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Dumidae A, Subkrasae C, Ardpairin J, Pansri S, Homkaew C, Gordon CN, Mangkit B, Thanwisai A, Vitta A. Assessment of the genetic diversity of lymnaeid (Gastropoda: Pulmonata) snails and their infection status with trematode cercariae in different regions of Thailand. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2024; 119:105576. [PMID: 38408586 DOI: 10.1016/j.meegid.2024.105576] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Revised: 02/01/2024] [Accepted: 02/21/2024] [Indexed: 02/28/2024]
Abstract
Lymnaeid snails are some of the most widespread snails and are the first intermediate host of trematode parasites that affect human and livestock health. A full understanding of the genetic relationship of hosts and parasites is of paramount importance for effective parasite management. The present study assessed the prevalence of trematode larvae in lymnaeid snails and examined the genetic diversity of these snails collected across Thailand. We collected 672 lymnaeid snails from 39 locations in 22 provinces of six regions in Thailand. Subsequently, cercarial infection in the snails was observed by using the shedding method. Lymnaeid snails released 5 types of trematode cercariae, namely, xiphidiocercariae, echinostome cercariae I, echinostome cercariae II, furcocercous cercariae, and strigea cercariae. The phylogenetic analysis based on ITS2 and 28S rDNA sequences revealed 5 cercaria types assigned to four trematode families, of which two belong to the group of human intestinal flukes. Combination of shell morphology and sequence analysis of the mitochondrial COI and 16S rDNA genes, the lymnaeid snails were classified into two species, Radix rubiginosa and Orientogalba viridis. Moreover, the combined dataset of mtDNA genes (COI + 16S rDNA) from R. rubiginosa and O. viridis revealed 32 and 15 different haplotypes, respectively, of which only a few haplotypes were infected with cercariae. The genetic diversity and genetic structure revealed that R. rubiginosa and O. viridis experienced a bottleneck phenomenon, and showed limited gene flow between populations. Population demographic history analyses revealed that R. rubiginosa and O. viridis experienced population reductions followed by recent population expansion. These findings may improve our understanding of parasite-lymnaeid evolutionary relationships, as well as the underlying molecular genetic basis, which is information that can be used for further effective control of the spread of trematode disease.
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Affiliation(s)
- Abdulhakam Dumidae
- Department of Microbiology and Parasitology, Faculty of Medical Science, Naresuan University, Phitsanulok 65000, Thailand
| | - Chanakan Subkrasae
- Department of Microbiology and Parasitology, Faculty of Medical Science, Naresuan University, Phitsanulok 65000, Thailand
| | - Jiranun Ardpairin
- Department of Microbiology and Parasitology, Faculty of Medical Science, Naresuan University, Phitsanulok 65000, Thailand
| | - Supawan Pansri
- Department of Microbiology and Parasitology, Faculty of Medical Science, Naresuan University, Phitsanulok 65000, Thailand
| | - Chanatinat Homkaew
- Department of Microbiology and Parasitology, Faculty of Medical Science, Naresuan University, Phitsanulok 65000, Thailand
| | - Chadaporn Nuchjangreed Gordon
- Department of Medical Sciences, Faculty of Allied Health Sciences, Burapha University, Chonburi Province 20131, Thailand
| | - Bandid Mangkit
- Department of Veterinary Technology, Faculty of Veterinary Technology, Kasetsart University, Bangkok, Thailand, 10900
| | - Aunchalee Thanwisai
- Department of Microbiology and Parasitology, Faculty of Medical Science, Naresuan University, Phitsanulok 65000, Thailand; Centre of Excellence in Medical Biotechnology (CEMB), Faculty of Medical Science, Naresuan University, Phitsanulok 65000, Thailand; Center of Excellence for Biodiversity, Faculty of Sciences, Naresuan University, Phitsanulok 65000, Thailand
| | - Apichat Vitta
- Department of Microbiology and Parasitology, Faculty of Medical Science, Naresuan University, Phitsanulok 65000, Thailand; Centre of Excellence in Medical Biotechnology (CEMB), Faculty of Medical Science, Naresuan University, Phitsanulok 65000, Thailand; Center of Excellence for Biodiversity, Faculty of Sciences, Naresuan University, Phitsanulok 65000, Thailand.
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2
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Dumidae A, Subkrasae C, Ardpairin J, Pansri S, Homkaew C, Thanwisai A, Vitta A. Genetic variation of the freshwater snail Indoplanorbis exustus (Gastropoda: Planorbidae) in Thailand, inferred from 18S and 28S rDNA sequences. Parasitol Res 2024; 123:93. [PMID: 38212518 DOI: 10.1007/s00436-024-08120-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Accepted: 01/07/2024] [Indexed: 01/13/2024]
Abstract
Indoplanorbis exustus, a freshwater pulmonate snail, is widely distributed in tropical and subtropical zones and plays a significant role as an intermediate host for trematode parasites. Various genetic markers have been used for species identification and phylogenetic studies of this snail. However, there are limited studies about their molecular genetics based on nuclear ribosomal DNA (rDNA) genes. A genetic analysis of I. exustus in Thailand was conducted based on the nuclear 18S rDNA (339 bp) and 28S rDNA (1036 bp) genes. Indoplanorbis snails were collected from 29 localities in 21 provinces covering six regions of Thailand. Nucleotide sequences from 44 snails together with sequences from the GenBank database were examined for phylogenetic relationships and genetic diversity. All sequences of the selected nucleotide regions exhibited a high level of similarity (99%) to the sequences of I. exustus in the GenBank database. The maximum likelihood tree based on the 18S and 28S rDNA fragment sequences of I. exustus in Thailand revealed only one group with clear separation from another genus in the family Planorbidae. The I. exustus 28S rDNA sequences showed intraspecific genetic divergence ranging from 0 to 0.78% and were classified into 8 different haplotypes. Conversely, the 18S rDNA data showed lower variation than the 28S rDNA data and revealed a single haplotype and intraspecific distances of zero among all sampled individuals. The haplotype network of 28S rDNA sequences of I. exustus in Thailand revealed six unique haplotypes and two haplotypes shared by at least two regions. Overall, both markers were successful in the identification of I. exustus. However, these markers, particularly the 18S rDNA, may not be suitable for genetic analysis within the species, particularly for population genetic studies, due to their limited variation as seen in this study. In summary, this study not only enhances understanding of genetic variation in I. exustus but is also useful for the selection of molecular markers in future genetic research.
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Affiliation(s)
- Abdulhakam Dumidae
- Department of Microbiology and Parasitology, Faculty of Medical Science, Naresuan University, Phitsanulok, 65000, Thailand
| | - Chanakan Subkrasae
- Department of Microbiology and Parasitology, Faculty of Medical Science, Naresuan University, Phitsanulok, 65000, Thailand
| | - Jiranun Ardpairin
- Department of Microbiology and Parasitology, Faculty of Medical Science, Naresuan University, Phitsanulok, 65000, Thailand
| | - Supawan Pansri
- Department of Microbiology and Parasitology, Faculty of Medical Science, Naresuan University, Phitsanulok, 65000, Thailand
| | - Chanatinat Homkaew
- Department of Microbiology and Parasitology, Faculty of Medical Science, Naresuan University, Phitsanulok, 65000, Thailand
| | - Aunchalee Thanwisai
- Department of Microbiology and Parasitology, Faculty of Medical Science, Naresuan University, Phitsanulok, 65000, Thailand
- Centre of Excellence in Medical Biotechnology (CEMB), Faculty of Medical Science, Naresuan University, Phitsanulok, 65000, Thailand
- Center of Excellence for Biodiversity, Faculty of Sciences, Naresuan University, Phitsanulok, 65000, Thailand
| | - Apichat Vitta
- Department of Microbiology and Parasitology, Faculty of Medical Science, Naresuan University, Phitsanulok, 65000, Thailand.
- Centre of Excellence in Medical Biotechnology (CEMB), Faculty of Medical Science, Naresuan University, Phitsanulok, 65000, Thailand.
- Center of Excellence for Biodiversity, Faculty of Sciences, Naresuan University, Phitsanulok, 65000, Thailand.
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3
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Wallén J, Norén K, Angerbjörn A, Eide NE, Landa A, Flagstad Ø. Context‐dependent demographic and genetic effects of translocation from a captive breeding project. Anim Conserv 2022. [DOI: 10.1111/acv.12831] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Affiliation(s)
- J. Wallén
- Department of Zoology Stockholm University Stockholm Sweden
| | - K. Norén
- Department of Zoology Stockholm University Stockholm Sweden
| | - A. Angerbjörn
- Department of Zoology Stockholm University Stockholm Sweden
| | - N. E. Eide
- Norwegian Institute for Nature Research Trondheim Norway
| | - A. Landa
- Norwegian Institute for Nature Research Bergen Norway
| | - Ø. Flagstad
- Norwegian Institute for Nature Research Trondheim Norway
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4
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Searching for genetic evidence of demographic decline in an arctic seabird: beware of overlapping generations. Heredity (Edinb) 2022; 128:364-376. [PMID: 35246618 PMCID: PMC9076905 DOI: 10.1038/s41437-022-00515-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Revised: 02/12/2022] [Accepted: 02/14/2022] [Indexed: 11/09/2022] Open
Abstract
Genetic data are useful for detecting sudden population declines in species that are difficult to study in the field. Yet this indirect approach has its own drawbacks, including population structure, mutation patterns, and generation overlap. The ivory gull (Pagophila eburnea), a long-lived Arctic seabird, is currently suffering from rapid alteration of its primary habitat (i.e., sea ice), and dramatic climatic events affecting reproduction and recruitment. However, ivory gulls live in remote areas, and it is difficult to assess the population trend of the species across its distribution. Here we present complementary microsatellite- and SNP-based genetic analyses to test a recent bottleneck genetic signal in ivory gulls over a large portion of their distribution. With attention to the potential effects of population structure, mutation patterns, and sample size, we found no significant signatures of population decline worldwide. At a finer scale, we found a significant bottleneck signal at one location in Canada. These results were compared with predictions from simulations showing how generation time and generation overlap can delay and reduce the bottleneck microsatellite heterozygosity excess signal. The consistency of the results obtained with independent methods strongly indicates that the species shows no genetic evidence of an overall decline in population size. However, drawing conclusions related to the species' population trends will require a better understanding of the effect of age structure in long-lived species. In addition, estimates of the effective global population size of ivory gulls were surprisingly low (~1000 ind.), suggesting that the evolutionary potential of the species is not assured.
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5
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Setzke C, Wong C, Russello MA. Genotyping-in-Thousands by sequencing of archival fish scales reveals maintenance of genetic variation following a severe demographic contraction in kokanee salmon. Sci Rep 2021; 11:22798. [PMID: 34815428 PMCID: PMC8611073 DOI: 10.1038/s41598-021-01958-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Accepted: 11/08/2021] [Indexed: 11/23/2022] Open
Abstract
Historical DNA analysis of archival samples has added new dimensions to population genetic studies, enabling spatiotemporal approaches for reconstructing population history and informing conservation management. Here we tested the efficacy of Genotyping-in-Thousands by sequencing (GT-seq) for collecting targeted single nucleotide polymorphism genotypic data from archival scale samples, and applied this approach to a study of kokanee salmon (Oncorhynchus nerka) in Kluane National Park and Reserve (KNPR; Yukon, Canada) that underwent a severe 12-year population decline followed by a rapid rebound. We genotyped archival scales sampled pre-crash and contemporary fin clips collected post-crash, revealing high coverage (> 90% average genotyping across all individuals) and low genotyping error (< 0.01% within-libraries, 0.60% among-libraries) despite the relatively poor quality of recovered DNA. We observed slight decreases in expected heterozygosity, allelic diversity, and effective population size post-crash, but none were significant, suggesting genetic diversity was retained despite the severe demographic contraction. Genotypic data also revealed the genetic distinctiveness of a now extirpated population just outside of KNPR, revealing biodiversity loss at the northern edge of the species distribution. More broadly, we demonstrated GT-seq as a valuable tool for collecting genome-wide data from archival samples to address basic questions in ecology and evolution, and inform applied research in wildlife conservation and fisheries management.
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Affiliation(s)
- Christopher Setzke
- Department of Biology, University of British Columbia, Okanagan Campus, 3247 University Way, Kelowna, BC, V1V 1V7, Canada
| | - Carmen Wong
- Parks Canada Yukon Field Unit, Suite 205 - 300 Main St, Whitehorse, YT, Y1A 2B5, Canada
| | - Michael A Russello
- Department of Biology, University of British Columbia, Okanagan Campus, 3247 University Way, Kelowna, BC, V1V 1V7, Canada.
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6
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Martínez-García L, Ferrari G, Oosting T, Ballantyne R, van der Jagt I, Ystgaard I, Harland J, Nicholson R, Hamilton-Dyer S, Baalsrud HT, Brieuc MSO, Atmore LM, Burns F, Schmölcke U, Jakobsen KS, Jentoft S, Orton D, Hufthammer AK, Barrett JH, Star B. Historical Demographic Processes Dominate Genetic Variation in Ancient Atlantic Cod Mitogenomes. Front Ecol Evol 2021. [DOI: 10.3389/fevo.2021.671281] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Ancient DNA (aDNA) approaches have been successfully used to infer the long-term impacts of climate change, domestication, and human exploitation in a range of terrestrial species. Nonetheless, studies investigating such impacts using aDNA in marine species are rare. Atlantic cod (Gadus morhua), is an economically important species that has experienced dramatic census population declines during the last century. Here, we investigated 48 ancient mitogenomes from historical specimens obtained from a range of archeological excavations in northern Europe dated up to 6,500 BCE. We compare these mitogenomes to those of 496 modern conspecifics sampled across the North Atlantic Ocean and adjacent seas. Our results confirm earlier observations of high levels of mitogenomic variation and a lack of mutation-drift equilibrium—suggestive of population expansion. Furthermore, our temporal comparison yields no evidence of measurable mitogenomic changes through time. Instead, our results indicate that mitogenomic variation in Atlantic cod reflects past demographic processes driven by major historical events (such as oscillations in sea level) and subsequent gene flow rather than contemporary fluctuations in stock abundance. Our results indicate that historical and contemporaneous anthropogenic pressures such as commercial fisheries have had little impact on mitogenomic diversity in a wide-spread marine species with high gene flow such as Atlantic cod. These observations do not contradict evidence that overfishing has had negative consequences for the abundance of Atlantic cod and the importance of genetic variation in implementing conservation strategies. Instead, these observations imply that any measures toward the demographic recovery of Atlantic cod in the eastern Atlantic, will not be constrained by recent loss of historical mitogenomic variation.
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7
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Becheler R, Guillemin M, Stoeckel S, Mauger S, Saunier A, Brante A, Destombe C, Valero M. After a catastrophe, a little bit of sex is better than nothing: Genetic consequences of a major earthquake on asexual and sexual populations. Evol Appl 2020; 13:2086-2100. [PMID: 32908606 PMCID: PMC7463374 DOI: 10.1111/eva.12967] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Revised: 03/04/2020] [Accepted: 03/05/2020] [Indexed: 11/27/2022] Open
Abstract
Catastrophic events can have profound effects on the demography of a population and consequently on genetic diversity. The dynamics of postcatastrophic recovery and the role of sexual versus asexual reproduction in buffering the effects of massive perturbations remain poorly understood, in part because the opportunity to document genetic diversity before and after such events is rare. Six natural (purely sexual) and seven cultivated (mainly clonal due to farming practices) populations of the red alga Agarophyton chilense were surveyed along the Chilean coast before, in the days after and 2 years after the 8.8 magnitude earthquake in 2010. The genetic diversity of sexual populations appeared sensitive to this massive perturbation, notably through the loss of rare alleles immediately after the earthquake. By 2012, the levels of diversity returned to those observed before the catastrophe, probably due to migration. In contrast, enhanced rates of clonality in cultivated populations conferred a surprising ability to buffer the instantaneous loss of diversity. After the earthquake, farmers increased the already high rate of clonality to maintain the few surviving beds, but most of them collapsed rapidly. Contrasting fates between sexual and clonal populations suggest that betting on strict clonality to sustain production is risky, probably because this extreme strategy hampered adaptation to the brutal environmental perturbation induced by the catastrophe.
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Affiliation(s)
- Ronan Becheler
- Centro de Conservación MarinaDepartamento de EcologíaFacultad de Ciencias BiológicasPontificia Universidad Católica de ChileCasillaChile
- UMI 3614Evolutionary Biology and Ecology of AlgaeCNRSSorbonne UniversitéUniversidad Austral de ChilePontificia Universidad Católica de ChileRoscoffFrance
| | - Marie‐Laure Guillemin
- UMI 3614Evolutionary Biology and Ecology of AlgaeCNRSSorbonne UniversitéUniversidad Austral de ChilePontificia Universidad Católica de ChileRoscoffFrance
- Instituto de Ciencias Ambientales y EvolutivasFacultad de CienciasUniversidad Austral de ChileValdiviaChile
| | - Solenn Stoeckel
- UMR1349 Institute for Genetics, Environment and Plant ProtectionINRALe RheuFrance
| | - Stéphane Mauger
- UMI 3614Evolutionary Biology and Ecology of AlgaeCNRSSorbonne UniversitéUniversidad Austral de ChilePontificia Universidad Católica de ChileRoscoffFrance
| | - Alice Saunier
- UMI 3614Evolutionary Biology and Ecology of AlgaeCNRSSorbonne UniversitéUniversidad Austral de ChilePontificia Universidad Católica de ChileRoscoffFrance
- Instituto de Ciencias Ambientales y EvolutivasFacultad de CienciasUniversidad Austral de ChileValdiviaChile
| | - Antonio Brante
- Departamento de EcologíaFacultad de CienciasUniversidad Católica de la Santísima Concepción (UCSC)ConcepciónChile
- Centro de Investigación en Biodiversidad y Ambientes Sustentables (CIBAS)UCSCConcepciónChile
| | - Christophe Destombe
- UMI 3614Evolutionary Biology and Ecology of AlgaeCNRSSorbonne UniversitéUniversidad Austral de ChilePontificia Universidad Católica de ChileRoscoffFrance
| | - Myriam Valero
- UMI 3614Evolutionary Biology and Ecology of AlgaeCNRSSorbonne UniversitéUniversidad Austral de ChilePontificia Universidad Católica de ChileRoscoffFrance
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8
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Prôa M, Nanova O. Severe population bottleneck and cranial morphology change in the Mednyi Island subspecies of Arctic fox Vulpes lagopus (Carnivora: Canidae). MAMMALIA 2020. [DOI: 10.1515/mammalia-2018-0165] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Abstract
Arctic foxes, Vulpes lagopus living on Mednyi Island suffered a drastic decline in population size in the late 1970s due to an outbreak of mange epizootic. This dramatic fall in numbers rendered the subspecies endangered, and the concomitant loss of variability resulted in a population bottleneck. Here, we investigate whether differences in cranial morphology between Mednyi Island Arctic foxes and Bering Island Arctic foxes could be attributed to the severe population bottleneck suffered by the Mednyi population in the 1970s. We used morphometric traits as proxies for genetic data to provide estimates of FST. Results show higher FST estimates for the Mednyi population than for the Bering population, which we interpret as a bottleneck signature. FST results also indicate a pattern of divergence between the two populations consistent with random genetic drift. Bottleneck detection is critical for the interpretation of the demographic history of the endangered Mednyi Island Arctic fox, with consequences for conservation management.
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Affiliation(s)
- Miguel Prôa
- Centro de Investigação em Antropologia e Saúde, Departamento de Ciências da Vida , Universidade de Coimbra , Apartado 3046 , 3001-401 Coimbra , Portugal
| | - Olga Nanova
- Zoological Museum , M.V. Lomonosov Moscow State University , Bol’shaya Nikitskaya, 2 , Moscow 125009 , Russia
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9
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Larsson P, von Seth J, Hagen IJ, Götherström A, Androsov S, Germonpré M, Bergfeldt N, Fedorov S, Eide NE, Sokolova N, Berteaux D, Angerbjörn A, Flagstad Ø, Plotnikov V, Norén K, Díez-Del-Molino D, Dussex N, Stanton DWG, Dalén L. Consequences of past climate change and recent human persecution on mitogenomic diversity in the arctic fox. Philos Trans R Soc Lond B Biol Sci 2019; 374:20190212. [PMID: 31679495 PMCID: PMC6863501 DOI: 10.1098/rstb.2019.0212] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Ancient DNA provides a powerful means to investigate the timing, rate and extent of population declines caused by extrinsic factors, such as past climate change and human activities. One species probably affected by both these factors is the arctic fox, which had a large distribution during the last glaciation that subsequently contracted at the start of the Holocene. More recently, the arctic fox population in Scandinavia went through a demographic bottleneck owing to human persecution. To investigate the consequences of these processes, we generated mitogenome sequences from a temporal dataset comprising Pleistocene, historical and modern arctic fox samples. We found no evidence that Pleistocene populations in mid-latitude Europe or Russia contributed to the present-day gene pool of the Scandinavian population, suggesting that postglacial climate warming led to local population extinctions. Furthermore, during the twentieth-century bottleneck in Scandinavia, at least half of the mitogenome haplotypes were lost, consistent with a 20-fold reduction in female effective population size. In conclusion, these results suggest that the arctic fox in mainland Western Europe has lost genetic diversity as a result of both past climate change and human persecution. Consequently, it might be particularly vulnerable to the future challenges posed by climate change. This article is part of a discussion meeting issue 'The past is a foreign country: how much can the fossil record actually inform conservation?'
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Affiliation(s)
- Petter Larsson
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden.,Department of Zoology, Stockholm University, Stockholm, Sweden
| | - Johanna von Seth
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden.,Department of Zoology, Stockholm University, Stockholm, Sweden
| | | | - Anders Götherström
- Department of Archaeology and Classical Studies, Stockholm University, Stockholm, Sweden
| | | | - Mietje Germonpré
- Operational Direction 'Earth and History of Life', Royal Belgian Institute of Natural Sciences, Brussels, Belgium
| | - Nora Bergfeldt
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden.,Department of Zoology, Stockholm University, Stockholm, Sweden
| | - Sergey Fedorov
- Mammoth Museum of Institute of Applied Ecology of the North, North-Eastern Federal University, Yakutsk, Republic Sakha (Yakutia), Russia
| | - Nina E Eide
- Norwegian Institute for Nature Research, Trondheim, Norway
| | - Natalia Sokolova
- Arctic Research Station of Institute of Plant and Animal Ecology, Ural Branch of Russian Academy of Sciences, Yamal-Nenets Autonomous District, Russia.,Arctic Research Center of Yamal-Nenets Autonomous District, Salekhard, Russia
| | - Dominique Berteaux
- Canada Research Chair on Northern Biodiversity and Centre for Northern Studies, Université du Québec à Rimouski, Rimouski, Canada
| | | | | | - Valeri Plotnikov
- Academy of Sciences of Sakha Republic, Lenin Avenue 33, Republic of Sakha, Yakutia, Russia
| | - Karin Norén
- Department of Zoology, Stockholm University, Stockholm, Sweden
| | - David Díez-Del-Molino
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden.,Department of Zoology, Stockholm University, Stockholm, Sweden
| | - Nicolas Dussex
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden
| | - David W G Stanton
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden
| | - Love Dalén
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden.,Department of Zoology, Stockholm University, Stockholm, Sweden
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10
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Lonsinger RC, Daniel D, Adams JR, Waits LP. Consideration of sample source for establishing reliable genetic microsatellite data from mammalian carnivore specimens held in natural history collections. J Mammal 2019. [DOI: 10.1093/jmammal/gyz112] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
AbstractSpecimens from natural history collections (NHCs) are increasingly being used for genetic studies and can provide information on extinct populations, facilitate comparisons of historical and contemporary populations, produce baseline data before environmental changes, and elucidate patterns of change. Destructive sampling for DNA may be in disagreement with NHC goals of long-term care and maintenance. Differentiating quality among sample sources can direct destructive sampling to the source predicted to yield the highest quality DNA and most reliable data, potentially reducing damage to specimens, laboratory costs, and genotyping errors. We used the kit fox (Vulpes macrotis) as a model species and evaluated the quality and reliability of genetic data obtained from carnivoran specimens via three different sample sources: cranial bones, nasal bones, and toepads. We quantified variation in microsatellite amplification success and genotyping error rates and assessed the reliability of source-specific genic data. Toepads had the highest amplification success rates and lowest genotyping error rates. Shorter loci had higher amplification success and lower allelic dropout rates than longer loci. There were substantial differences in the reliability of resulting multilocus genotypes. Toepads produced the most reliable data, required the fewest replicates, and therefore, had the lowest costs to achieve reliable data. Our results demonstrate that the quality of DNA obtained from specimens varies by sample source and can inform NHCs when evaluating requests for destructive sampling. Our results suggest that prior to large-scale specimen sampling, researchers should conduct pilot studies to differentiate among source-specific data reliability, identify high performing loci, reduce costs of analyses, and minimize destructive sampling.
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Affiliation(s)
- Robert C Lonsinger
- Department of Natural Resource Management, South Dakota State University, Brookings, SD, USA
| | - David Daniel
- Economics, Applied Statistics and International Business Department, New Mexico State University, Las Cruces, NM, USA
| | - Jennifer R Adams
- Department of Fish and Wildlife Sciences, University of Idaho, Moscow, ID, USA
| | - Lisette P Waits
- Department of Fish and Wildlife Sciences, University of Idaho, Moscow, ID, USA
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11
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Lacey EA, Takenaka R, LaBarbera K, Tammone MN. Ecological and demographic impacts of a recent volcanic eruption on two endemic patagonian rodents. PLoS One 2019; 14:e0213311. [PMID: 30845255 PMCID: PMC6405110 DOI: 10.1371/journal.pone.0213311] [Citation(s) in RCA: 5] [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: 11/13/2018] [Accepted: 02/18/2019] [Indexed: 11/18/2022] Open
Abstract
Catastrophic events can significantly impact the demographic processes that shape natural populations of organisms. However, linking the outcomes of such events to specific demographic parameters is often challenging due to a lack of detailed pre-event data. The eruption of the Puyehue-Cordon Caulle volcanic complex on 4 June 2011 had profound consequences for the biota of southwestern Argentina. Our long-term behavioral, ecological, and demographic studies of two species of tuco-tucos (Ctenomys sociabilis and C. haigi) that occur in the region most heavily impacted by ash fall from the eruption provided an unusual opportunity to assess the effects of this event on natural populations of mammals. The post-eruption density of the study population for each species was markedly reduced compared to pre-eruption values, with the relative magnitude of this reduction being greater for the group-living C. sociabilis. The more extensive data set for this species indicated that ash fall from the eruption altered the food resources available to these animals; differences in pre- and post-eruption stable isotope signatures for fur samples from C. sociabilis were consistent with observed changes in vegetation. Per capita female reproductive success was also reduced in this species during the first breeding season following the eruption. Based on our detailed demographic records for C. sociabilis, neither survival of yearling females from 2010 to 2011 nor the percentage of unmarked females in the study population in 2011 differed from pre-eruption values. Instead, the post-eruption decrease in population density for C. sociabilis appeared to reflect reduced within-population recruitment of juvenile females to the 2011 breeding population. Although the eruption did not result in the local extinction of either study population, the demographic consequences detected are likely to have impacted the effective sizes of these populations, creating important opportunities to link specific demographic parameters to previously reported decreases in genetic variability detected after this significant natural event.
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Affiliation(s)
- Eileen A. Lacey
- Museum of Vertebrate Zoology and Department of Integrative Biology, University of California, Berkeley, CA, United States of America
- * E-mail:
| | - Risa Takenaka
- Museum of Vertebrate Zoology and Department of Integrative Biology, University of California, Berkeley, CA, United States of America
| | - Katie LaBarbera
- Museum of Vertebrate Zoology and Department of Integrative Biology, University of California, Berkeley, CA, United States of America
| | - Mauro N. Tammone
- Programa de Estudios Aplicados a la Conservación del Parque Nacional Nahuel Huapi, Bariloche, Río Negro, Argentina
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12
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Jensen EL, Edwards DL, Garrick RC, Miller JM, Gibbs JP, Cayot LJ, Tapia W, Caccone A, Russello MA. Population genomics through time provides insights into the consequences of decline and rapid demographic recovery through head-starting in a Galapagos giant tortoise. Evol Appl 2018; 11:1811-1821. [PMID: 30459831 PMCID: PMC6231475 DOI: 10.1111/eva.12682] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Revised: 07/09/2018] [Accepted: 07/16/2018] [Indexed: 12/26/2022] Open
Abstract
Population genetic theory related to the consequences of rapid population decline is well-developed, but there are very few empirical studies where sampling was conducted before and after a known bottleneck event. Such knowledge is of particular importance for species restoration, given links between genetic diversity and the probability of long-term persistence. To directly evaluate the relationship between current genetic diversity and past demographic events, we collected genome-wide single nucleotide polymorphism data from prebottleneck historical (c.1906) and postbottleneck contemporary (c.2014) samples of Pinzón giant tortoises (Chelonoidis duncanensis; n = 25 and 149 individuals, respectively) endemic to a single island in the Galapagos. Pinzón giant tortoises had a historically large population size that was reduced to just 150-200 individuals in the mid 20th century. Since then, Pinzón's tortoise population has recovered through an ex situ head-start programme in which eggs or pre-emergent individuals were collected from natural nests on the island, reared ex situ in captivity until they were 4-5 years old and subsequently repatriated. We found that the extent and distribution of genetic variation in the historical and contemporary samples were very similar, with the latter group not exhibiting the characteristic genetic patterns of recent population decline. No population structure was detected either spatially or temporally. We estimated an effective population size (N e) of 58 (95% CI = 50-69) for the postbottleneck population; no prebottleneck N e point estimate was attainable (95% CI = 39-infinity) likely due to the sample size being lower than the true N e. Overall, the historical sample provided a valuable benchmark for evaluating the head-start captive breeding programme, revealing high retention of genetic variation and no skew in representation despite the documented bottleneck event. Moreover, this work demonstrates the effectiveness of head-starting in rescuing the Pinzón giant tortoise from almost certain extinction.
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Affiliation(s)
- Evelyn L. Jensen
- Department of BiologyUniversity of British Columbia OkanaganKelownaBritish ColumbiaCanada
- Present address:
Department of BiologyQueen's UniversityKingstonOntarioCanada
| | | | - Ryan C. Garrick
- Department of BiologyUniversity of MississippiOxfordMississippi
| | - Joshua M. Miller
- Department of Ecology and Evolutionary BiologyYale UniversityNew HavenConnecticut
| | - James P. Gibbs
- College of Environmental Science and ForestryState University of New YorkSyracuseNew York
| | | | - Washington Tapia
- Department of Applied ResearchGalapagos National Park ServicePuerto AyoraEcuador
- Galapagos ConservancySanta CruzEcuador
| | - Adalgisa Caccone
- Department of Ecology and Evolutionary BiologyYale UniversityNew HavenConnecticut
| | - Michael A. Russello
- Department of BiologyUniversity of British Columbia OkanaganKelownaBritish ColumbiaCanada
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13
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Lonsinger RC, Adams JR, Waits LP. Evaluating effective population size and genetic diversity of a declining kit fox population using contemporary and historical specimens. Ecol Evol 2018; 8:12011-12021. [PMID: 30598795 PMCID: PMC6303725 DOI: 10.1002/ece3.4660] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Revised: 09/24/2018] [Accepted: 10/03/2018] [Indexed: 01/06/2023] Open
Abstract
Loss of genetic diversity has serious conservation consequences (e.g., loss of adaptive potential, reduced population viability), but is difficult to evaluate without developing long-term, multigenerational datasets. Alternatively, historical samples can provide insights into changes in genetic diversity and effective population size (N e). Kit foxes (Vulpes macrotis) are a species of conservation concern across much of their range. In western Utah, kit fox abundance has declined precipitously from historical levels, causing concern about population persistence. We analyzed genetic samples from museum specimens and contemporary scats to evaluate temporal changes in (a) genetic diversity and (b) N e for kit foxes in western Utah, and (c) discuss our findings with respect to population risk and conservation. The N e of kit foxes in western Utah has decreased substantially. When compared to established conservation thresholds for N e (e.g., the 50/500 rule), observed levels suggest the population may be at risk of inbreeding depression and local extinction. In contrast, we found no significant decrease in genetic diversity associated with declining N e. We detected evidence of low levels of immigration into the population and suspect genetic diversity may have been maintained by this previously undescribed gene flow from adjacent populations. Low or intermittent immigration may serve to temper the potential short-term negative consequences of low N e. We recommend that kit fox conservation efforts focus on evaluating and maintaining landscape connectivity. We demonstrate how historical specimens can provide a baseline of comparison for contemporary populations, highlighting the importance of natural history collections to conservation during a period of declining funding and support.
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Affiliation(s)
- Robert C. Lonsinger
- Department of Natural Resource ManagementSouth Dakota State UniversityBrookingsSouth Dakota
| | - Jennifer R. Adams
- Department of Fish and Wildlife SciencesUniversity of IdahoMoscowIdaho
| | - Lisette P. Waits
- Department of Fish and Wildlife SciencesUniversity of IdahoMoscowIdaho
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14
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Fugassa MH, Petrigh RS, Fernández PM, Carballido Catalayud M, Belleli C. Fox parasites in pre-Columbian times: Evidence from the past to understand the current helminth assemblages. Acta Trop 2018; 185:380-384. [PMID: 29902423 DOI: 10.1016/j.actatropica.2018.06.007] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Revised: 05/22/2018] [Accepted: 06/09/2018] [Indexed: 11/19/2022]
Abstract
This work aims to increase the information on the entero-parasitism in Holocene carnivores, by examining coprolites found in Patagonia. Molecular analysis was conducted following the Authenticity Criteria to Determine Ancient DNA sequences. The nucleotide sequences showed 99% of identity with the Control Region sequences of Lycalopex culpaeus (culpeo fox). Coprolites were positive for gastrointestinal parasites. The presence of Alaria sp. and Clonorchis sp. represents the first record for pre-Columbian America. The parasitological findings suggest the importance of these carnivores for the dissemination of their own parasites and those to their prey in rockshelters, areas with high re-use of space.
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Affiliation(s)
- M H Fugassa
- Lab. de Parasitología de Sitios Arqueológicos, Universidad Nacional de Mar del Plata, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas, Argentina.
| | - R S Petrigh
- Lab. de Parasitología de Sitios Arqueológicos, Universidad Nacional de Mar del Plata, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas, Argentina
| | - P M Fernández
- Consejo Nacional de Investigaciones Científicas y Técnicas, Argentina; Instituto Nacional de Antropología y Pensamiento Latinoamericano, Argentina; Universidad de Buenos Aires, Argentina
| | - M Carballido Catalayud
- Consejo Nacional de Investigaciones Científicas y Técnicas, Argentina; Instituto Nacional de Antropología y Pensamiento Latinoamericano, Argentina; Universidad de Buenos Aires, Argentina
| | - C Belleli
- Instituto Nacional de Antropología y Pensamiento Latinoamericano, Argentina; Universidad de Buenos Aires, Argentina
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15
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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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16
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McDonough MM, Parker LD, Rotzel McInerney N, Campana MG, Maldonado JE. Performance of commonly requested destructive museum samples for mammalian genomic studies. J Mammal 2018. [DOI: 10.1093/jmammal/gyy080] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Affiliation(s)
- Molly M McDonough
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
- Center for Conservation Genomics, Smithsonian Conservation Biology Institute, National Zoo, Washington, DC, USA
| | - Lillian D Parker
- Center for Conservation Genomics, Smithsonian Conservation Biology Institute, National Zoo, Washington, DC, USA
- Environmental Science and Policy Department, George Mason University, Fairfax, VA, USA
| | - Nancy Rotzel McInerney
- Center for Conservation Genomics, Smithsonian Conservation Biology Institute, National Zoo, Washington, DC, USA
| | - Michael G Campana
- Center for Conservation Genomics, Smithsonian Conservation Biology Institute, National Zoo, Washington, DC, USA
- Environmental Science and Policy Department, George Mason University, Fairfax, VA, USA
| | - Jesús E Maldonado
- Center for Conservation Genomics, Smithsonian Conservation Biology Institute, National Zoo, Washington, DC, USA
- Environmental Science and Policy Department, George Mason University, Fairfax, VA, USA
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17
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Significant loss of mitochondrial diversity within the last century due to extinction of peripheral populations in eastern gorillas. Sci Rep 2018; 8:6551. [PMID: 29695730 PMCID: PMC5917027 DOI: 10.1038/s41598-018-24497-7] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2017] [Accepted: 04/03/2018] [Indexed: 12/12/2022] Open
Abstract
Species and populations are disappearing at an alarming rate as a direct result of human activities. Loss of genetic diversity associated with population decline directly impacts species' long-term survival. Therefore, preserving genetic diversity is of considerable conservation importance. However, to assist in conservation efforts, it is important to understand how genetic diversity is spatially distributed and how it changes due to anthropogenic pressures. In this study, we use historical museum and modern faecal samples of two critically endangered eastern gorilla taxa, Grauer's (Gorilla beringei graueri) and mountain gorillas (Gorilla beringei beringei), to directly infer temporal changes in genetic diversity within the last century. Using over 100 complete mitochondrial genomes, we observe a significant decline in haplotype and nucleotide diversity in Grauer's gorillas. By including historical samples from now extinct populations we show that this decline can be attributed to the loss of peripheral populations rather than a decrease in genetic diversity within the core range of the species. By directly quantifying genetic changes in the recent past, our study shows that human activities have severely impacted eastern gorilla genetic diversity within only four to five generations. This rapid loss calls for dedicated conservation actions, which should include preservation of the remaining peripheral populations.
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18
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Jensen EL, Miller JM, Edwards DL, Garrick RC, Tapia W, Caccone A, Russello MA. Temporal Mitogenomics of the Galapagos Giant Tortoise from Pinzón Reveals Potential Biases in Population Genetic Inference. J Hered 2018; 109:631-640. [DOI: 10.1093/jhered/esy016] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2017] [Accepted: 04/03/2018] [Indexed: 11/13/2022] Open
Affiliation(s)
- Evelyn L Jensen
- Department of Biology, University of British Columbia Okanagan, Kelowna, BC, Canada
| | - Joshua M Miller
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT
| | | | - Ryan C Garrick
- Department of Biology, University of Mississippi, Oxford, MS
| | - Washington Tapia
- Department of Applied Research, Galapagos National Park Service, Puerto Ayora, Galápagos, Ecuador
- Galapagos Conservancy, Santa Cruz, Galápagos, Ecuador
| | - Adalgisa Caccone
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT
| | - Michael A Russello
- Department of Biology, University of British Columbia Okanagan, Kelowna, BC, Canada
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19
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Genetic diversity through time and space: diversity and demographic history from natural history specimens and serially sampled contemporary populations of the threatened Gouldian finch (Erythrura gouldiae). CONSERV GENET 2018. [DOI: 10.1007/s10592-018-1051-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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20
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van der Valk T, Lona Durazo F, Dalén L, Guschanski K. Whole mitochondrial genome capture from faecal samples and museum-preserved specimens. Mol Ecol Resour 2017; 17:e111-e121. [DOI: 10.1111/1755-0998.12699] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2017] [Revised: 06/20/2017] [Accepted: 06/28/2017] [Indexed: 01/01/2023]
Affiliation(s)
- Tom van der Valk
- Animal Ecology; Department of Ecology and Genetics; Evolutionary Biology Centre; Uppsala University; Uppsala Sweden
| | - Frida Lona Durazo
- Animal Ecology; Department of Ecology and Genetics; Evolutionary Biology Centre; Uppsala University; Uppsala Sweden
| | - Love Dalén
- Department of Bioinformatics and Genetics; Swedish Museum of Natural History; Stockholm Sweden
| | - Katerina Guschanski
- Animal Ecology; Department of Ecology and Genetics; Evolutionary Biology Centre; Uppsala University; Uppsala Sweden
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21
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Krojerová-Prokešová J, Barančeková M, Kawata Y, Oshida T, Igota H, Koubek P. Genetic differentiation between introduced Central European sika and source populations in Japan: effects of isolation and demographic events. Biol Invasions 2017. [DOI: 10.1007/s10530-017-1424-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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22
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Tammone MN, Lavin BR, Pardiñas UFJ, Lacey EA. Post-extinction discovery of a population of the highly endemic colonial tuco-tuco (Ctenomys sociabilis). J Mammal 2016. [DOI: 10.1093/jmammal/gyw146] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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23
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Norén K, Godoy E, Dalén L, Meijer T, Angerbjörn A. Inbreeding depression in a critically endangered carnivore. Mol Ecol 2016; 25:3309-18. [DOI: 10.1111/mec.13674] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2015] [Revised: 03/12/2016] [Accepted: 04/13/2016] [Indexed: 10/21/2022]
Affiliation(s)
- Karin Norén
- Department of Zoology; Stockholm University; SE-10691 Stockholm Sweden
| | - Erika Godoy
- Department of Zoology; Stockholm University; SE-10691 Stockholm Sweden
| | - Love Dalén
- Department of Zoology; Stockholm University; SE-10691 Stockholm Sweden
- Department of Bioinformatics and Genetics; Swedish Museum of Natural History; SE-10405 Stockholm Sweden
| | - Tomas Meijer
- Department of Zoology; Stockholm University; SE-10691 Stockholm Sweden
- Department of Pathology and Wildlife Diseases; National Veterinary Institute; SE-751 89 Uppsala Sweden
| | - Anders Angerbjörn
- Department of Zoology; Stockholm University; SE-10691 Stockholm Sweden
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24
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Reduced Genetic Diversity and Increased Structure in American Mink on the Swedish Coast following Invasive Species Control. PLoS One 2016; 11:e0157972. [PMID: 27333328 PMCID: PMC4917106 DOI: 10.1371/journal.pone.0157972] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2016] [Accepted: 06/08/2016] [Indexed: 11/19/2022] Open
Abstract
Eradication and population reductions are often used to mitigate the negative impacts of non-native invasive species on native biodiversity. However, monitoring the effectiveness of non-native species control programmes is necessary to evaluate the efficacy of these measures. Genetic monitoring could provide valuable insights into temporal changes in demographic, ecological, and evolutionary processes in invasive populations being subject to control programmes. Such programmes should cause a decrease in effective population size and/or in genetic diversity of the targeted non-native species and an increase in population genetic structuring over time. We used microsatellite DNA data from American mink (Neovison vison) to determine whether the removal of this predator on the Koster Islands archipelago and the nearby Swedish mainland affected genetic variation over six consecutive years of mink culling by trappers as part of a population control programme. We found that on Koster Islands allelic richness decreased (from on average 4.53 to 3.55), genetic structuring increased, and effective population size did not change. In contrast, the mink population from the Swedish coast showed no changes in genetic diversity or structure, suggesting the stability of this population over 6 years of culling. Effective population size did not change over time but was higher on the coast than on the islands across all years. Migration rates from the islands to the coast were almost two times higher than from the coast to the islands. Most migrants leaving the coast were localised on the southern edge of the archipelago, as expected from the direction of the sea current between the two sites. Genetic monitoring provided valuable information on temporal changes in the population of American mink suggesting that this approach can be used to evaluate and improve control programmes of invasive vertebrates.
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25
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Basto MP, Santos-Reis M, Simões L, Grilo C, Cardoso L, Cortes H, Bruford MW, Fernandes C. Assessing Genetic Structure in Common but Ecologically Distinct Carnivores: The Stone Marten and Red Fox. PLoS One 2016; 11:e0145165. [PMID: 26727497 PMCID: PMC4699814 DOI: 10.1371/journal.pone.0145165] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2014] [Accepted: 11/30/2015] [Indexed: 11/23/2022] Open
Abstract
The identification of populations and spatial genetic patterns is important for ecological and conservation research, and spatially explicit individual-based methods have been recognised as powerful tools in this context. Mammalian carnivores are intrinsically vulnerable to habitat fragmentation but not much is known about the genetic consequences of fragmentation in common species. Stone martens (Martes foina) and red foxes (Vulpes vulpes) share a widespread Palearctic distribution and are considered habitat generalists, but in the Iberian Peninsula stone martens tend to occur in higher quality habitats. We compared their genetic structure in Portugal to see if they are consistent with their differences in ecological plasticity, and also to illustrate an approach to explicitly delineate the spatial boundaries of consistently identified genetic units. We analysed microsatellite data using spatial Bayesian clustering methods (implemented in the software BAPS, GENELAND and TESS), a progressive partitioning approach and a multivariate technique (Spatial Principal Components Analysis-sPCA). Three consensus Bayesian clusters were identified for the stone marten. No consensus was achieved for the red fox, but one cluster was the most probable clustering solution. Progressive partitioning and sPCA suggested additional clusters in the stone marten but they were not consistent among methods and were geographically incoherent. The contrasting results between the two species are consistent with the literature reporting stricter ecological requirements of the stone marten in the Iberian Peninsula. The observed genetic structure in the stone marten may have been influenced by landscape features, particularly rivers, and fragmentation. We suggest that an approach based on a consensus clustering solution of multiple different algorithms may provide an objective and effective means to delineate potential boundaries of inferred subpopulations. sPCA and progressive partitioning offer further verification of possible population structure and may be useful for revealing cryptic spatial genetic patterns worth further investigation.
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Affiliation(s)
- Mafalda P. Basto
- Ce3C – Centre for Ecology, Evolution and Environmental Changes, Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal
- Cardiff School of Biosciences, Cardiff University, Cardiff, United Kingdom
- * E-mail:
| | - Margarida Santos-Reis
- Ce3C – Centre for Ecology, Evolution and Environmental Changes, Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal
| | - Luciana Simões
- Ce3C – Centre for Ecology, Evolution and Environmental Changes, Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal
| | - Clara Grilo
- Centro Brasileiro de Estudos em Ecologia de Estradas/Programa de Pós-graduação em Ecologia Aplicada, Universidade Federal de Lavras, Lavras, Minas Gerais, Brasil
| | - Luís Cardoso
- Departamento de Ciências Veterinárias, Escola de Ciências Agrárias e Veterinárias, Universidade de Trás-os-Montes e Alto Douro (UTAD), Vila Real, Portugal
| | - Helder Cortes
- Laboratório de Parasitologia Victor Caeiro, Instituto de Ciências Agrárias e Ambientais Mediterrânicas (ICAAM), Universidade de Évora, Évora, Portugal
| | - Michael W. Bruford
- Cardiff School of Biosciences, Cardiff University, Cardiff, United Kingdom
| | - Carlos Fernandes
- Ce3C – Centre for Ecology, Evolution and Environmental Changes, Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal
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26
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Norén K, Statham MJ, Ågren EO, Isomursu M, Flagstad Ø, Eide NE, Berg TBG, Bech-Sanderhoff L, Sacks BN. Genetic footprints reveal geographic patterns of expansion in Fennoscandian red foxes. GLOBAL CHANGE BIOLOGY 2015; 21:3299-3312. [PMID: 26058388 DOI: 10.1111/gcb.12922] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2014] [Accepted: 01/29/2015] [Indexed: 06/04/2023]
Abstract
Population expansions of boreal species are among the most substantial ecological consequences of climate change, potentially transforming both structure and processes of northern ecosystems. Despite their importance, little is known about expansion dynamics of boreal species. Red foxes (Vulpes vulpes) are forecasted to become a keystone species in northern Europe, a process stemming from population expansions that began in the 19th century. To identify the relative roles of geographic and demographic factors and the sources of northern European red fox population expansion, we genotyped 21 microsatellite loci in modern and historical (1835-1941) Fennoscandian red foxes. Using Bayesian clustering and Bayesian inference of migration rates, we identified high connectivity and asymmetric migration rates across the region, consistent with source-sink dynamics, whereby more recently colonized sampling regions received immigrants from multiple sources. There were no clear clines in allele frequency or genetic diversity as would be expected from a unidirectional range expansion from south to north. Instead, migration inferences, demographic models and comparison to historical red fox genotypes suggested that the population expansion of the red fox is a consequence of dispersal from multiple sources, as well as in situ demographic growth. Together, these findings provide a rare glimpse into the anatomy of a boreal range expansion and enable informed predictions about future changes in boreal communities.
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Affiliation(s)
- Karin Norén
- Mammalian Ecology and Conservation Unit, Center for Veterinary Genetics, University of California Davis, Davis, CA, USA
- Department of Zoology, Stockholm University, SE-106 91, Stockholm, Sweden
| | - Mark J Statham
- Mammalian Ecology and Conservation Unit, Center for Veterinary Genetics, University of California Davis, Davis, CA, USA
| | - Erik O Ågren
- National Veterinary Institute, Department of Pathology and Wildlife Diseases, SE-751 89, Uppsala, Sweden
| | - Marja Isomursu
- Finnish Food Safety Authority Evira, Production Animal and Wildlife Health Research Unit, Elektroniikkatie 5, FIN-90590, Oulu, Finland
| | - Øystein Flagstad
- Norwegian Institute for Nature Research, N-7485, Trondheim, Norway
| | - Nina E Eide
- Norwegian Institute for Nature Research, N-7485, Trondheim, Norway
| | | | - Lene Bech-Sanderhoff
- Naturama - Modern Natural History, Dronningemaen 30, DK-5700, Svendborg, Denmark
| | - Benjamin N Sacks
- Mammalian Ecology and Conservation Unit, Center for Veterinary Genetics, University of California Davis, Davis, CA, USA
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27
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Xenikoudakis G, Ersmark E, Tison JL, Waits L, Kindberg J, Swenson JE, Dalén L. Consequences of a demographic bottleneck on genetic structure and variation in the Scandinavian brown bear. Mol Ecol 2015; 24:3441-54. [PMID: 26042479 DOI: 10.1111/mec.13239] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2014] [Revised: 05/07/2015] [Accepted: 05/08/2015] [Indexed: 11/30/2022]
Abstract
The Scandinavian brown bear went through a major decline in population size approximately 100 years ago, due to intense hunting. After being protected, the population subsequently recovered and today numbers in the thousands. The genetic diversity in the contemporary population has been investigated in considerable detail, and it has been shown that the population consists of several subpopulations that display relatively high levels of genetic variation. However, previous studies have been unable to resolve the degree to which the demographic bottleneck impacted the contemporary genetic structure and diversity. In this study, we used mitochondrial and microsatellite DNA markers from pre- and postbottleneck Scandinavian brown bear samples to investigate the effect of the bottleneck. Simulation and multivariate analysis suggested the same genetic structure for the historical and modern samples, which are clustered into three subpopulations in southern, central and northern Scandinavia. However, the southern subpopulation appears to have gone through a marked change in allele frequencies. When comparing the mitochondrial DNA diversity in the whole population, we found a major decline in haplotype numbers across the bottleneck. However, the loss of autosomal genetic diversity was less pronounced, although a significant decline in allelic richness was observed in the southern subpopulation. Approximate Bayesian computations provided clear support for a decline in effective population size during the bottleneck, in both the southern and northern subpopulations. These results have implications for the future management of the Scandinavian brown bear because they indicate a recent loss in genetic diversity and also that the current genetic structure may have been caused by historical ecological processes rather than recent anthropogenic persecution.
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Affiliation(s)
- G Xenikoudakis
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, SE-10405, Stockholm, Sweden.,Department of Zoology, Stockholm University, SE-106 91, Stockholm, Sweden
| | - E Ersmark
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, SE-10405, Stockholm, Sweden.,Department of Zoology, Stockholm University, SE-106 91, Stockholm, Sweden
| | - J-L Tison
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, SE-10405, Stockholm, Sweden
| | - L Waits
- Department of Fish and Wildlife Sciences, University of Idaho, 875 Perimeter Drive MS 1136, Moscow, ID, 83844, USA
| | - J Kindberg
- Department of Wildlife, Fish, and Environmental Studies, Swedish University of Agricultural Sciences, SE-90183, Umeå, Sweden
| | - J E Swenson
- Department of Ecology and Natural Resource Management, Norwegian University of Life Sciences, NO-1432, Ås, Norway.,Norwegian Institute for Nature Research, PO Box 5685 Sluppen, NO-7485, Trondheim, Norway
| | - L Dalén
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, SE-10405, Stockholm, Sweden
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Tison JL, Blennow V, Palkopoulou E, Gustafsson P, Roos A, Dalén L. Population structure and recent temporal changes in genetic variation in Eurasian otters from Sweden. CONSERV GENET 2014. [DOI: 10.1007/s10592-014-0664-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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29
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Jansson E, Harmoinen J, Ruokonen M, Aspi J. Living on the edge: reconstructing the genetic history of the Finnish wolf population. BMC Evol Biol 2014; 14:64. [PMID: 24678616 PMCID: PMC4033686 DOI: 10.1186/1471-2148-14-64] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2014] [Accepted: 03/05/2014] [Indexed: 11/19/2022] Open
Abstract
Background Many western European carnivore populations became almost or completely eradicated during the last ~200 years, but are now recovering. Extirpation of wolves started in Finland in the 19th century, and for more than 150 years the population size of wolves has remained small. To investigate historical patterns of genetic variation, we extracted DNA from 114 wolf samples collected in zoological museums over the last ~150 years. Fifteen microsatellite loci were used to look at genotypic variation in this historical sample. Additionally, we amplified a 430 bp sequence of mtDNA control region from the same samples. Contemporary wolf samples (N = 298) obtained after the population recovery in the mid-1990s, were used as a reference. Results Our analyses of mtDNA revealed reduced variation in the mtDNA control region through the loss of historical haplotypes observed prior to wolf declines. Heterozygosity at autosomal microsatellite loci did not decrease significantly. However, almost 20% of microsatellite alleles were unique to wolves collected before the 1960s. The genetic composition of the population changed gradually with the largest changes occurring prior to 1920. Half of the oldest historical samples formed a distinguishable genetic cluster not detected in the modern-day Finnish or Russian samples, and might therefore represent northern genetic variation lost from today’s gene pool. Point estimates of Ne were small (13.2 and 20.5) suggesting population fragmentation. Evidence of a genetic population bottleneck was also detected. Conclusions Our genetic analyses confirm changes in the genetic composition of the Finnish wolf population through time, despite the geographic interconnectivity to a much larger population in Russia. Our results emphasize the need for restoration of the historical connectivity between the present wolf populations to secure long-term viability. This might be challenging, however, because the management policies between Western and Eastern Europe often differ greatly. Additionally, wolf conservation is still a rather controversial issue, and anthropogenic pressure towards wolves remains strong.
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Affiliation(s)
| | | | | | - Jouni Aspi
- Department of Biology, University of Oulu, P,O, Box 3000, FIN-90014 Oulu, Finland.
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30
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Janecka JE, Tewes ME, Laack L, Caso A, Grassman LI, Honeycutt RL. Loss of genetic diversity among ocelots in the United States during the 20th century linked to human induced population reductions. PLoS One 2014; 9:e89384. [PMID: 24586737 PMCID: PMC3935880 DOI: 10.1371/journal.pone.0089384] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2013] [Accepted: 01/20/2014] [Indexed: 11/18/2022] Open
Abstract
Ocelots (Leopardus pardalis) in the United States currently exhibit low levels of genetic diversity. One hypothesis for this observation is that habitat fragmentation, resulting from human induced changes in the landscape during the 20(th) century, created island populations with highly reduced gene flow and increased genetic drift and inbreeding. In an effort to investigate this, we used a portion of the mitochondrial control region and 11 autosomal microsatellite loci to examine historical levels of genetic diversity and infer temporal changes in ocelot populations between 1853 and 2005. Levels of genetic diversity were higher in historical ocelot populations than in extant populations from Texas. The earliest documented loss of mitochondrial haplotype diversity occurred at Laguna Atascosa National Wildlife Refuge. The second extant population inhabiting private lands in Willacy County retained higher levels of genetic diversity through the 1990s, but subsequently lost diversity over the next decade. A similar pattern was observed for autosomal microsatellite loci. This supports the argument that low levels of genetic diversity in Texas are related to human induced population reductions and fragmentation, both of which threaten the remaining ocelots in the United States. At this time, the best means of mitigating the continued erosion of genetic variation are translocation of individuals either from larger populations in Mexico to Texas, or between the Texas populations.
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Affiliation(s)
- Jan E. Janecka
- Caesar Kleberg Wildlife Research Institute, Texas A & M University-Kingsville, Kingsville, Texas, United States of America
| | - Michael E. Tewes
- Caesar Kleberg Wildlife Research Institute, Texas A & M University-Kingsville, Kingsville, Texas, United States of America
| | - Linda Laack
- Laguna Atascosa National Wildlife Refuge, Rio Hondo, Texas, United States of America
| | - Arturo Caso
- Caesar Kleberg Wildlife Research Institute, Texas A & M University-Kingsville, Kingsville, Texas, United States of America
| | - Lon I. Grassman
- Caesar Kleberg Wildlife Research Institute, Texas A & M University-Kingsville, Kingsville, Texas, United States of America
| | - Rodney L. Honeycutt
- Natural Science Division, Pepperdine University, Malibu, California, United States of America
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Kuhn K, Schwenk K, Both C, Canal D, Johansson US, van der Mije S, Töpfer T, Päckert M. Differentiation in neutral genes and a candidate gene in the pied flycatcher: using biological archives to track global climate change. Ecol Evol 2013; 3:4799-814. [PMID: 24363905 PMCID: PMC3867912 DOI: 10.1002/ece3.855] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2013] [Revised: 09/25/2013] [Accepted: 09/25/2013] [Indexed: 11/11/2022] Open
Abstract
Global climate change is one of the major driving forces for adaptive shifts in migration and breeding phenology and possibly impacts demographic changes if a species fails to adapt sufficiently. In Western Europe, pied flycatchers (Ficedula hypoleuca) have insufficiently adapted their breeding phenology to the ongoing advance of food peaks within their breeding area and consequently suffered local population declines. We address the question whether this population decline led to a loss of genetic variation, using two neutral marker sets (mitochondrial control region and microsatellites), and one potentially selectively non-neutral marker (avian Clock gene). We report temporal changes in genetic diversity in extant populations and biological archives over more than a century, using samples from sites differing in the extent of climate change. Comparing genetic differentiation over this period revealed that only the recent Dutch population, which underwent population declines, showed slightly lower genetic variation than the historic Dutch population. As that loss of variation was only moderate and not observed in all markers, current gene flow across Western and Central European populations might have compensated local loss of variation over the last decades. A comparison of genetic differentiation in neutral loci versus the Clock gene locus provided evidence for stabilizing selection. Furthermore, in all genetic markers, we found a greater genetic differentiation in space than in time. This pattern suggests that local adaptation or historic processes might have a stronger effect on the population structure and genetic variation in the pied flycatcher than recent global climate changes.
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Affiliation(s)
- Kerstin Kuhn
- Biodiversity and Climate Research CentreSenckenberganlage 25, Frankfurt a. Main, D-60325, Germany
- Ecology and Evolution, Johann Wolfgang Goethe-UniversitätMax-von-Laue-Straße 13, Frankfurt am Main, D-60438, Germany
| | - Klaus Schwenk
- Biodiversity and Climate Research CentreSenckenberganlage 25, Frankfurt a. Main, D-60325, Germany
- Institute of Environmental Sciences, University of Koblenz-LandauFortstraße 7, Landau in der Pfalz, 76829, Germany
| | - Christiaan Both
- Centre for Ecological and Evolutionary Studies (CEES), University of GroningenPO Box 11103, Groningen, 9700 CC, The Netherlands
| | - David Canal
- Department of Evolutionary Ecology, Estación Biológica de Doñana, CSICAv. Américo Vespucio s/n, Sevilla, 41092, Spain
| | - Ulf S Johansson
- Department of Zoology, Swedish Museum of Natural HistoryPO Box 50007, Stockholm, SE 10405, Sweden
| | | | - Till Töpfer
- Biodiversity and Climate Research CentreSenckenberganlage 25, Frankfurt a. Main, D-60325, Germany
- Museum of Zoology, Senckenberg Natural History CollectionsKönigsbrücker Landstraße 159, Dresden, D-01109, Germany
| | - Martin Päckert
- Biodiversity and Climate Research CentreSenckenberganlage 25, Frankfurt a. Main, D-60325, Germany
- Museum of Zoology, Senckenberg Natural History CollectionsKönigsbrücker Landstraße 159, Dresden, D-01109, Germany
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Fugassa MH, Gonzalez Olivera EA, Petrigh RS. First palaeoparasitological record of a dioctophymatid egg in an archaeological sample from Patagonia. Acta Trop 2013; 128:175-7. [PMID: 23774319 DOI: 10.1016/j.actatropica.2013.06.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2013] [Revised: 05/31/2013] [Accepted: 06/05/2013] [Indexed: 10/26/2022]
Abstract
The collection of parasitological information from ancient material requires an exhaustive study of samples. In 2005, cestode and nematode eggs were found in a coprolite sample tentatively assigned to a canid. The sample was obtained from the layer of the archaeological site located in Cerro Casa de Piedra, Santa Cruz Province, Argentina, and dated from 6540±110 years before present. The aim of the present work was to reexamine this fixed sample in order to confirm the presence of these parasites. The palaeoparasitological results support our previous findings. Interestingly, another parasite was also confirmed: a dioctophymatid nematode. Dioctophyma renale has been reported in several modern carnivores in the Southern Hemisphere but in ancient materials, it has only been reported in human coprolites from Switzerland. This report constitutes the first evidence of the presence of a dioctophymatid nematode parasite dioctophymatid nematode in American pre-Columbian times. The results obtained in this work show the importance of revising earlier palaeoparasitological results.
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33
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Mondol S, Bruford MW, Ramakrishnan U. Demographic loss, genetic structure and the conservation implications for Indian tigers. Proc Biol Sci 2013; 280:20130496. [PMID: 23677341 PMCID: PMC3673047 DOI: 10.1098/rspb.2013.0496] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2013] [Accepted: 04/23/2013] [Indexed: 11/12/2022] Open
Abstract
India is home to approximately 60 per cent of the world's remaining wild tigers, a species that has declined in the last few centuries to occupy less than 7 per cent of its former geographical range. While Indian tiger numbers have somewhat stabilized in recent years, they remain low and populations are highly fragmented. Therefore, the application of evidence-based demographic and genetic management to enhance the remaining populations is a priority. In this context, and using genetic data from historical and modern tigers, we investigated anthropogenic impacts on genetic variation in Indian tigers using mitochondrial and nuclear genetic markers. We found a very high number of historical mitochondrial DNA variants, 93 per cent of which are not detected in modern populations. Population differentiation was higher in modern tigers. Simulations incorporating historical data support population decline, and suggest high population structure in extant populations. Decreased connectivity and habitat loss as a result of ongoing fragmentation in the Indian subcontinent has therefore resulted in a loss of genetic variants and increased genetic differentiation among tiger populations. These results highlight that anthropogenic fragmentation and species-specific demographic processes can interact to alter the partitioning of genetic variation over very short time scales. We conclude that ongoing strategies to maximize the size of some tiger populations, at the expense of losing others, is an inadequate conservation strategy, as it could result in a loss of genetic diversity that may be of adaptive significance for this emblematic species.
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Affiliation(s)
- Samrat Mondol
- National Centre for Biological Sciences, TIFR, GKVK Campus, Bellary Road, Bangalore 560065, India
| | | | - Uma Ramakrishnan
- National Centre for Biological Sciences, TIFR, GKVK Campus, Bellary Road, Bangalore 560065, India
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34
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Lee PLM, Prys-Jones RP. Extracting DNA from museum bird eggs, and whole genome amplification of archive DNA. Mol Ecol Resour 2013; 8:551-60. [PMID: 21585832 DOI: 10.1111/j.1471-8286.2007.02042.x] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We present a comprehensive protocol for extracting DNA from egg membranes and other internal debris recovered from the interior of blown museum bird eggs. A variety of commercially available DNA extraction methods were found to be applicable. DNA sequencing of polymerase chain reaction (PCR) products for a 176-bp fragment of mitochondrial DNA was successful for most egg samples (> 78%) even though the amount of DNA extracted (mean = 14.71 ± 4.55 ng/µL) was significantly less than that obtained for bird skin samples (mean = 67.88 ± 4.77 ng/µL). For PCR and sequencing of snipe (Gallinago) DNA, we provide eight new primers for the 'DNA barcode' region of COI mtDNA. In various combinations, the primers target a range of PCR products sized from 72 bp to the full 'barcode' of 751 bp. Not all possible combinations were tested with archive snipe DNA, but we found a significantly better success rate of PCR amplification for a shorter 176-bp target compared with a larger 288-bp fragment (67% vs. 39%). Finally, we explored the feasibility of whole genome amplification (WGA) for extending the use of archive DNA in PCR and sequencing applications. Of two WGA approaches, a PCR-based method was found to be able to amplify whole genomic DNA from archive skins and eggs from museum bird collections. After WGA, significantly more archive egg samples produced visible PCR products on agarose (56.9% before WGA vs. 79.0% after WGA). However, overall sequencing success did not improve significantly (78.8% compared with 83.0%).
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Affiliation(s)
- Patricia L M Lee
- Department of Biological Sciences, Institute of Environmental Sustainability, Swansea University, Swansea SA2 8PP, UK, Bird Group, Department of Zoology, The Natural History Museum, Tring HP23 6AP, Herts, UK
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35
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Ploshnitsa AI, Goltsman ME, Happ GM, Macdonald DW, Kennedy LJ. Historical and modern neutral genetic variability in
M
ednyi
A
rctic foxes passed through a severe bottleneck. J Zool (1987) 2012. [DOI: 10.1111/j.1469-7998.2012.00964.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- A. I. Ploshnitsa
- Biology Faculty, Department of Vertebrate Zoology Lomonosov Moscow State University Moscow Russia
| | - M. E. Goltsman
- Biology Faculty, Department of Vertebrate Zoology Lomonosov Moscow State University Moscow Russia
| | - G. M. Happ
- Institute of Arctic Biology University of Alaska Fairbanks AK USA
| | - D. W. Macdonald
- Wildlife Conservation Research Unit, Department of Zoology, The Recananti‐Kaplan Centre, Tubney House University of Oxford Tubney UK
| | - L. J. Kennedy
- Centre for Integrated Genomic Medical Research The University of Manchester Manchester UK
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36
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Ochoa A, Gasca J, Ceballos GJ, Eguiarte LE. Spatiotemporal population genetics of the endangered Perote ground squirrel (Xerospermophilus perotensis) in a fragmented landscape. J Mammal 2012. [DOI: 10.1644/11-mamm-a-371.1] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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37
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Mellows A, Barnett R, Dalén L, Sandoval-Castellanos E, Linderholm A, McGovern TH, Church MJ, Larson G. The impact of past climate change on genetic variation and population connectivity in the Icelandic arctic fox. Proc Biol Sci 2012; 279:4568-73. [PMID: 22977155 DOI: 10.1098/rspb.2012.1796] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Previous studies have suggested that the presence of sea ice is an important factor in facilitating migration and determining the degree of genetic isolation among contemporary arctic fox populations. Because the extent of sea ice is dependent upon global temperatures, periods of significant cooling would have had a major impact on fox population connectivity and genetic variation. We tested this hypothesis by extracting and sequencing mitochondrial control region sequences from 17 arctic foxes excavated from two late-ninth-century to twelfth-century AD archaeological sites in northeast Iceland, both of which predate the Little Ice Age (approx. sixteenth to nineteenth century). Despite the fact that five haplotypes have been observed in modern Icelandic foxes, a single haplotype was shared among all of the ancient individuals. Results from simulations within an approximate Bayesian computation framework suggest that the rapid increase in Icelandic arctic fox haplotype diversity can only be explained by sea-ice-mediated fox immigration facilitated by the Little Ice Age.
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Affiliation(s)
- Andrew Mellows
- Department of Archaeology, Durham Evolution and Ancient DNA, Durham University, South Road, Durham DH1 3LE, UK
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38
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Nyström V, Humphrey J, Skoglund P, McKeown NJ, Vartanyan S, Shaw PW, Lidén K, Jakobsson M, Barnes I, Angerbjörn A, Lister A, Dalén L. Microsatellite genotyping reveals end-Pleistocene decline in mammoth autosomal genetic variation. Mol Ecol 2012; 21:3391-402. [PMID: 22443459 DOI: 10.1111/j.1365-294x.2012.05525.x] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The last glaciation was a dynamic period with strong impact on the demography of many species and populations. In recent years, mitochondrial DNA sequences retrieved from radiocarbon-dated remains have provided novel insights into the history of Late Pleistocene populations. However, genotyping of loci from the nuclear genome may provide enhanced resolution of population-level changes. Here, we use four autosomal microsatellite DNA markers to investigate the demographic history of woolly mammoths (Mammuthus primigenius) in north-eastern Siberia from before 60 000 years ago up until the species' final disappearance c.4000 years ago. We identified two genetic groups, implying a marked temporal genetic differentiation between samples with radiocarbon ages older than 12 thousand radiocarbon years before present (ka) and those younger than 9ka. Simulation-based analysis indicates that this dramatic change in genetic composition, which included a decrease in individual heterozygosity of approximately 30%, was due to a multifold reduction in effective population size. A corresponding reduction in genetic variation was also detected in the mitochondrial DNA, where about 65% of the diversity was lost. We observed no further loss in genetic variation during the Holocene, which suggests a rapid final extinction event.
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Affiliation(s)
- Veronica Nyström
- Department of Zoology, Stockholm University, S-106 91 Stockholm, Sweden.
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Abstract
Natural history museums around the world hold millions of animal and plant specimens that are potentially amenable to genetic analyses. With more and more populations and species becoming extinct, the importance of these specimens for phylogenetic and phylogeographic analyses is rapidly increasing. However, as most DNA extraction methods damage the specimens, nondestructive extraction methods are useful to balance the demands of molecular biologists, morphologists, and museum curators. Here, I describe a method for nondestructive DNA extraction from bony specimens (i.e., bones and teeth). In this method, the specimens are soaked in extraction buffer, and DNA is then purified from the soaking solution using adsorption to silica. The method reliably yields mitochondrial and often also nuclear DNA. The method has been adapted to DNA extraction from other types of specimens such as arthropods.
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Affiliation(s)
- Michael Hofreiter
- Department of Biology, The University of York, Wentworth Way, Heslington, York, YO10 5DD, UK.
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Ploshnitsa AI, Goltsman ME, Macdonald DW, Kennedy LJ, Sommer S. Impact of historical founder effects and a recent bottleneck on MHC variability in Commander Arctic foxes (Vulpes lagopus). Ecol Evol 2012; 2:165-80. [PMID: 22408734 PMCID: PMC3297186 DOI: 10.1002/ece3.42] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2011] [Revised: 08/24/2011] [Accepted: 08/26/2011] [Indexed: 11/11/2022] Open
Abstract
Populations of Arctic foxes (Vulpes lagopus) have been isolated on two of the Commander Islands (Bering and Mednyi) from the circumpolar distributed mainland population since the Pleistocene. In 1970-1980, an epizootic outbreak of mange caused a severe population decline on Mednyi Island. Genes of the major histocompatibility complex (MHC) play a primary role in infectious disease resistance. The main objectives of our study were to compare contemporary variation of MHC class II in mainland and island Arctic foxes, and to document the effects of the isolation and the recent bottleneck on MHC polymorphism by analyzing samples from historical and contemporary Arctic foxes. In 184 individuals, we found 25 unique MHC class II DRB and DQB alleles, and identified evidence of balancing selection maintaining allelic lineages over time at both loci. Twenty different MHC alleles were observed in mainland foxes and eight in Bering Island foxes. The historical Mednyi population contained five alleles and all contemporary individuals were monomorphic at both DRB and DQB. Our data indicate that despite positive and diversifying selection leading to elevated rates of amino acid replacement in functionally important antigen-binding sites, below a certain population size, balancing selection may not be strong enough to maintain genetic diversity in functionally important genes. This may have important fitness consequences and might explain the high pathogen susceptibility in some island populations. This is the first study that compares MHC diversity before and after a bottleneck in a wild canid population using DNA from museum samples.
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Geffen E, Kam M, Hefner R, Hersteinsson P, Angerbjörn A, Dalèn L, Fuglei E, Norèn K, Adams JR, Vucetich J, Meier TJ, Mech LD, Vonholdt BM, Stahler DR, Wayne RK. Kin encounter rate and inbreeding avoidance in canids. Mol Ecol 2011; 20:5348-58. [PMID: 22077191 DOI: 10.1111/j.1365-294x.2011.05358.x] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Mating with close kin can lead to inbreeding depression through the expression of recessive deleterious alleles and loss of heterozygosity. Mate selection may be affected by kin encounter rate, and inbreeding avoidance may not be uniform but associated with age and social system. Specifically, selection for kin recognition and inbreeding avoidance may be more developed in species that live in family groups or breed cooperatively. To test this hypothesis, we compared kin encounter rate and the proportion of related breeding pairs in noninbred and highly inbred canid populations. The chance of randomly encountering a full sib ranged between 1-8% and 20-22% in noninbred and inbred canid populations, respectively. We show that regardless of encounter rate, outside natal groups mates were selected independent of relatedness. Within natal groups, there was a significant avoidance of mating with a relative. Lack of discrimination against mating with close relatives outside packs suggests that the rate of inbreeding in canids is related to the proximity of close relatives, which could explain the high degree of inbreeding depression observed in some populations. The idea that kin encounter rate and social organization can explain the lack of inbreeding avoidance in some species is intriguing and may have implications for the management of populations at risk.
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Affiliation(s)
- Eli Geffen
- Department of Zoology, Tel Aviv University, Tel Aviv 69978, Israel.
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Rodríguez R, Ramírez O, Valdiosera CE, García N, Alda F, Madurell-Malapeira J, Marmi J, Doadrio I, Willerslev E, Götherström A, Arsuaga JL, Thomas MG, Lalueza-Fox C, Dalén L. 50,000 years of genetic uniformity in the critically endangered Iberian lynx. Mol Ecol 2011; 20:3785-95. [PMID: 21864323 DOI: 10.1111/j.1365-294x.2011.05231.x] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
Low genetic diversity in the endangered Iberian lynx, including lack of mitochondrial control region variation, is thought to result from historical or Pleistocene/Holocene population bottlenecks, and to indicate poor long-term viability. We find no variability in control region sequences from 19 Iberian lynx remains from across the Iberian Peninsula and spanning the last 50,000 years. This is best explained by continuously small female effective population size through time. We conclude that low genetic variability in the Iberian lynx is not in itself a threat to long-term viability, and so should not preclude conservation efforts.
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Affiliation(s)
- Ricardo Rodríguez
- Centro Mixto, Universidad Complutense de Madrid-Instituto de Salud Carlos III de Evolución y Comportamiento Humanos, Avda. Monforte de Lemos 5, Pabellón 14. 28029 Madrid, Spain.
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Beneteau CL, Walter RP, Mandrak NE, Heath DD. Range expansion by invasion: genetic characterization of invasion of the greenside darter (Etheostoma blennioides) at the northern edge of its distribution. Biol Invasions 2011. [DOI: 10.1007/s10530-011-9996-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Bluemel JK, Andrew King R, Virant-Doberlet M, Symondson WOC. Primers for identification of type and other archived specimens of Aphrodes leafhoppers (Hemiptera, Cicadellidae). Mol Ecol Resour 2011; 11:770-4. [PMID: 21457478 DOI: 10.1111/j.1755-0998.2011.03008.x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Primers were developed for leafhoppers of the genus Aphrodes amplifying 84-244 bp fragments of the mitochondrial cytochrome oxidase subunit I gene. DNA was extracted from legs of over 100-year-old archived museum specimens, amplified and sequenced. The fragments contain sufficient variation to unequivocally identify the different species. The majority of the analysed museum specimens, including three specimens of the syntype series for the UK endemic species A. aestuarina (Edwards 1908), were found to have been assigned to the wrong species. This work clearly underlines the need to validate museum specimens using molecular methods where identity is in doubt, based on reliable standards for species discrimination.
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Affiliation(s)
- Joanna K Bluemel
- Cardiff School of Biosciences, Cardiff University, Biomedical Sciences Building, Museum Avenue, Cardiff CF103AX, UK.
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46
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Endoparasites in the endangered Fennoscandian population of arctic foxes (Vulpes lagopus). EUR J WILDLIFE RES 2011. [DOI: 10.1007/s10344-011-0505-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Meijer T, Norén K, Angerbjörn A. The impact of maternal experience on post-weaning survival in an endangered arctic fox population. EUR J WILDLIFE RES 2010. [DOI: 10.1007/s10344-010-0463-0] [Citation(s) in RCA: 16] [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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48
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Norén K, Carmichael L, Dalén L, Hersteinsson P, Samelius G, Fuglei E, Kapel CMO, Menyushina I, Strobeck C, Angerbjörn A. Arctic fox Vulpes lagopus population structure: circumpolar patterns and processes. OIKOS 2010. [DOI: 10.1111/j.1600-0706.2010.18766.x] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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49
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Petersen SD, Manseau M, Wilson PJ. Bottlenecks, isolation, and life at the northern range limit: Peary caribou on Ellesmere Island, Canada. J Mammal 2010. [DOI: 10.1644/09-mamm-a-231.1] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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50
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Shirley MD, Elmhagen B, Lurz PW, Rushton SP, Angerbjörn A. Modelling the spatial population dynamics of arctic foxes: the effects of red foxes and microtine cycles. CAN J ZOOL 2009. [DOI: 10.1139/z09-104] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The Fennoscandian arctic fox ( Vulpes lagopus (L., 1758)) population is critically endangered, possibly because of increased interference competition from red foxes ( Vulpes vulpes (L., 1758)) and fading cycles in microtine rodents, which cause food shortage. It is not known how these factors drive arctic fox population trends. To test their role in arctic fox decline, we developed a spatially explicit and individual-based model that allowed us to simulate fox interactions and food availability in a real landscape. A sensitivity analysis revealed that simulated arctic fox population size and den occupancy were strongly correlated with fecundity and mortality during the microtine crash phase, but also with red fox status. Model simulations suggested that arctic fox population trends depended on microtine cycles and that arctic fox distributions were restricted by red fox presence. We compared the model predictions with field data collected at Vindelfjällen, Sweden. The model recreated the observed arctic fox trend only with the inclusion of arctic fox avoidance of red fox home ranges. The results indicate that avoidance behaviours can affect population trends and hence that relatively small numbers of red foxes can have a strong negative impact on arctic fox population size and distribution.
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Affiliation(s)
- Mark D.F. Shirley
- Institute for Research on Environment and Sustainability, Newcastle University, Newcastle upon Tyne NE1 7RU, UK
- Department of Zoology, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Bodil Elmhagen
- Institute for Research on Environment and Sustainability, Newcastle University, Newcastle upon Tyne NE1 7RU, UK
- Department of Zoology, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Peter W.W. Lurz
- Institute for Research on Environment and Sustainability, Newcastle University, Newcastle upon Tyne NE1 7RU, UK
- Department of Zoology, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Steve P. Rushton
- Institute for Research on Environment and Sustainability, Newcastle University, Newcastle upon Tyne NE1 7RU, UK
- Department of Zoology, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Anders Angerbjörn
- Institute for Research on Environment and Sustainability, Newcastle University, Newcastle upon Tyne NE1 7RU, UK
- Department of Zoology, Stockholm University, SE-106 91 Stockholm, Sweden
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