishing on an exploited reef fish, Plectropomus leopardus, Lacepède (the common coral trout). To determine population structure, we genotyped 417 Great Barrier Reef coral trout from four populations sampled in 2 years (1996 and 2004) at nine microsatellite loci. To test for exploitation effects, we additionally genotyped 869 individuals from a single cohort (ages 3-5) across eight different reefs, including fished and control populations. Genetic structure differed substantially in the two sampled years, with only 1 year exhibiting isolation by distance. Thus, genetic drift likely plays a role in shaping population genetic structure in this species. Although we found no loss of genetic diversity associated with exploitation, our relatedness patterns show that pulse fishing likely affects population genetics. Additionally, genetic structure in the cohort samples likely reflected spatial variation in recruitment contributing to genetic structure at the population level. Overall, we show that fishing does impact coral reef fishes, highlighting the importance of repeated widespread sampling to accurately characterize the genetic structure of reef fishes, as well as the power of analysing cohorts to avoid the impacts of recruitment-related genetic swamping. The high temporal and spatial variability in genetic structure, combined with possible selection effects, will make conservation/management of reef fish species complex.
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Affiliation(s)
- Zahra S. Taboun
- Great Lakes Institute for Environmental Research (GLIER)University of WindsorWindsorOntarioCanada
| | - Ryan P. Walter
- Department of Biological ScienceCalifornia State University, FullertonFullertonCAUSA
| | - Jennifer R. Ovenden
- Molecular Fisheries LaboratorySchool of Biomedical SciencesUniversity of QueenslandBrisbaneQueenslandAustralia
| | - Daniel D. Heath
- Great Lakes Institute for Environmental Research (GLIER)University of WindsorWindsorOntarioCanada
- Department of Integrative BiologyUniversity of WindsorWindsorOntarioCanada
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Bamford CCG, Warwick-Evans V, Staniland IJ, Jackson JA, Trathan PN. Wintertime overlaps between female Antarctic fur seals (Arctocephalus gazella) and the krill fishery at South Georgia, South Atlantic. PLoS One 2021; 16:e0248071. [PMID: 33662029 PMCID: PMC7932113 DOI: 10.1371/journal.pone.0248071] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Accepted: 02/18/2021] [Indexed: 11/24/2022] Open
Abstract
The diet of Antarctic fur seals (Arctocephalus gazella) at South Georgia is dominated by Antarctic krill (Euphausia superba). During the breeding season, foraging trips by lactating female fur seals are constrained by their need to return to land to provision their pups. Post-breeding, seals disperse in order to feed and recover condition; estimates indicate c.70% of females remain near to South Georgia, whilst others head west towards the Patagonian Shelf or south to the ice-edge. The krill fishery at South Georgia operates only during the winter, providing the potential for fur seal: fishery interaction during these months. Here we use available winter (May to September) tracking data from Platform Terminal Transmitter (PTT) tags deployed on female fur seals at Bird Island, South Georgia. We develop habitat models describing their distribution during the winters of 1999 and 2003 with the aim of visualising and quantifying the degree of spatial overlap between female fur seals and krill harvesting in South Georgia waters. We show that spatial distribution of fur seals around South Georgia is extensive, and that the krill fishery overlaps with small, highly localised areas of available fur seal habitat. From these findings we discuss the implications for management, and future work.
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Affiliation(s)
- Connor C. G. Bamford
- British Antarctic Survey, High Cross, Cambridge, United Kingdom
- University of Southampton, Southampton, United Kingdom
| | | | - Iain J. Staniland
- British Antarctic Survey, High Cross, Cambridge, United Kingdom
- International Whaling Commission, The Red House, Impington, Cambridge, United Kingdom
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Jackson JA, Kennedy A, Moore M, Andriolo A, Bamford CCG, Calderan S, Cheeseman T, Gittins G, Groch K, Kelly N, Leaper R, Leslie MS, Lurcock S, Miller BS, Richardson J, Rowntree V, Smith P, Stepien E, Stowasser G, Trathan P, Vermeulen E, Zerbini AN, Carroll EL. Have whales returned to a historical hotspot of industrial whaling? The pattern of southern right whale Eubalaena australis recovery at South Georgia. ENDANGER SPECIES RES 2020. [DOI: 10.3354/esr01072] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Around 176500 whales were killed in the sub-Antarctic waters off South Georgia (South Atlantic) between 1904 and 1965. In recent decades, whales have once again become summer visitors, with the southern right whale (SRW) the most commonly reported species until 2011. Here, we assess the distribution, temporal pattern, health status and likely prey of SRWs in these waters, combining observations from a summertime vessel-based expedition to South Georgia, stable isotope data collected from SRWs and putative prey and sightings reports collated by the South Georgia Museum. The expedition used directional acoustics and visual surveys to localise whales and collected skin biopsies and photo-IDs. During 76 h of visual observation effort over 19 expedition days, SRWs were encountered 15 times (~31 individuals). Photo-IDs, combined with publicly contributed images from commercial vessels, were reconciled and quality-controlled to form a catalogue of 6 fully (i.e. both sides) identified SRWs and 26 SRWs identified by either left or right sides. No photo-ID matches were found with lower-latitude calving grounds, but 3 whales had gull lesions supporting a direct link with Península Valdés, Argentina. The isotopic position of SRWs in the South Georgia food web suggests feeding on a combination of copepod and krill species. Opportunistic reports of SRW sightings and associated group sizes remain steady over time, while humpback whales provide a strong contrast, with increased sighting rates and group sizes seen since 2013. These data suggest a plateau in SRWs and an increasing humpback whale presence in South Georgia waters following the cessation of whaling.
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Affiliation(s)
- JA Jackson
- British Antarctic Survey, High Cross, Cambridge CB3 0ET, UK For a full list of affiliations see Supplement 1 at www.int-res.com/articles/suppl/n043p323_supp1.pdf
| | | | | | | | - CCG Bamford
- British Antarctic Survey, High Cross, Cambridge CB3 0ET, UK For a full list of affiliations see Supplement 1 at www.int-res.com/articles/suppl/n043p323_supp1.pdf
| | | | | | | | | | | | | | | | | | | | | | | | | | | | - G Stowasser
- British Antarctic Survey, High Cross, Cambridge CB3 0ET, UK For a full list of affiliations see Supplement 1 at www.int-res.com/articles/suppl/n043p323_supp1.pdf
| | - P Trathan
- British Antarctic Survey, High Cross, Cambridge CB3 0ET, UK For a full list of affiliations see Supplement 1 at www.int-res.com/articles/suppl/n043p323_supp1.pdf
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12
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Bestley S, Ropert-Coudert Y, Bengtson Nash S, Brooks CM, Cotté C, Dewar M, Friedlaender AS, Jackson JA, Labrousse S, Lowther AD, McMahon CR, Phillips RA, Pistorius P, Puskic PS, Reis AODA, Reisinger RR, Santos M, Tarszisz E, Tixier P, Trathan PN, Wege M, Wienecke B. Marine Ecosystem Assessment for the Southern Ocean: Birds and Marine Mammals in a Changing Climate. Front Ecol Evol 2020. [DOI: 10.3389/fevo.2020.566936] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
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An 85K SNP Array Uncovers Inbreeding and Cryptic Relatedness in an Antarctic Fur Seal Breeding Colony. G3-GENES GENOMES GENETICS 2020; 10:2787-2799. [PMID: 32540866 PMCID: PMC7407454 DOI: 10.1534/g3.120.401268] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
High density single nucleotide polymorphism (SNP) arrays allow large numbers of individuals to be rapidly and cost-effectively genotyped at large numbers of genetic markers. However, despite being widely used in studies of humans and domesticated plants and animals, SNP arrays are lacking for most wild organisms. We developed a custom 85K Affymetrix Axiom array for an intensively studied pinniped, the Antarctic fur seal (Arctocephalus gazella). SNPs were discovered from a combination of genomic and transcriptomic resources and filtered according to strict criteria. Out of a total of 85,359 SNPs tiled on the array, 75,601 (88.6%) successfully converted and were polymorphic in 270 animals from a breeding colony at Bird Island in South Georgia. Evidence was found for inbreeding, with three genomic inbreeding coefficients being strongly intercorrelated and the proportion of the genome in runs of homozygosity being non-zero in all individuals. Furthermore, analysis of genomic relatedness coefficients identified previously unknown first-degree relatives and multiple second-degree relatives among a sample of ostensibly unrelated individuals. Such “cryptic relatedness” within fur seal breeding colonies may increase the likelihood of consanguineous matings and could therefore have implications for understanding fitness variation and mate choice. Finally, we demonstrate the cross-amplification potential of the array in three related pinniped species. Overall, our SNP array will facilitate future studies of Antarctic fur seals and has the potential to serve as a more general resource for the wider pinniped research community.
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Antarctic fur seal (Arctocephalus gazella) annual migration and temporal patterns of on-shore occurrence of leucistic individuals on King George Island. Polar Biol 2020. [DOI: 10.1007/s00300-020-02694-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
AbstractNon-invasive tracking the on-shore occurrence of the atypically pigmented animals and determination of land residency duration of leucistic seals would help us find out more about the rotation of the migrating population. During seven austral summer seasons (2011–2018), by counting the animals every 10 days at the Cape Lions Rump shore, King George Island, South Shetlands, in the Antarctic Specially Protected Area No. 151 and the adjacent ice-free land (31.52 km2) we registered fourteen leucistic individuals per a total of 43,919 animals. Moreover, daily monitoring of local fauna resulted in further 33 leucistic animals (together 47, in all seasons). Whilst the results of 10-day censuses of the total population were similar inter-seasonally, a tendency for increased occurrence of leucistic individuals in successive seasons was revealed. Generally, the number of animals increased significantly as season progressed. Since leucistic individuals stayed on-shore for 1–2 days usually, it can be hypothesised that the observation of migrating Antarctic fur seals every 3 days does not involve the same individuals. Also, additional every 5-day censuses taken in one season in ASPA 151 resulted in a higher seasonal number of animals, which proves that more frequent counts help us estimate population abundance more efficiently. Thus, every 5-day counts are proposed as a feasible and justified method of population monitoring.
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15
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Paijmans AJ, Stoffel MA, Bester MN, Cleary AC, De Bruyn PJN, Forcada J, Goebel ME, Goldsworthy SD, Guinet C, Lydersen C, Kovacs KM, Lowther A, Hoffman JI. The genetic legacy of extreme exploitation in a polar vertebrate. Sci Rep 2020; 10:5089. [PMID: 32198403 PMCID: PMC7083876 DOI: 10.1038/s41598-020-61560-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Accepted: 01/24/2020] [Indexed: 12/12/2022] Open
Abstract
Understanding the effects of human exploitation on the genetic composition of wild populations is important for predicting species persistence and adaptive potential. We therefore investigated the genetic legacy of large-scale commercial harvesting by reconstructing, on a global scale, the recent demographic history of the Antarctic fur seal (Arctocephalus gazella), a species that was hunted to the brink of extinction by 18th and 19th century sealers. Molecular genetic data from over 2,000 individuals sampled from all eight major breeding locations across the species' circumpolar geographic distribution, show that at least four relict populations around Antarctica survived commercial hunting. Coalescent simulations suggest that all of these populations experienced severe bottlenecks down to effective population sizes of around 150-200. Nevertheless, comparably high levels of neutral genetic variability were retained as these declines are unlikely to have been strong enough to deplete allelic richness by more than around 15%. These findings suggest that even dramatic short-term declines need not necessarily result in major losses of diversity, and explain the apparent contradiction between the high genetic diversity of this species and its extreme exploitation history.
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Affiliation(s)
- Anneke J Paijmans
- Department of Animal Behaviour, Bielefeld University, 33501, Bielefeld, Germany.
| | - Martin A Stoffel
- Department of Animal Behaviour, Bielefeld University, 33501, Bielefeld, Germany
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, EH9 3FL, United Kingdom
| | - Marthán N Bester
- Department of Zoology and Entomology, Mammal Research Institute, University of Pretoria, Private Bag X20, Hatfield, 0028, South Africa
| | - Alison C Cleary
- Norwegian Polar Institute, Fram Centre, 9296, Tromsø, Norway
- Department of Natural Sciences, University of Agder, 4630, Kristiansand, Norway
| | - P J Nico De Bruyn
- Department of Zoology and Entomology, Mammal Research Institute, University of Pretoria, Private Bag X20, Hatfield, 0028, South Africa
| | - Jaume Forcada
- British Antarctic Survey, High Cross, Madingley Road, Cambridge, CB3 OET, UK
| | - Michael E Goebel
- Antarctic Ecosystem Research Division, Southwest Fisheries Science Center, National Marine Fisheries, National Oceanographic and Atmospheric Administration, 8901 La Jolla Shores Drive, La Jolla, CA, 92037, USA
- Institute of Marine Science, University of California Santa Cruz, 1156 High Street, Santa Cruz, CA, 95064, USA
| | - Simon D Goldsworthy
- South Australian Research and Development Institute, 2 Hamra Avenue, West Beach, South Australia, 5024, Australia
- School of Biological Sciences, The University of Adelaide, Adelaide, South Australia, 5005, Australia
| | - Christophe Guinet
- Centre d'Etudes Biologiques de Chizé (CEBC), CNRS and Université de La Rochelle - UMR 7372, 79360, Villiers en Bois, France
| | | | - Kit M Kovacs
- Norwegian Polar Institute, Fram Centre, 9296, Tromsø, Norway
| | - Andrew Lowther
- Norwegian Polar Institute, Fram Centre, 9296, Tromsø, Norway
| | - Joseph I Hoffman
- Department of Animal Behaviour, Bielefeld University, 33501, Bielefeld, Germany.
- British Antarctic Survey, High Cross, Madingley Road, Cambridge, CB3 OET, UK.
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16
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Foley CM, Lynch HJ. A method to estimate pre-exploitation population size. CONSERVATION BIOLOGY : THE JOURNAL OF THE SOCIETY FOR CONSERVATION BIOLOGY 2020; 34:256-265. [PMID: 31460682 DOI: 10.1111/cobi.13416] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Revised: 03/15/2019] [Accepted: 07/03/2019] [Indexed: 06/10/2023]
Abstract
Antarctic fur seals (Arctocephalus gazella) were commercially exploited on the subantarctic island of South Georgia for over 100 years and nearly driven to extinction. Since the cessation of harvesting, however, their populations have rebounded, and they are now often considered a nuisance species whose impact on the terrestrial landscape should be mitigated. Any evaluation of their current population requires the context provided by their historic, pre-exploitation abundance, lest ecologists fall prey to shifting baseline syndrome in which their perspective on current abundance is compared only with an altered state resulting from past anthropogenic disturbance. Estimating pre-exploitation abundance is critical to defining species recovery and setting recovery targets, both of which are needed for the International Union for the Conservation of Nature's recent efforts to develop a green list of recovering species. To address this issue, we reconstructed the South Georgia fur seal harvest from 1786 to 1908 from ship logbooks and other historical records and interpolated missing harvest data as necessary with a generalized linear model fit to the historical record. Using an approximate Bayesian computation framework, harvest data, and a stochastic age-structured population model, we estimated the pre-exploitation abundance of Antarctic fur seals on South Georgia was 2.5 million females (95% CI 1.5-3.5 million). This estimate is similar to recent abundance estimates, and suggests current populations, and the ecological consequences of so many fur seals on the island, may be similar to conditions prior to human harvest. Although the historic archive on the fur sealing era is unavoidably patchy, the use of archival records is essential for reconstructing the past and, correspondingly, to understanding the present. Article impact statement: Defining species recovery requires an understanding of baseline population state, which can be estimated through statistical methods.
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Affiliation(s)
- Catherine M Foley
- Hawai'i Institute of Marine Biology, University of Hawai'i at Mānoa, P.O. Box 1346, Kāne'ohe, HI 96744, USA
| | - Heather J Lynch
- Department of Ecology and Evolution, Stony Brook University, 650 Life Sciences Building, Stony Brook, NY, 11794, U.S.A
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17
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Nagel R, Forcada J, Hoffman JI. Complete mitochondrial genome of the Antarctic fur seal ( Arctocephalus gazella). Mitochondrial DNA B Resour 2019; 4:2936-2937. [PMID: 33365800 PMCID: PMC7706844 DOI: 10.1080/23802359.2019.1662751] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
The Antarctic fur seal (Arctocephalus gazella) is an abundant Antarctic otariid. Here, we present the complete mitochondrial DNA sequence of this species, which includes 13 protein-coding genes, 22 transfer RNA genes, 2 ribosomal RNA genes, and the control region for a total length of 16,156 bp. A phylogenetic analysis including all 25 publically available pinniped mitogenomes nested the Antarctic fur seal within the Otariid clade, which was clearly resolved from the Phocidae and Odobenidae.
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Affiliation(s)
- Rebecca Nagel
- Department of Animal Behaviour, Bielefeld University, Bielefeld, Germany
| | | | - Joseph I Hoffman
- Department of Animal Behaviour, Bielefeld University, Bielefeld, Germany.,British Antarctic Survey, Cambridge, UK
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18
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Iwahori A, Kitamura JI, Kawamura K. Genetic Characteristics of the Japanese Serow Capricornis crispus in the Kii Mountain Range, Central Japan. Zoolog Sci 2019; 36:306-315. [PMID: 34664901 DOI: 10.2108/zs180187] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2018] [Accepted: 02/28/2019] [Indexed: 11/17/2022]
Abstract
The Japanese serow, Capricornis crispus, is an indigenous bovid species exclusively inhabiting mountain regions in the main Japanese islands, excepting Hokkaido. It had decreased in abundance to its lowest level due to overhunting and deforestation, with its distribution severely fragmented from the middle of the 20th century, many populations of C. crispus currently facing the risk of extinction. The Kii Mountain Range (KM) on Honshu is one such location that has seen a drastic population decline of C. crispus. In this study, we examined genetic characteristics of C. crispus in KM and neighboring regions of the Chubu district, using mtDNA and microsatellite markers, in order to devise strategies for its conservation. Results for mtDNA were characterized by low nucleotide diversity with five endemic and two dominant haplotypes shared by individuals in neighboring regions. A Bayesian skyline plot indicated a gradual increase after the last glacial maximum. For microsatellites, the genetic diversity of C. crispus in KM was comparable to Shizuoka and higher than Shikoku. Recent genetic bottlenecks were strongly suggested in C. crispus in KM. Bayesian clustering showed a genetic cline between KM and neighboring regions, where multivariate analysis suggested three local populations. A Mantel test indicated male-biased dispersal. These results indicate that C. crispus in KM and neighboring regions constitute multiple local populations, connected through restricted gene flow. For the conservation of C. crispus, it is important to define small-scale conservation units, among which genetic connectivity should be facilitated to prevent further loss of genetic diversity.
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Affiliation(s)
- Arisa Iwahori
- Faculty of Bioresources, Mie University, Tsu, Mie 514-8507, Japan
| | | | - Kouichi Kawamura
- Faculty of Bioresources, Mie University, Tsu, Mie 514-8507, Japan,
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19
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Pirog A, Jaquemet S, Ravigné V, Cliff G, Clua E, Holmes BJ, Hussey NE, Nevill JEG, Temple AJ, Berggren P, Vigliola L, Magalon H. Genetic population structure and demography of an apex predator, the tiger shark Galeocerdo cuvier. Ecol Evol 2019; 9:5551-5571. [PMID: 31160982 PMCID: PMC6540675 DOI: 10.1002/ece3.5111] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Revised: 01/20/2019] [Accepted: 02/26/2019] [Indexed: 12/16/2022] Open
Abstract
Population genetics has been increasingly applied to study large sharks over the last decade. Whilst large shark species are often difficult to study with direct methods, improved knowledge is needed for both population management and conservation, especially for species vulnerable to anthropogenic and climatic impacts. The tiger shark, Galeocerdo cuvier, is an apex predator known to play important direct and indirect roles in tropical and subtropical marine ecosystems. While the global and Indo-West Pacific population genetic structure of this species has recently been investigated, questions remain over population structure and demographic history within the western Indian (WIO) and within the western Pacific Oceans (WPO). To address the knowledge gap in tiger shark regional population structures, the genetic diversity of 286 individuals sampled in seven localities was investigated using 27 microsatellite loci and three mitochondrial genes (CR,COI, and cytb). A weak genetic differentiation was observed between the WIO and the WPO, suggesting high genetic connectivity. This result agrees with previous studies and highlights the importance of the pelagic behavior of this species to ensure gene flow. Using approximate Bayesian computation to couple information from both nuclear and mitochondrial markers, evidence of a recent bottleneck in the Holocene (2,000-3,000 years ago) was found, which is the most probable cause for the low genetic diversity observed. A contemporary effective population size as low as 111 [43,369] was estimated during the bottleneck. Together, these results indicate low genetic diversity that may reflect a vulnerable population sensitive to regional pressures. Conservation measures are thus needed to protect a species that is classified as Near Threatened.
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Affiliation(s)
- Agathe Pirog
- UMR ENTROPIE (Université de La Réunion/IRD/CNRS)Université de La RéunionSaint Denis, La RéunionFrance
| | - Sébastien Jaquemet
- UMR ENTROPIE (Université de La Réunion/IRD/CNRS)Université de La RéunionSaint Denis, La RéunionFrance
| | | | - Geremy Cliff
- KwaZulu‐Natal Sharks BoardUmhlanga RocksSouth Africa
- School of Life SciencesUniversity of KwaZulu‐NatalDurbanSouth Africa
| | - Eric Clua
- EPHE‐CNRS‐UPVDCNRS UPVDUSR 3278 CRIOBEPSL Research UniversityPerpignanFrance
- Laboratoire d'Excellence CORAILPerpignanFrance
| | - Bonnie J. Holmes
- School of Biological SciencesUniversity of Queensland, St LuciaBrisbaneQueenslandAustralia
| | - Nigel E. Hussey
- Biological SciencesUniversity of WindsorWindsorOntarioCanada
| | | | - Andrew J. Temple
- School of Natural and Environmental SciencesNewcastle UniversityNewcastle‐upon‐TyneUK
| | - Per Berggren
- School of Natural and Environmental SciencesNewcastle UniversityNewcastle‐upon‐TyneUK
| | - Laurent Vigliola
- Laboratoire d'Excellence CORAILPerpignanFrance
- UMR ENTROPIE (Université de La Réunion/IRD/CNRS)Institut de Recherche pour le DéveloppementNouméaNouvelle CalédonieFrance
| | - Hélène Magalon
- UMR ENTROPIE (Université de La Réunion/IRD/CNRS)Université de La RéunionSaint Denis, La RéunionFrance
- Laboratoire d'Excellence CORAILPerpignanFrance
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20
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Sovic M, Fries A, Martin SA, Lisle Gibbs H. Genetic signatures of small effective population sizes and demographic declines in an endangered rattlesnake, Sistrurus catenatus. Evol Appl 2019; 12:664-678. [PMID: 30976301 PMCID: PMC6439488 DOI: 10.1111/eva.12731] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2018] [Revised: 09/28/2018] [Accepted: 10/01/2018] [Indexed: 12/15/2022] Open
Abstract
Endangered species that exist in small isolated populations are at elevated risk of losing adaptive variation due to genetic drift. Analyses that estimate short-term effective population sizes, characterize historical demographic processes, and project the trajectory of genetic variation into the future are useful for predicting how levels of genetic diversity may change. Here, we use data from two independent types of genetic markers (single nucleotide polymorphisms [SNPs] and microsatellites) to evaluate genetic diversity in 17 populations spanning the geographic range of the endangered eastern massasauga rattlesnake (Sistrurus catenatus). First, we use SNP data to confirm previous reports that these populations exhibit high levels of genetic structure (overall Fst = 0.25). Second, we show that most populations have contemporary Ne estimates <50. Heterozygosity-fitness correlations in these populations provided no evidence for a genetic cost to living in small populations, though these tests may lack power. Third, model-based demographic analyses of individual populations indicate that all have experienced declines, with the onset of many of these declines occurring over timescales consistent with anthropogenic impacts (<200 years). Finally, forward simulations of the expected loss of variation in relatively large (Ne = 50) and small (Ne = 10) populations indicate they will lose a substantial amount of their current standing neutral variation (63% and 99%, respectively) over the next 100 years. Our results argue that drift has a significant and increasing impact on levels of genetic variation in isolated populations of this snake, and efforts to assess and mitigate associated impacts on adaptive variation should be components of the management of this endangered reptile.
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Affiliation(s)
- Michael Sovic
- Department of Evolution, Ecology and Organismal Biology and Ohio Biodiversity Conservation PartnershipThe Ohio State UniversityColumbusOhio
- Present address:
College of PharmacyThe Ohio State UniversityColumbusOhio
| | - Anthony Fries
- Department of Evolution, Ecology and Organismal Biology and Ohio Biodiversity Conservation PartnershipThe Ohio State UniversityColumbusOhio
- United States Air Force School of Aerospace MedicineWright‐Patterson AFBColumbusOhio
| | - Scott A. Martin
- Department of Evolution, Ecology and Organismal Biology and Ohio Biodiversity Conservation PartnershipThe Ohio State UniversityColumbusOhio
| | - H. Lisle Gibbs
- Department of Evolution, Ecology and Organismal Biology and Ohio Biodiversity Conservation PartnershipThe Ohio State UniversityColumbusOhio
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21
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Japaud A, Bouchon C, Magalon H, Fauvelot C. Geographic distances and ocean currents influence Caribbean Acropora palmata population connectivity in the Lesser Antilles. CONSERV GENET 2019. [DOI: 10.1007/s10592-019-01145-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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22
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Stoffel MA, Humble E, Paijmans AJ, Acevedo-Whitehouse K, Chilvers BL, Dickerson B, Galimberti F, Gemmell NJ, Goldsworthy SD, Nichols HJ, Krüger O, Negro S, Osborne A, Pastor T, Robertson BC, Sanvito S, Schultz JK, Shafer ABA, Wolf JBW, Hoffman JI. Demographic histories and genetic diversity across pinnipeds are shaped by human exploitation, ecology and life-history. Nat Commun 2018; 9:4836. [PMID: 30446730 PMCID: PMC6240053 DOI: 10.1038/s41467-018-06695-z] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2018] [Accepted: 09/18/2018] [Indexed: 12/22/2022] Open
Abstract
A central paradigm in conservation biology is that population bottlenecks reduce genetic diversity and population viability. In an era of biodiversity loss and climate change, understanding the determinants and consequences of bottlenecks is therefore an important challenge. However, as most studies focus on single species, the multitude of potential drivers and the consequences of bottlenecks remain elusive. Here, we combined genetic data from over 11,000 individuals of 30 pinniped species with demographic, ecological and life history data to evaluate the consequences of commercial exploitation by 18th and 19th century sealers. We show that around one third of these species exhibit strong signatures of recent population declines. Bottleneck strength is associated with breeding habitat and mating system variation, and together with global abundance explains much of the variation in genetic diversity across species. Overall, bottleneck intensity is unrelated to IUCN status, although the three most heavily bottlenecked species are endangered. Our study reveals an unforeseen interplay between human exploitation, animal biology, demographic declines and genetic diversity. Historical hunting has caused documented declines in pinnipeds, but the extent to which hunting caused genetic bottlenecks among species was unknown. Here, the authors show evidence of severe bottlenecks in several pinniped species, particularly those that breed on land.
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Affiliation(s)
- M A Stoffel
- Department of Animal Behaviour, Bielefeld University, Postfach 100131, 33501, Bielefeld, Germany.,School of Natural Sciences and Psychology, Faculty of Science, Liverpool John Moores University, Liverpool, L3 3AF, UK
| | - E Humble
- Department of Animal Behaviour, Bielefeld University, Postfach 100131, 33501, Bielefeld, Germany.,British Antarctic Survey, High Cross, Madingley Road, Cambridge, CB3 OET, UK
| | - A J Paijmans
- Department of Animal Behaviour, Bielefeld University, Postfach 100131, 33501, Bielefeld, Germany
| | - K Acevedo-Whitehouse
- Unit for Basic and Applied Microbiology, School of Natural Sciences, Autonomous University of Queretaro, Avenida de las Ciencias S/N, Queretaro, 76230, Mexico
| | - B L Chilvers
- Wildbase, Institute of Veterinary, Animal and Biomedical Science, Massey University, Private Bag 11222, Palmerston North, 4442, New Zealand
| | - B Dickerson
- National Marine Mammal Laboratory, Alaska Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, Seattle, 98115, WA, USA
| | - F Galimberti
- Elephant Seal Research Group, Sea Lion Island, FIQQ 1ZZ, Falkland Islands
| | - N J Gemmell
- Department of Anatomy, University of Otago, PO Box 56, Dunedin, 9054, New Zealand
| | - S D Goldsworthy
- South Australian Research and Development Institute, West Beach, SA, 5024, Australia
| | - H J Nichols
- School of Natural Sciences and Psychology, Faculty of Science, Liverpool John Moores University, Liverpool, L3 3AF, UK.,Department of Animal Behaviour Bielefeld University, Postfach 100131 33501, Bielefeld, Germany.,Department of Biosciences, Swansea University, Swansea, SA2 8PP, UK
| | - O Krüger
- Department of Animal Behaviour, Bielefeld University, Postfach 100131, 33501, Bielefeld, Germany
| | - S Negro
- UMR de Génétique Quantitative et Évolution - Le Moulon, INRA, Université Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, Gif-sur-Yvette, 91190, France.,GIGA-R, Medical Genomics - BIO3, Université of Liège, Liège, 4000, Belgium
| | - A Osborne
- School of Biological Sciences, University of Canterbury, Private Bag 4800, Christchurch, New Zealand, 8140
| | - T Pastor
- EUROPARC Federation, Carretera de l'Església, 92, 08017, Barcelona, Spain
| | - B C Robertson
- Department of Zoology, University of Otago, PO Box 56, Dunedin, 9054, New Zealand
| | - S Sanvito
- Elephant Seal Research Group, Sea Lion Island, FIQQ 1ZZ, Falkland Islands
| | - J K Schultz
- National Marine Fisheries Service, National Oceanic and Atmospheric Administration, 1315 East West Highway, Silver Spring, MD, 20910, USA
| | - A B A Shafer
- Forensic Science & Environmental Life Sciences, Trent University, Peterborough, ON, Canada, K9J 7B8
| | - J B W Wolf
- Division of Evolutionary Biology, Faculty of Biology, LMU Munich, Planegg-Martinstried, Munich, 82152, Germany.,Science of Life Laboratory and Department of Evolutionary Biology, Uppsala University, Uppsala, 752 36, Sweden
| | - J I Hoffman
- Department of Animal Behaviour, Bielefeld University, Postfach 100131, 33501, Bielefeld, Germany. .,British Antarctic Survey, High Cross, Madingley Road, Cambridge, CB3 OET, UK.
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23
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Hoffman JI, Bauer E, Paijmans AJ, Humble E, Beckmann LM, Kubetschek C, Christaller F, Kröcker N, Fuchs B, Moreras A, Shihlomule YD, Bester MN, Cleary AC, De Bruyn PJN, Forcada J, Goebel ME, Goldsworthy SD, Guinet C, Hoelzel AR, Lydersen C, Kovacs KM, Lowther A. A global cline in a colour polymorphism suggests a limited contribution of gene flow towards the recovery of a heavily exploited marine mammal. ROYAL SOCIETY OPEN SCIENCE 2018; 5:181227. [PMID: 30473858 PMCID: PMC6227926 DOI: 10.1098/rsos.181227] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Accepted: 09/18/2018] [Indexed: 06/09/2023]
Abstract
Evaluating how populations are connected by migration is important for understanding species resilience because gene flow can facilitate recovery from demographic declines. We therefore investigated the extent to which migration may have contributed to the global recovery of the Antarctic fur seal (Arctocephalus gazella), a circumpolar distributed marine mammal that was brought to the brink of extinction by the sealing industry in the eighteenth and nineteenth centuries. It is widely believed that animals emigrating from South Georgia, where a relict population escaped sealing, contributed to the re-establishment of formerly occupied breeding colonies across the geographical range of the species. To investigate this, we interrogated a genetic polymorphism (S291F) in the melanocortin 1 receptor gene, which is responsible for a cream-coloured phenotype that is relatively abundant at South Georgia and which appears to have recently spread to localities as far afield as Marion Island in the sub-Antarctic Indian Ocean. By sequencing a short region of this gene in 1492 pups from eight breeding colonies, we showed that S291F frequency rapidly declines with increasing geographical distance from South Georgia, consistent with locally restricted gene flow from South Georgia mainly to the South Shetland Islands and Bouvetøya. The S291F allele was not detected farther afield, suggesting that although emigrants from South Georgia may have been locally important, they are unlikely to have played a major role in the recovery of geographically more distant populations.
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Affiliation(s)
- J. I. Hoffman
- Department of Animal Behaviour, Bielefeld University, 33501 Bielefeld, Germany
- British Antarctic Survey, High Cross, Madingley Road, Cambridge CB3 OET, UK
| | - E. Bauer
- Department of Animal Behaviour, Bielefeld University, 33501 Bielefeld, Germany
| | - A. J. Paijmans
- Department of Animal Behaviour, Bielefeld University, 33501 Bielefeld, Germany
| | - E. Humble
- Department of Animal Behaviour, Bielefeld University, 33501 Bielefeld, Germany
| | - L. M. Beckmann
- Department of Animal Behaviour, Bielefeld University, 33501 Bielefeld, Germany
| | - C. Kubetschek
- Department of Animal Behaviour, Bielefeld University, 33501 Bielefeld, Germany
| | - F. Christaller
- Department of Animal Behaviour, Bielefeld University, 33501 Bielefeld, Germany
| | - N. Kröcker
- Department of Animal Behaviour, Bielefeld University, 33501 Bielefeld, Germany
| | - B. Fuchs
- Department of Animal Behaviour, Bielefeld University, 33501 Bielefeld, Germany
| | - A. Moreras
- Department of Animal Behaviour, Bielefeld University, 33501 Bielefeld, Germany
| | - Y. D. Shihlomule
- Department of Zoology and Entomology, Mammal Research Institute, University of Pretoria, Private Bag X20, Hatfield 0028, South Africa
| | - M. N. Bester
- Department of Zoology and Entomology, Mammal Research Institute, University of Pretoria, Private Bag X20, Hatfield 0028, South Africa
| | - A. C. Cleary
- Norwegian Polar Institute, Fram Centre, 9296 Tromsø, Norway
| | - P. J. N. De Bruyn
- Department of Zoology and Entomology, Mammal Research Institute, University of Pretoria, Private Bag X20, Hatfield 0028, South Africa
| | - J. Forcada
- British Antarctic Survey, High Cross, Madingley Road, Cambridge CB3 OET, UK
| | - M. E. Goebel
- Antarctic Ecosystem Research Division, Southwest Fisheries Science Center, National Marine Fisheries, National Oceanographic and Atmospheric Administration, 8901 La Jolla Shores Drive, La Jolla, CA 92037, USA
| | - S. D. Goldsworthy
- South Australian Research and Development Institute, 2 Hamra Avenue, West Beach, South Australia 5024, Australia
| | - C. Guinet
- Centre d'Etudes Biologiques de Chizé (CEBC), CNRS and Université de La Rochelle - UMR 7372, 79360 Villiers en Bois, France
| | - A. R. Hoelzel
- Department of Biosciences, Durham University, South Road, Durham DH1 3LE, UK
| | - C. Lydersen
- Norwegian Polar Institute, Fram Centre, 9296 Tromsø, Norway
| | - K. M. Kovacs
- Norwegian Polar Institute, Fram Centre, 9296 Tromsø, Norway
| | - A. Lowther
- Norwegian Polar Institute, Fram Centre, 9296 Tromsø, Norway
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24
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Dussex N, Taylor HR, Stovall WR, Rutherford K, Dodds KG, Clarke SM, Gemmell NJ. Reduced representation sequencing detects only subtle regional structure in a heavily exploited and rapidly recolonizing marine mammal species. Ecol Evol 2018; 8:8736-8749. [PMID: 30271541 PMCID: PMC6157699 DOI: 10.1002/ece3.4411] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Revised: 05/17/2018] [Accepted: 05/29/2018] [Indexed: 12/20/2022] Open
Abstract
Next-generation reduced representation sequencing (RRS) approaches show great potential for resolving the structure of wild populations. However, the population structure of species that have shown rapid demographic recovery following severe population bottlenecks may still prove difficult to resolve due to high gene flow between subpopulations. Here, we tested the effectiveness of the RRS method Genotyping-By-Sequencing (GBS) for describing the population structure of the New Zealand fur seal (NZFS, Arctocephalus forsteri), a species that was heavily exploited by the 19th century commercial sealing industry and has since rapidly recolonized most of its former range from a few isolated colonies. Using 26,026 neutral single nucleotide polymorphisms (SNPs), we assessed genetic variation within and between NZFS colonies. We identified low levels of population differentiation across the species range (<1% of variation explained by regional differences) suggesting a state of near panmixia. Nonetheless, we observed subtle population substructure between West Coast and Southern East Coast colonies and a weak, but significant (p = 0.01), isolation-by-distance pattern among the eight colonies studied. Furthermore, our demographic reconstructions supported severe bottlenecks with potential 10-fold and 250-fold declines in response to Polynesian and European hunting, respectively. Finally, we were able to assign individuals treated as unknowns to their regions of origin with high confidence (96%) using our SNP data. Our results indicate that while it may be difficult to detect population structure in species that have experienced rapid recovery, next-generation markers and methods are powerful tools for resolving fine-scale structure and informing conservation and management efforts.
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Affiliation(s)
- Nicolas Dussex
- Department of AnatomyUniversity of OtagoDunedinNew Zealand
- Department of Bioinformatics and GeneticsSwedish Museum of Natural HistoryStockholmSweden
| | | | | | - Kim Rutherford
- Department of AnatomyUniversity of OtagoDunedinNew Zealand
| | - Ken G. Dodds
- Invermay Agricultural CentreAgResearchPuddle AlleyMosgielNew Zealand
| | - Shannon M. Clarke
- Invermay Agricultural CentreAgResearchPuddle AlleyMosgielNew Zealand
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RAD Sequencing and a Hybrid Antarctic Fur Seal Genome Assembly Reveal Rapidly Decaying Linkage Disequilibrium, Global Population Structure and Evidence for Inbreeding. G3-GENES GENOMES GENETICS 2018; 8:2709-2722. [PMID: 29954843 PMCID: PMC6071602 DOI: 10.1534/g3.118.200171] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Recent advances in high throughput sequencing have transformed the study of wild organisms by facilitating the generation of high quality genome assemblies and dense genetic marker datasets. These resources have the potential to significantly advance our understanding of diverse phenomena at the level of species, populations and individuals, ranging from patterns of synteny through rates of linkage disequilibrium (LD) decay and population structure to individual inbreeding. Consequently, we used PacBio sequencing to refine an existing Antarctic fur seal (Arctocephalus gazella) genome assembly and genotyped 83 individuals from six populations using restriction site associated DNA (RAD) sequencing. The resulting hybrid genome comprised 6,169 scaffolds with an N50 of 6.21 Mb and provided clear evidence for the conservation of large chromosomal segments between the fur seal and dog (Canis lupus familiaris). Focusing on the most extensively sampled population of South Georgia, we found that LD decayed rapidly, reaching the background level by around 400 kb, consistent with other vertebrates but at odds with the notion that fur seals experienced a strong historical bottleneck. We also found evidence for population structuring, with four main Antarctic island groups being resolved. Finally, appreciable variance in individual inbreeding could be detected, reflecting the strong polygyny and site fidelity of the species. Overall, our study contributes important resources for future genomic studies of fur seals and other pinnipeds while also providing a clear example of how high throughput sequencing can generate diverse biological insights at multiple levels of organization.
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Cypriano-Souza AL, da Silva TF, Engel MH, Bonatto SL. Effective population size and the genetic consequences of commercial whaling on the humpback whales (Megaptera novaeangliae) from Southwestern Atlantic Ocean. Genet Mol Biol 2018; 41:253-262. [PMID: 29668011 PMCID: PMC5913722 DOI: 10.1590/1678-4685-gmb-2017-0052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2017] [Accepted: 08/01/2017] [Indexed: 11/21/2022] Open
Abstract
Genotypes of 10 microsatellite loci of 420 humpback whales from the Southwestern Atlantic Ocean population were used to estimate for the first time its contemporary effective (Ne) and census (Nc) population sizes and to test the genetic effect of commercial whaling. The results are in agreement with our previous studies that found high genetic diversity for this breeding population. Using an approximate Bayesian computation approach, the scenario of constant Ne was significantly supported over scenarios with moderate to strong size changes during the commercial whaling period. The previous generation Nc (Ne multiplied by 3.6), which should corresponds to the years between around 1980 and 1990, was estimated between ~2,600 and 6,800 whales (point estimate ~4,000), and is broadly compatible with the recent abundance surveys extrapolated to the past using a growth rate of 7.4% per annum. The long-term Nc in the constant scenario (point estimate ~15,000) was broadly compatible (considering the confidence interval) with pre-whaling catch records estimates (point estimate ~25,000). Overall, our results shown that the Southwestern Atlantic Ocean humpback whale population is genetically very diverse and resisted well to the strong population reduction during commercial whaling.
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Affiliation(s)
- Ana Lúcia Cypriano-Souza
- Faculdade de Biociências, Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Porto Alegre, RS, Brazil.,Projeto Baleia Jubarte/Instituto Baleia Jubarte, Caravelas, BA, Brazil
| | - Tiago Ferraz da Silva
- Faculdade de Biociências, Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Porto Alegre, RS, Brazil.,Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo (USP), São Paulo, SP, Brazil
| | - Márcia H Engel
- Projeto Baleia Jubarte/Instituto Baleia Jubarte, Caravelas, BA, Brazil
| | - Sandro L Bonatto
- Faculdade de Biociências, Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Porto Alegre, RS, Brazil
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Genetic diversity from pre-bottleneck to recovery in two sympatric pinniped species in the Northwest Atlantic. CONSERV GENET 2017. [DOI: 10.1007/s10592-017-1032-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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Cabrera AA, Palsbøll PJ. Inferring past demographic changes from contemporary genetic data: A simulation-based evaluation of the ABC methods implemented indiyabc. Mol Ecol Resour 2017; 17:e94-e110. [DOI: 10.1111/1755-0998.12696] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2016] [Revised: 06/12/2017] [Accepted: 06/20/2017] [Indexed: 01/19/2023]
Affiliation(s)
- Andrea A. Cabrera
- Marine Evolution and Conservation; Groningen Institute of Evolutionary Life Sciences; University of Groningen; Groningen The Netherlands
| | - Per J. Palsbøll
- Marine Evolution and Conservation; Groningen Institute of Evolutionary Life Sciences; University of Groningen; Groningen The Netherlands
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Moon KL, Chown SL, Fraser CI. Reconsidering connectivity in the sub-Antarctic. Biol Rev Camb Philos Soc 2017; 92:2164-2181. [DOI: 10.1111/brv.12327] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2016] [Revised: 02/09/2017] [Accepted: 02/15/2017] [Indexed: 12/21/2022]
Affiliation(s)
- Katherine L. Moon
- School of Biological Sciences; Monash University; Clayton 3800 Australia
- Fenner School of Environment and Society; Australian National University; Acton 2601 Australia
| | - Steven L. Chown
- School of Biological Sciences; Monash University; Clayton 3800 Australia
| | - Ceridwen I. Fraser
- Fenner School of Environment and Society; Australian National University; Acton 2601 Australia
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Miura O, Kanaya G, Nakai S, Itoh H, Chiba S, Makino W, Nishimura T, Kojima S, Urabe J. Ecological and genetic impact of the 2011 Tohoku Earthquake Tsunami on intertidal mud snails. Sci Rep 2017; 7:44375. [PMID: 28281698 PMCID: PMC5345064 DOI: 10.1038/srep44375] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Accepted: 02/07/2017] [Indexed: 11/13/2022] Open
Abstract
Natural disturbances often destroy local populations and can considerably affect the genetic properties of these populations. The 2011 Tohoku Earthquake Tsunami greatly damaged local populations of various coastal organisms, including the mud snail Batillaria attramentaria, which was an abundant macroinvertebrate on the tidal flats in the Tohoku region. To evaluate the impact of the tsunami on the ecology and population genetic properties of these snails, we monitored the density, shell size, and microsatellite DNA variation of B. attramentaria for more than ten years (2005–2015) throughout the disturbance event. We found that the density of snails declined immediately after the tsunami. Bayesian inference of the genetically effective population size (Ne) demonstrated that the Ne declined by 60–99% at the study sites exposed to the tsunami. However, we found that their genetic diversity was not significantly reduced after the tsunami. The maintenance of genetic diversity is essential for long-term survival of local populations, and thus, the observed genetic robustness could play a key role in the persistence of snail populations in this region which has been devastated by similar tsunamis every 500–800 years. Our findings have significant implications for understanding the sustainability of populations damaged by natural disturbances.
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Affiliation(s)
- Osamu Miura
- Faculty of Agriculture and Marine Science, Kochi University, 200 Monobe, Nankoku, Kochi 783-8502, Japan
| | - Gen Kanaya
- National Institute for Environmental Studies, 16-2 Onogawa, Tsukuba, Ibaraki 305-8506, Japan
| | - Shizuko Nakai
- Department of Marine Science and Resources, College of Bioresource Sciences Nihon University, 1866 Kameino, Fujisawa, Kanagawa 252-0880, Japan
| | - Hajime Itoh
- Atmosphere and Ocean Research Institute, The University of Tokyo, 5-1-5, Kashiwanoha, Kashiwa, Chiba 277-8564, Japan
| | - Satoshi Chiba
- Department of Environmental Life Sciences, Graduate School of Life Sciences, Tohoku University, Kawauchi 41, Aoba-ku, Sendai, Miyagi 980-0862, Japan
| | - Wataru Makino
- Division of Ecology and Evolutionary Biology, Graduate School of Life Sciences, Tohoku University, Sendai, Miyagi 980-8578, Japan
| | - Tomohiro Nishimura
- Laboratory of Aquatic Environmental Science, Faculty of Agriculture, Kochi University, Nankoku, Kochi 783-8502, Japan
| | - Shigeaki Kojima
- Atmosphere and Ocean Research Institute, The University of Tokyo, 5-1-5, Kashiwanoha, Kashiwa, Chiba 277-8564, Japan
| | - Jotaro Urabe
- Division of Ecology and Evolutionary Biology, Graduate School of Life Sciences, Tohoku University, Sendai, Miyagi 980-8578, Japan
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Dussex N, Robertson BC, Salis AT, Kalinin A, Best H, Gemmell NJ. Low Spatial Genetic Differentiation Associated with Rapid Recolonization in the New Zealand Fur Seal Arctocephalus forsteri. J Hered 2016; 107:581-592. [PMID: 27563072 DOI: 10.1093/jhered/esw056] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2016] [Accepted: 08/15/2016] [Indexed: 11/14/2022] Open
Abstract
Population declines resulting from anthropogenic activities are of major consequence for the long-term survival of species because the resulting loss of genetic diversity can lead to extinction via the effects of inbreeding depression, fixation of deleterious mutations, and loss of adaptive potential. Otariid pinnipeds have been exploited commercially to near extinction with some species showing higher demographic resilience and recolonization potential than others. The New Zealand fur seal (NZFS) was heavily impacted by commercial sealing between the late 18th and early 19th centuries, but has recolonized its former range in southern Australia. The species has also recolonized its former range in New Zealand, yet little is known about the pattern of recolonization. Here, we first used 11 microsatellite markers (n = 383) to investigate the contemporary population structure and dispersal patterns in the NZFS (Arctocephalus forsteri). Secondly, we model postsealing recolonization with 1 additional mtDNA cytochrome b (n = 261) marker. Our data identified 3 genetic clusters: an Australian, a subantarctic, and a New Zealand one, with a weak and probably transient subdivision within the latter cluster. Demographic history scenarios supported a recolonization of the New Zealand coastline from remote west coast colonies, which is consistent with contemporary gene flow and with the species' high resilience. The present data suggest the management of distinct genetic units in the North and South of New Zealand along a genetic gradient. Assignment of individuals to their colony of origin was limited (32%) with the present data indicating the current microsatellite markers are unlikely sufficient to assign fisheries bycatch of NZFSs to colonies.
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Affiliation(s)
- Nicolas Dussex
- From the Department of Zoology, University of Otago, Dunedin, New Zealand (Dussex, Robertson, and Salis); Allan Wilson Centre, Dunedin, New Zealand (Dussex and Gemmell); Department of Anatomy, University of Otago, PO Box 913, Dunedin 9054, New Zealand (Dussex and Gemmell); School of Biological Sciences, University of Canterbury, Christchurch, New Zealand (Robertson, Kalinin, and Gemmell); and Marine Conservation Unit, Department of Conservation, Wellington, New Zealand (Best)
| | - Bruce C Robertson
- From the Department of Zoology, University of Otago, Dunedin, New Zealand (Dussex, Robertson, and Salis); Allan Wilson Centre, Dunedin, New Zealand (Dussex and Gemmell); Department of Anatomy, University of Otago, PO Box 913, Dunedin 9054, New Zealand (Dussex and Gemmell); School of Biological Sciences, University of Canterbury, Christchurch, New Zealand (Robertson, Kalinin, and Gemmell); and Marine Conservation Unit, Department of Conservation, Wellington, New Zealand (Best)
| | - Alexander T Salis
- From the Department of Zoology, University of Otago, Dunedin, New Zealand (Dussex, Robertson, and Salis); Allan Wilson Centre, Dunedin, New Zealand (Dussex and Gemmell); Department of Anatomy, University of Otago, PO Box 913, Dunedin 9054, New Zealand (Dussex and Gemmell); School of Biological Sciences, University of Canterbury, Christchurch, New Zealand (Robertson, Kalinin, and Gemmell); and Marine Conservation Unit, Department of Conservation, Wellington, New Zealand (Best)
| | - Aleksandr Kalinin
- From the Department of Zoology, University of Otago, Dunedin, New Zealand (Dussex, Robertson, and Salis); Allan Wilson Centre, Dunedin, New Zealand (Dussex and Gemmell); Department of Anatomy, University of Otago, PO Box 913, Dunedin 9054, New Zealand (Dussex and Gemmell); School of Biological Sciences, University of Canterbury, Christchurch, New Zealand (Robertson, Kalinin, and Gemmell); and Marine Conservation Unit, Department of Conservation, Wellington, New Zealand (Best)
| | - Hugh Best
- From the Department of Zoology, University of Otago, Dunedin, New Zealand (Dussex, Robertson, and Salis); Allan Wilson Centre, Dunedin, New Zealand (Dussex and Gemmell); Department of Anatomy, University of Otago, PO Box 913, Dunedin 9054, New Zealand (Dussex and Gemmell); School of Biological Sciences, University of Canterbury, Christchurch, New Zealand (Robertson, Kalinin, and Gemmell); and Marine Conservation Unit, Department of Conservation, Wellington, New Zealand (Best)
| | - Neil J Gemmell
- From the Department of Zoology, University of Otago, Dunedin, New Zealand (Dussex, Robertson, and Salis); Allan Wilson Centre, Dunedin, New Zealand (Dussex and Gemmell); Department of Anatomy, University of Otago, PO Box 913, Dunedin 9054, New Zealand (Dussex and Gemmell); School of Biological Sciences, University of Canterbury, Christchurch, New Zealand (Robertson, Kalinin, and Gemmell); and Marine Conservation Unit, Department of Conservation, Wellington, New Zealand (Best)
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32
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Peters L, Humble E, Kröcker N, Fuchs B, Forcada J, Hoffman JI. Born blonde: a recessive loss-of-function mutation in the melanocortin 1 receptor is associated with cream coat coloration in Antarctic fur seals. Ecol Evol 2016; 6:5705-17. [PMID: 27547348 PMCID: PMC4983585 DOI: 10.1002/ece3.2290] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2016] [Revised: 06/08/2016] [Accepted: 06/09/2016] [Indexed: 02/03/2023] Open
Abstract
Although the genetic basis of color variation has been extensively studied in humans and domestic animals, the genetic polymorphisms responsible for different color morphs remain to be elucidated in many wild vertebrate species. For example, hypopigmentation has been observed in numerous marine mammal species but the underlying mutations have not been identified. A particularly compelling candidate gene for explaining color polymorphism is the melanocortin 1 receptor (MC1R), which plays a key role in the regulation of pigment production. We therefore used Antarctic fur seals (Arctocephalus gazella) as a highly tractable marine mammal system with which to test for an association between nucleotide variation at the MC1R and melanin‐based coat color phenotypes. By sequencing 70 wild‐type individuals with dark‐colored coats and 26 hypopigmented individuals with cream‐colored coats, we identified a nonsynonymous mutation that results in the substitution of serine with phenylalanine at an evolutionarily highly conserved structural domain. All of the hypopigmented individuals were homozygous for the allele coding for phenylalanine, consistent with a recessive loss‐of‐function allele. In order to test for cryptic population structure, which can generate artefactual associations, and to evaluate whether homozygosity at the MC1R could be indicative of low genome‐wide heterozygosity, we also genotyped all of the individuals at 50 polymorphic microsatellite loci. We were unable to detect any population structure and also found that wild‐type and hypopigmented individuals did not differ significantly in their standardized multilocus heterozygosity. Such a lack of association implies that hypopigmented individuals are unlikely to suffer disproportionately from inbreeding depression, and hence, we have no reason to believe that they are at a selective disadvantage in the wider population.
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Affiliation(s)
- Lucy Peters
- Department of Animal Behaviour University of Bielefeld Postfach 100131 33501 Bielefeld Germany; College of Medical, Veterinary & Life Sciences University of Glasgow Graham Kerr Building Glasgow G12 8QQ UK
| | - Emily Humble
- Department of Animal Behaviour University of Bielefeld Postfach 100131 33501 Bielefeld Germany; British Antarctic Survey High Cross, Madingley Road Cambridge CB3 OET UK
| | - Nicole Kröcker
- Department of Animal Behaviour University of Bielefeld Postfach 100131 33501 Bielefeld Germany
| | - Birgit Fuchs
- Department of Animal Behaviour University of Bielefeld Postfach 100131 33501 Bielefeld Germany
| | - Jaume Forcada
- British Antarctic Survey High Cross, Madingley Road Cambridge CB3 OET UK
| | - Joseph I Hoffman
- Department of Animal Behaviour University of Bielefeld Postfach 100131 33501 Bielefeld Germany
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Hoffman JI, Kowalski GJ, Klimova A, Eberhart-Phillips LJ, Staniland IJ, Baylis AMM. Population structure and historical demography of South American sea lions provide insights into the catastrophic decline of a marine mammal population. ROYAL SOCIETY OPEN SCIENCE 2016; 3:160291. [PMID: 27493782 PMCID: PMC4968474 DOI: 10.1098/rsos.160291] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/29/2016] [Accepted: 06/23/2016] [Indexed: 06/06/2023]
Abstract
Understanding the causes of population decline is crucial for conservation management. We therefore used genetic analysis both to provide baseline data on population structure and to evaluate hypotheses for the catastrophic decline of the South American sea lion (Otaria flavescens) at the Falkland Islands (Malvinas) in the South Atlantic. We genotyped 259 animals from 23 colonies across the Falklands at 281 bp of the mitochondrial hypervariable region and 22 microsatellites. A weak signature of population structure was detected, genetic diversity was moderately high in comparison with other pinniped species, and no evidence was found for the decline being associated with a strong demographic bottleneck. By combining our mitochondrial data with published sequences from Argentina, Brazil, Chile and Peru, we also uncovered strong maternally directed population structure across the geographical range of the species. In particular, very few shared haplotypes were found between the Falklands and South America, and this was reflected in correspondingly low migration rate estimates. These findings do not support the prominent hypothesis that the decline was caused by migration to Argentina, where large-scale commercial harvesting operations claimed over half a million animals. Thus, our study not only provides baseline data for conservation management but also reveals the potential for genetic studies to shed light upon long-standing questions pertaining to the history and fate of natural populations.
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Affiliation(s)
- J. I. Hoffman
- Department of Animal Behaviour, University of Bielefeld, Postfach 100131, 33501 Bielefeld, Germany
| | - G. J. Kowalski
- Department of Animal Behaviour, University of Bielefeld, Postfach 100131, 33501 Bielefeld, Germany
- Animal Ecology Group, Institute of Biochemistry and Biology, University of Potsdam, Maulbeerallee 1, 14469, Potsdam, Germany
| | - A. Klimova
- Centro de Investigaciones Biológicas del Noroeste Baja California Sur, La Paz, Mexico
| | - L. J. Eberhart-Phillips
- Department of Animal Behaviour, University of Bielefeld, Postfach 100131, 33501 Bielefeld, Germany
| | - I. J. Staniland
- British Antarctic Survey, Natural Environment Research Council, High Cross, Madingley Road, Cambridge CB3 0ET, UK
| | - A. M. M. Baylis
- South Atlantic Environmental Research Institute, Stanley FIQQ1ZZ, Falkland Islands
- Falklands Conservation, Stanley FIQQ1ZZ, Falkland Islands
- Department of Biological Sciences, Macquarie University, Sydney, New South Wales 2109, Australia
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Xuereb ATJ, Rouse JD, Cunnington G, Lougheed SC. Population genetic structure at the northern range limit of the threatened eastern hog-nosed snake (Heterodon platirhinos). CONSERV GENET 2015. [DOI: 10.1007/s10592-015-0737-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Zhang W, Luo Z, Zhao M, Wu H. High genetic diversity in the endangered and narrowly distributed amphibian species Leptobrachium leishanense. Integr Zool 2015; 10:465-81. [PMID: 26037662 DOI: 10.1111/1749-4877.12142] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Threatened species typically have a small or declining population size, which make them highly susceptible to loss of genetic diversity through genetic drift and inbreeding. Genetic diversity determines the evolutionary potential of a species; therefore, maintaining the genetic diversity of threatened species is essential for their conservation. In this study, we assessed the genetic diversity of the adaptive major histocompatibility complex (MHC) genes in an endangered and narrowly distributed amphibian species, Leptobrachium leishanense in Southwest China. We compared the genetic variation of MHC class I genes with that observed in neutral markers (5 microsatellite loci and cytochrome b gene) to elucidate the relative roles of genetic drift and natural selection in shaping the current MHC polymorphism in this species. We found a high level of genetic diversity in this population at both MHC and neutral markers compared with other threatened amphibian species. Historical positive selection was evident in the MHC class I genes. The higher allelic richness in MHC markers compared with that of microsatellite loci suggests that selection rather than genetic drift plays a prominent role in shaping the MHC variation pattern, as drift can affect all the genome in a similar way but selection directly targets MHC genes. Although demographic analysis revealed no recent bottleneck events in L. leishanense, additional population decline will accelerate the dangerous status for this species. We suggest that the conservation management of L. leishanense should concentrate on maximizing the retention of genetic diversity through preventing their continuous population decline. Protecting their living habitats and forbidding illegal hunting are the most important measures for conservation of L. leishanense.
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Affiliation(s)
- Wei Zhang
- Institute of Evolution and Ecology, International Research Centre of Ecology and Environment, School of Life Sciences, Central China Normal University, Wuhan, China
| | - Zhenhua Luo
- Institute of Evolution and Ecology, International Research Centre of Ecology and Environment, School of Life Sciences, Central China Normal University, Wuhan, China
| | - Mian Zhao
- Institute of Evolution and Ecology, International Research Centre of Ecology and Environment, School of Life Sciences, Central China Normal University, Wuhan, China
| | - Hua Wu
- Institute of Evolution and Ecology, International Research Centre of Ecology and Environment, School of Life Sciences, Central China Normal University, Wuhan, China
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36
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Fine-scale matrilineal population structure in the Galapagos fur seal and its implications for conservation management. CONSERV GENET 2015. [DOI: 10.1007/s10592-015-0725-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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37
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Ancient and contemporary DNA reveal a pre-human decline but no population bottleneck associated with recent human persecution in the kea (Nestor notabilis). PLoS One 2015; 10:e0118522. [PMID: 25719752 PMCID: PMC4342260 DOI: 10.1371/journal.pone.0118522] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2014] [Accepted: 11/19/2014] [Indexed: 12/02/2022] Open
Abstract
The impact of population bottlenecks is an important factor to consider when assessing species survival. Population declines can considerably limit the evolutionary potential of species and make them more susceptible to stochastic events. New Zealand has a well documented history of decline of endemic avifauna related to human colonization. Here, we investigate the genetic effects of a recent population decline in the endangered kea (Nestor notabilis). Kea have undergone a long-lasting persecution between the late 1800s to 1970s where an estimated 150,000 kea were culled under a governmental bounty scheme. Kea now number 1,000–5,000 individuals in the wild and it is likely that the recent population decline may have reduced the genetic diversity of the species. Comparison of contemporary (n = 410), historical (n = 15) and fossil samples (n = 4) showed a loss of mitochondrial diversity since the end of the last glaciation (Otiran Glacial) but no loss of overall genetic diversity associated with the cull. Microsatellite data indicated a recent bottleneck for only one population and a range-wide decline in Ne dating back some 300 – 6,000 years ago, a period predating European arrival in NZ. These results suggest that despite a recent human persecution, kea might have experienced a large population decline before stabilizing in numbers prior to human settlement of New Zealand in response to Holocene changes in habitat distribution. Our study therefore highlights the need to understand the respective effects of climate change and human activities on endangered species dynamics when proposing conservation guidelines.
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Garrick RC, Kajdacsi B, Russello MA, Benavides E, Hyseni C, Gibbs JP, Tapia W, Caccone A. Naturally rare versus newly rare: demographic inferences on two timescales inform conservation of Galápagos giant tortoises. Ecol Evol 2015; 5:676-94. [PMID: 25691990 PMCID: PMC4328771 DOI: 10.1002/ece3.1388] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2014] [Revised: 11/26/2014] [Accepted: 12/01/2014] [Indexed: 02/05/2023] Open
Abstract
Long-term population history can influence the genetic effects of recent bottlenecks. Therefore, for threatened or endangered species, an understanding of the past is relevant when formulating conservation strategies. Levels of variation at neutral markers have been useful for estimating local effective population sizes (N e ) and inferring whether population sizes increased or decreased over time. Furthermore, analyses of genotypic, allelic frequency, and phylogenetic information can potentially be used to separate historical from recent demographic changes. For 15 populations of Galápagos giant tortoises (Chelonoidis sp.), we used 12 microsatellite loci and DNA sequences from the mitochondrial control region and a nuclear intron, to reconstruct demographic history on shallow (past ∽100 generations, ∽2500 years) and deep (pre-Holocene, >10 thousand years ago) timescales. At the deep timescale, three populations showed strong signals of growth, but with different magnitudes and timing, indicating different underlying causes. Furthermore, estimated historical N e of populations across the archipelago showed no correlation with island age or size, underscoring the complexity of predicting demographic history a priori. At the shallow timescale, all populations carried some signature of a genetic bottleneck, and for 12 populations, point estimates of contemporary N e were very small (i.e., < 50). On the basis of the comparison of these genetic estimates with published census size data, N e generally represented ∽0.16 of the census size. However, the variance in this ratio across populations was considerable. Overall, our data suggest that idiosyncratic and geographically localized forces shaped the demographic history of tortoise populations. Furthermore, from a conservation perspective, the separation of demographic events occurring on shallow versus deep timescales permits the identification of naturally rare versus newly rare populations; this distinction should facilitate prioritization of management action.
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Affiliation(s)
- Ryan C Garrick
- Department of Biology, University of MississippiOxford, Mississippi, 38677
| | - Brittney Kajdacsi
- Department of Ecology and Evolutionary Biology, Yale UniversityNew Haven, Connecticut, 06520
| | - Michael A Russello
- Department of Biology, University of British ColumbiaOkanagan Campus, Kelowna, British Columbia, V1V 1V7, Canada
| | - Edgar Benavides
- Department of Ecology and Evolutionary Biology, Yale UniversityNew Haven, Connecticut, 06520
| | - Chaz Hyseni
- Department of Biology, University of MississippiOxford, Mississippi, 38677
| | - James P Gibbs
- College of Environmental Science and Forestry, State University of New YorkSyracuse, New York, 13210
| | - Washington Tapia
- Department of Applied Research, Galápagos National Park ServicePuerto Ayora, Galápagos, Ecuador
- Biodiver S.A. ConsultoresKm 5 Vía a Baltra, Isla Santa Cruz, Galápagos, Ecuador
| | - Adalgisa Caccone
- Department of Ecology and Evolutionary Biology, Yale UniversityNew Haven, Connecticut, 06520
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Eberhart-Phillips LJ, Hoffman JI, Brede EG, Zefania S, Kamrad MJ, Székely T, Bruford MW. Contrasting genetic diversity and population structure among three sympatric Madagascan shorebirds: parallels with rarity, endemism, and dispersal. Ecol Evol 2015; 5:997-1010. [PMID: 25798218 PMCID: PMC4364815 DOI: 10.1002/ece3.1393] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2014] [Accepted: 12/15/2014] [Indexed: 01/12/2023] Open
Abstract
Understanding the relative contributions of intrinsic and extrinsic factors to population structure and genetic diversity is a central goal of conservation and evolutionary genetics. One way to achieve this is through comparative population genetic analysis of sympatric sister taxa, which allows evaluation of intrinsic factors such as population demography and life history while controlling for phylogenetic relatedness and geography. We used ten conserved microsatellites to explore the population structure and genetic diversity of three sympatric and closely related plover species in southwestern Madagascar: Kittlitz's plover (Charadrius pecuarius), white-fronted plover (C. marginatus), and Madagascar plover (C. thoracicus). Bayesian clustering revealed strong population structure in the rare and endemic Madagascar plover, intermediate population structure in the white-fronted plover, and no detectable population structure in the geographically widespread Kittlitz's plover. In contrast, allelic richness and heterozygosity were highest for the Kittlitz's plover, intermediate for the white-fronted plover and lowest for the Madagascar plover. No evidence was found in support of the “watershed mechanism” proposed to facilitate vicariant divergence of Madagascan lemurs and reptiles, which we attribute to the vagility of birds. However, we found a significant pattern of genetic isolation by distance among populations of the Madagascar plover, but not for the other two species. These findings suggest that interspecific variation in rarity, endemism, and dispersal propensity may influence genetic structure and diversity, even in highly vagile species.
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Affiliation(s)
| | - Joseph I Hoffman
- Department of Animal Behaviour, Bielefeld University Morgenbreede 45, 33615, Bielefeld, Germany
| | - Edward G Brede
- Biodiversity and Ecological Processes Group, Cardiff School of Biosciences, Cardiff University Cardiff, CF10 3AX, U.K
| | - Sama Zefania
- Department of Animal Biology, University of Toliara PO Box 185, Toliara, Madagascar
| | - Martina J Kamrad
- Department of Animal Behaviour, Bielefeld University Morgenbreede 45, 33615, Bielefeld, Germany
| | - Tamás Székely
- Department of Animal Behaviour, Bielefeld University Morgenbreede 45, 33615, Bielefeld, Germany ; Biodiversity Lab, Department of Biology and Biochemistry, University of Bath Bath, BA2 7AY, U.K
| | - Michael W Bruford
- Biodiversity and Ecological Processes Group, Cardiff School of Biosciences, Cardiff University Cardiff, CF10 3AX, U.K
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He L, Zhang A, Weese D, Li S, Li J, Zhang J. Demographic response of cutlassfish (Trichiurus japonicus and T. nanhaiensis) to fluctuating palaeo-climate and regional oceanographic conditions in the China seas. Sci Rep 2014; 4:6380. [PMID: 25223336 PMCID: PMC4165270 DOI: 10.1038/srep06380] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2014] [Accepted: 08/26/2014] [Indexed: 11/09/2022] Open
Abstract
Glacial cycles of the Quaternary have heavily influenced the demographic history of various species. To test the evolutionary impact of palaeo-geologic and climatic events on the demographic history of marine taxa from the coastal Western Pacific, we investigated the population structure and demographic history of two economically important fish (Trichiurus japonicus and T. nanhaiensis) that inhabit the continental shelves of the East China and northern South China Seas using the mitochondrial cytochrome b sequences and Bayesian Skyline Plot analyses. A molecular rate of 2.03% per million years, calibrated to the earliest flooding of the East China Sea shelf (70-140 kya), revealed a strong correlation between population sizes and primary production. Furthermore, comparison of the demographic history of T. japonicus populations from the East China and South China Seas provided evidence of the postglacial development of the Changjiang (Yangtze River) Delta. In the South China Sea, interspecific comparisons between T. japonicus and T. nanhaiensis indicated possible evolutionary responses to changes in palaeo-productivity that were influenced by East Asian winter monsoons. This study not only provides insight into the demographic history of cutlassfish but also reveals potential clues regarding the historic productivity and regional oceanographic conditions of the Western Pacific marginal seas.
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Affiliation(s)
- Lijun He
- 1] State Key Laboratory of Estuarine and Coastal Research, East China Normal University, Shanghai, 200062, P. R. China [2] East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Shanghai, 200090, P. R. China
| | - Aibing Zhang
- 1] College of Life Sciences, Capital Normal University, Beijing, 100048, P. R. China [2]
| | - David Weese
- 1] Department of Biological and Environmental Sciences, Georgia College &State University, Milledgeville, GA 31061, USA [2]
| | - Shengfa Li
- 1] East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Shanghai, 200090, P. R. China [2]
| | - Jiansheng Li
- East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Shanghai, 200090, P. R. China
| | - Jing Zhang
- State Key Laboratory of Estuarine and Coastal Research, East China Normal University, Shanghai, 200062, P. R. China
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Nyman T, Valtonen M, Aspi J, Ruokonen M, Kunnasranta M, Palo JU. Demographic histories and genetic diversities of Fennoscandian marine and landlocked ringed seal subspecies. Ecol Evol 2014; 4:3420-34. [PMID: 25535558 PMCID: PMC4228616 DOI: 10.1002/ece3.1193] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2014] [Revised: 07/21/2014] [Accepted: 07/22/2014] [Indexed: 11/18/2022] Open
Abstract
Island populations are on average smaller, genetically less diverse, and at a higher risk to go extinct than mainland populations. Low genetic diversity may elevate extinction probability, but the genetic component of the risk can be affected by the mode of diversity loss, which, in turn, is connected to the demographic history of the population. Here, we examined the history of genetic erosion in three Fennoscandian ringed seal subspecies, of which one inhabits the Baltic Sea 'mainland' and two the 'aquatic islands' composed of Lake Saimaa in Finland and Lake Ladoga in Russia. Both lakes were colonized by marine seals after their formation c. 9500 years ago, but Lake Ladoga is larger and more contiguous than Lake Saimaa. All three populations suffered dramatic declines during the 20th century, but the bottleneck was particularly severe in Lake Saimaa. Data from 17 microsatellite loci and mitochondrial control-region sequences show that Saimaa ringed seals have lost most of the genetic diversity present in their Baltic ancestors, while the Ladoga population has experienced only minor reductions. Using Approximate Bayesian computing analyses, we show that the genetic uniformity of the Saimaa subspecies derives from an extended founder event and subsequent slow erosion, rather than from the recent bottleneck. This suggests that the population has persisted for nearly 10,000 years despite having low genetic variation. The relatively high diversity of the Ladoga population appears to result from a high number of initial colonizers and a high post-colonization population size, but possibly also by a shorter isolation period and/or occasional gene flow from the Baltic Sea.
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Affiliation(s)
- Tommi Nyman
- Department of Biology, University of Eastern FinlandPO Box 111, Joensuu, FI-80101, Finland
- Institute for Systematic Botany, University of Zurich, Zollikerstrasse 107Zurich, CH-8008, Switzerland
| | - Mia Valtonen
- Department of Biology, University of Eastern FinlandPO Box 111, Joensuu, FI-80101, Finland
| | - Jouni Aspi
- Department of Biology, University of OuluPO Box 3000, Oulu, FI-90014, Finland
| | - Minna Ruokonen
- Department of Biology, University of OuluPO Box 3000, Oulu, FI-90014, Finland
| | - Mervi Kunnasranta
- Department of Biology, University of Eastern FinlandPO Box 111, Joensuu, FI-80101, Finland
| | - Jukka U Palo
- Laboratory of Forensic Biology, Hjelt Institute, University of HelsinkiPO Box 40, Helsinki, FI-00014, Finland
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Spurgin LG, Wright DJ, van der Velde M, Collar NJ, Komdeur J, Burke T, Richardson DS. Museum DNA reveals the demographic history of the endangered Seychelles warbler. Evol Appl 2014; 7:1134-43. [PMID: 25553073 PMCID: PMC4231601 DOI: 10.1111/eva.12191] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2014] [Accepted: 06/30/2014] [Indexed: 01/10/2023] Open
Abstract
The importance of evolutionary conservation – how understanding evolutionary forces can help guide conservation decisions – is widely recognized. However, the historical demography of many endangered species is unknown, despite the fact that this can have important implications for contemporary ecological processes and for extinction risk. Here, we reconstruct the population history of the Seychelles warbler (Acrocephalus sechellensis) – an ecological model species. By the 1960s, this species was on the brink of extinction, but its previous history is unknown. We used DNA samples from contemporary and museum specimens spanning 140 years to reconstruct bottleneck history. We found a 25% reduction in genetic diversity between museum and contemporary populations, and strong genetic structure. Simulations indicate that the Seychelles warbler was bottlenecked from a large population, with an ancestral Ne of several thousands falling to <50 within the last century. Such a rapid decline, due to anthropogenic factors, has important implications for extinction risk in the Seychelles warbler, and our results will inform conservation practices. Reconstructing the population history of this species also allows us to better understand patterns of genetic diversity, inbreeding and promiscuity in the contemporary populations. Our approaches can be applied across species to test ecological hypotheses and inform conservation.
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Affiliation(s)
- Lewis G Spurgin
- School of Biological Sciences, University of East Anglia Norwich, Norfolk, UK ; Behavioural Ecology and Self-organization Group, Centre for Ecological and Evolutionary Studies, University of Groningen Groningen, The Netherlands
| | - David J Wright
- School of Biological Sciences, University of East Anglia Norwich, Norfolk, UK ; Department of Animal and Plant Sciences, NERC Biomolecular Analysis Facility, University of Sheffield Sheffield, UK
| | - Marco van der Velde
- Behavioural Ecology and Self-organization Group, Centre for Ecological and Evolutionary Studies, University of Groningen Groningen, The Netherlands
| | - Nigel J Collar
- School of Biological Sciences, University of East Anglia Norwich, Norfolk, UK ; BirdLife International Cambridge, UK
| | - Jan Komdeur
- Behavioural Ecology and Self-organization Group, Centre for Ecological and Evolutionary Studies, University of Groningen Groningen, The Netherlands
| | - Terry Burke
- Department of Animal and Plant Sciences, NERC Biomolecular Analysis Facility, University of Sheffield Sheffield, UK
| | - David S Richardson
- School of Biological Sciences, University of East Anglia Norwich, Norfolk, UK ; Nature Seychelles Roche Caiman, Mahé, Republic of Seychelles
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Klimova A, Phillips CD, Fietz K, Olsen MT, Harwood J, Amos W, Hoffman JI. Global population structure and demographic history of the grey seal. Mol Ecol 2014; 23:3999-4017. [PMID: 25041117 DOI: 10.1111/mec.12850] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2014] [Revised: 06/04/2014] [Accepted: 06/25/2014] [Indexed: 02/06/2023]
Abstract
Although the grey seal Halichoerus grypus is one of the most familiar and intensively studied of all pinniped species, its global population structure remains to be elucidated. Little is also known about how the species as a whole may have historically responded to climate-driven changes in habitat availability and anthropogenic exploitation. We therefore analysed samples from over 1500 individuals collected from 22 colonies spanning the Western and Eastern Atlantic and the Baltic Sea regions, represented by 350 bp of the mitochondrial hypervariable region and up to nine microsatellites. Strong population structure was observed at both types of marker, and highly asymmetrical patterns of gene flow were also inferred, with the Orkney Islands being identified as a source of emigrants to other areas in the Eastern Atlantic. The Baltic and Eastern Atlantic regions were estimated to have diverged a little over 10 000 years ago, consistent with the last proposed isolation of the Baltic Sea. Approximate Bayesian computation also identified genetic signals consistent with postglacial population expansion across much of the species range, suggesting that grey seals are highly responsive to changes in habitat availability.
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Affiliation(s)
- A Klimova
- Department of Animal Behaviour, University of Bielefeld, Postfach 100131, 33501, Bielefeld, Germany
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Chakraborty D, Sinha A, Ramakrishnan U. Mixed fortunes: ancient expansion and recent decline in population size of a subtropical montane primate, the Arunachal macaque Macaca munzala. PLoS One 2014; 9:e97061. [PMID: 25054863 PMCID: PMC4108313 DOI: 10.1371/journal.pone.0097061] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2013] [Accepted: 04/14/2014] [Indexed: 11/18/2022] Open
Abstract
Quaternary glacial oscillations are known to have caused population size fluctuations in many temperate species. Species from subtropical and tropical regions are, however, considerably less studied, despite representing most of the biodiversity hotspots in the world including many highly threatened by anthropogenic activities such as hunting. These regions, consequently, pose a significant knowledge gap in terms of how their fauna have typically responded to past climatic changes. We studied an endangered primate, the Arunachal macaque Macaca munzala, from the subtropical southern edge of the Tibetan plateau, a part of the Eastern Himalaya biodiversity hotspot, also known to be highly threatened due to rampant hunting. We employed a 534 bp-long mitochondrial DNA sequence and 22 autosomal microsatellite loci to investigate the factors that have potentially shaped the demographic history of the species. Analysing the genetic data with traditional statistical methods and advance Bayesian inferential approaches, we demonstrate a limited effect of past glacial fluctuations on the demographic history of the species before the last glacial maximum, approximately 20,000 years ago. This was, however, immediately followed by a significant population expansion possibly due to warmer climatic conditions, approximately 15,000 years ago. These changes may thus represent an apparent balance between that displayed by the relatively climatically stable tropics and those of the more severe, temperate environments of the past. This study also draws attention to the possibility that a cold-tolerant species like the Arunachal macaque, which could withstand historical climate fluctuations and grow once the climate became conducive, may actually be extremely vulnerable to anthropogenic exploitation, as is perhaps indicated by its Holocene ca. 30-fold population decline, approximately 3,500 years ago. Our study thus provides a quantitative appraisal of these demographically important events, emphasising the ability to potentially infer the occurrence of two separate historical events from contemporary genetic data.
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Affiliation(s)
- Debapriyo Chakraborty
- Nature Conservation Foundation, Gokulam Park, Mysore, India
- National Centre for Biological Sciences, GKVK Campus, Bangalore, India
- * E-mail:
| | - Anindya Sinha
- Nature Conservation Foundation, Gokulam Park, Mysore, India
- National Centre for Biological Sciences, GKVK Campus, Bangalore, India
- National Institute of Advanced Studies, Indian Institute of Science Campus, Bangalore, India
| | - Uma Ramakrishnan
- National Centre for Biological Sciences, GKVK Campus, Bangalore, India
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Nikolic N, Chevalet C. Detecting past changes of effective population size. Evol Appl 2014; 7:663-81. [PMID: 25067949 PMCID: PMC4105917 DOI: 10.1111/eva.12170] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2013] [Accepted: 04/21/2014] [Indexed: 12/03/2022] Open
Abstract
Understanding and predicting population abundance is a major challenge confronting scientists. Several genetic models have been developed using microsatellite markers to estimate the present and ancestral effective population sizes. However, to get an overview on the evolution of population requires that past fluctuation of population size be traceable. To address the question, we developed a new model estimating the past changes of effective population size from microsatellite by resolving coalescence theory and using approximate likelihoods in a Monte Carlo Markov Chain approach. The efficiency of the model and its sensitivity to gene flow and to assumptions on the mutational process were checked using simulated data and analysis. The model was found especially useful to provide evidence of transient changes of population size in the past. The times at which some past demographic events cannot be detected because they are too ancient and the risk that gene flow may suggest the false detection of a bottleneck are discussed considering the distribution of coalescence times. The method was applied on real data sets from several Atlantic salmon populations. The method called VarEff (Variation of Effective size) was implemented in the R package VarEff and is made available at https://qgsp.jouy.inra.fr and at http://cran.r-project.org/web/packages/VarEff.
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Affiliation(s)
| | - Claude Chevalet
- INRA Génétique, Physiologie et Systèmes d'ElevageCastanet-Tolosan, France
- Université de Toulouse INP, ENSAT, Génétique, Physiologie et Systémes d'ElevageCastanet-Tolosan, France
- Université de Toulouse INP, ENVT, Génétique, Physiologie et Systémes d'ElevageToulouse, France
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Torres-Florez JP, Hucke-Gaete R, Rosenbaum H, Figueroa CC. High genetic diversity in a small population: the case of Chilean blue whales. Ecol Evol 2014; 4:1398-412. [PMID: 24834336 PMCID: PMC4020699 DOI: 10.1002/ece3.998] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2013] [Revised: 01/13/2014] [Accepted: 01/23/2014] [Indexed: 11/06/2022] Open
Abstract
It is generally assumed that species with low population sizes have lower genetic diversities than larger populations and vice versa. However, this would not be the case for long-lived species with long generation times, and which populations have declined due to anthropogenic effects, such as the blue whale (Balaenoptera musculus). This species was intensively decimated globally to near extinction during the 20th century. Along the Chilean coast, it is estimated that at least 4288 blue whales were hunted from an apparently pre-exploitation population size (k) of a maximum of 6200 individuals (Southeastern Pacific). Thus, here, we describe the mtDNA (control region) and nDNA (microsatellites) diversities of the Chilean blue whale aggregation site in order to verify the expectation of low genetic diversity in small populations. We then compare our findings with other blue whale aggregations in the Southern Hemisphere. Interestingly, although the estimated population size is small compared with the pre-whaling era, there is still considerable genetic diversity, even after the population crash, both in mitochondrial (N = 46) and nuclear (N = 52) markers (Hd = 0.890 and Ho = 0.692, respectively). Our results suggest that this diversity could be a consequence of the long generation times and the relatively short period of time elapsed since the end of whaling, which has been observed in other heavily-exploited whale populations. The genetic variability of blue whales on their southern Chile feeding grounds was similar to that found in other Southern Hemisphere blue whale feeding grounds. Our phylogenetic analysis of mtDNA haplotypes does not show extensive differentiation of populations among Southern Hemisphere blue whale feeding grounds. The present study suggests that although levels of genetic diversity are frequently used as estimators of population health, these parameters depend on the biology of the species and should be taken into account in a monitoring framework study to obtain a more complete picture of the conservation status of a population.
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Affiliation(s)
- Juan P Torres-Florez
- Instituto de Ciencias Ambientales y Evolutivas, Universidad Austral de ChileIndependencia 641, Valdivia, Chile
- Centro Ballena Azul/Blue whale CenterIndependencia 641, Valdivia, Chile
| | - Rodrigo Hucke-Gaete
- Centro Ballena Azul/Blue whale CenterIndependencia 641, Valdivia, Chile
- Instituto de Ciencias Marinas y Limnológicas, Universidad Austral de ChileIndependencia 641, Valdivia, Chile
| | - Howard Rosenbaum
- Ocean Giants Program, Wildlife Conservation Society2300 Southern Boulevard, Bronx, New York, 10460, USA
- Sackler Institute for Comparative Genomics, American Museum of Natural HistoryCentral Park West at 79th Street, New York, New York, 10024-5192, USA
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Gray MM, Wegmann D, Haasl RJ, White MA, Gabriel SI, Searle JB, Cuthbert RJ, Ryan PG, Payseur BA. Demographic history of a recent invasion of house mice on the isolated Island of Gough. Mol Ecol 2014; 23:1923-39. [PMID: 24617968 PMCID: PMC4086876 DOI: 10.1111/mec.12715] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2013] [Revised: 02/24/2014] [Accepted: 02/26/2014] [Indexed: 02/05/2023]
Abstract
Island populations provide natural laboratories for studying key contributors to evolutionary change, including natural selection, population size and the colonization of new environments. The demographic histories of island populations can be reconstructed from patterns of genetic diversity. House mice (Mus musculus) inhabit islands throughout the globe, making them an attractive system for studying island colonization from a genetic perspective. Gough Island, in the central South Atlantic Ocean, is one of the remotest islands in the world. House mice were introduced to Gough Island by sealers during the 19th century and display unusual phenotypes, including exceptionally large body size and carnivorous feeding behaviour. We describe genetic variation in Gough Island mice using mitochondrial sequences, nuclear sequences and microsatellites. Phylogenetic analysis of mitochondrial sequences suggested that Gough Island mice belong to Mus musculus domesticus, with the maternal lineage possibly originating in England or France. Cluster analyses of microsatellites revealed genetic membership for Gough Island mice in multiple coastal populations in Western Europe, suggesting admixed ancestry. Gough Island mice showed substantial reductions in mitochondrial and nuclear sequence variation and weak reductions in microsatellite diversity compared with Western European populations, consistent with a population bottleneck. Approximate Bayesian computation (ABC) estimated that mice recently colonized Gough Island (~100 years ago) and experienced a 98% reduction in population size followed by a rapid expansion. Our results indicate that the unusual phenotypes of Gough Island mice evolved rapidly, positioning these mice as useful models for understanding rapid phenotypic evolution.
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Affiliation(s)
- Melissa M. Gray
- Laboratory of Genetics, University of Wisconsin, Madison, WI 53706 USA
| | - Daniel Wegmann
- Department of Biology, University of Fribourg, Fribourg, Switzerland
| | - Ryan J. Haasl
- Laboratory of Genetics, University of Wisconsin, Madison, WI 53706 USA
| | - Michael A. White
- Laboratory of Genetics, University of Wisconsin, Madison, WI 53706 USA
- Divisions of Human Biology and Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109 USA
| | - Sofia I. Gabriel
- Centre for Environmental and Marine Studies, Departamento de Biologia Animal, Faculdade de Ciências da Universidade de Lisboa, 1749–016 Lisbon, Portugal
| | - Jeremy B. Searle
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY 14853-2701 USA
| | - Richard J. Cuthbert
- Royal Society for the Protection of Birds, The Lodge, Sandy, Bedfordshire, UK
| | - Peter G. Ryan
- Percy FitzPatrick Institute of African Ornithology, University of Cape Town, DST/NRF Centre of Excellence, Rondebosch 7701 South Africa
| | - Bret A. Payseur
- Laboratory of Genetics, University of Wisconsin, Madison, WI 53706 USA
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Karaiskou N, Tsakogiannis A, Gkagkavouzis K, Papika S, Latsoudis P, Kavakiotis I, Pantis J, Abatzopoulos TJ, Triantaphyllidis C, Triantafyllidis A. Greece: a Balkan subrefuge for a remnant red deer (cervus elaphus) population. J Hered 2014; 105:334-44. [PMID: 24558101 DOI: 10.1093/jhered/esu007] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
A number of phylogeographic studies have revealed the existence of multiple ice age refugia within the Balkan Peninsula, marking it as a biodiversity hotspot. Greece has been reported to harbor genetically differentiated lineages from the rest of Balkans for a number of mammal species. We therefore searched for distinct red deer lineages in Greece, by analyzing 78 samples originating from its last population in Parnitha Mountain (Central Greece). Additionally, we tested the impact of human-induced practices on this population. The presence of 2 discrete mtDNA lineages was inferred: 1) an abundant one not previously sampled in the Balkans and 2) a more restricted one shared with other Balkan populations, possibly the result of successful translocations of Eastern European individuals. Microsatellite-based analyses of 14 loci strongly support the existence of 2 subpopulations with relative frequencies similar to mitochondrial analyses. This study stresses the biogeographic importance of Central Greece as a separate Last Glacial Maximum period refugium within the Balkans. It also delineates the possible effects that recent translocations of red deer populations had on the genetic structuring within Parnitha. We suggest that the Greek red deer population of Parnitha is genetically distinct, and restocking programs should take this genetic evidence into consideration.
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Affiliation(s)
- Nikoleta Karaiskou
- the Department of Genetics, Developmental and Molecular Biology, School of Biology, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece
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Ciosi M, Masiga DK, Turner CMR. Laboratory colonisation and genetic bottlenecks in the tsetse fly Glossina pallidipes. PLoS Negl Trop Dis 2014; 8:e2697. [PMID: 24551260 PMCID: PMC3923722 DOI: 10.1371/journal.pntd.0002697] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2013] [Accepted: 12/31/2013] [Indexed: 02/08/2023] Open
Abstract
Background The IAEA colony is the only one available for mass rearing of Glossina pallidipes, a vector of human and animal African trypanosomiasis in eastern Africa. This colony is the source for Sterile Insect Technique (SIT) programs in East Africa. The source population of this colony is unclear and its genetic diversity has not previously been evaluated and compared to field populations. Methodology/Principal Findings We examined the genetic variation within and between the IAEA colony and its potential source populations in north Zimbabwe and the Kenya/Uganda border at 9 microsatellites loci to retrace the demographic history of the IAEA colony. We performed classical population genetics analyses and also combined historical and genetic data in a quantitative analysis using Approximate Bayesian Computation (ABC). There is no evidence of introgression from the north Zimbabwean population into the IAEA colony. Moreover, the ABC analyses revealed that the foundation and establishment of the colony was associated with a genetic bottleneck that has resulted in a loss of 35.7% of alleles and 54% of expected heterozygosity compared to its source population. Also, we show that tsetse control carried out in the 1990's is likely reduced the effective population size of the Kenya/Uganda border population. Conclusions/Significance All the analyses indicate that the area of origin of the IAEA colony is the Kenya/Uganda border and that a genetic bottleneck was associated with the foundation and establishment of the colony. Genetic diversity associated with traits that are important for SIT may potentially have been lost during this genetic bottleneck which could lead to a suboptimal competitiveness of the colony males in the field. The genetic diversity of the colony is lower than that of field populations and so, studies using colony flies should be interpreted with caution when drawing general conclusions about G. pallidipes biology. There is only one mass reared laboratory colony of Glossina pallidipes, a vector of human African trypanosomiasis and arguably the main vector of animal African trypanosomiasis in eastern Africa. This colony is the main one used for basic research on this species and is intended to be used for Sterile Insect Technique (SIT) programs for control of field populations. The origins of this colony are not clear and the extent to which it is genetically representative of the species is unknown. Using population genetics analyses to compare the current colony with two potential source populations we have shown that the colony is from the Kenya/Uganda border and that its foundation and establishment in the laboratory were associated with a genetic bottleneck, i.e. reduction of genetic variation due to increased genetic drift in a population of reduced size. As a consequence, the genetic diversity of the colony is lower than that of G. pallidipes field populations.
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Affiliation(s)
- Marc Ciosi
- Molecular Biology and Bioinformatics Unit, ICIPE, Nairobi, Kenya
- Institute of Infection, Immunity & Inflammation, University of Glasgow, Glasgow, United Kingdom
- * E-mail:
| | - Daniel K. Masiga
- Molecular Biology and Bioinformatics Unit, ICIPE, Nairobi, Kenya
- Institute of Infection, Immunity & Inflammation, University of Glasgow, Glasgow, United Kingdom
| | - Charles M. R. Turner
- Institute of Infection, Immunity & Inflammation, University of Glasgow, Glasgow, United Kingdom
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Bonin CA, Goebel ME, Hoffman JI, Burton RS. High male reproductive success in a low-density Antarctic fur seal (Arctocephalus gazella) breeding colony. Behav Ecol Sociobiol 2014. [DOI: 10.1007/s00265-013-1674-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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