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Xie M, Chen C, Wang Y, Li W, Yu L, Hong X, Zhu X. Conservation Genetics of the Asian Giant Soft-Shelled Turtle (Pelochelys cantorii) with Novel Microsatellite Multiplexes. Animals (Basel) 2022; 12:ani12243459. [PMID: 36552380 PMCID: PMC9774628 DOI: 10.3390/ani12243459] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Revised: 12/03/2022] [Accepted: 12/06/2022] [Indexed: 12/13/2022] Open
Abstract
To understand the genetic structure of the protected turtle species Pelochelys cantorii we used transcriptome data to design more than 30,000 tri- and tetranucleotide repeat microsatellite primer pairs, of which 230 pairs were used for laboratory experiments. After two screenings, only 10 microsatellite markers with good specificity, high amplification efficiency, and polymorphisms were obtained. Using the selected primers, two multiplex PCR systems were established to compare and analyze the genetic diversity of artificially assisted breeding generations from four parents (two females and two males) continuously bred over two years. A total of 25 alleles were detected among the 10 microsatellite loci of the offspring. The polymorphism information content (PIC) was 0.313-0.674, with an average of 0.401, among which two loci were highly polymorphic (PIC ≥ 0.5). The number of alleles was 2-5 and the number of effective alleles was 1.635-3.614. The observed heterozygosity was 0.341-0.813, with an average of 0.582, whereas the average expected heterozygosity was 0.389-0.725, with an average of 0.493. Moreover, on the basis of Nei's genetic distance and the Bayesian clustering algorithm, the 182 offspring were divided into two subgroups, and the results corresponded to the two maternal lines. This is the first study to investigate the molecular markers of P. cantorii, and the results obtained can be used to protect genetic resources and provide a genetic basis for the design of population recovery plans.
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Affiliation(s)
- Minmin Xie
- Key Laboratory of Tropical & Subtropical Fishery Resource Application & Cultivation of Ministry of Agriculture, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, China
- College of Wuxi Fisheries, Nanjing Agricultural University, Wuxi 214081, China
| | - Chen Chen
- Key Laboratory of Tropical & Subtropical Fishery Resource Application & Cultivation of Ministry of Agriculture, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, China
| | - Yakun Wang
- Key Laboratory of Tropical & Subtropical Fishery Resource Application & Cultivation of Ministry of Agriculture, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, China
| | - Wei Li
- Key Laboratory of Tropical & Subtropical Fishery Resource Application & Cultivation of Ministry of Agriculture, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, China
| | - Lingyun Yu
- Key Laboratory of Tropical & Subtropical Fishery Resource Application & Cultivation of Ministry of Agriculture, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, China
| | - Xiaoyou Hong
- Key Laboratory of Tropical & Subtropical Fishery Resource Application & Cultivation of Ministry of Agriculture, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, China
- Correspondence: (X.H.); (X.Z.)
| | - Xinping Zhu
- Key Laboratory of Tropical & Subtropical Fishery Resource Application & Cultivation of Ministry of Agriculture, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, China
- College of Wuxi Fisheries, Nanjing Agricultural University, Wuxi 214081, China
- Correspondence: (X.H.); (X.Z.)
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Mohr DW, Gaughran SJ, Paschall J, Naguib A, Pang AWC, Dudchenko O, Aiden EL, Church DM, Scott AF. A Chromosome-Length Assembly of the Hawaiian Monk Seal (Neomonachus schauinslandi): A History of “Genetic Purging” and Genomic Stability. Genes (Basel) 2022; 13:genes13071270. [PMID: 35886053 PMCID: PMC9323584 DOI: 10.3390/genes13071270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Revised: 06/29/2022] [Accepted: 07/07/2022] [Indexed: 12/04/2022] Open
Abstract
The Hawaiian monk seal (HMS) is the single extant species of tropical earless seals of the genus Neomonachus. The species survived a severe bottleneck in the late 19th century and experienced subsequent population declines until becoming the subject of a NOAA-led species recovery effort beginning in 1976 when the population was fewer than 1000 animals. Like other recovering species, the Hawaiian monk seal has been reported to have reduced genetic heterogeneity due to the bottleneck and subsequent inbreeding. Here, we report a chromosomal reference assembly for a male animal produced using a variety of methods. The final assembly consisted of 16 autosomes, an X, and portions of the Y chromosomes. We compared variants in this animal to other HMS and to a frequently sequenced human sample, confirming about 12% of the variation seen in man. To confirm that the reference animal was representative of the HMS, we compared his sequence to that of 10 other individuals and noted similarly low variation in all. Variation in the major histocompatibility (MHC) genes was nearly absent compared to the orthologous human loci. Demographic analysis predicts that Hawaiian monk seals have had a long history of small populations preceding the bottleneck, and their current low levels of heterozygosity may indicate specialization to a stable environment. When we compared our reference assembly to that of other species, we observed significant conservation of chromosomal architecture with other pinnipeds, especially other phocids. This reference should be a useful tool for future evolutionary studies as well as the long-term management of this species.
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Affiliation(s)
- David W. Mohr
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA; (D.W.M.); (J.P.)
| | - Stephen J. Gaughran
- Department of Ecology & Evolutionary Biology, Princeton University, Princeton, NJ 08544, USA;
| | - Justin Paschall
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA; (D.W.M.); (J.P.)
| | - Ahmed Naguib
- Bionano Genomics, Inc., 9640 Towne Centre Dr., Suite 100, San Diego, CA 92121, USA; (A.N.); (A.W.C.P.)
| | - Andy Wing Chun Pang
- Bionano Genomics, Inc., 9640 Towne Centre Dr., Suite 100, San Diego, CA 92121, USA; (A.N.); (A.W.C.P.)
| | - Olga Dudchenko
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; (O.D.); (E.L.A.)
- Center for Theoretical Biological Physics, Rice University, Houston, TX 77030, USA
| | - Erez Lieberman Aiden
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; (O.D.); (E.L.A.)
- Center for Theoretical Biological Physics, Rice University, Houston, TX 77030, USA
- UWA School of Agriculture and Environment, The University of Western Australia, Crawley, WA 6009, Australia
- Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai 201210, China
| | | | - Alan F. Scott
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA; (D.W.M.); (J.P.)
- Correspondence:
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Font-Porterias N, McNelis MG, Comas D, Hlusko LJ. Evidence of selection in the ectodysplasin pathway among endangered aquatic mammals. Integr Org Biol 2022; 4:obac018. [PMID: 35874492 PMCID: PMC9299678 DOI: 10.1093/iob/obac018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Revised: 05/06/2022] [Accepted: 05/21/2022] [Indexed: 11/13/2022] Open
Abstract
Synopsis The ectodysplasin pathway has been a target of evolution repeatedly. Genetic variation in the key genes of this pathway (EDA, EDAR, and EDARADD) results in a rich source of pleiotropic effects across ectodermally-derived structures, including teeth, hair, sweat glands, and mammary glands. In addition, a non-canonical Wnt pathway has a very similar functional role, making variation in the WNT10A gene also of evolutionary significance. The adaptation of mammals to aquatic environments has occurred independently in at least 4 orders, whose species occupy a wide geographic range (from equatorial to polar regions) and exhibit great phenotypic variation in ectodermally-derived structures, including the presence or absence of fur and extreme lactational strategies. The role of the ectodysplasin pathway in the adaptation to aquatic environments has been never explored in mammalian species. In the present study, we analyze the genetic variation in orthologous coding sequences from EDA, EDAR, EDARADD, and WNT10A genes together with ectodermally-derived phenotypic variation from 34 aquatic and non-aquatic mammalian species to assess signals of positive selection, gene-trait coevolution, and genetic convergence. Our study reveals strong evidence of positive selection in a proportion of coding sites in EDA and EDAR genes in 3 endangered aquatic mammals (the Hawaiian monk seal, the Yangtze finless porpoise, and the sea otter). We hypothesize functional implications potentially related to the adaptation to the low-latitude aquatic environment in the Hawaiian monk seal and the freshwater in the Yangtze finless porpoise. The signal in the sea otter is likely the result of an increased genetic drift after an intense bottleneck and reduction of genetic diversity. Besides positive selection, we have not detected robust signals of gene-trait coevolution or convergent amino acid shifts in the ectodysplasin pathway associated with shared phenotypic traits among aquatic mammals. This study provides new evidence of the evolutionary role of the ectodysplasin pathway and encourages further investigation, including functional studies, to fully resolve its relationship with mammalian aquatic adaptation. Spanish La vía de la ectodisplasina ha sido objeto de la evolución repetidamente. La variación genética en los principales genes de esta vía (EDA, EDAR y EDARADD) da como resultado una gran diversidad de efectos pleiotrópicos en las estructuras derivadas del ectodermo, incluidos los dientes, el cabello, las glándulas sudoríparas y las glándulas mamarias. Además, una vía wnt no canónica tiene un papel funcional muy similar, por lo que la variación en el gen WNT10A también tiene importancia evolutiva. La adaptación de los mamíferos a los entornes acuáticos se ha producido de forma independiente en al menos cuatro órdenes, cuyas especies ocupan un amplio rango geográfico (desde regiones ecuatoriales a polares) y presentan una gran variación fenotípica en las estructuras derivadas del ectodermo, incluyendo la presencia o ausencia de pelaje y estrategias de lactancia muy diferentes. El papel de la vía de la ectodisplasina en la adaptación a entornos acuáticos no se ha explorado nunca en especies de mamíferos. En este estudio, analizamos la variación genética en las secuencias codificantes ortólogas de los genes EDA, EDAR, EDARADD y WNT10A junto con la variación fenotípica derivada del ectodermo de 34 especies de mamíferos acuáticos y no acuáticos para evaluar señales de selección positiva, coevolución gen-rasgo y convergencia genética. Nuestro estudio revela señales de selección positiva en regiones de las secuencias codificantes de los genes EDA y EDAR en tres mamíferos acuáticos en peligro de extinción (la foca monje de Hawái, la marsopa lisa y la nutria marina). Estas señales podrían tener implicaciones funcionales potencialmente relacionadas con la adaptación al entorno acuático de baja latitud en la foca monje de Hawái y el agua dulce en la marsopa lisa. La señal en la nutria marina es probablemente el resultado de una mayor deriva genética tras un intenso un cuello de botella y una reducción de la diversidad genética. A parte de selección positiva, no hemos detectado señales sólidas de coevolución gen-rasgo o cambios convergentes de aminoácidos en la vía de la ectodisplasina asociados a rasgos fenotípicos compartidos entre mamíferos acuáticos. Este estudio proporciona nuevas evidencias del papel evolutivo de la vía de la ectodisplasina y quiere promover futuras investigaciones con estudios funcionales para acabar de resolver la relación de esta vía con la adaptación acuática de los mamíferos.
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Affiliation(s)
- Neus Font-Porterias
- Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Institut de Biologia Evolutiva (UPF-CSIC) , Barcelona , Spain
| | - Madeline G McNelis
- Department of Integrative Biology, University of California Berkeley , California , USA
| | - David Comas
- Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Institut de Biologia Evolutiva (UPF-CSIC) , Barcelona , Spain
| | - Leslea J Hlusko
- Department of Integrative Biology, University of California Berkeley , California , USA
- National Research Center on Human Evolution (CENIEH) , Burgos , Spain
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Hunt DAGA, DiBattista JD, Hendry AP. Effects of insularity on genetic diversity within and among natural populations. Ecol Evol 2022; 12:e8887. [PMID: 35571757 PMCID: PMC9077629 DOI: 10.1002/ece3.8887] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2022] [Accepted: 04/15/2022] [Indexed: 11/27/2022] Open
Abstract
We conducted a quantitative literature review of genetic diversity (GD) within and among populations in relation to categorical population size and isolation (together referred to as “insularity”). Using populations from within the same studies, we were able to control for between‐study variation in methodology, as well as demographic and life histories of focal species. Contrary to typical expectations, insularity had relatively minor effects on GD within and among populations, which points to the more important role of other factors in shaping evolutionary processes. Such effects of insularity were sometimes seen—particularly in study systems where GD was already high overall. That is, insularity influenced GD in a study system when GD was high even in non‐insular populations of the same study system—suggesting an important role for the “scope” of influences on GD. These conclusions were more robust for within population GD versus among population GD, although several biases might underlie this difference. Overall, our findings indicate that population‐level genetic assumptions need to be tested rather than assumed in nature, particularly for topics underlying current conservation management practices.
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Affiliation(s)
- David A. G. A. Hunt
- Redpath Museum and Department of Biology McGill University Montreal Quebec Canada
| | - Joseph D. DiBattista
- Australian Museum Research Institute Australian Museum Sydney New South Wales Australia
| | - Andrew P. Hendry
- Redpath Museum and Department of Biology McGill University Montreal Quebec Canada
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Antaky CC, Conklin EE, Toonen RJ, Knapp IS, Price MR. Unexpectedly high genetic diversity in a rare and endangered seabird in the Hawaiian Archipelago. PeerJ 2020; 8:e8463. [PMID: 32071808 PMCID: PMC7007978 DOI: 10.7717/peerj.8463] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Accepted: 12/26/2019] [Indexed: 11/20/2022] Open
Abstract
Seabirds in the order of Procellariiformes have one of the highest proportions of threatened species of any avian order. Species undergoing recovery may be predicted to have a genetic signature of a bottleneck, low genetic diversity, or higher rates of inbreeding. The Hawaiian Band-rumped Storm Petrel ('Akē'akē; Hydrobates castro), a long-lived philopatric seabird, suffered massive population declines resulting in its listing under the Endangered Species Act in 2016 as federally Endangered. We used high-throughput sequencing to assess patterns of genetic diversity and potential for inbreeding in remaining populations in the Hawaiian Islands. We compared a total of 24 individuals, including both historical and modern samples, collected from breeding colonies or downed individuals found on the islands of Kaua'i, O'ahu, Maui, and the Big Island of Hawai'i. Genetic analyses revealed little differentiation between breeding colonies on Kaua'i and the Big Island colonies. Although small sample sizes limit inferences regarding other island colonies, downed individuals from O'ahu and Maui did not assign to known breeding colonies, suggesting the existence of an additional distinct breeding population. The maintenance of genetic diversity in future generations is an important consideration for conservation management. This study provides a baseline of population structure for the remaining nesting colonies that could inform potential translocations of the Endangered H. castro.
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Affiliation(s)
- Carmen C. Antaky
- Department of Natural Resources and Environmental Management, University of Hawai‘i at Mānoa, Honolulu, HI, USA
| | - Emily E. Conklin
- Hawai‘i Institute of Marine Biology, University of Hawai‘i at Mānoa, Kāne‘ohe, HI, USA
| | - Robert J. Toonen
- Hawai‘i Institute of Marine Biology, University of Hawai‘i at Mānoa, Kāne‘ohe, HI, USA
| | - Ingrid S.S. Knapp
- Hawai‘i Institute of Marine Biology, University of Hawai‘i at Mānoa, Kāne‘ohe, HI, USA
| | - Melissa R. Price
- Department of Natural Resources and Environmental Management, University of Hawai‘i at Mānoa, Honolulu, HI, USA
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van den Burg MP, Meirmans PG, van Wagensveld TP, Kluskens B, Madden H, Welch ME, Breeuwer JAJ. The Lesser Antillean Iguana (Iguana delicatissima) on St. Eustatius: Genetically Depauperate and Threatened by Ongoing Hybridization. J Hered 2019; 109:426-437. [PMID: 29471487 DOI: 10.1093/jhered/esy008] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2017] [Accepted: 02/15/2018] [Indexed: 11/13/2022] Open
Abstract
The Lesser Antillean Iguana (Iguana delicatissima) is an endangered species threatened by habitat loss and hybridization with non-native Green Iguanas (Iguana iguana). Iguana delicatissima has been extirpated on several islands, and the Green Iguana has invaded most islands with extant populations. Information is essential to protect this species from extinction. We collected data on 293 iguanas including 17 juveniles from St. Eustasius, one of the few remaining I. delicatissima strongholds. Genetic data were leveraged to test for hybridization presence with the Green Iguana using both mitochondrial and nuclear genes, including 16 microsatellite loci. The microsatellites were also analyzed to estimate genetic diversity, population structure, and effective population size. Using molecular and morphological data, we identified 286 I. delicatissima individuals captured during our first fieldwork effort, and 7 non-native iguanas captured during a second effort, showing hybridization occurs within this population. Comparing homologous microsatellites used in studies on Dominica and Chancel, the I. delicatissima population on St. Eustatius has extremely low genetic diversity (HO = 0.051; HE = 0.057), suggesting this population is genetically depauperate. Furthermore, there is significant evidence for inbreeding (FIS = 0.12) and weak spatial genetic structure (FST = 0.021, P = 0.002) within this population. Besides immediate threats including hybridization, this population's low genetic diversity, presence of physiological abnormalities and low recruitment could indicate presence of inbreeding depression that threatens its long-term survival. We conclude there is a continued region-wide threat to I. delicatissima and highlight the need for immediate conservation action to stop the continuing spread of Green Iguanas and to eliminate hybridization from St. Eustatius.
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Affiliation(s)
- Matthijs P van den Burg
- Institute of Biodiversity and Ecosystem Dynamics (IBED), University of Amsterdam, Amsterdam, The Netherlands
| | - Patrick G Meirmans
- Institute of Biodiversity and Ecosystem Dynamics (IBED), University of Amsterdam, Amsterdam, The Netherlands
| | | | - Bart Kluskens
- Reptile, Amphibian & Fish Conservation the Netherlands, Nijmegen, The Netherlands
| | - Hannah Madden
- St. Eustatius National Park Foundation, Gallows Bay, St. Eustatius, Caribbean Netherlands.,Caribbean Netherlands Science Institute, St. Eustatius, Caribbean Netherlands
| | - Mark E Welch
- Department of Biological Sciences, Mississippi State University, Mississippi, USA
| | - Johannes A J Breeuwer
- Institute of Biodiversity and Ecosystem Dynamics (IBED), University of Amsterdam, Amsterdam, The Netherlands
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Cammen KM, Rasher DB, Steneck RS. Predator recovery, shifting baselines, and the adaptive management challenges they create. Ecosphere 2019. [DOI: 10.1002/ecs2.2579] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
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Lait LA, Marshall HD, Carr SM. Phylogeographic mitogenomics of Atlantic cod Gadus morhua: Variation in and among trans-Atlantic, trans-Laurentian, Northern cod, and landlocked fjord populations. Ecol Evol 2018; 8:6420-6437. [PMID: 30038745 PMCID: PMC6053584 DOI: 10.1002/ece3.3873] [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: 08/26/2017] [Revised: 12/21/2017] [Accepted: 01/01/2018] [Indexed: 01/16/2023] Open
Abstract
The historical phylogeography, biogeography, and ecology of Atlantic cod (Gadus morhua) have been impacted by cyclic Pleistocene glaciations, where drops in sea temperatures led to sequestering of water in ice sheets, emergence of continental shelves, and changes to ocean currents. High-resolution, whole-genome mitogenomic phylogeography can help to elucidate this history. We identified eight major haplogroups among 153 fish from 14 populations by Bayesian, parsimony, and distance methods, including one that extends the species coalescent back to ca. 330 kya. Fish from the Barents and Baltic Seas tend to occur in basal haplogroups versus more recent distribution of fish in the Northwest Atlantic. There was significant differentiation in the majority of trans-Atlantic comparisons (ΦST = .029-.180), but little or none in pairwise comparisons within the Northwest Atlantic of individual populations (ΦST = .000-.060) or defined management stocks (ΦST = .000-.023). Monte Carlo randomization tests of population phylogeography showed significantly nonrandom trans-Atlantic phylogeography versus absence of such structure within various partitions of trans-Laurentian, Northern cod (NAFO 2J3KL) and other management stocks, and Flemish Cap populations. A landlocked meromictic fjord on Baffin Island comprised multiple identical or near-identical mitogenomes in two major polyphyletic clades, and was significantly differentiated from all other populations (ΦST = .153-.340). The phylogeography supports a hypothesis of an eastern origin of genetic diversity ca. 200-250 kya, rapid expansion of a western superhaplogroup comprising four haplogroups ca. 150 kya, and recent postglacial founder populations.
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Affiliation(s)
- Linda A. Lait
- Genetics, Evolution, and Molecular Systematics LaboratoryDepartment of BiologyMemorial University of NewfoundlandSt. John'sNLCanada
- Centre for Biodiversity Genomics, Department of Integrative BiologyUniversity of GuelphGuelphONCanada
| | - H. Dawn Marshall
- Genetics, Evolution, and Molecular Systematics LaboratoryDepartment of BiologyMemorial University of NewfoundlandSt. John'sNLCanada
| | - Steven M. Carr
- Genetics, Evolution, and Molecular Systematics LaboratoryDepartment of BiologyMemorial University of NewfoundlandSt. John'sNLCanada
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Matsui M, Komada N, Yamada K, Takada M, Nishikawa K, Tominaga A, Tanaka-Ueno T. Genetic Uniformity of Japanese Giant Salamander (Amphibia, Caudata) from Kiso River, Central Japan. CURRENT HERPETOLOGY 2018. [DOI: 10.5358/hsj.37.23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Masafumi Matsui
- Graduate School of Human and Environmental Studies, Kyoto University, Sakyo-ku, Kyoto 606-8501, JAPAN
| | - Noritomo Komada
- Faculty of Human Life and Environmental Sciences, Nagoya Women's University, Shioji-cho 3-40, Mizuho-ku, Nagoya 467-8610, JAPAN
| | - Kumiko Yamada
- Faculty of Human Life and Environmental Sciences, Nagoya Women's University, Shioji-cho 3-40, Mizuho-ku, Nagoya 467-8610, JAPAN
| | - Makoto Takada
- The United Graduate School of Agricultural Science, Gifu University, Yanagido 1-1, Gifu 501-1193, JAPAN
| | - Kanto Nishikawa
- Graduate School of Human and Environmental Studies, Kyoto University, Sakyo-ku, Kyoto 606-8501, JAPAN
| | - Atsushi Tominaga
- Faculty of Education, University of the Ryukyus, Senbaru 1, Nishihara, Okinawa 903-0213, JAPAN
| | - Tomoko Tanaka-Ueno
- Laboratory of Biology, Meiji Gakuin University, Kamikurata-cho 1518, Totsuka-ku, Yokohama 244-8539, JAPAN
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Robinson SJ, Barbieri MM, Murphy S, Baker JD, Harting AL, Craft ME, Littnan CL. Model recommendations meet management reality: implementation and evaluation of a network-informed vaccination effort for endangered Hawaiian monk seals. Proc Biol Sci 2018; 285:20171899. [PMID: 29321294 PMCID: PMC5784189 DOI: 10.1098/rspb.2017.1899] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2017] [Accepted: 12/04/2017] [Indexed: 11/23/2022] Open
Abstract
Where disease threatens endangered wildlife populations, substantial resources are required for management actions such as vaccination. While network models provide a promising tool for identifying key spreaders and prioritizing efforts to maximize efficiency, population-scale vaccination remains rare, providing few opportunities to evaluate performance of model-informed strategies under realistic scenarios. Because the endangered Hawaiian monk seal could be heavily impacted by disease threats such as morbillivirus, we implemented a prophylactic vaccination programme. We used contact networks to prioritize vaccinating animals with high contact rates. We used dynamic network models to simulate morbillivirus outbreaks under real and idealized vaccination scenarios. We then evaluated the efficacy of model recommendations in this real-world vaccination project. We found that deviating from the model recommendations decreased the efficiency; requiring 44% more vaccinations to achieve a given decrease in outbreak size. However, we gained protection more quickly by vaccinating available animals rather than waiting to encounter priority seals. This work demonstrates the value of network models, but also makes trade-offs clear. If vaccines were limited but time was ample, vaccinating only priority animals would maximize herd protection. However, where time is the limiting factor, vaccinating additional lower-priority animals could more quickly protect the population.
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Affiliation(s)
- Stacie J Robinson
- NOAA National Marine Fisheries Service, Pacific Islands Fisheries Science Center, 1845 Wasp Boulevard, Honolulu, HI, USA
| | - Michelle M Barbieri
- NOAA National Marine Fisheries Service, Pacific Islands Fisheries Science Center, 1845 Wasp Boulevard, Honolulu, HI, USA
| | | | - Jason D Baker
- NOAA National Marine Fisheries Service, Pacific Islands Fisheries Science Center, 1845 Wasp Boulevard, Honolulu, HI, USA
| | | | - Meggan E Craft
- College of Veterinary Medicine, University of Minnesota, St Paul, MN, USA
| | - Charles L Littnan
- NOAA National Marine Fisheries Service, Pacific Islands Fisheries Science Center, 1845 Wasp Boulevard, Honolulu, HI, USA
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11
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Conservation genetics of an ex situ population of Primula reinii var. rhodotricha, an endangered primrose endemic to Japan on a limestone mountain. CONSERV GENET 2017. [DOI: 10.1007/s10592-017-0966-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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12
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Abadía-Cardoso A, Freimer NB, Deiner K, Garza JC. Molecular Population Genetics of the Northern Elephant Seal Mirounga angustirostris. J Hered 2017; 108:618-627. [PMID: 28821186 PMCID: PMC5892393 DOI: 10.1093/jhered/esx053] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2016] [Accepted: 06/21/2017] [Indexed: 11/13/2022] Open
Abstract
The northern elephant seal, Mirounga angustirostris, was heavily hunted and declared extinct in the 19th century. However, a colony remained on remote Guadalupe Island, Mexico and the species has since repopulated most of its historical distribution. Here, we present a comprehensive evaluation of genetic variation in the species. First, we assess the effect of the demographic bottleneck on microsatellite variability and compare it with that found in other pinnipeds, demonstrating levels of variation similar to that in species that continue to be threatened with extinction. Next, we use sequence data from these markers to demonstrate that some of the limited polymorphism predates the bottleneck. However, most contemporary variation appears to have arisen recently and persisted due to exponential growth. We also describe how we use the range in allele size of microsatellites to estimate ancestral effective population size before the bottleneck, demonstrating a large reduction in effective size. We then employ a classical method for bacteria to estimate the microsatellite mutation rate in the species, deriving an estimate that is extremely similar to that estimated for a similar set of loci in humans, indicating consistency of microsatellite mutation rates in mammals. Finally, we find slight significant structure between some geographically separated colonies, although its biological significance is unclear. This work demonstrates that genetic analysis can be useful for evaluating the population biology of the northern elephant seal, in spite of the bottleneck that removed most genetic variation from the species.
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Affiliation(s)
- Alicia Abadía-Cardoso
- Facultad de Ciencias Marinas, Universidad Autónoma de Baja California, Carretera Tijuana-Ensenada Km 103, Pedregal Playitas, 22860 Ensenada, BC, Mexico; University of California, Santa Cruz, 110 McAllister Way, Santa Cruz, CA 95060; Southwest Fisheries Science Center, National Marine Fisheries Service, 110 McAllister Way, Santa Cruz, CA 95060; Center for Neurobehavioral Genetics, University of California, Los Angeles, 695 Charles E. Young Drive South, Los Angeles, CA 90095. Department of Ecology and Evolutionary Biology, Cornell University, 215 Tower Rd., Ithaca, NY 14850
| | - Nelson B Freimer
- Facultad de Ciencias Marinas, Universidad Autónoma de Baja California, Carretera Tijuana-Ensenada Km 103, Pedregal Playitas, 22860 Ensenada, BC, Mexico; University of California, Santa Cruz, 110 McAllister Way, Santa Cruz, CA 95060; Southwest Fisheries Science Center, National Marine Fisheries Service, 110 McAllister Way, Santa Cruz, CA 95060; Center for Neurobehavioral Genetics, University of California, Los Angeles, 695 Charles E. Young Drive South, Los Angeles, CA 90095. Department of Ecology and Evolutionary Biology, Cornell University, 215 Tower Rd., Ithaca, NY 14850
| | - Kristy Deiner
- Facultad de Ciencias Marinas, Universidad Autónoma de Baja California, Carretera Tijuana-Ensenada Km 103, Pedregal Playitas, 22860 Ensenada, BC, Mexico; University of California, Santa Cruz, 110 McAllister Way, Santa Cruz, CA 95060; Southwest Fisheries Science Center, National Marine Fisheries Service, 110 McAllister Way, Santa Cruz, CA 95060; Center for Neurobehavioral Genetics, University of California, Los Angeles, 695 Charles E. Young Drive South, Los Angeles, CA 90095. Department of Ecology and Evolutionary Biology, Cornell University, 215 Tower Rd., Ithaca, NY 14850
| | - John Carlos Garza
- Facultad de Ciencias Marinas, Universidad Autónoma de Baja California, Carretera Tijuana-Ensenada Km 103, Pedregal Playitas, 22860 Ensenada, BC, Mexico; University of California, Santa Cruz, 110 McAllister Way, Santa Cruz, CA 95060; Southwest Fisheries Science Center, National Marine Fisheries Service, 110 McAllister Way, Santa Cruz, CA 95060; Center for Neurobehavioral Genetics, University of California, Los Angeles, 695 Charles E. Young Drive South, Los Angeles, CA 90095. Department of Ecology and Evolutionary Biology, Cornell University, 215 Tower Rd., Ithaca, NY 14850
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Emami-Khoyi A, Paterson AM, Hartley DA, Boren LJ, Cruickshank RH, Ross JG, Murphy EC, Else TA. Mitogenomics data reveal effective population size, historical bottlenecks, and the effects of hunting on New Zealand fur seals (Arctocephalus forsteri). Mitochondrial DNA A DNA Mapp Seq Anal 2017; 29:567-580. [PMID: 28539070 DOI: 10.1080/24701394.2017.1325478] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
The New Zealand fur seal (Arctocephalus forsteri) passed through a population bottleneck due to commercial sealing during the eighteenth to nineteenth centuries. To facilitate future management options, we reconstructed the demographic history of New Zealand fur seals in a Bayesian framework using maternally inherited, mitochondrial DNA sequences. Mitogenomic data suggested two separate clades (most recent common ancestor 5000 years ago) of New Zealand fur seals that survived large-scale human harvest. Mitochondrial haplotype diversity was high, with 45 singletons identified from 46 individuals although mean nucleotide diversity was low (0.012 ± 0.0061). Variation was not constrained geographically. Analyses of mitogenomes support the hypothesis for a population bottleneck approximately 35 generations ago, which coincides with the peak of commercial sealing. Mitogenomic data are consistent with a pre-human effective population size of approximately 30,000 that first declined to around 10,000 (due to the impact of Polynesian colonization, particularly in the first 100 years of their arrival into New Zealand), and then to 100-200 breeding individuals during peak of commercial sealing.
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Affiliation(s)
- Arsalan Emami-Khoyi
- a Center for Ecological Genomics and Wildlife Conservation , University of Johannesburg , Auckland Park , South Africa.,b Department of Ecology , Lincoln University , Lincoln , New Zealand
| | - Adrian M Paterson
- b Department of Ecology , Lincoln University , Lincoln , New Zealand
| | | | - Laura J Boren
- d New Zealand Department of Conservation , Wellington-Te Aro , New Zealand
| | | | - James G Ross
- b Department of Ecology , Lincoln University , Lincoln , New Zealand.,e Centre for Wildlife Management and Conservation , Lincoln University , Lincoln , New Zealand
| | - Elaine C Murphy
- b Department of Ecology , Lincoln University , Lincoln , New Zealand.,e Centre for Wildlife Management and Conservation , Lincoln University , Lincoln , New Zealand
| | - Terry-Ann Else
- f Department of Basic Science , Touro University , NV , USA
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MODELING A MORBILLIVIRUS OUTBREAK IN HAWAIIAN MONK SEALS (NEOMONACHUS SCHAUINSLANDI) TO AID IN THE DESIGN OF MITIGATION PROGRAMS. J Wildl Dis 2017; 53:736-748. [PMID: 28463627 DOI: 10.7589/2016-10-238] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
We developed a stochastic susceptible-exposed-infectious-removed (SEIR) model to simulate a range of plausible morbillivirus outbreak scenarios in a randomly mixing population of 170 endangered Hawaiian monk seals (Neomonachus schauinslandi). We then modeled realistic vaccination and quarantine measures to determine the potential efficacy of such mitigation efforts. Morbillivirus outbreaks represent substantial risk to monk seals-91% of simulated baseline outbreaks grew (R0>1), and in one-third of the scenarios all, or nearly all, individuals were infected. Simulated vaccination efforts in response to an outbreak were not effective in substantially reducing infections, largely because of the prolonged interval between vaccination and immunity. Prophylactic vaccination, in contrast, could be an effective tool for preventing outbreaks. Herd immunity is practically achievable because of the small sizes of monk seal populations and the animals' accessibility on shore. Adding realistic spatial structure to the model, as informed by movement of seals tracked in the main Hawaiian Islands with the use of telemetry, greatly reduced the simulated impact of outbreaks (≤10 seals were infected in 62% of spatially structured simulations). Although response vaccination remained relatively ineffective, spatial segregation allowed herd immunity to be achieved through prophylactic vaccination with less effort. In a randomly mixing population of 170 seals, 86% would need to be vaccinated to achieve herd immunity in 95% of simulated outbreaks, compared to only approximately 60% in three spatially segregated subgroups with the same combined abundance. Simulations indicate that quarantining a modest number (up to 20) of ill seals has the potential to extinguish even fast-growing outbreaks rapidly. The efficacy of quarantine, however, is highly dependent upon rapid detection and response. We conclude that prophylactic vaccination combined with a quarantine program supported by vigilant surveillance and rapid, reliable diagnosis could greatly mitigate the threat of a morbillivirus outbreak in Hawaiian monk seals.
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Spencer PBS, Sandover S, Nihill K, Wale CH, How RA, Schmitt LH. Living in isolation: ecological, demographic and genetic patterns in northern Australia’s top marsupial predator on Koolan Island. AUSTRALIAN MAMMALOGY 2017. [DOI: 10.1071/am16004] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Koolan Island supports an abundant population of the threatened northern quoll (Dasyurus hallucatus). We used a mark–release–recapture program that produced 2089 captures from 2009 to 2012 to examine demographic and genetic parameters in this insular population and compare to other localities. Every captured female was either lactating or carrying up to eight young over the breeding season, July–September. Unlike several other populations, males on Koolan Island can survive long after breeding, but never into a second breeding season. Females can survive and reproduce for two successive annual breeding seasons and occasionally survive to a third. There is marked sexual dimorphism but it is less pronounced, and both sexes are smaller than their mainland counterparts. Quolls were recorded moving over 4 km and apparent abundance was far higher on Koolan Island than the mainland. Genetic analyses of nuclear and mitochondrial markers demonstrate a distinctive signature. Koolan island has only 34% of the allelic richness of the entire species, and only 38% of the alleles in Kimberley mainland and near-shore island populations. There is no evidence of recent or long-term population decline. Kimberley island faunas have distinctive demographic and genetic profiles that should be appraised before considering translocations for conservation purposes.
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Mihnovets AN, Schultz JK, Wultsch C, Littnan CL, Amato G. A novel microsatellite multiplex assay for the endangered Hawaiian monk seal (Neomonachus schauinslandi). CONSERV GENET RESOUR 2016. [DOI: 10.1007/s12686-016-0517-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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ESTIMATING CONTACT RATES OF HAWAIIAN MONK SEALS (NEOMONACHUS SCHAUINSLANDI) USING SOCIAL NETWORK ANALYSIS. J Wildl Dis 2016; 52:533-43. [PMID: 27195686 DOI: 10.7589/2015-10-286] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Understanding disease transmission dynamics, which are in part mediated by rates and patterns of social contact, is fundamental to predicting the likelihood, rate of spread, impacts, and mitigation of disease outbreaks in wildlife populations. Contact rates, which are important parameters required for epidemiologic models, are difficult to estimate. The endangered Hawaiian monk seal (Neomonachus schauinslandi) may be particularly vulnerable to morbillivirus outbreaks, due to its low abundance, lack of genetic diversity, and history of isolation from mammalian diseases. Morbillivirus epizootics have had devastating effects on other seal populations. We constructed social networks based on visual observations of individually identifiable monk seals associating onshore to estimate contact rates, assuming random mixing, and also to investigate contact patterns of different age and sex classes. Contact rates estimated from two island populations in 4 yr were remarkably similar, indicating any two individuals have about a one in 1,000 chance of making contact on any given day. Further, contact patterns within and among age and sex classes were statistically different from random. The methods we used could be broadly applied to empirically derive contact rates using association data. These rates are critical for epidemiologic modelling to simulate wildlife disease outbreaks and to inform science-based prevention and mitigation programs.
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Taylor HR. The use and abuse of genetic marker-based estimates of relatedness and inbreeding. Ecol Evol 2015; 5:3140-50. [PMID: 26357542 PMCID: PMC4559056 DOI: 10.1002/ece3.1541] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2015] [Revised: 05/05/2015] [Accepted: 05/18/2015] [Indexed: 01/10/2023] Open
Abstract
Genetic marker-based estimators remain a popular tool for measuring relatedness (r xy ) and inbreeding (F) coefficients at both the population and individual level. The performance of these estimators fluctuates with the number and variability of markers available, and the relatedness composition and demographic history of a population. Several methods are available to evaluate the reliability of the estimates of r xy and F, some of which are implemented in the program COANCESTRY. I used the simulation module in COANCESTRY since assess the performance of marker-based estimators of r xy and F in a species with very low genetic diversity, New Zealand's little spotted kiwi (Apteryx owenii). I also conducted a review of published papers that have used COANCESTRY as its release to assess whether and how the reliability of the estimates of r xy and F produced by genetic markers are being measured and reported in published studies. My simulation results show that even when the correlation between true (simulated) and estimated r xy or F is relatively high (Pearson's r = 0.66-0.72 and 0.81-0.85, respectively) the imprecision of the estimates renders them highly unreliable on an individual basis. The literature review demonstrates that the majority of studies do not report the reliability of marker-based estimates of r xy and F. There is currently no standard practice for selecting the best estimator for a given data set or reporting an estimator's performance. This could lead to experimental results being interpreted out of context and render the robustness of conclusions based on measures of r xy and F debatable.
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Affiliation(s)
- Helen R Taylor
- Allan Wilson Centre, School of Biological Sciences, Victoria University of WellingtonKelburn Parade, Wellington, New Zealand
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Wang XJ, Shi DC, Wang XY, Wang J, Sun YS, Liu JQ. Evolutionary Migration of the Disjunct Salt Cress Eutrema salsugineum (= Thellungiella salsuginea, Brassicaceae) between Asia and North America. PLoS One 2015; 10:e0124010. [PMID: 25970468 PMCID: PMC4430283 DOI: 10.1371/journal.pone.0124010] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2014] [Accepted: 03/09/2015] [Indexed: 12/14/2022] Open
Abstract
Eutrema salsugineum (= Thellungiella salsuginea Brassicaceae), a species growing in highly saline habitats, is a good model for use in salt-stress research. However, its evolutionary migrations and genetic variations within and between disjunct regions from central Asia to northern China and North America remain largely unknown. We examined genetic variations and phylogeographic patterns of this species by sequencing ITS, 9 chloroplast (cp) DNA fragments (4379 bp) and 10 unlinked nuclear loci (6510 bp) of 24 populations across its distributional range. All markers suggested the high genetic poverty of this species and the limited number of genetic variations recovered was congruently partitioned between central Asia, northern China and North America. Further modelling of nuclear population-genetic data based on approximate bayesian computation (ABC) analyses indicated that the long-distance dispersals after the recent origin of E. salsugineum may have occurred from central Asia to the other two regions respectively within 20000 years. The fast demographic expansions should have occurred in northern China in a more recent past. Our study highlights the importance of using ABC analyses and nuclear population genetic data to trace evolutionary migrations of the disjunct distributions of the plants in the recent past.
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Affiliation(s)
- Xiao-Juan Wang
- MOE Key Laboratory for Bio-resources and Eco-environment, College of Life Science, Sichuan University, Chengdu, China
| | - Da-Chuan Shi
- Molecular Ecology Group, Key Laboratory of Arid and Grassland Ecology, School of Life Science, Lanzhou University, Lanzhou, China
| | - Xin-Yu Wang
- MOE Key Laboratory for Bio-resources and Eco-environment, College of Life Science, Sichuan University, Chengdu, China
| | - Juan Wang
- Molecular Ecology Group, Key Laboratory of Arid and Grassland Ecology, School of Life Science, Lanzhou University, Lanzhou, China
| | - Yong-Shuai Sun
- MOE Key Laboratory for Bio-resources and Eco-environment, College of Life Science, Sichuan University, Chengdu, China
| | - Jian-Quan Liu
- MOE Key Laboratory for Bio-resources and Eco-environment, College of Life Science, Sichuan University, Chengdu, China
- Molecular Ecology Group, Key Laboratory of Arid and Grassland Ecology, School of Life Science, Lanzhou University, Lanzhou, China
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Extremely low microsatellite diversity but distinct population structure in a long-lived threatened species, the Australian lungfish Neoceratodus forsteri (Dipnoi). PLoS One 2015; 10:e0121858. [PMID: 25853492 PMCID: PMC4390199 DOI: 10.1371/journal.pone.0121858] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2014] [Accepted: 02/16/2015] [Indexed: 11/24/2022] Open
Abstract
The Australian lungfish is a unique living representative of an ancient dipnoan lineage, listed as ‘vulnerable’ to extinction under Australia’s Environment Protection and Biodiversity Conservation Act 1999. Historical accounts indicate this species occurred naturally in two adjacent river systems in Australia, the Burnett and Mary. Current day populations in other rivers are thought to have arisen by translocation from these source populations. Early genetic work detected very little variation and so had limited power to answer questions relevant for management including how genetic variation is partitioned within and among sub-populations. In this study, we use newly developed microsatellite markers to examine samples from the Burnett and Mary Rivers, as well as from two populations thought to be of translocated origin, Brisbane and North Pine. We test whether there is significant genetic structure among and within river drainages; assign putatively translocated populations to potential source populations; and estimate effective population sizes. Eleven polymorphic microsatellite loci genotyped in 218 individuals gave an average within-population heterozygosity of 0.39 which is low relative to other threatened taxa and for freshwater fishes in general. Based on FST values (average over loci = 0.11) and STRUCTURE analyses, we identify three distinct populations in the natural range, one in the Burnett and two distinct populations in the Mary. These analyses also support the hypothesis that the Mary River is the likely source of translocated populations in the Brisbane and North Pine rivers, which agrees with historical published records of a translocation event giving rise to these populations. We were unable to obtain bounded estimates of effective population size, as we have too few genotype combinations, although point estimates were low, ranging from 29 - 129. We recommend that, in order to preserve any local adaptation in the three distinct populations that they be managed separately.
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Duignan PJ, Van Bressem MF, Baker JD, Barbieri M, Colegrove KM, De Guise S, de Swart RL, Di Guardo G, Dobson A, Duprex WP, Early G, Fauquier D, Goldstein T, Goodman SJ, Grenfell B, Groch KR, Gulland F, Hall A, Jensen BA, Lamy K, Matassa K, Mazzariol S, Morris SE, Nielsen O, Rotstein D, Rowles TK, Saliki JT, Siebert U, Waltzek T, Wellehan JF. Phocine distemper virus: current knowledge and future directions. Viruses 2014; 6:5093-134. [PMID: 25533658 PMCID: PMC4276944 DOI: 10.3390/v6125093] [Citation(s) in RCA: 65] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2014] [Revised: 12/05/2014] [Accepted: 12/11/2014] [Indexed: 11/16/2022] Open
Abstract
Phocine distemper virus (PDV) was first recognized in 1988 following a massive epidemic in harbor and grey seals in north-western Europe. Since then, the epidemiology of infection in North Atlantic and Arctic pinnipeds has been investigated. In the western North Atlantic endemic infection in harp and grey seals predates the European epidemic, with relatively small, localized mortality events occurring primarily in harbor seals. By contrast, PDV seems not to have become established in European harbor seals following the 1988 epidemic and a second event of similar magnitude and extent occurred in 2002. PDV is a distinct species within the Morbillivirus genus with minor sequence variation between outbreaks over time. There is now mounting evidence of PDV-like viruses in the North Pacific/Western Arctic with serological and molecular evidence of infection in pinnipeds and sea otters. However, despite the absence of associated mortality in the region, there is concern that the virus may infect the large Pacific harbor seal and northern elephant seal populations or the endangered Hawaiian monk seals. Here, we review the current state of knowledge on PDV with particular focus on developments in diagnostics, pathogenesis, immune response, vaccine development, phylogenetics and modeling over the past 20 years.
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Affiliation(s)
- Pádraig J. Duignan
- Department of Ecosystem and Public Health, University of Calgary, Calgary, AB T2N 4Z6, Canada; E-Mails: (P.D.); (K.L.)
| | - Marie-Françoise Van Bressem
- Cetacean Conservation Medicine Group (CMED), Peruvian Centre for Cetacean Research (CEPEC), Pucusana, Lima 20, Peru; E-Mail:
| | - Jason D. Baker
- Pacific Islands Fisheries Science Center, National Marine Fisheries Service, NOAA, 1845 WASP Blvd., Building 176, Honolulu, Hawaii 96818, USA; E-Mails: (J.D.B.); (M.B.)
| | - Michelle Barbieri
- Pacific Islands Fisheries Science Center, National Marine Fisheries Service, NOAA, 1845 WASP Blvd., Building 176, Honolulu, Hawaii 96818, USA; E-Mails: (J.D.B.); (M.B.)
- The Marine Mammal Centre, Sausalito, CA 94965, USA; E-Mail:
| | - Kathleen M. Colegrove
- Zoological Pathology Program, College of Veterinary Medicine, University of Illinois Urbana-Champaign, Maywood, IL 60153, USA; E-Mail:
| | - Sylvain De Guise
- Department of Pathobiology and Veterinary Science, and Connecticut Sea Grant College Program, University of Connecticut, Storrs, CT 06269, USA; E-Mail:
| | - Rik L. de Swart
- Department of Viroscience, Erasmus MC, 3015 CN Rotterdam, The Netherlands; E-Mail:
| | - Giovanni Di Guardo
- Faculty of Veterinary Medicine, University of Teramo, 64100 Teramo, Italy; E-Mail:
| | - Andrew Dobson
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ 08544-2016, USA; E-Mails: (A.D.); (B.G.); (S.E.M.)
| | - W. Paul Duprex
- Department of Microbiology, Boston University School of Medicine, Boston University, 620 Albany Street, Boston, MA 02118, USA; E-Mail:
| | - Greg Early
- Greg Early, Integrated Statistics, 87 Water St, Woods Hole, MA 02543, USA; E-Mail:
| | - Deborah Fauquier
- National Marine Fisheries Service/National Oceanographic and Atmospheric Administration, Marine Mammal Health and Stranding Response Program, Silver Spring, MD 20910, USA; E-Mails: (D.F.); (T.K.R.)
| | - Tracey Goldstein
- One Health Institute, School of Veterinary Medicine, University of California, Davis, CA 95616, USA; E-Mail:
| | - Simon J. Goodman
- School of Biology, University of Leeds, Leeds LS2 9JT, UK; E-Mail:
| | - Bryan Grenfell
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ 08544-2016, USA; E-Mails: (A.D.); (B.G.); (S.E.M.)
- Fogarty International Center, National Institutes of Health, Bethesda, MD 20892-2220, USA
| | - Kátia R. Groch
- Department of Pathology, School of Veterinary Medicine and Animal Science, University of São Paulo, São Paulo 05508-270, Brazil; E-Mail:
| | - Frances Gulland
- The Marine Mammal Centre, Sausalito, CA 94965, USA; E-Mail:
- Marine Mammal Commission, 4340 East-West Highway, Bethesda, MD 20814, USA
| | - Ailsa Hall
- Sea Mammal Research Unit, Scottish Oceans Institute, University of St. Andrews, St. Andrews, Fife KY16 8LB, UK; E-Mail:
| | - Brenda A. Jensen
- Department of Natural Sciences, Hawai’i Pacific University, Kaneohe, HI 96744, USA; E-Mail:
| | - Karina Lamy
- Department of Ecosystem and Public Health, University of Calgary, Calgary, AB T2N 4Z6, Canada; E-Mails: (P.D.); (K.L.)
| | - Keith Matassa
- Keith Matassa, Pacific Marine Mammal Center, 20612 Laguna Canyon Road, Laguna Beach, CA 92651, USA; E-Mail:
| | - Sandro Mazzariol
- Department of Comparative Biomedicine and Food Science, University of Padua, 35020 Legnaro Padua, Italy; E-Mail:
| | - Sinead E. Morris
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ 08544-2016, USA; E-Mails: (A.D.); (B.G.); (S.E.M.)
| | - Ole Nielsen
- Department of Fisheries and Oceans Canada, Central and Arctic Region, 501 University Crescent, Winnipeg, MB R3T 2N6, Canada; E-Mail:
| | - David Rotstein
- David Rotstein, Marine Mammal Pathology Services, 19117 Bloomfield Road, Olney, MD 20832, USA; E-Mail:
| | - Teresa K. Rowles
- National Marine Fisheries Service/National Oceanographic and Atmospheric Administration, Marine Mammal Health and Stranding Response Program, Silver Spring, MD 20910, USA; E-Mails: (D.F.); (T.K.R.)
| | - Jeremy T. Saliki
- Athens Veterinary Diagnostic Laboratory, College of Veterinary Medicine, University of Georgia, GA 30602, USA; E-Mail:
| | - Ursula Siebert
- Institute for Terrestrial and Aquatic Wildlife Research, University of Veterinary Medicine Hannover 30173, Germany; E-Mail:
| | - Thomas Waltzek
- Department of Infectious Diseases and Pathology, College of Veterinary Medicine, University of Florida, FL 32611, USA; E-Mail:
| | - James F.X. Wellehan
- Department of Small Animal Clinical Sciences, College of Veterinary Medicine, University of Florida, FL 32610, USA; E-Mail:
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Discovery of a New, Disjunct Population of a Narrowly Distributed Salamander (Taricha rivularis) in California Presents Conservation Challenges. J HERPETOL 2014. [DOI: 10.1670/13-066] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Valtonen M, Palo JU, Aspi J, Ruokonen M, Kunnasranta M, Nyman T. Causes and consequences of fine-scale population structure in a critically endangered freshwater seal. BMC Ecol 2014; 14:22. [PMID: 25005257 PMCID: PMC4106222 DOI: 10.1186/1472-6785-14-22] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2014] [Accepted: 07/03/2014] [Indexed: 11/10/2022] Open
Abstract
Background Small, genetically uniform populations may face an elevated risk of extinction due to reduced environmental adaptability and individual fitness. Fragmentation can intensify these genetic adversities and, therefore, dispersal and gene flow among subpopulations within an isolated population is often essential for maintaining its viability. Using microsatellite and mtDNA data, we examined genetic diversity, spatial differentiation, interregional gene flow, and effective population sizes in the critically endangered Saimaa ringed seal (Phoca hispida saimensis), which is endemic to the large but highly fragmented Lake Saimaa in southeastern Finland. Results Microsatellite diversity within the subspecies (HE = 0.36) ranks among the lowest thus far recorded within the order Pinnipedia, with signs of ongoing loss of individual heterozygosity, reflecting very low effective subpopulation sizes. Bayesian assignment analyses of the microsatellite data revealed clear genetic differentiation among the main breeding areas, but interregional structuring was substantially weaker in biparentally inherited microsatellites (FST = 0.107) than in maternally inherited mtDNA (FST = 0.444), indicating a sevenfold difference in the gene flow mediated by males versus females. Conclusions Genetic structuring in the population appears to arise from the joint effects of multiple factors, including small effective subpopulation sizes, a fragmented lacustrine habitat, and behavioural dispersal limitation. The fine-scale differentiation found in the landlocked Saimaa ringed seal is especially surprising when contrasted with marine ringed seals, which often exhibit near-panmixia among subpopulations separated by hundreds or even thousands of kilometres. Our results demonstrate that population structures of endangered animals cannot be predicted based on data on even closely related species or subspecies.
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Affiliation(s)
- Mia Valtonen
- Department of Biology, University of Eastern Finland, Joensuu, Finland.
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Scheel DM, Slater GJ, Kolokotronis SO, Potter CW, Rotstein DS, Tsangaras K, Greenwood AD, Helgen KM. Biogeography and taxonomy of extinct and endangered monk seals illuminated by ancient DNA and skull morphology. Zookeys 2014:1-33. [PMID: 24899841 PMCID: PMC4042687 DOI: 10.3897/zookeys.409.6244] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2013] [Accepted: 04/19/2014] [Indexed: 11/12/2022] Open
Abstract
Extinctions and declines of large marine vertebrates have major ecological impacts and are of critical concern in marine environments. The Caribbean monk seal, Monachus tropicalis, last definitively reported in 1952, was one of the few marine mammal species to become extinct in historical times. Despite its importance for understanding the evolutionary biogeography of southern phocids, the relationships of M. tropicalis to the two living species of critically endangered monk seals have not been resolved. In this study we present the first molecular data for M. tropicalis, derived from museum skins. Phylogenetic analysis of cytochrome b sequences indicates that M. tropicalis was more closely related to the Hawaiian rather than the Mediterranean monk seal. Divergence time estimation implicates the formation of the Panamanian Isthmus in the speciation of Caribbean and Hawaiian monk seals. Molecular, morphological and temporal divergence between the Mediterranean and “New World monk seals” (Hawaiian and Caribbean) is profound, equivalent to or greater than between sister genera of phocids. As a result, we classify the Caribbean and Hawaiian monk seals together in a newly erected genus, Neomonachus. The two genera of extant monk seals (Monachus and Neomonachus) represent old evolutionary lineages each represented by a single critically endangered species, both warranting continuing and concerted conservation attention and investment if they are to avoid the fate of their Caribbean relative.
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Affiliation(s)
- Dirk-Martin Scheel
- Leibniz Institute for Zoo and Wildlife Research, Alfred-Kowalke-Str. 17, 10315 Berlin, Germany
| | - Graham J Slater
- Division of Mammals, Smithsonian Institution, National Museum of Natural History, 10th Street and Constitution Ave, NW, Washington, DC 20560-0108, USA ; Department of Paleobiology, Smithsonian Institution, National Museum of Natural History, 10th Street and Constitution Ave, NW, Washington, DC 20560-0108, USA
| | | | - Charles W Potter
- Division of Mammals, Smithsonian Institution, National Museum of Natural History, 10th Street and Constitution Ave, NW, Washington, DC 20560-0108, USA
| | - David S Rotstein
- Marine Mammal Pathology Services, 19117 Bloomfield Road, Olney, MD 20832, USA
| | - Kyriakos Tsangaras
- Leibniz Institute for Zoo and Wildlife Research, Alfred-Kowalke-Str. 17, 10315 Berlin, Germany
| | - Alex D Greenwood
- Leibniz Institute for Zoo and Wildlife Research, Alfred-Kowalke-Str. 17, 10315 Berlin, Germany
| | - Kristofer M Helgen
- Division of Mammals, Smithsonian Institution, National Museum of Natural History, 10th Street and Constitution Ave, NW, Washington, DC 20560-0108, USA
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Remarkably low genetic diversity and strong population structure in common bottlenose dolphins (Tursiops truncatus) from coastal waters of the Southwestern Atlantic Ocean. CONSERV GENET 2014. [DOI: 10.1007/s10592-014-0586-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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Agnarsson I, Avilés L, Maddison WP. Loss of genetic variability in social spiders: genetic and phylogenetic consequences of population subdivision and inbreeding. J Evol Biol 2012; 26:27-37. [PMID: 23145542 PMCID: PMC3588177 DOI: 10.1111/jeb.12022] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2012] [Accepted: 09/20/2012] [Indexed: 11/29/2022]
Abstract
The consequences of population subdivision and inbreeding have been studied in many organisms, particularly in plants. However, most studies focus on the short-term consequences, such as inbreeding depression. To investigate the consequences of both population fragmentation and inbreeding for genetic variability in the longer term, we here make use of a natural inbreeding experiment in spiders, where sociality and accompanying population subdivision and inbreeding have evolved repeatedly. We use mitochondrial and nuclear data to infer phylogenetic relationships among 170 individuals of Anelosimus spiders representing 23 species. We then compare relative mitochondrial and nuclear genetic variability of the inbred social species and their outbred relatives. We focus on four independently derived social species and four subsocial species, including two outbred–inbred sister species pairs. We find that social species have 50% reduced mitochondrial sequence divergence. As inbreeding is not expected to reduce genetic variability in the maternally inherited mitochondrial genome, this suggests the loss of variation due to strong population subdivision, founder effects, small effective population sizes (colonies as individuals) and lineage turnover. Social species have < 10% of the nuclear genetic variability of the outbred species, also suggesting the loss of genetic variability through founder effects and/or inbreeding. Inbred sociality hence may result in reduction in variability through various processes. Sociality in most Anelosimus species probably arose relatively recently (0.1–2 mya), with even the oldest social lineages having failed to diversify. This is consistent with the hypothesis that inbred spider sociality represents an evolutionary dead end. Heterosis underlies a species potential to respond to environmental change and/or disease. Inbreeding and loss of genetic variability may thus limit diversification in social Anelosimus lineages and similarly pose a threat to many wild populations subject to habitat fragmentation or reduced population sizes.
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Affiliation(s)
- I Agnarsson
- Department of Biology, University of Vermont, Burlington, VT, USA.
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Kyrkjeeide MO, Hassel K, Flatberg KI, Stenøien HK. The rare peat moss Sphagnum wulfianum (Sphagnaceae) did not survive the last glacial period in northern European refugia. AMERICAN JOURNAL OF BOTANY 2012; 99:677-689. [PMID: 22473975 DOI: 10.3732/ajb.1100410] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
PREMISE OF THE STUDY Organisms may survive unfavorable conditions either by moving to more favorable areas by means of dispersal or by adapting to stressful environments. Pleistocene glacial periods represent extremely unfavorable conditions for the majority of life forms, especially sessile organisms. Many studies have revealed placements of refugial areas and postglacial colonization patterns of seed plants, but little is still known about areas of long-term survival and historical migration routes of bryophytes. Given overall differences in stress tolerance between seed plants and bryophytes, it is of interest to know whether bryophytes have survived periods of extreme climatic conditions better then seed plants in northern areas. METHODS The haploid and rarely spore-producing peat moss Sphagnum wulfianum is mostly found in areas that were covered by ice during the last glacial maximum. Twelve microsatellite markers were amplified from 43 populations (367 shoots) of this species, and data were analyzed using population genetic diversity statistics, Bayesian clustering methods, and coalescence-based inference tools to estimate historical and demographic parameters. KEY RESULTS Genetic diversity within populations was low, but populations were highly differentiated, with two main genetic clusters being recognized. CONCLUSION The two main genetic groups have diverged quite recently in the Holocene, and the pattern of genetic variability and structuring gives no support for survival in Scandinavian refugia during the last glacial period in this species. The dispersal ability of this plant thus seems surprisingly high despite its infrequent spore production.
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Affiliation(s)
- Magni Olsen Kyrkjeeide
- Systematics and Evolution Group, Section of Natural History, Museum of Natural History and Archaeology, Norwegian University of Science and Technology, Trondheim, Norway.
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Extremely low genetic diversity indicating the endangered status of Ranodon sibiricus (Amphibia: Caudata) and implications for phylogeography. PLoS One 2012; 7:e33378. [PMID: 22428037 PMCID: PMC3299782 DOI: 10.1371/journal.pone.0033378] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2011] [Accepted: 02/08/2012] [Indexed: 10/29/2022] Open
Abstract
BACKGROUND The Siberian salamander (Ranodon sibiricus), distributed in geographically isolated areas of Central Asia, is an ideal alpine species for studies of conservation and phylogeography. However, there are few data regarding the genetic diversity in R. sibiricus populations. METHODOLOGY/PRINCIPAL FINDINGS We used two genetic markers (mtDNA and microsatellites) to survey all six populations of R. sibiricus in China. Both of the markers revealed extreme genetic uniformity among these populations. There were only three haplotypes in the mtDNA, and the overall nucleotide diversity in the mtDNA was 0.00064, ranging from 0.00000 to 0.00091 for the six populations. Although we recovered 70 sequences containing microsatellite repeats, there were only two loci that displayed polymorphism. We used the approximate Bayesian computation (ABC) method to study the demographic history of the populations. This analysis suggested that the extant populations diverged from the ancestral population approximately 120 years ago and that the historical population size was much larger than the present population size; i.e., R. sibiricus has experienced dramatic population declines. CONCLUSION/SIGNIFICANCE Our findings suggest that the genetic diversity in the R. sibiricus populations is the lowest among all investigated amphibians. We conclude that the isolation of R. sibiricus populations occurred recently and was a result of recent human activity and/or climatic changes. The Pleistocene glaciation oscillations may have facilitated intraspecies genetic homogeneity rather than enhanced divergence. A low genomic evolutionary rate and elevated inbreeding frequency may have also contributed to the low genetic variation observed in this species. Our findings indicate the urgency of implementing a protection plan for this endangered species.
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Ureña-Aranda CA, de los Monteros AE. The genetic crisis of the Mexican Bolson Tortoise (Gopherus flavomarginatus: Testudinidae). AMPHIBIA-REPTILIA 2012. [DOI: 10.1163/156853811x621508] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Gopherusflavomarginatus(Testudinidae) is endemic to a series of discontinuous, isolated basins collectively known as the Bolson de Mapimí in the Chihuahuan Desert. Its numbers declined after catastrophic levels of exploitation during the mid-20th century. However currently, the Bolson Tortoise appears to be on a path to recovery owing to intensive, sustained conservation efforts. We sequenced an 842-bp-long fragment of the D-loop from 76 individuals distributed throughout the species’ range. The results revealed only two haplotypes. An AMOVA showed that 95% of the variance occurred among populations, whereas the remaining 5% was explained by genetic differences within populations. Tectonic processes together with ecological transformation during the Pleistocene and Holocene may be responsible for the reduction in this species’ genetic variation. A bottleneck during which a significant percentage of the haplotype diversity was lost would result in genetic homogeneity. Although there is demographic growth, the lack of genetic diversity is indicative of the potential crisis that the Bolson Tortoise is facing, and awareness must be brought to this situation.
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Affiliation(s)
- Cinthya Alejandra Ureña-Aranda
- Laboratorio de Sistemática Filogenética, Departamento de Biología Evolutiva, Instituto de Ecología, A. C., Carretera antigua a Coatepec No. 351, Xalapa, Veracruz 91070, México
| | - Alejandro Espinosa de los Monteros
- Laboratorio de Sistemática Filogenética, Departamento de Biología Evolutiva, Instituto de Ecología, A. C., Carretera antigua a Coatepec No. 351, Xalapa, Veracruz 91070, México
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Langen K, Schwarzer J, Kullmann H, Bakker TCM, Thünken T. Microsatellite support for active inbreeding in a cichlid fish. PLoS One 2011; 6:e24689. [PMID: 21980351 PMCID: PMC3184091 DOI: 10.1371/journal.pone.0024689] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2011] [Accepted: 08/18/2011] [Indexed: 11/21/2022] Open
Abstract
In wild animal populations, the degree of inbreeding differs between species and within species between populations. Because mating with kin often results in inbreeding depression, observed inbreeding is usually regarded to be caused by limited outbreeding opportunities due to demographic factors like small population size or population substructuring. However, theory predicts inclusive benefits from mating with kin, and thus part of the observed variation in inbreeding might be due to active inbreeding preferences. Although some recent studies indeed report kin mating preferences, the evidence is still highly ambiguous. Here, we investigate inbreeding in a natural population of the West African cichlid fish Pelvicachromis taeniatus which showed clear kin mating preferences in standardized laboratory experiments but no inbreeding depression. The presented microsatellite analysis reveals that the natural population has, in comparison to two reference populations, a reduced allelic diversity (A = 3) resulting in a low heterozygosity (Ho = 0.167) pointing to a highly inbred population. Furthermore, we found a significant heterozygote deficit not only at population (Fis = 0.116) but also at subpopulation level (Fis = 0.081) suggesting that inbreeding is not only a by-product of population substructuring but possibly a consequence of behavioral kin preferences.
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Affiliation(s)
- Kathrin Langen
- Institute for Evolutionary Biology and Ecology, University of Bonn, Bonn, Germany.
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Schultz JK, Becker BL, Johanos TC, Lopez JU, Kashinsky L. Dizygotic twinning in the Hawaiian monk seal. J Mammal 2011. [DOI: 10.1644/10-mamm-a-275.1] [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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ROBERTSON BC, CHILVERS BL. The population decline of the New Zealand sea lion Phocarctos hookeri: a review of possible causes. Mamm Rev 2011. [DOI: 10.1111/j.1365-2907.2011.00186.x] [Citation(s) in RCA: 74] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Schultz JK, Baker JD, Toonen RJ, Harting AL, Bowen BW. Range-wide genetic connectivity of the Hawaiian monk seal and implications for translocation. CONSERVATION BIOLOGY : THE JOURNAL OF THE SOCIETY FOR CONSERVATION BIOLOGY 2011; 25:124-132. [PMID: 21166713 DOI: 10.1111/j.1523-1739.2010.01615.x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
The Hawaiian monk seal (Monachus schauinslandi) is one of the most critically endangered marine mammals. Less than 1200 individuals remain, and the species is declining at a rate of approximately 4% per year as a result of juvenile starvation, shark predation, and entanglement in marine debris. Some of these problems may be alleviated by translocation; however, if island breeding aggregates are effectively isolated subpopulations, moving individuals may disrupt local adaptations. In these circumstances, managers must balance the pragmatic need of increasing survival with theoretical concerns about genetic viability. To assess range-wide population structure of the Hawaiian monk seal, we examined an unprecedented, near-complete genetic inventory of the species (n =1897 seals, sampled over 14 years) at 18 microsatellite loci. Genetic variation was not spatially partitioned ((w) =-0.03, p = 1.0), and a Bayesian clustering method provided evidence of one panmictic population (K =1). Pairwise F(ST) comparisons (among 7 island aggregates over 14 annual cohorts) did not reveal temporally stable, spatial reproductive isolation. Our results coupled with long-term tag-resight data confirm seal movement and gene flow throughout the Hawaiian Archipelago. Thus, human-mediated translocation of seals among locations is not likely to result in genetic incompatibilities.
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Affiliation(s)
- Jennifer K Schultz
- Hawaii Institute of Marine Biology, School of Ocean and Earth Science and Technology, University of Hawaii, Kaneohe, HI 96744, U.S.A.
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Toonen RJ, Andrews KR, Baums IB, Bird CE, Concepcion GT, Daly-Engel TS, Eble JA, Faucci A, Gaither MR, Iacchei M, Puritz JB, Schultz JK, Skillings DJ, Timmers MA, Bowen BW. Defining Boundaries for Ecosystem-Based Management: A Multispecies Case Study of Marine Connectivity across the Hawaiian Archipelago. JOURNAL OF MARINE BIOLOGY 2011; 2011:460173. [PMID: 25505913 PMCID: PMC4260462 DOI: 10.1155/2011/460173] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Determining the geographic scale at which to apply ecosystem-based management (EBM) has proven to be an obstacle for many marine conservation programs. Generalizations based on geographic proximity, taxonomy, or life history characteristics provide little predictive power in determining overall patterns of connectivity, and therefore offer little in terms of delineating boundaries for marine spatial management areas. Here, we provide a case study of 27 taxonomically and ecologically diverse species (including reef fishes, marine mammals, gastropods, echinoderms, cnidarians, crustaceans, and an elasmobranch) that reveal four concordant barriers to dispersal within the Hawaiian Archipelago which are not detected in single-species exemplar studies. We contend that this multispecies approach to determine concordant patterns of connectivity is an objective and logical way in which to define the minimum number of management units and that EBM in the Hawaiian Archipelago requires at least five spatially managed regions.
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Affiliation(s)
- Robert J. Toonen
- Hawai’i Institute of Marine Biology, School of Ocean and Earth Science and Technology, University of Hawai’i at Mānoa, P.O. Box 1346 Kāne’ohe, HI 96744, USA
| | - Kimberly R. Andrews
- Hawai’i Institute of Marine Biology, School of Ocean and Earth Science and Technology, University of Hawai’i at Mānoa, P.O. Box 1346 Kāne’ohe, HI 96744, USA
- Department of Zoology, University of Hawai’i at Mānoa, Honolulu, HI 96822, USA
| | - Iliana B. Baums
- Department of Biology, Pennsylvania State University, University Park, PA 16802, USA
| | - Christopher E. Bird
- Hawai’i Institute of Marine Biology, School of Ocean and Earth Science and Technology, University of Hawai’i at Mānoa, P.O. Box 1346 Kāne’ohe, HI 96744, USA
| | - Gregory T. Concepcion
- Hawai’i Institute of Marine Biology, School of Ocean and Earth Science and Technology, University of Hawai’i at Mānoa, P.O. Box 1346 Kāne’ohe, HI 96744, USA
- Department of Zoology, University of Hawai’i at Mānoa, Honolulu, HI 96822, USA
| | - Toby S. Daly-Engel
- Hawai’i Institute of Marine Biology, School of Ocean and Earth Science and Technology, University of Hawai’i at Mānoa, P.O. Box 1346 Kāne’ohe, HI 96744, USA
- Department of Zoology, University of Hawai’i at Mānoa, Honolulu, HI 96822, USA
| | - Jeff A. Eble
- Hawai’i Institute of Marine Biology, School of Ocean and Earth Science and Technology, University of Hawai’i at Mānoa, P.O. Box 1346 Kāne’ohe, HI 96744, USA
- Department of Zoology, University of Hawai’i at Mānoa, Honolulu, HI 96822, USA
| | - Anuschka Faucci
- Department of Biology, University of Hawai’i at Mānoa, Honolulu, HI 96822, USA
| | - Michelle R. Gaither
- Hawai’i Institute of Marine Biology, School of Ocean and Earth Science and Technology, University of Hawai’i at Mānoa, P.O. Box 1346 Kāne’ohe, HI 96744, USA
- Department of Zoology, University of Hawai’i at Mānoa, Honolulu, HI 96822, USA
| | - Matthew Iacchei
- Hawai’i Institute of Marine Biology, School of Ocean and Earth Science and Technology, University of Hawai’i at Mānoa, P.O. Box 1346 Kāne’ohe, HI 96744, USA
- Department of Zoology, University of Hawai’i at Mānoa, Honolulu, HI 96822, USA
| | - Jonathan B. Puritz
- Hawai’i Institute of Marine Biology, School of Ocean and Earth Science and Technology, University of Hawai’i at Mānoa, P.O. Box 1346 Kāne’ohe, HI 96744, USA
- Department of Zoology, University of Hawai’i at Mānoa, Honolulu, HI 96822, USA
| | - Jennifer K. Schultz
- Hawai’i Institute of Marine Biology, School of Ocean and Earth Science and Technology, University of Hawai’i at Mānoa, P.O. Box 1346 Kāne’ohe, HI 96744, USA
| | - Derek J. Skillings
- Hawai’i Institute of Marine Biology, School of Ocean and Earth Science and Technology, University of Hawai’i at Mānoa, P.O. Box 1346 Kāne’ohe, HI 96744, USA
- Department of Zoology, University of Hawai’i at Mānoa, Honolulu, HI 96822, USA
| | - Molly A. Timmers
- Joint Institute for Marine and Atmospheric Research, University of Hawai’i at Mānoa, Honolulu, HI 96822, USA
| | - Brian W. Bowen
- Hawai’i Institute of Marine Biology, School of Ocean and Earth Science and Technology, University of Hawai’i at Mānoa, P.O. Box 1346 Kāne’ohe, HI 96744, USA
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Branch OH, Sutton PL, Barnes C, Castro JC, Hussin J, Awadalla P, Hijar G. Plasmodium falciparum genetic diversity maintained and amplified over 5 years of a low transmission endemic in the Peruvian Amazon. Mol Biol Evol 2010; 28:1973-86. [PMID: 21109587 PMCID: PMC3112368 DOI: 10.1093/molbev/msq311] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Plasmodium falciparum entered into the Peruvian Amazon in 1994, sparking an epidemic between 1995 and 1998. Since 2000, there has been sustained low P. falciparum transmission. The Malaria Immunology and Genetics in the Amazon project has longitudinally followed members of the community of Zungarococha (N = 1,945, 4 villages) with active household and health center-based visits each year since 2003. We examined parasite population structure and traced the parasite genetic diversity temporally and spatially. We genotyped infections over 5 years (2003–2007) using 14 microsatellite (MS) markers scattered across ten different chromosomes. Despite low transmission, there was considerable genetic diversity, which we compared with other geographic regions. We detected 182 different haplotypes from 302 parasites in 217 infections. Structure v2.2 identified five clusters (subpopulations) of phylogenetically related clones. To consider genetic diversity on a more detailed level, we defined haplotype families (hapfams) by grouping haplotypes with three or less loci differences. We identified 34 different hapfams identified. The Fst statistic and heterozygosity analysis showed the five clusters were maintained in each village throughout this time. A minimum spanning network (MSN), stratified by the year of detection, showed that haplotypes within hapfams had allele differences and haplotypes within a cluster definition were more separated in the later years (2006–2007). We modeled hapfam detection and loss, accounting for sample size and stochastic fluctuations in frequencies overtime. Principle component analysis of genetic variation revealed patterns of genetic structure with time rather than village. The population structure, genetic diversity, appearance/disappearance of the different haplotypes from 2003 to 2007 provides a genome-wide “real-time” perspective of P. falciparum parasites in a low transmission region.
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Affiliation(s)
- Oralee H Branch
- Department of Medical Parasitology, New York University, USA.
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Genome-Wide Loss of Diversity in the Critically Endangered Hawaiian Monk Seal. DIVERSITY-BASEL 2010. [DOI: 10.3390/d2060863] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Hoffman JI, Forcada J, Amos W. Exploring the mechanisms underlying a heterozygosity-fitness correlation for canine size in the Antarctic fur seal Arctocephalus gazella. ACTA ACUST UNITED AC 2010; 101:539-52. [PMID: 20457623 DOI: 10.1093/jhered/esq046] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
Although heterozygosity-fitness correlations (HFCs) are widely reported in the literature, most studies use too few markers to allow the proximate mechanisms to be convincingly resolved. Two competing hypotheses have been proposed: the general effect hypothesis, in which marker heterozygosity correlates with genome-wide heterozygosity and hence the inbreeding coefficient f, and the local effect hypothesis, in which one or more of the markers by chance exhibit associative overdominance. To explore the relative contributions of general and local effects in a free-ranging marine mammal population, we revisited a strong HFC found using 9 microsatellite loci for canine tooth size in 84 male Antarctic fur seals Arctocephalus gazella (Hoffman JI, Hanson N, Forcada J, Trathan PN, Amos W. 2010. Getting long in the tooth: a strong positive correlation between canine size and heterozygosity in the Antarctic fur seal Arctocephalus gazella. J Hered.). Increasing the number of markers to 76, we find that heterozygosity is uncorrelated across loci, indicating that inbred individuals are rare or absent. Similarly, while the HFC based on overall heterozygosity is lost, stochastic simulations indicate that when an HFC is due to inbreeding depression, increasing marker number invariably strengthens the HFC. Together these observations argue strongly that the original HFC was not due to inbreeding depression. In contrast, a subset of markers show individually significant effects, and these are nonrandomly distributed across the marker panel, being preferentially associated with markers cloned from other species. Using basic alignment search tool searches, we were able to locate 94% of loci to unique locations in the dog genome, but the local genes are functionally diverse, and the majority cannot be linked directly to growth. Our results suggest that inbreeding depression contributes little if at all to the relationship between heterozygosity and tooth size but that instead the primary mechanism involves associative overdominance. These findings contribute to a growing body of evidence suggesting that general effects are likely to be uncommon in natural populations.
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Affiliation(s)
- Joseph I Hoffman
- Department of Zoology, University of Cambridge, Cambridge CB2 3EJ, UK.
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Pitcher BJ, Ahonen H, Harcourt RG, Charrier I. Delayed onset of vocal recognition in Australian sea lion pups (Neophoca cinerea). Naturwissenschaften 2009; 96:901-9. [DOI: 10.1007/s00114-009-0546-5] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2009] [Revised: 04/08/2009] [Accepted: 04/08/2009] [Indexed: 11/28/2022]
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