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Femerling G, van Oosterhout C, Feng S, Bristol RM, Zhang G, Groombridge J, P Gilbert MT, Morales HE. Genetic Load and Adaptive Potential of a Recovered Avian Species that Narrowly Avoided Extinction. Mol Biol Evol 2023; 40:msad256. [PMID: 37995319 DOI: 10.1093/molbev/msad256] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Revised: 10/26/2023] [Accepted: 11/16/2023] [Indexed: 11/25/2023] Open
Abstract
High genetic diversity is a good predictor of long-term population viability, yet some species persevere despite having low genetic diversity. Here we study the genomic erosion of the Seychelles paradise flycatcher (Terpsiphone corvina), a species that narrowly avoided extinction after having declined to 28 individuals in the 1960s. The species recovered unassisted to over 250 individuals in the 1990s and was downlisted from Critically Endangered to Vulnerable in the International Union for the Conservation of Nature Red List in 2020. By comparing historical, prebottleneck (130+ years old) and modern genomes, we uncovered a 10-fold loss of genetic diversity. Highly deleterious mutations were partly purged during the bottleneck, but mildly deleterious mutations accumulated. The genome shows signs of historical inbreeding during the bottleneck in the 1960s, but low levels of recent inbreeding after demographic recovery. Computer simulations suggest that the species long-term small Ne reduced the masked genetic load and made the species more resilient to inbreeding and extinction. However, the reduction in genetic diversity due to the chronically small Ne and the severe bottleneck is likely to have reduced the species adaptive potential to face environmental change, which together with a higher load, compromises its long-term population viability. Thus, small ancestral Ne offers short-term bottleneck resilience but hampers long-term adaptability to environmental shifts. In light of rapid global rates of population decline, our work shows that species can continue to suffer the effect of their decline even after recovery, highlighting the importance of considering genomic erosion and computer modeling in conservation assessments.
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Affiliation(s)
- Georgette Femerling
- Section for Hologenomics, Globe Institute, University of Copenhagen, Copenhagen, Denmark
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, México
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada
| | | | - Shaohong Feng
- Center for Evolutionary & Organismal Biology, Zhejiang University School of Medicine, Hangzhou, China
- Liangzhu Laboratory, Zhejiang University Medical Center, Hangzhou, China
- Innovation Center of Yangtze River Delta, Zhejiang University, Jiashan, China
| | - Rachel M Bristol
- Mahe, Seychelles
- Division of Human and Social Sciences, Durrell Institute of Conservation and Ecology, School of Anthropology and Conservation, University of Kent, Canterbury, Kent, CT2 7NR, UK
| | - Guojie Zhang
- Center for Evolutionary & Organismal Biology, Zhejiang University School of Medicine, Hangzhou, China
- Liangzhu Laboratory, Zhejiang University Medical Center, Hangzhou, China
- Innovation Center of Yangtze River Delta, Zhejiang University, Jiashan, China
| | - Jim Groombridge
- Division of Human and Social Sciences, Durrell Institute of Conservation and Ecology, School of Anthropology and Conservation, University of Kent, Canterbury, Kent, CT2 7NR, UK
| | - M Thomas P Gilbert
- Section for Hologenomics, Globe Institute, University of Copenhagen, Copenhagen, Denmark
- University Museum, NTNU, Trondheim, Norway
| | - Hernán E Morales
- Section for Hologenomics, Globe Institute, University of Copenhagen, Copenhagen, Denmark
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2
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Ham-Dueñas JG, Canales-del-Castillo R, Voelker G, Ruvalcaba-Ortega I, Aguirre-Calderón CE, González-Rojas JI. Adaptive genetic diversity and evidence of population genetic structure in the endangered Sierra Madre Sparrow (Xenospiza baileyi). PLoS One 2020; 15:e0232282. [PMID: 32352998 PMCID: PMC7192469 DOI: 10.1371/journal.pone.0232282] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Accepted: 04/10/2020] [Indexed: 12/13/2022] Open
Abstract
The magnitude and distribution of genetic diversity through space and time can provide useful information relating to evolutionary potential and conservation status in threatened species. In assessing genetic diversity in species that are of conservation concern, several studies have focused on the use of Toll-like receptors (TLRs). TLRs are innate immune genes related to pathogen resistance, and polymorphisms may reflect not only levels of functional diversity, but may also be used to assess genetic diversity within and among populations. Here, we combined four potentially adaptive markers (TLRs) with one mitochondrial (COI) marker to evaluate genetic variation in the endangered Sierra Madre Sparrow (Xenospiza baileyi). This species offers an ideal model to investigate population and evolutionary genetic processes that may be occurring in a habitat restricted endangered species with disjunct populations (Mexico City and Durango), the census sizes of which differ by an order of magnitude. TLRs diversity in the Sierra Madre Sparrow was relatively high, which was not expected given its two small, geographically isolated populations. Genetic diversity was different (but not significantly so) between the two populations, with less diversity seen in the smaller Durango population. Population genetic structure between populations was due to isolation and different selective forces acting on different TLRs; population structure was also evident in COI. Reduction of genetic diversity in COI was observed over 20 years in the Durango population, a result likely caused by habitat loss, a factor which may be the main cause of diversity decline generally. Our results provide information related to the ways in which adaptive variation can be altered by demographic changes due to human-mediated habitat alterations. Furthermore, our findings may help to guide conservation schemes for both populations and their restricted habitat.
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Affiliation(s)
- José G. Ham-Dueñas
- Laboratorio de Biología de la Conservación y Desarrollo Sustentable. Cd. Universitaria, Universidad Autónoma de Nuevo León, Facultad de Ciencias Biológicas, San Nicolás de los Garza, Nuevo León, México
| | - Ricardo Canales-del-Castillo
- Laboratorio de Biología de la Conservación y Desarrollo Sustentable. Cd. Universitaria, Universidad Autónoma de Nuevo León, Facultad de Ciencias Biológicas, San Nicolás de los Garza, Nuevo León, México
- * E-mail:
| | - Gary Voelker
- Department of Wildlife and Fisheries Sciences, Biodiversity Research and Teaching Collections, Texas A&M University, College Station, Texas, United States of America
| | - Irene Ruvalcaba-Ortega
- Laboratorio de Biología de la Conservación y Desarrollo Sustentable. Cd. Universitaria, Universidad Autónoma de Nuevo León, Facultad de Ciencias Biológicas, San Nicolás de los Garza, Nuevo León, México
| | | | - José I. González-Rojas
- Laboratorio de Biología de la Conservación y Desarrollo Sustentable. Cd. Universitaria, Universidad Autónoma de Nuevo León, Facultad de Ciencias Biológicas, San Nicolás de los Garza, Nuevo León, México
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3
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Dussex N, von Seth J, Knapp M, Kardailsky O, Robertson BC, Dalén L. Complete genomes of two extinct New Zealand passerines show responses to climate fluctuations but no evidence for genomic erosion prior to extinction. Biol Lett 2019; 15:20190491. [PMID: 31480938 DOI: 10.1098/rsbl.2019.0491] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Human intervention, pre-human climate change (or a combination of both), as well as genetic effects, contribute to species extinctions. While many species from oceanic islands have gone extinct due to direct human impacts, the effects of pre-human climate change and human settlement on the genomic diversity of insular species and the role that loss of genomic diversity played in their extinctions remains largely unexplored. To address this question, we sequenced whole genomes of two extinct New Zealand passerines, the huia (Heteralocha acutirostris) and South Island kōkako (Callaeas cinereus). Both species showed similar demographic trajectories throughout the Pleistocene. However, the South Island kōkako continued to decline after the last glaciation, while the huia experienced some recovery. Moreover, there was no indication of inbreeding resulting from recent mating among closely related individuals in either species. This latter result indicates that population fragmentation associated with forest clearing by Maōri may not have been strong enough to lead to an increase in inbreeding and exposure to genomic erosion. While genomic erosion may not have directly contributed to their extinctions, further habitat fragmentation and the introduction of mammalian predators by Europeans may have been an important driver of extinction in huia and South Island kōkako.
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Affiliation(s)
- Nicolas Dussex
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Box 50007, Stockholm 10405, Sweden.,Department of Anatomy, University of Otago, PO Box 913, Dunedin 9016, New Zealand
| | - Johanna von Seth
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Box 50007, Stockholm 10405, Sweden.,Department of Zoology, Stockholm University, Stockholm 10691, Sweden
| | - Michael Knapp
- Department of Anatomy, University of Otago, PO Box 913, Dunedin 9016, New Zealand
| | - Olga Kardailsky
- Department of Anatomy, University of Otago, PO Box 913, Dunedin 9016, New Zealand
| | - Bruce C Robertson
- Department of Zoology, University of Otago, PO Box 56, Dunedin 9016, New Zealand
| | - Love Dalén
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Box 50007, Stockholm 10405, Sweden
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Affiliation(s)
- Graham P. Wallis
- Department of Zoology, University of Otago, Dunedin, New Zealand
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5
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Nelson NJ, Briskie JV, Constantine R, Monks J, Wallis GP, Watts C, Wotton DM. The winners: species that have benefited from 30 years of conservation action. J R Soc N Z 2018. [DOI: 10.1080/03036758.2018.1518249] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Affiliation(s)
- Nicola J. Nelson
- School of Biological Sciences, Victoria University of Wellington, Wellington, New Zealand
| | - James V. Briskie
- Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | | | - Joanne Monks
- Biodiversity Group, New Zealand Department of Conservation, Dunedin, New Zealand
| | - Graham P. Wallis
- Department of Zoology, University of Otago, Dunedin, New Zealand
| | - Corinne Watts
- Manaaki Whenua – Landcare Research, Hamilton, New Zealand
| | - Debra M. Wotton
- Biological Sciences, University of Canterbury, Christchurch, New Zealand
- Moa’s Ark Research, Wellington, New Zealand
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6
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Dufresnes C, Miquel C, Remollino N, Biollaz F, Salamin N, Taberlet P, Fumagalli L. Howling from the past: historical phylogeography and diversity losses in European grey wolves. Proc Biol Sci 2018; 285:rspb.2018.1148. [PMID: 30068681 DOI: 10.1098/rspb.2018.1148] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Accepted: 07/06/2018] [Indexed: 12/18/2022] Open
Abstract
Genetic bottlenecks resulting from human-induced population declines make alarming symbols for the irreversible loss of our natural legacy worldwide. The grey wolf (Canis lupus) is an iconic example of extreme declines driven by anthropogenic factors. Here, we assessed the genetic signatures of 150 years of wolf persecution throughout the Western Palaearctic by high-throughput mitochondrial DNA sequencing of historical specimens in an unprecedented spatio-temporal framework. Despite Late Pleistocene bottlenecks, we show that historical genetic variation had remained high throughout Europe until the last several hundred years. In Western Europe, where wolves nearly got fully exterminated, diversity dramatically collapsed at the turn of the twentieth century and recolonization from few homogeneous relict populations induced drastic shifts of genetic composition. By contrast, little genetic displacement and steady levels of diversity were maintained in Eastern European regions, where human persecution had lesser effects on wolf demography. By comparing prehistoric, historic and modern patterns of genetic diversity, our study hence traces the timeframe and the active human role in the decline of the grey wolf, an emblematic yet controversial animal which symbolizes the complex relationship between human societies and nature conservation.
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Affiliation(s)
- Christophe Dufresnes
- Laboratory for Conservation Biology, Department of Ecology and Evolution University of Lausanne, Biophore Building, CH-1015 Lausanne, Switzerland.,Department of Animal and Plant Sciences, University of Sheffield, Alfred Denny Building, Western Bank, Sheffield S10 2TN, UK
| | - Christian Miquel
- Laboratoire d'Écologie Alpine (LECA), UMR5553, BP53, 38041 Grenoble, Cedex 9, France
| | - Nadège Remollino
- Laboratory for Conservation Biology, Department of Ecology and Evolution University of Lausanne, Biophore Building, CH-1015 Lausanne, Switzerland
| | - François Biollaz
- Laboratory for Conservation Biology, Department of Ecology and Evolution University of Lausanne, Biophore Building, CH-1015 Lausanne, Switzerland.,Route Pra de Louetse 32, 1968 Mase, Switzerland
| | - Nicolas Salamin
- Department of Ecology and Evolution University of Lausanne, Biophore Building, CH-1015 Lausanne, Switzerland.,Department of Computational Biology University of Lausanne, Biophore Building, CH-1015 Lausanne, Switzerland
| | - Pierre Taberlet
- Laboratoire d'Écologie Alpine (LECA), UMR5553, BP53, 38041 Grenoble, Cedex 9, France
| | - Luca Fumagalli
- Laboratory for Conservation Biology, Department of Ecology and Evolution University of Lausanne, Biophore Building, CH-1015 Lausanne, Switzerland
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7
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Peacock MM, Hekkala ER, Kirchoff VS, Heki LG. Return of a giant: DNA from archival museum samples helps to identify a unique cutthroat trout lineage formerly thought to be extinct. ROYAL SOCIETY OPEN SCIENCE 2017; 4:171253. [PMID: 29291110 PMCID: PMC5717685 DOI: 10.1098/rsos.171253] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Accepted: 10/13/2017] [Indexed: 05/05/2023]
Abstract
Currently one small, native population of the culturally and ecologically important Lahontan cutthroat trout (Oncorhynchus clarkii henshawi, LCT, Federally listed) remains in the Truckee River watershed of northwestern Nevada and northeastern California. The majority of populations in this watershed were extirpated in the 1940s due to invasive species, overharvest, anthropogenic water consumption and changing precipitation regimes. In 1977, a population of cutthroat trout discovered in the Pilot Peak Mountains in the Bonneville basin of Utah, was putatively identified as the extirpated LCT lacustrine lineage native to Pyramid Lake in the Truckee River basin based on morphological and meristic characters. Our phylogenetic and Bayesian genotype clustering analyses of museum specimens collected from the large lakes (1872-1913) and contemporary samples collected from populations throughout the extant range provide evidence in support of a genetically distinct Truckee River basin origin for this population. Analysis of museum samples alone identified three distinct genotype clusters and historical connectivity among water bodies within the Truckee River basin. Baseline data from museum collections indicate that the extant Pilot Peak strain represents a remnant of the extirpated lacustrine lineage. Given the limitations on high-quality data when working with a sparse number of preserved museum samples, we acknowledge that, in the end, this may be a more complicated story. However, the paucity of remnant populations in the Truckee River watershed, in combination with data on the distribution of morphological, meristic and genetic data for Lahontan cutthroat trout, suggests that recovery strategies, particularly in the large lacustrine habitats should consider this lineage as an important part of the genetic legacy of this species.
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Affiliation(s)
- Mary M. Peacock
- Department of Biology, University of Nevada, Reno, NV 89557, USA
- Ecology, Evolution, and Conservation Biology Interdisciplinary Program, University of Nevada, Reno, NV 89557, USA
| | - Evon R. Hekkala
- Department of Biological Sciences, Fordham University, New York, NY 10458, USA
| | - Veronica S. Kirchoff
- Department of Biology, University of Nevada, Reno, NV 89557, USA
- United States Department of Agriculture, Agricultural Research Service, Reno, NV 89512, USA
| | - Lisa G. Heki
- United States Fish and Wildlife Service, Lahontan National Fish Hatchery Complex, 1340 Financial Blvd, Suite 234, Reno, NV 89502, USA
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8
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Mills LS. Some matchmaking advice when translocated immigrants are a population's last hope. Anim Conserv 2017. [DOI: 10.1111/acv.12333] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- L. Scott Mills
- Wildlife Biology Program and Office of Research and Creative Scholarship
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9
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Bergner LM, Dussex N, Jamieson IG, Robertson BC. European Colonization, Not Polynesian Arrival, Impacted Population Size and Genetic Diversity in the Critically Endangered New Zealand Kākāpō. J Hered 2016; 107:593-602. [DOI: 10.1093/jhered/esw065] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2016] [Accepted: 09/14/2016] [Indexed: 11/13/2022] Open
Abstract
Abstract
Island endemic species are often vulnerable to decline and extinction following human settlement, and the genetic study of historical museum specimens can be useful in understanding these processes. The kākāpō (Strigops habroptilus) is a critically endangered New Zealand parrot that was formerly widespread and abundant. It is well established that both Polynesian and European colonization of New Zealand impacted the native avifauna, but the timeframe and severity of impacts have differed depending on species. Here, we investigated the relative importance of the 2 waves of human settlement on kākāpō decline, using microsatellites and mitochondrial DNA (mtDNA) to characterize recent kākāpō genetic and demographic history. We analyzed samples from 49 contemporary individuals and 54 museum specimens dating from 1884 to 1985. Genetic diversity decreased significantly between historical and contemporary kākāpō, with a decline in mean number of microsatellite alleles from 6.15 to 3.08 and in number of mtDNA haplotypes from 17 to 3. Modeling of demographic history indicated a recent population bottleneck linked to the period of European colonization (approximately 5 generations ago) but did not support a major decline linked to Polynesian settlement. Effective population size estimates were also larger for historical than contemporary kākāpō. Our findings inform contemporary kākāpō management by indicating the timeframe and possible cause of the bottleneck, which has implications for the management of extant genetic diversity. We demonstrate the broader utility of a historical perspective in understanding causes of decline and managing extinction risk in contemporary endangered species.
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Affiliation(s)
- Laura M. Bergner
- From the Allan Wilson Centre for Molecular Ecology and Evolution, Department of Zoology, University of Otago, 340 Great King Street, Dunedin 9016, New Zealand (Bergner, Dussex, Jamieson, and Robertson) and Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow G12 8QQ, UK (Bergner)
| | - Nicolas Dussex
- From the Allan Wilson Centre for Molecular Ecology and Evolution, Department of Zoology, University of Otago, 340 Great King Street, Dunedin 9016, New Zealand (Bergner, Dussex, Jamieson, and Robertson) and Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow G12 8QQ, UK (Bergner)
| | - Ian G. Jamieson
- From the Allan Wilson Centre for Molecular Ecology and Evolution, Department of Zoology, University of Otago, 340 Great King Street, Dunedin 9016, New Zealand (Bergner, Dussex, Jamieson, and Robertson) and Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow G12 8QQ, UK (Bergner)
| | - Bruce C. Robertson
- From the Allan Wilson Centre for Molecular Ecology and Evolution, Department of Zoology, University of Otago, 340 Great King Street, Dunedin 9016, New Zealand (Bergner, Dussex, Jamieson, and Robertson) and Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow G12 8QQ, UK (Bergner)
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10
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Sutton JT, Robertson BC, Jamieson IG. MHC variation reflects the bottleneck histories of New Zealand passerines. Mol Ecol 2015; 24:362-73. [PMID: 25488544 DOI: 10.1111/mec.13039] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2014] [Revised: 12/01/2014] [Accepted: 12/03/2014] [Indexed: 11/27/2022]
Abstract
Most empirical evidence suggests that balancing selection does not counter the effects of genetic drift in shaping postbottleneck major histocompatibility complex (MHC) genetic diversity when population declines are severe or prolonged. However, few studies have been able to include data from historical specimens, or to compare populations/species with different bottleneck histories. In this study, we examined MHC class II B and microsatellite diversity in four New Zealand passerine (songbird) species that experienced moderate to very severe declines. We compared diversity from historical samples (collected c. 1884-1938) to present-day populations. Using a Bayesian framework, we found that the change in genetic diversity from historical to contemporary samples was affected by three main factors: (i) whether the data were based on MHC or microsatellite markers, (ii) species (as a surrogate for bottleneck severity) and (iii) whether the comparison between historical and contemporary samples was made using historical samples originating from the mainland, or using historical samples originating from islands. The greatest losses in genetic diversity occurred for the most severely bottlenecked species, particularly between historical mainland and contemporary samples. Additionally, where loss of diversity occurred, the change was greater for MHC genes compared to microsatellite loci.
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Affiliation(s)
- Jolene T Sutton
- Department of Zoology, Allan Wilson Centre for Molecular Ecology and Evolution, University of Otago, 340 Great King Street, PO Box 56, Dunedin, 9054, New Zealand; Department of Biology, University of Hawai'i at Mānoa, Edmondson Hall, 2538 McCarthy Mall, Honolulu, HI, 96822-2233, USA
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Grueber CE, Knafler GJ, King TM, Senior AM, Grosser S, Robertson B, Weston KA, Brekke P, Harris CLW, Jamieson IG. Toll-like receptor diversity in 10 threatened bird species: relationship with microsatellite heterozygosity. CONSERV GENET 2015. [DOI: 10.1007/s10592-014-0685-x] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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12
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Bristol RM, Tucker R, Dawson DA, Horsburgh G, Prys-Jones RP, Frantz AC, Krupa A, Shah NJ, Burke T, Groombridge JJ. Comparison of historical bottleneck effects and genetic consequences of re-introduction in a critically endangered island passerine. Mol Ecol 2013; 22:4644-62. [DOI: 10.1111/mec.12429] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2012] [Revised: 06/21/2013] [Accepted: 06/24/2013] [Indexed: 11/26/2022]
Affiliation(s)
- Rachel M. Bristol
- Durrell Institute of Conservation and Ecology; School of Anthropology and Conservation; University of Kent; Marlowe Building Canterbury CT2 7NR UK
- NERC Biomolecular Analysis Facility; Department of Animal and Plant Sciences; University of Sheffield; Western Bank; Alfred Denny Building Sheffield South Yorkshire S20 2TN UK
| | - Rachel Tucker
- Durrell Institute of Conservation and Ecology; School of Anthropology and Conservation; University of Kent; Marlowe Building Canterbury CT2 7NR UK
- NERC Biomolecular Analysis Facility; Department of Animal and Plant Sciences; University of Sheffield; Western Bank; Alfred Denny Building Sheffield South Yorkshire S20 2TN UK
- Imperial College London; Silwood Park Campus, Buckhurst Road Ascot Berkshire SL5 7PY UK
| | - Deborah A. Dawson
- NERC Biomolecular Analysis Facility; Department of Animal and Plant Sciences; University of Sheffield; Western Bank; Alfred Denny Building Sheffield South Yorkshire S20 2TN UK
| | - Gavin Horsburgh
- NERC Biomolecular Analysis Facility; Department of Animal and Plant Sciences; University of Sheffield; Western Bank; Alfred Denny Building Sheffield South Yorkshire S20 2TN UK
| | - Robert P. Prys-Jones
- Bird Group; Department of Life Sciences; Natural History Museum; Akeman St Tring Herts HP23 6AP UK
| | - Alain C. Frantz
- NERC Biomolecular Analysis Facility; Department of Animal and Plant Sciences; University of Sheffield; Western Bank; Alfred Denny Building Sheffield South Yorkshire S20 2TN UK
| | - Andy Krupa
- NERC Biomolecular Analysis Facility; Department of Animal and Plant Sciences; University of Sheffield; Western Bank; Alfred Denny Building Sheffield South Yorkshire S20 2TN UK
| | - Nirmal J. Shah
- Nature Seychelles; Centre for Environment and Education; Roche Caiman PO Box 1310 Mahé Seychelles
| | - Terry Burke
- NERC Biomolecular Analysis Facility; Department of Animal and Plant Sciences; University of Sheffield; Western Bank; Alfred Denny Building Sheffield South Yorkshire S20 2TN UK
| | - Jim J. Groombridge
- Durrell Institute of Conservation and Ecology; School of Anthropology and Conservation; University of Kent; Marlowe Building Canterbury CT2 7NR UK
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Grueber CE, Wallis GP, Jamieson IG. Genetic drift outweighs natural selection at toll-like receptor (TLR) immunity loci in a re-introduced population of a threatened species. Mol Ecol 2013; 22:4470-82. [DOI: 10.1111/mec.12404] [Citation(s) in RCA: 70] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2013] [Revised: 05/14/2013] [Accepted: 05/23/2013] [Indexed: 01/22/2023]
Affiliation(s)
| | - Graham P. Wallis
- Department of Zoology; University of Otago; PO Box 56 Dunedin 9054 New Zealand
| | - Ian G. Jamieson
- Department of Zoology; University of Otago; PO Box 56 Dunedin 9054 New Zealand
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14
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Johnston SE, Lindqvist M, Niemelä E, Orell P, Erkinaro J, Kent MP, Lien S, Vähä JP, Vasemägi A, Primmer CR. Fish scales and SNP chips: SNP genotyping and allele frequency estimation in individual and pooled DNA from historical samples of Atlantic salmon (Salmo salar). BMC Genomics 2013; 14:439. [PMID: 23819691 PMCID: PMC3716687 DOI: 10.1186/1471-2164-14-439] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2013] [Accepted: 06/18/2013] [Indexed: 12/02/2022] Open
Abstract
Background DNA extracted from historical samples is an important resource for understanding genetic consequences of anthropogenic influences and long-term environmental change. However, such samples generally yield DNA of a lower amount and quality, and the extent to which DNA degradation affects SNP genotyping success and allele frequency estimation is not well understood. We conducted high density SNP genotyping and allele frequency estimation in both individual DNA samples and pooled DNA samples extracted from dried Atlantic salmon (Salmo salar) scales stored at room temperature for up to 35 years, and assessed genotyping success, repeatability and accuracy of allele frequency estimation using a high density SNP genotyping array. Results In individual DNA samples, genotyping success and repeatability was very high (> 0.973 and > 0.998, respectively) in samples stored for up to 35 years; both increased with the proportion of DNA of fragment size > 1000 bp. In pooled DNA samples, allele frequency estimation was highly repeatable (Repeatability = 0.986) and highly correlated with empirical allele frequency measures (Mean Adjusted R2 = 0.991); allele frequency could be accurately estimated in > 95% of pooled DNA samples with a reference group of at least 30 individuals. SNPs located in polyploid regions of the genome were more sensitive to DNA degradation: older samples had lower genotyping success at these loci, and a larger reference panel of individuals was required to accurately estimate allele frequencies. Conclusions SNP genotyping was highly successful in degraded DNA samples, paving the way for the use of degraded samples in SNP genotyping projects. DNA pooling provides the potential for large scale population genetic studies with fewer assays, provided enough reference individuals are also genotyped and DNA quality is properly assessed beforehand. We provide recommendations for future studies intending to conduct high-throughput SNP genotyping and allele frequency estimation in historical samples.
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Sutton JT, Robertson BC, Grueber CE, Stanton JAL, Jamieson IG. Characterization of MHC class II B polymorphism in bottlenecked New Zealand saddlebacks reveals low levels of genetic diversity. Immunogenetics 2013; 65:619-33. [DOI: 10.1007/s00251-013-0708-7] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2012] [Accepted: 04/23/2013] [Indexed: 12/13/2022]
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16
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Ralston J, Kirchman JJ. Predicted range shifts in North American boreal forest birds and the effect of climate change on genetic diversity in blackpoll warblers (Setophaga striata). CONSERV GENET 2012. [DOI: 10.1007/s10592-012-0418-y] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Unraveling natural versus anthropogenic effects on genetic diversity within the southeastern beach mouse (Peromyscus polionotus niveiventris). CONSERV GENET 2012. [DOI: 10.1007/s10592-012-0417-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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18
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Jamieson IG, Allendorf FW. How does the 50/500 rule apply to MVPs? Trends Ecol Evol 2012; 27:578-84. [PMID: 22868005 DOI: 10.1016/j.tree.2012.07.001] [Citation(s) in RCA: 139] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2012] [Revised: 07/03/2012] [Accepted: 07/05/2012] [Indexed: 11/19/2022]
Affiliation(s)
- Ian G Jamieson
- Allan Wilson Centre, Department of Zoology, University of Otago, Dunedin, New Zealand.
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19
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Grueber CE, Wallis GP, King TM, Jamieson IG. Variation at innate immunity Toll-like receptor genes in a bottlenecked population of a New Zealand robin. PLoS One 2012; 7:e45011. [PMID: 23024782 PMCID: PMC3443209 DOI: 10.1371/journal.pone.0045011] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2012] [Accepted: 08/16/2012] [Indexed: 11/22/2022] Open
Abstract
Toll-like receptors (TLRs) are an ancient family of genes encoding transmembrane proteins that bind pathogen-specific molecules and initiate both innate and adaptive aspects of the immune response. Our goal was to determine whether these genes show sufficient genetic diversity in a bottlenecked population to be a useful addition or alternative to the more commonly employed major histocompatibility complex (MHC) genotyping in a conservation genetics context. We amplified all known avian TLR genes in a severely bottlenecked population of New Zealand's Stewart Island robin (Petroica australis rakiura), for which reduced microsatellite diversity was previously observed. We genotyped 17-24 birds from a reintroduced island population (including the 12 founders) for nine genes, seven of which were polymorphic. We observed a total of 24 single-nucleotide polymorphisms overall, 15 of which were non-synonymous, representing up to five amino-acid variants at a locus. One locus (TLR1LB) showed evidence of past directional selection. Results also confirmed a passerine duplication of TLR7. The levels of TLR diversity that we observe are sufficient to justify their further use in addressing conservation genetic questions, even in bottlenecked populations.
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Farrington HL, Petren K. A century of genetic change and metapopulation dynamics in the Galápagos warbler finches (Certhidea). Evolution 2011; 65:3148-61. [PMID: 22023582 DOI: 10.1111/j.1558-5646.2011.01385.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Populations that are connected by immigrants play an important role in evolutionary and conservation biology, yet we have little direct evidence of how such metapopulations change genetically over evolutionary time. We compared historic (1894-1906) to modern (1988-2006) genetic variation in 11 populations of warbler finches at 14 microsatellite loci. Although several lines of evidence suggest that Darwin's finches may be in decline, we found that the genetic diversity of warbler finches has not generally declined, and broad-scale patterns of variation remained similar over time. Contrary to expectations, inferred population sizes have generally increased over time (6-8%) as have immigration rates (8-16%), which may reflect a recent increase in the frequency and intensity of El Niño events. Individual island populations showed significant declines (18-19%) and also substantial gains (18-20%) in allelic richness over time. Changes in genetic diversity were correlated with changes in immigration rates, but did not correspond to population size or human disturbance. These results reflect the expected stabilizing properties of whole metapopulations over time. However, the dramatic and unpredictable changes observed in individual populations during this short time interval suggests that care should be taken when monitoring individual population fragments with snapshots of genetic variation.
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Affiliation(s)
- Heather L Farrington
- Department of Biological Sciences, University of Cincinnati, OH 45221-0006, USA.
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21
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Population genetic structure of the endangered Eastern Bristlebird, Dasyornis brachypterus; implications for conservation. CONSERV GENET 2011. [DOI: 10.1007/s10592-011-0210-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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22
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Ortego J, Yannic G, Shafer ABA, Mainguy J, Festa-Bianchet M, Coltman DW, Côté SD. Temporal dynamics of genetic variability in a mountain goat (Oreamnos americanus) population. Mol Ecol 2011; 20:1601-11. [PMID: 21366746 DOI: 10.1111/j.1365-294x.2011.05022.x] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
The association between population dynamics and genetic variability is of fundamental importance for both evolutionary and conservation biology. We combined long-term population monitoring and molecular genetic data from 123 offspring and their parents at 28 microsatellite loci to investigate changes in genetic diversity over 14 cohorts in a small and relatively isolated population of mountain goats (Oreamnos americanus) during a period of demographic increase. Offspring heterozygosity decreased while parental genetic similarity and inbreeding coefficients (F(IS) ) increased over the study period (1995-2008). Immigrants introduced three novel alleles into the population and matings between residents and immigrants produced more heterozygous offspring than local crosses, suggesting that immigration can increase population genetic variability. The population experienced genetic drift over the study period, reflected by a reduced allelic richness over time and an 'isolation-by-time' pattern of genetic structure. The temporal decline of individual genetic diversity despite increasing population size probably resulted from a combination of genetic drift due to small effective population size, inbreeding and insufficient counterbalancing by immigration. This study highlights the importance of long-term genetic monitoring to understand how demographic processes influence temporal changes of genetic diversity in long-lived organisms.
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Affiliation(s)
- Joaquín Ortego
- Département de biologie and Centre d'études nordiques, Université Laval, 1045 avenue de Médecine, Québec, Canada.
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Jamieson IG. Founder effects, inbreeding, and loss of genetic diversity in four avian reintroduction programs. CONSERVATION BIOLOGY : THE JOURNAL OF THE SOCIETY FOR CONSERVATION BIOLOGY 2011; 25:115-123. [PMID: 20825445 DOI: 10.1111/j.1523-1739.2010.01574.x] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
The number of individuals translocated and released as part of a reintroduction is often small, as is the final established population, because the reintroduction site is typically small. Small founder and small resulting populations can result in population bottlenecks, which are associated with increased rates of inbreeding and loss of genetic diversity, both of which can affect the long-term viability of reintroduced populations. I used information derived from pedigrees of four monogamous bird species reintroduced onto two different islands (220 and 259 ha) in New Zealand to compare the pattern of inbreeding and loss of genetic diversity among the reintroduced populations. Although reintroduced populations founded with few individuals had higher levels of inbreeding, as predicted, other factors, including biased sex ratio and skewed breeding success, contributed to high levels of inbreeding and loss of genetic diversity. Of the 10-58 individuals released, 4-25 genetic founders contributed at least one living descendent and yielded approximately 3-11 founder-genome equivalents (number of genetic founders assuming an equal contribution of offspring and no random loss of alleles across generations) after seven breeding seasons. This range is much lower than the 20 founder-genome equivalents recommended for captive-bred populations. Although the level of inbreeding in one reintroduced population initially reached three times that of a closely related species, the long-term estimated rate of inbreeding of this one population was approximately one-third that of the other species due to differences in carrying capacities of the respective reintroduction sites. The increasing number of reintroductions to suitable areas that are smaller than those I examined here suggests that it might be useful to develop long-term strategies and guidelines for reintroduction programs, which would minimize inbreeding and maintain genetic diversity.
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Affiliation(s)
- Ian G Jamieson
- Department of Zoology, University of Otago, Dunedin, New Zealand.
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BREKKE PATRICIA, BENNETT PETERM, SANTURE ANNAW, EWEN JOHNG. High genetic diversity in the remnant island population of hihi and the genetic consequences of re-introduction. Mol Ecol 2010; 20:29-45. [DOI: 10.1111/j.1365-294x.2010.04923.x] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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Alley MR, Hale KA, Cash W, Ha HJ, Howe L. Concurrent avian malaria and avipox virus infection in translocated South Island saddlebacks (Philesturnus carunculatus carunculatus). N Z Vet J 2010; 58:218-23. [PMID: 20676161 DOI: 10.1080/00480169.2010.68868] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
CASE HISTORY Outbreaks of mortality in South Island saddlebacks (Philesturnus carunculatus carunculatus) that had been translocated to two offshore islands in the Marlborough Sounds of New Zealand were investigated during the summers of 2002 and 2007. Both outbreaks were associated with a severe decrease in numbers of saddlebacks of up to 60% of approximately 200 birds. CLINICAL AND PATHOLOGICAL FINDINGS Many of the surviving birds were in poor condition, and had skin lesions on the legs and head. Necropsy showed pale liver and lungs, and a swollen spleen. Histopathology revealed schizonts resembling Plasmodium spp. within the cytoplasm of many hepatocytes and splenic histiocytes. The skin lesions consisted of epithelial proliferations containing numerous Bollinger bodies typical of avipox virus (APV) infection. Two different APV were isolated, using PCR, from two different birds exhibiting skin lesions. Each isolate had 100% sequence homology with APV members from either Clade A or Clade B. In addition, PCR analysis revealed that the Plasmodium elongatum present in infected birds belonged to a strain that was endemic in the population of North Island saddlebacks (Philesturnus carunculatus rufusater). DIAGNOSIS Concurrent infections with Plasmodium spp. haemoparasites and APV were identified as the likely cause of death in the birds examined. CONCLUSIONS AND CLINICAL RELEVANCE Although the Plasmodium spp. identified is thought to be endemic to saddlebacks in New Zealand, the affected birds were likely to be immunocompromised by concurrent APV infection or through lack of genetic diversity. Both the introduced mosquito Culex quinquefasicatus and the native mosquito Culex pervigilans are likely vectors for both these diseases, and the provision of water supplies less favourable to mosquito-breeding is recommended.
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Affiliation(s)
- M R Alley
- New Zealand Wildlife Health Centre, Massey University, Palmerston North, New Zealand.
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Hoeck PEA, Bollmer JL, Parker PG, Keller LF. Differentiation with drift: a spatio-temporal genetic analysis of Galapagos mockingbird populations (Mimus spp.). Philos Trans R Soc Lond B Biol Sci 2010; 365:1127-38. [PMID: 20194174 DOI: 10.1098/rstb.2009.0311] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Small and isolated island populations provide ideal systems to study the effects of limited population size, genetic drift and gene flow on genetic diversity. We assessed genetic diversity within and differentiation among 19 mockingbird populations on 15 Galápagos islands, covering all four endemic species, using 16 microsatellite loci. We tested for signs of drift and gene flow, and used historic specimens to assess genetic change over the last century and to estimate effective population sizes. Within-population genetic diversity and effective population sizes varied substantially among island populations and correlated strongly with island size, suggesting that island size serves as a good predictor for effective population size. Genetic differentiation among populations was pronounced and increased with geographical distance. A century of genetic drift did not change genetic diversity on an archipelago-wide scale, but genetic drift led to loss of genetic diversity in small populations, especially in one of the two remaining populations of the endangered Floreana mockingbird. Unlike in other Galápagos bird species such as the Darwin's finches, gene flow among mockingbird populations was low. The clear pattern of genetically distinct populations reflects the effects of genetic drift and suggests that Galápagos mockingbirds are evolving in relative isolation.
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Affiliation(s)
- Paquita E A Hoeck
- Zoological Museum, University of Zurich, , Winterthurerstrasse 190, 8057 Zurich, Switzerland.
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Parker KA, Hauber ME, Brunton DH. Contemporary cultural evolution of a conspecific recognition signal following serial translocations. Evolution 2010; 64:2431-41. [PMID: 20394665 DOI: 10.1111/j.1558-5646.2010.01013.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
The divergence of conspecific recognition signals (CRS) among isolated populations facilitates the evolution of behavioral barriers to gene flow. The influence of CRS evolution on signal effectiveness in isolated populations can be assessed by testing the salience of changes in CRS from surviving ancestral populations but founder events are rarely detected. The population history of the North Island (NI) saddleback Philesturnus rufusater is absolutely known following conservation translocations which increased the number of populations from 1 to 15. With one exception there is no gene flow between these populations. The translocations have generated interisland divergence of male rhythmical song (MRS), a culturally transmitted CRS. We conducted an experimental test of behavioral discrimination in NI saddlebacks exposed to familiar and unfamiliar MRS and found that responses were significantly stronger for familiar MRS, consistent with a model of contemporary cultural evolution leading to discrimination between geographic song variants. Significantly, this result demonstrates the rapid tempo with which discrimination of CRS might evolve within isolated populations and supports both bottleneck and cultural mutation hypotheses in CRS evolution. The evolutionary implications of contemporary cultural evolution in the production and perception of CRS merit debate on the time frames over which conservation management is evaluated.
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Affiliation(s)
- Kevin A Parker
- The Ecology and Conservation Group, Institute for Natural Sciences, Massey University, Private Bag 102904, North Shore Mail Centre, Auckland 1309, New Zealand.
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28
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Boessenkool S, Star B, Scofield RP, Seddon PJ, Waters JM. Lost in translation or deliberate falsification? Genetic analyses reveal erroneous museum data for historic penguin specimens. Proc Biol Sci 2009; 277:1057-64. [PMID: 20007185 DOI: 10.1098/rspb.2009.1837] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Historic museum specimens are increasingly used to answer a wide variety of questions in scientific research. Nevertheless, the scientific value of these specimens depends on the authenticity of the data associated with them. Here we use individual-based genetic analyses to demonstrate erroneous locality information for archive specimens from the late nineteenth century. Specifically, using 10 microsatellite markers, we analysed 350 contemporary and 43 historic yellow-eyed penguin (Megadyptes antipodes) specimens from New Zealand's South Island and sub-Antarctic regions. Factorial correspondence analysis and an assignment test strongly suggest that eight of the historic specimens purportedly of sub-Antarctic origin were in fact collected from the South Island. Interestingly, all eight specimens were obtained by the same collector, and all are currently held in the same museum collection. Further inspection of the specimen labels and evaluation of sub-Antarctic voyages did not reveal whether the erroneous data are caused by incorrect labelling or whether deliberate falsification was at play. This study highlights a promising extension to the well-known applications of assignment tests in molecular ecology, which can complement methods that are currently being applied for error detection in specimen data. Our results also serve as a warning to all who use archive specimens to invest time in the verification of collection information.
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Affiliation(s)
- Sanne Boessenkool
- Department of Zoology, University of Otago, 340 Great King Street, Dunedin, New Zealand.
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ROLLINS LEEANN, WOOLNOUGH ANDREWP, WILTON ALANN, SINCLAIR RON, SHERWIN WILLIAMB. Invasive species can't cover their tracks: using microsatellites to assist management of starling (Sturnus vulgaris) populations in Western Australia. Mol Ecol 2009; 18:1560-73. [DOI: 10.1111/j.1365-294x.2009.04132.x] [Citation(s) in RCA: 77] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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Jamieson IG, Taylor SS, Tracy LN, Kokko H, Armstrong DP. Why some species of birds do not avoid inbreeding: insights from New Zealand robins and saddlebacks. Behav Ecol 2009. [DOI: 10.1093/beheco/arp034] [Citation(s) in RCA: 65] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Johnson JA, Tingay RE, Culver M, Hailer F, Clarke ML, Mindell DP. Long-term survival despite low genetic diversity in the critically endangered Madagascar fish-eagle. Mol Ecol 2009; 18:54-63. [PMID: 19140964 DOI: 10.1111/j.1365-294x.2008.04012.x] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
The critically endangered Madagascar fish-eagle (Haliaeetus vociferoides) is considered to be one of the rarest birds of prey globally and at significant risk of extinction. In the most recent census, only 222 adult individuals were recorded with an estimated total breeding population of no more than 100-120 pairs. Here, levels of Madagascar fish-eagle population genetic diversity based on 47 microsatellite loci were compared with its sister species, the African fish-eagle (Haliaeetus vocifer), and 16 of these loci were also characterized in the white-tailed eagle (Haliaeetus albicilla) and the bald eagle (Haliaeetus leucocephalus). Overall, extremely low genetic diversity was observed in the Madagascar fish-eagle compared to other surveyed Haliaeetus species. Determining whether this low diversity is the result of a recent bottleneck or a more historic event has important implications for their conservation. Using a Bayesian coalescent-based method, we show that Madagascar fish-eagles have maintained a small effective population size for hundreds to thousands of years and that its low level of neutral genetic diversity is not the result of a recent bottleneck. Therefore, efforts made to prevent Madagascar fish-eagle extinction should place high priority on maintenance of habitat requirements and reducing direct and indirect human persecution. Given the current rate of deforestation in Madagascar, we further recommend that the population be expanded to occupy a larger geographical distribution. This will help the population persist when exposed to stochastic factors (e.g. climate and disease) that may threaten a species consisting of only 200 adult individuals while inhabiting a rapidly changing landscape.
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Affiliation(s)
- Jeff A Johnson
- The Peregrine Fund, 5668 West Flying Hawk Lane, Boise, ID 83709, USA.
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Ortego J, Aparicio JM, Cordero PJ, Calabuig G. Individual genetic diversity correlates with the size and spatial isolation of natal colonies in a bird metapopulation. Proc Biol Sci 2008; 275:2039-47. [PMID: 18505717 PMCID: PMC2596367 DOI: 10.1098/rspb.2008.0475] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2008] [Revised: 05/06/2008] [Accepted: 05/08/2008] [Indexed: 11/12/2022] Open
Abstract
The genetic consequences of small population size and isolation are of central concern in both population and conservation biology. Organisms with a metapopulation structure generally show effective population sizes that are much smaller than the number of mature individuals and this can reduce genetic diversity especially in small sized and isolated subpopulations. Here, we examine the association between heterozygosity and the size and spatial isolation of natal colonies in a metapopulation of lesser kestrels (Falco naumanni). For this purpose, we used capture-mark-recapture data to determine the patterns of immigration into the studied colonies, and 11 highly polymorphic microsatellite markers that allowed us to estimate genetic diversity of locally born individuals. We found that individuals born in smaller and more isolated colonies were genetically less diverse. These colonies received a lower number of immigrants, supporting the idea that both reduced gene flow and small population size are responsible for the genetic pattern observed. Our results are particularly intriguing because the lesser kestrel is a vagile and migratory species with great movement capacity and dispersal potential. Overall, this study provides evidence of the association between individual heterozygosity and the size and spatial isolation of natal colonies in a highly mobile vertebrate showing relatively frequent dispersal and low genetic differentiation among local subpopulations.
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Affiliation(s)
- Joaquín Ortego
- Grupo de Investigación de la Biodiversidad Genética y Cultural, Instituto de Investigación en Recursos Cinegéticos, Ronda de Toledo s/n, Ciudad Real, Spain.
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GRUEBER CATHERINEE, WALLIS GRAHAMP, JAMIESON IANG. Heterozygosity-fitness correlations and their relevance to studies on inbreeding depression in threatened species. Mol Ecol 2008; 17:3978-84. [DOI: 10.1111/j.1365-294x.2008.03910.x] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Massaro M, Starling-Windhof A, Briskie JV, Martin TE. Introduced mammalian predators induce behavioural changes in parental care in an endemic New Zealand bird. PLoS One 2008; 3:e2331. [PMID: 18523640 PMCID: PMC2396284 DOI: 10.1371/journal.pone.0002331] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2008] [Accepted: 04/28/2008] [Indexed: 11/19/2022] Open
Abstract
The introduction of predatory mammals to oceanic islands has led to the extinction of many endemic birds. Although introduced predators should favour changes that reduce predation risk in surviving bird species, the ability of island birds to respond to such novel changes remains unstudied. We tested whether novel predation risk imposed by introduced mammalian predators has altered the parental behaviour of the endemic New Zealand bellbird (Anthornis melanura). We examined parental behaviour of bellbirds at three woodland sites in New Zealand that differed in predation risk: 1) a mainland site with exotic predators present (high predation risk), 2) a mainland site with exotic predators experimentally removed (low risk recently) and, 3) an off-shore island where exotic predators were never introduced (low risk always). We also compared parental behaviour of bellbirds with two closely related Tasmanian honeyeaters (Phylidonyris spp.) that evolved with native nest predators (high risk always). Increased nest predation risk has been postulated to favour reduced parental activity, and we tested whether island bellbirds responded to variation in predation risk. We found that females spent more time on the nest per incubating bout with increased risk of predation, a strategy that minimised activity at the nest during incubation. Parental activity during the nestling period, measured as number of feeding visits/hr, also decreased with increasing nest predation risk across sites, and was lowest among the honeyeaters in Tasmania that evolved with native predators. These results demonstrate that some island birds are able to respond to increased risk of predation by novel predators in ways that appear adaptive. We suggest that conservation efforts may be more effective if they take advantage of the ability of island birds to respond to novel predators, especially when the elimination of exotic predators is not possible.
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Affiliation(s)
- Melanie Massaro
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand.
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TAYLOR SABRINAS, JAMIESON IANG. No evidence for loss of genetic variation following sequential translocations in extant populations of a genetically depauperate species. Mol Ecol 2007; 17:545-56. [DOI: 10.1111/j.1365-294x.2007.03591.x] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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