1
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Judson BJ, Kristjánsson BK, Leblanc CA, Ferguson MM. The role of neutral and adaptive evolutionary processes on patterns of genetic diversity across small cave-dwelling populations of Icelandic Arctic charr ( Salvelinus alpinus). Ecol Evol 2024; 14:e11363. [PMID: 38770124 PMCID: PMC11103641 DOI: 10.1002/ece3.11363] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Revised: 04/10/2024] [Accepted: 04/12/2024] [Indexed: 05/22/2024] Open
Abstract
Understanding the adaptability of small populations in the face of environmental change is a central problem in evolutionary biology. Solving this problem is challenging because neutral evolutionary processes that operate on historical and contemporary timescales can override the effects of selection in small populations. We assessed the effects of isolation by colonization (IBC), isolation by dispersal limitation (IBDL) as reflected by a pattern of isolation by distance (IBD), and isolation by adaptation (IBA) and the roles of genetic drift and gene flow on patterns of genetic differentiation among 19 cave-dwelling populations of Icelandic Arctic charr (Salvelinus alpinus). We detected evidence of IBC based on the genetic affinity of nearby cave populations and the genetic relationships between the cave populations and the presumed ancestral population in the lake. A pattern of IBD was evident regardless of whether high-level genetic structuring (IBC) was taken into account. Genetic signatures of bottlenecks and lower genetic diversity in smaller populations indicate the effect of drift. Estimates of gene flow and fish movement suggest that gene flow is limited to nearby populations. In contrast, we found little evidence of IBA as patterns of local ecological and phenotypic variation showed little association with genetic differentiation among populations. Thus, patterns of genetic variation in these small populations likely reflect localized gene flow and genetic drift superimposed onto a larger-scale structure that is largely a result of colonization history. Our simultaneous assessment of the effects of neutral and adaptive processes in a tractable and replicated system has yielded novel insights into the evolution of small populations on both historical and contemporary timescales and over a smaller spatial scale than is typically studied.
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Affiliation(s)
- Braden J. Judson
- Department of Integrative BiologyUniversity of GuelphGuelphOntarioCanada
| | | | | | - Moira M. Ferguson
- Department of Integrative BiologyUniversity of GuelphGuelphOntarioCanada
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2
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Matthews G, Farquhar JE, White CR, Chapple DG. Does thermal biology differ between two colour pattern morphs of a widespread Australian lizard? J Therm Biol 2023; 114:103579. [PMID: 37344018 DOI: 10.1016/j.jtherbio.2023.103579] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 04/17/2023] [Accepted: 04/18/2023] [Indexed: 06/23/2023]
Abstract
Alternative phenotypes allow individuals to pursue different adaptive pathways in response to the same selective challenge. Colour polymorphic species with geographically varying morph frequencies may reflect multiple adaptations to spatial variables such as temperature and climate. We examined whether thermal biology differed between colour morphs of an Australian lizard, the delicate skink, Lampropholis delicata. The delicate skink has two colour pattern morphs, with frequencies varying across latitude and sex: plain (darker, more common at temperate latitudes, more common in males) or striped (lighter, more common at lower latitudes, more common in females). We tested heating and cooling rate, sprint speed, thermal preference, field body temperature and metabolic rate in both morphs and sexes to determine any link between colour and morph frequency distribution. Plain individuals heated more quickly, but other thermal traits showed little variation among morphs. Lampropholis delicata colour influences rates of heat exchange, but the relationship does not appear to be adaptive, suggesting that behavioural thermoregulation homogenises body temperature in the field. While we find no substantial evidence of thermal differences between the two colour morphs, morph-specific behaviour may buffer against differences in heat exchange. Latitudinal variation in species colour may be driven by selection pressures other than temperature.
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Affiliation(s)
- Genevieve Matthews
- School of Biological Sciences, Monash University, Clayton, Victoria, 3800, Australia
| | - Jules E Farquhar
- School of Biological Sciences, Monash University, Clayton, Victoria, 3800, Australia
| | - Craig R White
- School of Biological Sciences, Monash University, Clayton, Victoria, 3800, Australia; Centre for Geometric Biology, Monash University, Clayton, Victoria, 3800, Australia
| | - David G Chapple
- School of Biological Sciences, Monash University, Clayton, Victoria, 3800, Australia.
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3
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Chen C, Zhan C, Wang Y. Do functional and phylogenetic nestedness follow the same mechanisms as taxonomic nestedness? Evidence from amphibians in the largest archipelago of China. J Anim Ecol 2022; 91:2424-2436. [PMID: 36260356 DOI: 10.1111/1365-2656.13824] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Accepted: 09/19/2022] [Indexed: 12/14/2022]
Abstract
Nested subset pattern (nestedness) has been raised to explain the distribution of species on islands and habitat fragments for over 60 years. However, previous studies on nestedness focused on species richness and composition and overlooked the role of species traits and phylogeny in generating and explaining nestedness. To address this gap, we sampled amphibians on 37 land-bridge islands in the largest archipelago of China, the Zhoushan Archipelago, to explore nestedness as well as the underlying causal processes through three facets of diversity, that is, taxonomic, functional and phylogenetic diversity. The taxonomic nestedness was measured through organizing the species incidence matrix to achieve a maximum value, while the functional and phylogenetic nestedness were quantified by incorporating the similarity of species in terms of their ecological traits and phylogeny. We also obtained six island characteristics and seven species traits as predictors of nestedness. Amphibian metacommunities were significantly nested in these three facets of diversity. When relating different predictors to nestedness, island area, habitat diversity and species traits were highly correlated with taxonomic nestedness. Moreover, island area and habitat diversity significantly influenced functional and phylogenetic nestedness. Therefore, the results support the selective extinction and habitat nestedness hypotheses. Interestingly, although we did not observe significant influences of island isolation on taxonomic nestedness, functional and phylogenetic diversities were significantly higher than expected when matrices were ordered by increasing distance to mainland. The result suggests that there are more functionally and phylogenetically diverse species on less-isolated islands, reflecting a selective colonization process overlooked by the traditional analysis of taxonomic nestedness. Although the three facets of nestedness and underlying processes were largely congruent, we detected the distance-related functional and phylogenetic nestedness for amphibian assemblages. Therefore, we highlight that a framework that simultaneously considers taxonomic, functional and phylogenetic nestedness can contribute to a complementary understanding of nestedness processes. In addition, it also improves our ability to conserve insular biodiversity from different perspectives.
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Affiliation(s)
- Chuanwu Chen
- Laboratory of Island Biogeography and Conservation Biology, College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Chengxiu Zhan
- Laboratory of Island Biogeography and Conservation Biology, College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Yanping Wang
- Laboratory of Island Biogeography and Conservation Biology, College of Life Sciences, Nanjing Normal University, Nanjing, China
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4
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Zhao N, Ma Z, Jiang Y, Shi Y, Xie Y, Wang Y, Wu S, Liu S, Wang S. Geographical patterns of Fejervarya limnocharis gut microbiota by latitude along mainland China’s coastline. Front Microbiol 2022; 13:1062302. [DOI: 10.3389/fmicb.2022.1062302] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Accepted: 11/02/2022] [Indexed: 11/18/2022] Open
Abstract
The gut microbiota affects many aspects of host biology and plays key roles in the coevolutionary association with its host. Geographical gradients may play a certain role on gut microbiota variation in the natural environment. However, the distribution pattern of amphibian gut microbiota in the latitudinal gradient remains largely unexplored. Here, we sampled six natural populations of Fejervarya limnocharis along the eastern coastline of mainland China (spanning 20°–30° N = 1,300 km) using 16S rRNA amplicon sequencing to characterize the gut microbiota. First of all, a significant correlation between gut microbial diversity and latitude was observed in our research system. Second, we discovered that latitude influenced the composition of the gut microbiota of F. limnocharis. Finally, we detected that geographical distance could not determine gut microbiota composition in F. limnocharis. These results indicate that latitude can play an important role in shaping the gut microbial diversity of amphibian. Our study offers the first evidence that gut microbial diversity of amphibian presents a latitudinal pattern and highlights the need for increased numbers of individuals to be sampled during microbiome studies in wild populations along environmental gradients.
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5
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Tolone M, Sardina MT, Senczuk G, Chessari G, Criscione A, Moscarelli A, Riggio S, Rizzuto I, Di Gerlando R, Portolano B, Mastrangelo S. Genomic Tools for the Characterization of Local Animal Genetic Resources: Application in Mascaruna Goat. Animals (Basel) 2022; 12:2840. [PMID: 36290231 PMCID: PMC9597745 DOI: 10.3390/ani12202840] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Revised: 10/13/2022] [Accepted: 10/18/2022] [Indexed: 02/06/2024] Open
Abstract
Italy contains a large number of local goat populations, some of which do not have a recognized genetic structure. The "Mascaruna" is a goat population reared for milk production in Sicily. In this study, a total of 72 individuals were genotyped with the Illumina Goat_IGGC_65K_v2 BeadChip with the aim to characterize the genetic diversity, population structure and relatedness with another 31 Italian goat populations. The results displayed a moderate level of genetic variability for Mascaruna, in concordance with the estimated values for Italian goats. Runs of homozygosity islands are linked to genes involved in milk production, immune response and local adaptation. Population structure analyses separated Mascaruna from the other goat populations, indicating a clear genetic differentiation. Although they are not conclusive, our current results represent a starting point for the creation of monitoring and conservation plans. Additional analyses and a wider sampling would contribute to refine and validate these results. Finally, our study describing the diversity and structure of Mascaruna confirms the usefulness of applied genomic analyses as valid tools for the study of the local uncharacterized genetic resources.
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Affiliation(s)
- Marco Tolone
- Dipartimento Scienze Agrarie, Alimentari e Forestali, University of Palermo, 90128 Palermo, Italy
| | - Maria Teresa Sardina
- Dipartimento Scienze Agrarie, Alimentari e Forestali, University of Palermo, 90128 Palermo, Italy
| | - Gabriele Senczuk
- Dipartimento di Agricoltura, Ambiente e Alimenti, University of Molise, 86100 Campobasso, Italy
| | - Giorgio Chessari
- Dipartimento Agricoltura, Alimentazione e Ambiente, University of Catania, 95131 Catania, Italy
| | - Andrea Criscione
- Dipartimento Agricoltura, Alimentazione e Ambiente, University of Catania, 95131 Catania, Italy
| | - Angelo Moscarelli
- Dipartimento Scienze Agrarie, Alimentari e Forestali, University of Palermo, 90128 Palermo, Italy
| | - Silvia Riggio
- Dipartimento Scienze Agrarie, Alimentari e Forestali, University of Palermo, 90128 Palermo, Italy
| | - Ilaria Rizzuto
- Dipartimento Scienze Agrarie, Alimentari e Forestali, University of Palermo, 90128 Palermo, Italy
| | - Rosalia Di Gerlando
- Dipartimento Scienze Agrarie, Alimentari e Forestali, University of Palermo, 90128 Palermo, Italy
| | - Baldassare Portolano
- Dipartimento Scienze Agrarie, Alimentari e Forestali, University of Palermo, 90128 Palermo, Italy
| | - Salvatore Mastrangelo
- Dipartimento Scienze Agrarie, Alimentari e Forestali, University of Palermo, 90128 Palermo, Italy
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6
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Contrasting genetic diversity between Planchonella obovata sensu lato (Sapotaceae) on old continental and young oceanic island populations in Japan. PLoS One 2022; 17:e0273871. [PMID: 36054192 PMCID: PMC9439235 DOI: 10.1371/journal.pone.0273871] [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: 02/08/2022] [Accepted: 08/16/2022] [Indexed: 11/23/2022] Open
Abstract
Genetic diversity of plant populations on islands is likely to be influenced by characteristics such as island origin (oceanic or continental) and their age, size, and distance to continental landmasses. In Japan, Planchonella obovata sensu lato which is found on both continental and oceanic islands of varying age, size, and distance to East Asian continental areas—is an ideal system in which to investigate the factors influencing genetic diversity of island plant species. In this study, we examined the genetic diversity of P. obovata s.l. populations, in the context of the species population genetic structure, demography, and between island migration, from 668 individuals, 28 populations and 14 islands including both continental (the Yaeyama Islands) and oceanic islands (the Daito, Bonin, and Volcano Islands) using 11 microsatellite markers. The Yaeyama and Volcano Islands respectively had the highest and lowest genetic diversity, and island origin and age significantly affected genetic diversity. Clustering analysis revealed that populations were grouped into Bonin, Volcano, and Yaeyama + Daito groups. However, Bonin and Volcano groups were distinct despite the relatively short geographical distance between them. Approximate Bayesian Computation analysis suggested that the population size was stable in Bonin and Yaeyama + Daito groups, whereas population reduction occurred in Volcano group, and migration between groups were very limited. Younger oceanic islands showed lower genetic diversity, probably due to limited gene flow and a lack of time to accumulate unique alleles. Genetic structure was generally consistent with the geographic pattern of the islands, but in Volcano, a limited number of founders and limited gene flow among islands are likely to have caused the large genetic divergence observed.
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7
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Devillard S, Jacquier M, Vandel JM, Léger F, Duhayer J, Pardonnet S, Say L, Ruette S. Genetic variability and population size covary positively across nine badgers (Meles meles) populations in France. MAMMAL RES 2022. [DOI: 10.1007/s13364-021-00614-2] [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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8
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Abstract
The nearly neutral theory is a common framework to describe natural selection at the molecular level. This theory emphasizes the importance of slightly deleterious mutations by recognizing their ability to segregate and eventually get fixed due to genetic drift in spite of the presence of purifying selection. As genetic drift is stronger in smaller than in larger populations, a correlation between population size and molecular measures of natural selection is expected within the nearly neutral theory. However, this hypothesis was originally formulated under equilibrium conditions. As most natural populations are not in equilibrium, testing the relationship empirically may lead to confounded outcomes. Demographic nonequilibria, for instance following a change in population size, are common scenarios that are expected to push the selection–drift relationship off equilibrium. By explicitly modeling the effects of a change in population size on allele frequency trajectories in the Poisson random field framework, we obtain analytical solutions of the nonstationary allele frequency spectrum. This enables us to derive exact results of measures of natural selection and effective population size in a demographic nonequilibrium. The study of their time-dependent relationship reveals a substantial deviation from the equilibrium selection–drift balance after a change in population size. Moreover, we show that the deviation is sensitive to the combination of different measures. These results therefore constitute relevant tools for empirical studies to choose suitable measures for investigating the selection–drift relationship in natural populations. Additionally, our new modeling approach extends existing population genetics theory and can serve as foundation for methodological developments.
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Affiliation(s)
- Rebekka Müller
- Department of Mathematics, Uppsala University, 752 37 Uppsala, Sweden
| | - Ingemar Kaj
- Department of Mathematics, Uppsala University, 752 37 Uppsala, Sweden
| | - Carina F. Mugal
- Department of Ecology and Genetics, Uppsala University, 752 36 Uppsala, Sweden
- Corresponding author: E-mail:
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9
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Yao Z, Wang X, Wang K, Yu W, Deng P, Dong J, Li Y, Cui K, Liu Y. Chloroplast and Nuclear Genetic Diversity Explain the Limited Distribution of Endangered and Endemic Thuja sutchuenensis in China. Front Genet 2021; 12:801229. [PMID: 35003229 PMCID: PMC8733598 DOI: 10.3389/fgene.2021.801229] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Accepted: 11/30/2021] [Indexed: 11/13/2022] Open
Abstract
Narrow-ranged species face challenges from natural disasters and human activities, and to address why species distributes only in a limited region is of great significance. Here we investigated the genetic diversity, gene flow, and genetic differentiation in six wild and three cultivated populations of Thuja sutchuenensis, a species that survive only in the Daba mountain chain, using chloroplast simple sequence repeats (cpSSR) and nuclear restriction site-associated DNA sequencing (nRAD-seq). Wild T. sutchuenensis populations were from a common ancestral population at 203 ka, indicating they reached the Daba mountain chain before the start of population contraction at the Last Interglacial (LIG, ∼120-140 ka). T. sutchuenensis populations showed relatively high chloroplast but low nuclear genetic diversity. The genetic differentiation of nRAD-seq in any pairwise comparisons were low, while the cpSSR genetic differentiation values varied with pairwise comparisons of populations. High gene flow and low genetic differentiation resulted in a weak isolation-by-distance effect. The genetic diversity and differentiation of T. sutchuenensis explained its survival in the Daba mountain chain, while its narrow ecological niche from the relatively isolated and unique environment in the "refugia" limited its distribution.
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Affiliation(s)
- Zhi Yao
- State Environmental Protection Key Laboratory of Regional Eco-Process and Function Assessment, Chinese Research Academy of Environmental Sciences, Beijing, China
- Hunan Provincial Collaborative Innovation Center for Field Weeds Control, Hunan University of Humanities, Science and Technology, Loudi, China
| | - Xinyu Wang
- State Environmental Protection Key Laboratory of Regional Eco-Process and Function Assessment, Chinese Research Academy of Environmental Sciences, Beijing, China
| | - Kailai Wang
- State Environmental Protection Key Laboratory of Regional Eco-Process and Function Assessment, Chinese Research Academy of Environmental Sciences, Beijing, China
| | - Wenhao Yu
- State Environmental Protection Key Laboratory of Regional Eco-Process and Function Assessment, Chinese Research Academy of Environmental Sciences, Beijing, China
| | - Purong Deng
- State Environmental Protection Key Laboratory of Regional Eco-Process and Function Assessment, Chinese Research Academy of Environmental Sciences, Beijing, China
| | - Jinyi Dong
- State Environmental Protection Key Laboratory of Regional Eco-Process and Function Assessment, Chinese Research Academy of Environmental Sciences, Beijing, China
- Hunan Provincial Collaborative Innovation Center for Field Weeds Control, Hunan University of Humanities, Science and Technology, Loudi, China
| | - Yonghua Li
- State Environmental Protection Key Laboratory of Regional Eco-Process and Function Assessment, Chinese Research Academy of Environmental Sciences, Beijing, China
| | - Kaifeng Cui
- Changbai Mountain Academy of Sciences, Joint Key Laboratory of Community and Biodiversity for Jilin Province and Changbai Mountain, Jilin, China
| | - Yongbo Liu
- State Environmental Protection Key Laboratory of Regional Eco-Process and Function Assessment, Chinese Research Academy of Environmental Sciences, Beijing, China
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10
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Jin L, Liao WB, Merilä J. Genomic evidence for adaptive differentiation among
Microhyla fissipes
populations: Implications for conservation. DIVERS DISTRIB 2021. [DOI: 10.1111/ddi.13433] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Affiliation(s)
- Long Jin
- Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education) China West Normal University Nanchong China
| | - Wen Bo Liao
- Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education) China West Normal University Nanchong China
| | - Juha Merilä
- Ecological Genetics Research Unit, Organismal and Evolutionary Biology Programme Faculty of Biological and Environmental Sciences FI‐00014 University of Helsinki Helsinki Finland
- Research Division for Ecology and Biodiversity School Biological Sciences The University of Hong KongHong Kong SAR
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11
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Wen G, Jin L, Wu Y, Wang X, Fu J, Qi Y. Low diversity, little genetic structure but no inbreeding in a high-density island endemic pit-viper Gloydius shedaoensis. Curr Zool 2021; 68:526-534. [DOI: 10.1093/cz/zoab084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Accepted: 10/06/2021] [Indexed: 11/13/2022] Open
Abstract
Abstract
Island species and their ecosystems play an important role in global biodiversity preservation, and many vulnerable island species are conservation priorities. Although insular habitat likely facilitates the species diversification process, it may also aggravate the fragility of these species with high risk of inbreeding. The Shedao pit-viper Gloydius shedaoensis is an island endemic species with an extremely high population density, which has been categorized as vulnerable in the IUCN (International Union for the Conservation of Nature and Natural Resources) Red List. We collected 13,148 SNP (Single Nucleotide Polymorphism) from across its genome and examined its genetic diversity and demographic history. The Shedao pit-viper has a low genetic diversity but shows no sign of inbreeding. Furthermore, population genetic structure analysis, including the neighbor-joining tree, principal coordinate analysis, clustering, and spatial autocorrelation, revealed a general lack of spatial structure. Only the isolation by distance residues suggested a weak patchiness. Overall, the population is nearly panmictic and gene flow is evenly distributed across the island. A large number of individuals, small size of the island, and the lack of population structure likely all contribute to the lack of inbreeding in this species. We also detected signs of male-biased dispersal, which likely is another inbreeding avoidance strategy. Historical demographic analysis suggested that the historical population size and distribution of the species are much larger than their current ones. The multiple transgressive–regressive events since the Late Pleistocene are likely the main cause of the population size changes. Taken together, our results provide a basic scientific foundation for the conservation of this interesting and important species.
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Affiliation(s)
- Guannan Wen
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China
| | - Long Jin
- Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education), China West Normal University, Nanchong 637009, China
| | - Yayong Wu
- College of Life Sciences and Food Engineering, Yibin University, Yibin 644007, China
| | - Xiaoping Wang
- Nature Conservation of Snake Island and Laotieshan Mountain, Dalian 116041, China
| | - Jinzhong Fu
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China
- Department of Integrative Biology, University of Guelph, Guelph, Ontario N1G 2W1, Canada
| | - Yin Qi
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China
- Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education), China West Normal University, Nanchong 637009, China
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12
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Jiang L, Kon T, Chen C, Ichikawa R, Zheng Q, Pei L, Takemura I, Nsobi LH, Tabata H, Pan H, Omori Y, Ogura A. Whole-genome sequencing of endangered Zhoushan cattle suggests its origin and the association of MC1R with black coat colour. Sci Rep 2021; 11:17359. [PMID: 34462508 PMCID: PMC8405626 DOI: 10.1038/s41598-021-96896-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Accepted: 08/05/2021] [Indexed: 12/04/2022] Open
Abstract
Zhoushan cattle are an endangered cattle breed in the Zhoushan islands in China. Since Zhoushan cattle have been bred in isolation, they show unique characteristics, such as dark black coat colour. However, no studies have been conducted on the genome of Zhoushan cattle. Here, we performed whole-genome sequencing of seven individuals of Zhoushan cattle and nine cattle in Wenling, geographically close to the Zhoushan islands. By integrating our data and publicly-available data, we found that Zhoushan cattle are genetically highly similar to Bos indicus cattle in south-eastern China. Furthermore, by identifying the genomic regions shared between Zhoushan cattle and Angus cattle, a Bos taurus breed, we found that the p.F195L mutation in melanocyte-stimulating hormone receptor (MC1R) could be associated with their dark black coat colour. Taken together, our results provide a valuable resource for characterising the uniqueness of Zhoushan cattle.
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Affiliation(s)
- Lihua Jiang
- National Engineering Research Center of Marine Facilities Aquaculture, Zhejiang Ocean University, Zhoushan, 316022, China. .,Genomic Diversity Laboratory, Graduate School of Bioscience, Nagahama Institute of Bioscience and Technology, Nagahama, Shiga, 526-0829, Japan.
| | - Tetsuo Kon
- Laboratory of Functional Genomics, Graduate School of Bioscience, Nagahama Institute of Bioscience and Technology, Nagahama, Shiga, 526-0829, Japan
| | - Chunyan Chen
- National Engineering Research Center of Marine Facilities Aquaculture, Zhejiang Ocean University, Zhoushan, 316022, China
| | - Ryota Ichikawa
- Laboratory of Functional Genomics, Graduate School of Bioscience, Nagahama Institute of Bioscience and Technology, Nagahama, Shiga, 526-0829, Japan
| | - Qiyuan Zheng
- Zhoushan Sanxing Zhoushan Cattle Protection Institute, Zhoushan City, 316000, China
| | - Liyi Pei
- National Engineering Research Center of Marine Facilities Aquaculture, Zhejiang Ocean University, Zhoushan, 316022, China
| | - Ikuyo Takemura
- Genomic Diversity Laboratory, Graduate School of Bioscience, Nagahama Institute of Bioscience and Technology, Nagahama, Shiga, 526-0829, Japan
| | - Lauden Hagai Nsobi
- National Engineering Research Center of Marine Facilities Aquaculture, Zhejiang Ocean University, Zhoushan, 316022, China
| | - Hiromasa Tabata
- Genomic Diversity Laboratory, Graduate School of Bioscience, Nagahama Institute of Bioscience and Technology, Nagahama, Shiga, 526-0829, Japan
| | - Hao Pan
- Genomic Diversity Laboratory, Graduate School of Bioscience, Nagahama Institute of Bioscience and Technology, Nagahama, Shiga, 526-0829, Japan
| | - Yoshihiro Omori
- Laboratory of Functional Genomics, Graduate School of Bioscience, Nagahama Institute of Bioscience and Technology, Nagahama, Shiga, 526-0829, Japan
| | - Atsushi Ogura
- Genomic Diversity Laboratory, Graduate School of Bioscience, Nagahama Institute of Bioscience and Technology, Nagahama, Shiga, 526-0829, Japan.
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13
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Li W, Hou X, Xu C, Qin M, Wang S, Wei L, Wang Y, Liu X, Li Y. Validating eDNA measurements of the richness and abundance of anurans at a large scale. J Anim Ecol 2021; 90:1466-1479. [PMID: 33694188 DOI: 10.1111/1365-2656.13468] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Accepted: 02/17/2021] [Indexed: 02/06/2023]
Abstract
In some situations, environmental DNA (eDNA) metabarcoding is a more accurate tool for measuring species richness of a taxon than conventional methods. Whether this tool can reliably estimate the abundance of a taxon remains unresolved. We examined the reliability of metabarcoding for measuring anuran diversity compared to a commonly used traditional line transect method (TLTM) through the replicate sampling of three visits across 71 waterbodies (ponds or reservoirs) in Liuheng, China. We also investigated the relative contributions of species-specific characteristics and the physiochemical properties of a waterbody on the relative read count across species and waterbodies. We found that eDNA metabarcoding had a higher detection probability for each of seven anuran species found in the sampling region than TLTM. Furthermore, the relative read count estimated by metabarcoding was positively correlated with the density or relative density of individuals identified with the TLTM across waterbodies for every species. Species-specific characteristics of anurans, such as density, relative density, body mass, biomass and relative biomass, accounted for substantial variations in the read count across species and waterbodies, while physiochemical factors, including pH, temperature, water volume, vegetation and elevation, had little effect on the read count. Our results based on robust sampling suggest that metabarcoding enables more reliable and efficient measurements of anuran occurrence at a large scale during a short-term survey (within 15 days) than that obtained by the TLTM, and offers an alternative tool for quantifications of anuran abundance. Density or biomass is better and more reliable indicator of anuran abundance associated with read count than relative density or relative biomass.
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Affiliation(s)
- Wenhao Li
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, The Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Xianglei Hou
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, The Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Chunxia Xu
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, The Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Mingshuo Qin
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, The Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Supen Wang
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, The Chinese Academy of Sciences, Beijing, China
| | - Li Wei
- College of Ecology, Lishui University, Lishui, China
| | - Yanping Wang
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Science, Nanjing Normal University, Nanjing, China
| | - Xuan Liu
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, The Chinese Academy of Sciences, Beijing, China
| | - Yiming Li
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, The Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
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14
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Shi M, Wang Y, Duan T, Qian X, Zeng T, Zhang D. In situ glacial survival maintains high genetic diversity of Mussaenda kwangtungensis on continental islands in subtropical China. Ecol Evol 2020; 10:11304-11321. [PMID: 33144966 PMCID: PMC7593160 DOI: 10.1002/ece3.6768] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Revised: 07/06/2020] [Accepted: 08/18/2020] [Indexed: 11/23/2022] Open
Abstract
Generally, island populations are predicted to have less genetic variation than their mainland relatives. However, a growing number of studies have nevertheless reported exceptions, indicating that the relationships were impacted by several factors, for example, historical processes. In the present study, we chose a group of subtropical islands located in South China as the study system, which are quite younger and much closer to the mainland than most of the previous studied island systems, to test the hypothesis that in situ glacial survival contributes to high levels of genetic diversity in island populations. We conducted a comparison of genetic variation between 12 island and 11 nearby mainland populations of Mussaenda kwangtungensis using eleven nuclear microsatellite and three chloroplast markers, evaluated effects of the island area and distance to mainland on genetic diversity of island populations, and simulated the potential distribution over the past by ecological niche modeling, together with the genetic data to detect the role of islands during the glacial periods. The island populations displayed comparable levels of genetic diversity and differentiation with mainland populations, overall high levels of unique polymorphisms, and the greatest values of specific within-population genetic diversity. No significant correlation was detected between genetic diversity of island populations and distance to mainland, as well as area of islands, except that allelic richness was significantly positively correlated with the area of islands. Nuclear microsatellites revealed two main clusters, largely corresponding to islands and inland populations, which divergence dated to a time of island formation by ABC analysis. Ecological niche modeling predicted a highly climatic suitability on islands during the last glacial maximum (LGM). Our results suggest that the islands have acted as refugia during the LGM and highlight the role of in situ glacial survival in maintaining high levels of genetic diversity of M. kwangtungensis in continental islands of subtropical China.
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Affiliation(s)
- Miaomiao Shi
- Key Laboratory of Plant Resources Conservation and Sustainable UtilizationSouth China Botanical GardenChinese Academy of SciencesGuangzhouChina
- Center of Conservation BiologyCore Botanical GardensChinese Academy of SciencesGuangzhouChina
| | - Yuyuan Wang
- Key Laboratory of Plant Resources Conservation and Sustainable UtilizationSouth China Botanical GardenChinese Academy of SciencesGuangzhouChina
- University of Chinese Academy of SciencesBeijingChina
| | | | - Xin Qian
- College of Life SciencesFujian Agriculture and Forestry UniversityFuzhouChina
| | - Tong Zeng
- Key Laboratory of Plant Resources Conservation and Sustainable UtilizationSouth China Botanical GardenChinese Academy of SciencesGuangzhouChina
- University of Chinese Academy of SciencesBeijingChina
| | - Dianxiang Zhang
- Key Laboratory of Plant Resources Conservation and Sustainable UtilizationSouth China Botanical GardenChinese Academy of SciencesGuangzhouChina
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15
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Yu W, Wu B, Wang X, Yao Z, Li Y, Liu Y. Scale-dependent effects of habitat fragmentation on the genetic diversity of Actinidia chinensis populations in China. HORTICULTURE RESEARCH 2020; 7:172. [PMID: 33082978 PMCID: PMC7553913 DOI: 10.1038/s41438-020-00401-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Revised: 07/25/2020] [Accepted: 08/04/2020] [Indexed: 05/04/2023]
Abstract
Spatial scale partly explains the differentiated effects of habitat fragmentation on plant biodiversity, but the mechanisms remain unclear. To investigate the effects of habitat fragmentation on genetic diversity at different scales, we sampled Actinidia chinensis Planch. at broad and fine scales, China. The broad-scale sampling included five mountain populations and one oceanic island population (Zhoushan Archipelago), and the fine-scale sampling covered 11 lake islands and three neighboring land populations in Thousand-Island Lake (TIL). These populations were genotyped at 30 microsatellite loci, and genetic diversity, gene flow, and genetic differentiation were evaluated. Genetic differentiation was positively related to geographical distance at the broad scale, indicating an isolation-by-distance effect of habitat fragmentation on genetic diversity. The oceanic population differed from the mainland populations and experienced recent bottleneck events, but it showed high gene flow with low genetic differentiation from a mountain population connected by the Yangtze River. At the fine scale, no negative genetic effects of habitat fragmentation were found because seed dispersal with water facilitates gene flow between islands. The population size of A. chinensis was positively correlated with the area of TIL islands, supporting island biogeography theory, but no correlation was found between genetic diversity and island area. Our results highlight the scale-dependent effects of habitat fragmentation on genetic diversity and the importance of connectivity between island-like isolated habitats at both the broad and fine scales.
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Affiliation(s)
- Wenhao Yu
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, 8 Dayangfang, 100012 Beijing, China
| | - Baofeng Wu
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, 8 Dayangfang, 100012 Beijing, China
| | - Xinyu Wang
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, 8 Dayangfang, 100012 Beijing, China
| | - Zhi Yao
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, 8 Dayangfang, 100012 Beijing, China
| | - Yonghua Li
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, 8 Dayangfang, 100012 Beijing, China
| | - Yongbo Liu
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, 8 Dayangfang, 100012 Beijing, China
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16
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Igawa T, Sugawara H, Honda M, Tominaga A, Oumi S, Katsuren S, Ota H, Matsui M, Sumida M. Detecting inter- and intra-island genetic diversity: population structure of the endangered crocodile newt, Echinotriton andersoni, in the Ryukyus. CONSERV GENET 2019. [DOI: 10.1007/s10592-019-01219-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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17
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Comparative phylogeography of two hemipteran species (Geisha distinctissima and Megacopta cribraria) in the Zhoushan Archipelago of China reveals contrasting genetic structures despite concordant historical demographies. Heredity (Edinb) 2019; 124:207-222. [PMID: 31501533 DOI: 10.1038/s41437-019-0265-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Revised: 08/06/2019] [Accepted: 08/22/2019] [Indexed: 11/08/2022] Open
Abstract
Continental islands are useful models to explore the roles of shared historical factors in the evolution of sympatric species. However, China's largest continental group of islands, the Zhoushan Archipelago, was neglected by most studies focusing on biodiversity hotspots. Here we investigated the phylogeographic patterns and the historical demography of two sympatric hemipteran insects (Geisha distinctissima and Megacopta cribraria), which shared historical factors in the Zhoushan Archipelago. The results based on mtDNA (COX1, COX2-COX3, and CYTB) and nDNA (28S and ITS2) showed that G. distinctissima diverged into three genetic lineages (L1-L3) ~8.9-13.7 thousand years ago (kya), which coincided with the period of island isolation. However, the three lineages exhibit no clear phylogeographic patterns for frequent asymmetrical gene flow (starting around 5 kya) from the mainland and adjacent islands to other distant islands due to subsequent human activities. In contrast, only one genetic lineage exists for M. cribraria, without any phylogeographic structures. The ancestral range in the mainland as well as in neighboring islands, together with the frequent asymmetrical gene flow of M. cribraria (from the mainland and neighboring islands to more distant islands) within the last 5000 years suggests that human activities may have lead to the colonization of this species in the Zhoushan Archipelago. The contrasting genetic structures indicate shared historical factors but independent evolutionary histories for the two sympatric species in the Zhoushan Archipelago. Our demographic analysis clearly showed that both species underwent population expansion before 5 kya during the post-LGM (Last Glacial Maximum), which indicates that the two species shared concordant historical demographies. This result suggests that the population size of the two species was affected similarly by the climatic oscillations of post-LGM in Eastern China. Together, our findings reveal that the two insect species in the Zhoushan Archipelago exhibit contrasting genetic structures despite concordant historical demographies, which provides an important framework for the exploration of the evolution patterns of sympatric species in the continental island.
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18
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Costanzi J, Steifetten Ø. Island biogeography theory explains the genetic diversity of a fragmented rock ptarmigan ( Lagopus muta) population. Ecol Evol 2019; 9:3837-3849. [PMID: 31015970 PMCID: PMC6468070 DOI: 10.1002/ece3.5007] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2018] [Revised: 01/31/2019] [Accepted: 02/04/2019] [Indexed: 01/20/2023] Open
Abstract
The island biogeography theory is one of the major theories in ecology, and its applicability to natural systems is well documented. The core model of the theory, the equilibrium model of island biogeography, predicts that species diversity on an island is positively related to the size of the island, but negatively related by the island's distance to the mainland. In recent years, ecologists have begun to apply this model when investigating genetic diversity, arguing that genetic and species diversity might be influenced by similar ecological processes. However, most studies have focused on oceanic islands, but knowledge on how the theory applies to islands located on the mainland (e.g., mountain islands, forest islands) is scarce. In this study, we examined how the size and degree of isolation of mountain islands would affect the genetic diversity of an alpine bird, the rock ptarmigan (Lagopus muta). Within our study area, we defined the largest contiguous mountain area as the mainland, while smaller mountains surrounding the mainland were defined as islands. We found that the observed heterozygosity (H o) was significantly higher, and the inbreeding coefficient (F is) significantly lower, on the mainland compared to islands. There was a positive significant relationship between the unbiased expected heterozygosity (H n.b.) and island size (log km2), but a negative significant relationship between H o and the cost distance to the mainland. Our results are consistent with the equilibrium model of island biogeography and show that the model is well suited for investigating genetic diversity among islands, but also on islands located on the mainland.
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Affiliation(s)
- Jean‐Marc Costanzi
- Department of Natural Sciences and Environmental HealthUniversity of South‐Eastern NorwayBø i TelemarkNorway
| | - Øyvind Steifetten
- Department of Natural Sciences and Environmental HealthUniversity of South‐Eastern NorwayBø i TelemarkNorway
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19
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Wang S, Liu C, Wu J, Xu C, Zhang J, Bai C, Gao X, Liu X, Li X, Zhu W, Li Y. Propagule pressure and hunting pressure jointly determine genetic evolution in insular populations of a global frog invader. Sci Rep 2019; 9:448. [PMID: 30679623 PMCID: PMC6345768 DOI: 10.1038/s41598-018-37007-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Accepted: 11/26/2018] [Indexed: 12/24/2022] Open
Abstract
Islands are often considered to be more susceptible to biological invasions and to suffer greater impacts from invaders than mainland areas, and this difference is generally attributed to differences in species introductions, ecological factors or human activities between islands and mainland areas. Genetic variation, as a good estimate of evolutionary potential, can influence the invasion process and impacts of alien species. However, few studies have compared the genetic diversity of alien species between islands and a corresponding mainland. Here, we examined the genetic variation and differentiation in feral populations (30 sampled individuals/population) of a globally invasive species (the American bullfrog, Lithobates catesbeianus) that was extensively farmed on 14 islands in the Zhoushan Archipelago of China and in three nearby regions on the mainland. We quantified the relative importance of propagule pressure and hunting pressures on the genetic variation of bullfrog populations and found that insular populations have greater genetic variation than their mainland counterparts. Although genetic differentiation between the populations was observed, no evidence of recent bottlenecks or population expansion in any of the tested population was found. Our results suggest that the propagule pressures of bullfrogs escaping from farms, multiple releases and hunting pressure influence the genetic variation among bullfrog populations. These results might have important implications for understanding the establishment and evolution of alien species on islands and for the management of invasive species.
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Affiliation(s)
- Supen Wang
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, 1 Beichen West Road, Chaoyang District, Beijing, 100101, China
| | - Conghui Liu
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, 1 Beichen West Road, Chaoyang District, Beijing, 100101, China.,University of Chinese Academy of Sciences, 19 Yuquan Road, Shijingshan, Beijing, 100049, China
| | - Jun Wu
- Nanjing Institute of Environmental Sciences under Ministry of Environmental Protection of China, No. 8 Jiang Wang Miao Street, Nanjing, 210042, PR China
| | - Chunxia Xu
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, 1 Beichen West Road, Chaoyang District, Beijing, 100101, China.,University of Chinese Academy of Sciences, 19 Yuquan Road, Shijingshan, Beijing, 100049, China
| | - Jiaqi Zhang
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, 1 Beichen West Road, Chaoyang District, Beijing, 100101, China.,University of Chinese Academy of Sciences, 19 Yuquan Road, Shijingshan, Beijing, 100049, China
| | - Changming Bai
- Key Laboratory of Sustainable Development of Marine Fisheries, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, 266071, China
| | - Xu Gao
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, 1 Beichen West Road, Chaoyang District, Beijing, 100101, China.,University of Chinese Academy of Sciences, 19 Yuquan Road, Shijingshan, Beijing, 100049, China
| | - Xuan Liu
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, 1 Beichen West Road, Chaoyang District, Beijing, 100101, China
| | - Xianping Li
- College of Resources and Environmental Science, Nanjing Agricultural University, Nanjing, 210095, China
| | - Wei Zhu
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, 1 Beichen West Road, Chaoyang District, Beijing, 100101, China.,University of Chinese Academy of Sciences, 19 Yuquan Road, Shijingshan, Beijing, 100049, China
| | - Yiming Li
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, 1 Beichen West Road, Chaoyang District, Beijing, 100101, China. .,University of Chinese Academy of Sciences, 19 Yuquan Road, Shijingshan, Beijing, 100049, China.
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20
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Wang S, Fan L, Liu C, Li J, Gao X, Zhu W, Li Y. The origin of invasion of an alien frog species in Tibet, China. Curr Zool 2018; 63:615-621. [PMID: 29492022 PMCID: PMC5804215 DOI: 10.1093/cz/zow117] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2016] [Accepted: 12/10/2016] [Indexed: 11/15/2022] Open
Abstract
Identifying the origins of alien species has important implications for effectively controlling the spread of alien species. The black-spotted frog Pelophylax nigromaculatus, originally from East Asia, has become an alien species on the Tibetan Plateau (TP). In this study, we collected 300 individuals of P. nigromaculatus from 13 native regions and 2 invasive regions (including Nyingchi and Lhasa) on the TP. To identify the source region of the TP introductions, we sequenced portions of the mitochondrial cyt b gene. We sequenced a ∼600-bp portion of the mitochondrial cyt b gene to identify 69 haplotypes (124 polymorphic sites) in all sampled populations. According to the network results, we suggest that the P. nigromaculatus found on the TP was most likely originated from Chongqing by human introduction. Furthermore, we found that the genetic diversity was significantly lower for invasive than for native sites due to founder effects. Our study provides genetic evidence that this alien species invaded the cold environment of high elevations and expanded the distribution of P. nigromaculatus in China.
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Affiliation(s)
- Supen Wang
- Institute of Zoology, Chinese Academy of Sciences, Key Laboratory of Animal Ecology and Conservation Biology, Beijing 100101, China
| | - Liqing Fan
- Institute of Plateau Ecology, Tibet Agriculture and Animal Husbandry College, Bayi Town, Linzhi County, Xizang Province 860000, China
- National Forest Ecosystem Observation & Research Station of Tibet Linzhi, Linzhi 860000, China
| | - Conghui Liu
- Institute of Zoology, Chinese Academy of Sciences, Key Laboratory of Animal Ecology and Conservation Biology, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jiaqi Li
- Nanjing Institute of Environmental Sciences under Ministry of Environmental Protection of China, Nanjing 210042, China
| | - Xu Gao
- Institute of Zoology, Chinese Academy of Sciences, Key Laboratory of Animal Ecology and Conservation Biology, Beijing 100101, China
- Institute of Plateau Ecology, Tibet Agriculture and Animal Husbandry College, Bayi Town, Linzhi County, Xizang Province 860000, China
| | - Wei Zhu
- Institute of Zoology, Chinese Academy of Sciences, Key Laboratory of Animal Ecology and Conservation Biology, Beijing 100101, China
- Institute of Plateau Ecology, Tibet Agriculture and Animal Husbandry College, Bayi Town, Linzhi County, Xizang Province 860000, China
| | - Yiming Li
- Institute of Zoology, Chinese Academy of Sciences, Key Laboratory of Animal Ecology and Conservation Biology, Beijing 100101, China
- Institute of Plateau Ecology, Tibet Agriculture and Animal Husbandry College, Bayi Town, Linzhi County, Xizang Province 860000, China
- Address correspondence to Yiming Li. E-mail:
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21
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Wang S, Liu C, Wilson AB, Zhao N, Li X, Zhu W, Gao X, Liu X, Li Y. Pathogen richness and abundance predict patterns of adaptive major histocompatibility complex variation in insular amphibians. Mol Ecol 2017; 26:4671-4685. [PMID: 28734069 DOI: 10.1111/mec.14242] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2016] [Revised: 06/01/2017] [Accepted: 06/19/2017] [Indexed: 12/26/2022]
Abstract
The identification of the factors responsible for genetic variation and differentiation at adaptive loci can provide important insights into the evolutionary process and is crucial for the effective management of threatened species. We studied the impact of environmental viral richness and abundance on functional diversity and differentiation of the MHC class Ia locus in populations of the black-spotted pond frog (Pelophylax nigromaculatus), an IUCN-listed species, on 24 land-bridge islands of the Zhoushan Archipelago and three nearby mainland sites. We found a high proportion of private MHC alleles in mainland and insular populations, corresponding to 32 distinct functional supertypes, and strong positive selection on MHC antigen-binding sites in all populations. Viral pathogen diversity and abundance were reduced at island sites relative to the mainland, and islands housed distinctive viral communities. Standardized MHC diversity at island sites exceeded that found at neutral microsatellites, and the representation of key functional supertypes was positively correlated with the abundance of specific viruses in the environment (Frog virus 3 and Ambystoma tigrinum virus). These results indicate that pathogen-driven diversifying selection can play an important role in maintaining functionally important MHC variation following island isolation, highlighting the importance of considering functionally important genetic variation and host-pathogen associations in conservation planning and management.
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Affiliation(s)
- Supen Wang
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Conghui Liu
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Anthony B Wilson
- Department of Biology, Brooklyn College and The Graduate Center, City University of New York, Brooklyn, NY, USA
| | - Na Zhao
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Xianping Li
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Wei Zhu
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Xu Gao
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Xuan Liu
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Yiming Li
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
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22
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Sato JJ, Tasaka Y, Tasaka R, Gunji K, Yamamoto Y, Takada Y, Uematsu Y, Sakai E, Tateishi T, Yamaguchi Y. Effects of Isolation by Continental Islands in the Seto Inland Sea, Japan, on Genetic Diversity of the Large Japanese Field Mouse, Apodemus speciosus (Rodentia: Muridae), Inferred from the Mitochondrial Dloop Region. Zoolog Sci 2017; 34:112-121. [DOI: 10.2108/zs160113] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Affiliation(s)
- Jun J. Sato
- Laboratory of Animal Cell Technology, Faculty of Life Science and Technology, Fukuyama University, Higashimura-cho, Aza, Sanzo, 985, Fukuyama 729-0292, Japan
| | - Yurina Tasaka
- Laboratory of Animal Cell Technology, Faculty of Life Science and Technology, Fukuyama University, Higashimura-cho, Aza, Sanzo, 985, Fukuyama 729-0292, Japan
| | - Ryoya Tasaka
- Laboratory of Animal Cell Technology, Faculty of Life Science and Technology, Fukuyama University, Higashimura-cho, Aza, Sanzo, 985, Fukuyama 729-0292, Japan
| | - Kentaro Gunji
- Laboratory of Animal Cell Technology, Faculty of Life Science and Technology, Fukuyama University, Higashimura-cho, Aza, Sanzo, 985, Fukuyama 729-0292, Japan
| | - Yuya Yamamoto
- Laboratory of Animal Cell Technology, Faculty of Life Science and Technology, Fukuyama University, Higashimura-cho, Aza, Sanzo, 985, Fukuyama 729-0292, Japan
| | - Yasushi Takada
- Department of Anatomy, School of Dentistry, Aichi-Gakuin University, Kusumoto-cho, Chikusa-ku, Nagoya 464-8650, Japan
| | - Yasushi Uematsu
- Department of Anatomy, School of Dentistry, Aichi-Gakuin University, Kusumoto-cho, Chikusa-ku, Nagoya 464-8650, Japan
| | - Eiichi Sakai
- Department of Dental Hygiene, Aichi-Gakuin University, Kusumoto-cho, Chikusa-ku, Nagoya 464-8650, Japan
| | | | - Yasunori Yamaguchi
- Laboratory of Animal Cell Technology, Faculty of Life Science and Technology, Fukuyama University, Higashimura-cho, Aza, Sanzo, 985, Fukuyama 729-0292, Japan
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23
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Lourenço A, Álvarez D, Wang IJ, Velo-Antón G. Trapped within the city: integrating demography, time since isolation and population-specific traits to assess the genetic effects of urbanization. Mol Ecol 2017; 26:1498-1514. [DOI: 10.1111/mec.14019] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2016] [Revised: 01/04/2017] [Accepted: 01/05/2017] [Indexed: 01/05/2023]
Affiliation(s)
- André Lourenço
- Departamento de Biologia da Faculdade de Ciências da Universidade do Porto; Rua Campo Alegre 4169-007 Porto Portugal
- CIBIO/InBIO; Centro de Investigação em Biodiversidade e Recursos Genéticos da Universidade do Porto; Instituto de Ciências Agrárias de Vairão; Rua Padre Armando Quintas 7 4485-661 Vairão Portugal
| | - David Álvarez
- Ecology Unit; Department of Organisms and Systems Biology; University of Oviedo; C/ Catedrático Rodrigo Uría 33071 Oviedo Spain
| | - Ian J. Wang
- Department of Environmental Science, Policy and Management; University of California; 130 Mulford Hall #3114 Berkeley CA 94705 USA
| | - Guillermo Velo-Antón
- CIBIO/InBIO; Centro de Investigação em Biodiversidade e Recursos Genéticos da Universidade do Porto; Instituto de Ciências Agrárias de Vairão; Rua Padre Armando Quintas 7 4485-661 Vairão Portugal
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24
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Abstract
Biological networks pervade nature. They describe systems throughout all levels of biological organization, from molecules regulating metabolism to species interactions that shape ecosystem dynamics. The network thinking revealed recurrent organizational patterns in complex biological systems, such as the formation of semi-independent groups of connected elements (modularity) and non-random distributions of interactions among elements. Other structural patterns, such as nestedness, have been primarily assessed in ecological networks formed by two non-overlapping sets of elements; information on its occurrence on other levels of organization is lacking. Nestedness occurs when interactions of less connected elements form proper subsets of the interactions of more connected elements. Only recently these properties began to be appreciated in one-mode networks (where all elements can interact) which describe a much wider variety of biological phenomena. Here, we compute nestedness in a diverse collection of one-mode networked systems from six different levels of biological organization depicting gene and protein interactions, complex phenotypes, animal societies, metapopulations, food webs and vertebrate metacommunities. Our findings suggest that nestedness emerge independently of interaction type or biological scale and reveal that disparate systems can share nested organization features characterized by inclusive subsets of interacting elements with decreasing connectedness. We primarily explore the implications of a nested structure for each of these studied systems, then theorize on how nested networks are assembled. We hypothesize that nestedness emerges across scales due to processes that, although system-dependent, may share a general compromise between two features: specificity (the number of interactions the elements of the system can have) and affinity (how these elements can be connected to each other). Our findings suggesting occurrence of nestedness throughout biological scales can stimulate the debate on how pervasive nestedness may be in nature, while the theoretical emergent principles can aid further research on commonalities of biological networks.
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25
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Lillie M, Dubey S, Shine R, Belov K. Variation in Major Histocompatibility Complex diversity in invasive cane toad populations. WILDLIFE RESEARCH 2017. [DOI: 10.1071/wr17055] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Context The cane toad (Rhinella marina), a native species of central and southern America, was introduced to Australia in 1935 as a biocontrol agent after a complex history of prior introductions. The population rapidly expanded and has since spread through much of the Australian landmass, with severe impacts on the endemic wildlife, primarily via toxicity to predators. The invasion process has taken its toll on the cane toad, with changes in the immunological capacity across the Australian invasive population. Aims To investigate the immunogenetic underpinnings of these changes, we studied the diversity of the Major Histocompatiblity Complex (MHC) genes in introduced cane toad populations. Methods We studied the diversity of two MHC genes (the classical class I UA locus and a class II DAB locus) and compared these with neutral microsatellite markers in toads from the Australian site of introduction and the Australian invasion front. We also included toads from Hawai’i, the original source of the Australian toads, to infer founder effect. Key results Diversity across all markers was low across Australian and Hawai’ian samples, consistent with a reduction in genetic diversity through multiple founder effects during the course of the successive translocations. In Australia, allelic diversity at the microsatellite markers and the UA locus was reduced at the invasion front, whereas all three alleles at the DAB locus were maintained in the invasion-front toads. Conclusions Loss of allelic diversity observed at the microsatellite markers and the UA locus could be the result of drift and bottlenecking along the invasion process, however, the persistence of DAB diversity warrants further investigation to disentangle the evolutionary forces influencing this locus. Implications Through the use of different molecular markers, we provide a preliminary description of the adaptive genetic processes occurring in this invasive population. The extremely limited MHC diversity may represent low immunogenetic competence across the Australian population, which could be exploited for invasive species management.
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26
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Decline in territory size and fecundity as a response to carrying capacity in an endangered songbird. Oecologia 2016; 183:597-606. [PMID: 27873065 DOI: 10.1007/s00442-016-3763-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2016] [Accepted: 10/26/2016] [Indexed: 10/20/2022]
Abstract
Density-dependent processes are fundamental mechanisms for the regulation of populations. Ecological theories differ in their predictions on whether increasing population density leads to individual adjustments of survival and reproductive output or to dominance and monopolization of resources. Here, we use a natural experiment to examine which factors limit population growth in the only remaining population of the endangered pale-headed brush finch (Atlapetes pallidiceps). For three distinct phases (a phase of population suppression, 2001-2002; expansion due to conservation management, 2003-2008; and equilibrium phase, 2009-2014), we estimated demographic parameters with an integrated population model using population size, the proportion of successfully breeding pairs and their productivity, territory size, and mark-recapture data of adult birds. A low proportion of successful breeders due to brood parasitism (0.42, 95% credible interval 0.26-0.59) limited population growth before 2003; subsequent culling of the brood parasite resulted in a two-fold increase of the proportion of successful breeders during the 'expansion phase'. When the population approached the carrying capacity of its habitat, territory size declined by more than 50% and fecundity declined from 1.9 (1.54-2.27) to 1.3 (1.12-1.53) chicks per breeding pair, but the proportion of successful breeders remained constant (expansion phase: 0.85; 0.76-0.93; equilibrium phase: 0.86; 0.79-0.92). This study demonstrates that limiting resources can lead to individual adjustments instead of despotic behavior, and the individual reduction of reproductive output at high population densities is consistent with the slow life-history of many tropical species.
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27
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Dalton DL, Vermaak E, Smit-Robinson HA, Kotze A. Lack of diversity at innate immunity Toll-like receptor genes in the Critically Endangered White-winged Flufftail (Sarothrura ayresi). Sci Rep 2016; 6:36757. [PMID: 27827442 PMCID: PMC5101489 DOI: 10.1038/srep36757] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2016] [Accepted: 10/20/2016] [Indexed: 02/07/2023] Open
Abstract
The White-winged Flufftail (Sarothrura ayresi) population is listed as globally Critically Endangered. White-winged Flufftails are only known to occur, with any regularity, in the high-altitude wetlands of South Africa and Ethiopia. Threats to the species include the limited number of suitable breeding sites in Ethiopia and severe habitat degradation and loss both in Ethiopia and South Africa. Toll-like receptors (TLRs) are increasingly being studied in a variety of taxa as a broader approach to determine functional genetic diversity. In this study, we confirm low genetic diversity in the innate immune regions of the White-winged Flufftail similar to that observed in other bird species that have undergone population bottlenecks. Low TLR diversity in White-winged Flufftail indicates that this species is more likely to be threatened by changes to the environment that would potentially expose the species to new diseases. Thus, conservation efforts should be directed towards maintaining pristine habitat for White-winged Flufftail in its current distribution range. To date, no studies on immunogenetic variation in White-winged Flufftail have been conducted and to our knowledge, this is the first study of TLR genetic diversity in a critically endangered species.
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Affiliation(s)
- Desire L. Dalton
- National Zoological Gardens of South Africa, P.O. Box 754, Pretoria, 0001, South Africa
- Genetics Department, University of the Free State, P.O. Box 339, Bloemfontein, 9300, South Africa
| | - Elaine Vermaak
- National Zoological Gardens of South Africa, P.O. Box 754, Pretoria, 0001, South Africa
| | - Hanneline A. Smit-Robinson
- BirdLife South Africa, Private Bag X5000 Parklands 2121, Gauteng, South Africa
- Applied Behavioural Ecological & Ecosystem Research Unit (ABEERU), UNISA, Private Bag X6, Florida, 1717, South Africa
| | - Antoinette Kotze
- National Zoological Gardens of South Africa, P.O. Box 754, Pretoria, 0001, South Africa
- Genetics Department, University of the Free State, P.O. Box 339, Bloemfontein, 9300, South Africa
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28
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Shine R, Wang S, Madani G, Armstrong KN, Zhang L, Li YM. Using genetic data to predict the vulnerability of a native predator to a toxic invader. ENDANGER SPECIES RES 2016. [DOI: 10.3354/esr00745] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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29
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Hudson MA, Young RP, D'Urban Jackson J, Orozco-terWengel P, Martin L, James A, Sulton M, Garcia G, Griffiths RA, Thomas R, Magin C, Bruford MW, Cunningham AA. Dynamics and genetics of a disease-driven species decline to near extinction: lessons for conservation. Sci Rep 2016; 6:30772. [PMID: 27485994 PMCID: PMC4971493 DOI: 10.1038/srep30772] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2016] [Accepted: 07/07/2016] [Indexed: 12/05/2022] Open
Abstract
Amphibian chytridiomycosis has caused precipitous declines in hundreds of species worldwide. By tracking mountain chicken (Leptodactylus fallax) populations before, during and after the emergence of chytridiomycosis, we quantified the real-time species level impacts of this disease. We report a range-wide species decline amongst the fastest ever recorded, with a loss of over 85% of the population in fewer than 18 months on Dominica and near extinction on Montserrat. Genetic diversity declined in the wild, but emergency measures to establish a captive assurance population captured a representative sample of genetic diversity from Montserrat. If the Convention on Biological Diversity’s targets are to be met, it is important to evaluate the reasons why they appear consistently unattainable. The emergence of chytridiomycosis in the mountain chicken was predictable, but the decline could not be prevented. There is an urgent need to build mitigation capacity where amphibians are at risk from chytridiomycosis.
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Affiliation(s)
- M A Hudson
- Institute of Zoology, Zoological Society of London, Regent's Park, London NW1 4RY, UK.,Durrell Institute of Conservation and Ecology, School of Anthropology and Conservation, University of Kent, Canterbury, Kent CT2 7NR, UK.,Durrell Wildlife Conservation Trust, Les Augres Manor, Trinity, Jersey, Channel Islands, UK
| | - R P Young
- Durrell Wildlife Conservation Trust, Les Augres Manor, Trinity, Jersey, Channel Islands, UK.,Department of Life Sciences, Imperial College London, Silwood Park Campus, Buckhurst Road, Ascot, Berkshire SL5 7PY, UK
| | - J D'Urban Jackson
- School of Biosciences, Cardiff University, The Sir Martin Evans Building, Museum Avenue, Cardiff CF10 3AX, UK.,Department of Biology &Biochemistry, University of Bath, Claverton Down, Bath BA2 7AY, UK
| | - P Orozco-terWengel
- School of Biosciences, Cardiff University, The Sir Martin Evans Building, Museum Avenue, Cardiff CF10 3AX, UK
| | - L Martin
- Department of Environment, Montserrat Ministry of Agriculture, Housing, Lands and Environment, Montserrat, West Indies
| | - A James
- Forestry, Wildlife and Parks Division, Dominica Ministry of Agriculture and Fisheries, Botanical Gardens, Roseau, Commonwealth of Dominica, West Indies
| | - M Sulton
- Forestry, Wildlife and Parks Division, Dominica Ministry of Agriculture and Fisheries, Botanical Gardens, Roseau, Commonwealth of Dominica, West Indies
| | - G Garcia
- Chester Zoo, Cedar House, Caughall Road, Upton by Chester, Chester CH2 1LH, UK
| | - R A Griffiths
- Durrell Wildlife Conservation Trust, Les Augres Manor, Trinity, Jersey, Channel Islands, UK
| | - R Thomas
- Division of Agriculture, Dominica Ministry of Agriculture and Fisheries, Botanical Gardens, Roseau, Commonwealth of Dominica, West Indies
| | - C Magin
- The Royal Society for the Protection of Birds, The Lodge, Sandy, Bedfordshire SG19 2DL, UK
| | - M W Bruford
- School of Biosciences, Cardiff University, The Sir Martin Evans Building, Museum Avenue, Cardiff CF10 3AX, UK.,Sustainable Places Research Institute, Cardiff University, Cardiff CF10 3BB, UK
| | - A A Cunningham
- Institute of Zoology, Zoological Society of London, Regent's Park, London NW1 4RY, UK
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30
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Loaiza-Piedrahíta JD, Bock BC, Páez VP. Demography of the Andean Dart Frog (Andinobates opisthomelas, Dendrobatidae) in Eastern Antioquia, Colombia. SOUTH AMERICAN JOURNAL OF HERPETOLOGY 2016. [DOI: 10.2994/sajh-d-16-00009.1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
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31
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Roth S, Jehle R. High genetic diversity of common toad (Bufo bufo) populations under strong natural fragmentation on a Northern archipelago. Ecol Evol 2016; 6:1626-36. [PMID: 27087930 PMCID: PMC4801968 DOI: 10.1002/ece3.1957] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2015] [Revised: 12/15/2015] [Accepted: 12/16/2015] [Indexed: 02/02/2023] Open
Abstract
The last decades have shown a surge in studies focusing on the interplay between fragmented habitats, genetic variation, and conservation. In the present study, we consider the case of a temperate pond-breeding anuran (the common toad Bufo bufo) inhabiting a naturally strongly fragmented habitat at the Northern fringe of the species' range: islands offshore the Norwegian coast. A total of 475 individuals from 19 populations (three mainland populations and 16 populations on seven adjacent islands) were genetically characterized using nine microsatellite markers. As expected for a highly fragmented habitat, genetic distances between populations were high (pairwise F st values ranging between 0.06 and 0.33), with however little differences between populations separated by ocean and populations separated by terrestrial habitat (mainland and on islands). Despite a distinct cline in genetic variation from mainland populations to peripheral islands, the study populations were characterized by overall high genetic variation, in line with effective population sizes derived from single-sample estimators which were on average about 20 individuals. Taken together, our results reinforce the notion that spatial and temporal scales of fragmentation need to be considered when studying the interplay between landscape fragmentation and genetic erosion.
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Affiliation(s)
- Steffen Roth
- The Natural History Collections University Museum of Bergen Bergen N-5020 Norway
| | - Robert Jehle
- School of Environment and Life Sciences University of Salford Salford M5 4WT UK
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Li SL, Vasemägi A, Ramula S. Genetic variation facilitates seedling establishment but not population growth rate of a perennial invader. ANNALS OF BOTANY 2016; 117:187-194. [PMID: 26420202 PMCID: PMC4701146 DOI: 10.1093/aob/mcv145] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2015] [Revised: 06/22/2015] [Accepted: 08/17/2015] [Indexed: 06/05/2023]
Abstract
BACKGROUND AND AIMS Assessing the demographic consequences of genetic variation is fundamental to invasion biology. However, genetic and demographic approaches are rarely combined to explore the effects of genetic variation on invasive populations in natural environments. This study combined population genetics, demographic data and a greenhouse experiment to investigate the consequences of genetic variation for the population fitness of the perennial, invasive herb Lupinus polyphyllus. METHODS Genetic and demographic data were collected from 37 L. polyphyllus populations representing different latitudes in Finland, and genetic variation was characterized based on 13 microsatellite loci. Associations between genetic variation and population size, population density, latitude and habitat were investigated. Genetic variation was then explored in relation to four fitness components (establishment, survival, growth, fecundity) measured at the population level, and the long-term population growth rate (λ). For a subset of populations genetic variation was also examined in relation to the temporal variability of λ. A further assessment was made of the role of natural selection in the observed variation of certain fitness components among populations under greenhouse conditions. KEY RESULTS It was found that genetic variation correlated positively with population size, particularly at higher latitudes, and differed among habitat types. Average seedling establishment per population increased with genetic variation in the field, but not under greenhouse conditions. Quantitative genetic divergence (Q(ST)) based on seedling establishment in the greenhouse was smaller than allelic genetic divergence (F'(ST)), indicating that unifying selection has a prominent role in this fitness component. Genetic variation was not associated with average survival, growth or fecundity measured at the population level, λ or its variability. CONCLUSIONS The study suggests that although genetic variation may facilitate plant invasions by increasing seedling establishment, it may not necessarily affect the long-term population growth rate. Therefore, established invasions may be able to grow equally well regardless of their genetic diversity.
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Affiliation(s)
- Shou-Li Li
- Section of Ecology, Department of Biology, University of Turku, 20014 Turku, Finland, Department of Biology and Center for Infectious Disease Dynamics, The Pennsylvania State University, University Park, Pennsylvania, USA,
| | - Anti Vasemägi
- Division of Genetics and Physiology, Department of Biology, University of Turku, 20014 Turku, Finland, Department of Aquaculture, Estonian University of Life Sciences, Tartu, Estonia and
| | - Satu Ramula
- Section of Ecology, Department of Biology, University of Turku, 20014 Turku, Finland, Aronia Coastal Zone Research Team, Åbo Akademi University and Novia University of Applied Sciences, Raseborgsvägen 9, 10600 Ekenäs, Finland
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Harradine EL, Andrew ME, Thomas JW, How RA, Schmitt LH, Spencer PBS. Importance of dispersal routes that minimize open-ocean movement to the genetic structure of island populations. CONSERVATION BIOLOGY : THE JOURNAL OF THE SOCIETY FOR CONSERVATION BIOLOGY 2015; 29:1704-1714. [PMID: 26171679 DOI: 10.1111/cobi.12555] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2014] [Accepted: 04/23/2015] [Indexed: 06/04/2023]
Abstract
Islands present a unique scenario in conservation biology, offering refuge yet imposing limitations on insular populations. The Kimberley region of northwestern Australia has more than 2500 islands that have recently come into focus as substantial conservation resources. It is therefore of great interest for managers to understand the driving forces of genetic structure of species within these island archipelagos. We used the ubiquitous bar-shouldered skink (Ctenotus inornatus) as a model species to represent the influence of landscape factors on genetic structure across the Kimberley islands. On 41 islands and 4 mainland locations in a remote area of Australia, we genotyped individuals across 18 nuclear (microsatellite) markers. Measures of genetic differentiation and diversity were used in two complementary analyses. We used circuit theory and Mantel tests to examine the influence of the landscape matrix on population connectivity and linear regression and model selection based on Akaike's information criterion to investigate landscape controls on genetic diversity. Genetic differentiation between islands was best predicted with circuit-theory models that accounted for the large difference in resistance to dispersal between land and ocean. In contrast, straight-line distances were unrelated to either resistance distances or genetic differentiation. Instead, connectivity was determined by island-hopping routes that allow organisms to minimize the distance of difficult ocean passages. Island populations of C. inornatus retained varying degrees of genetic diversity (NA = 1.83 - 7.39), but it was greatest on islands closer to the mainland, in terms of resistance-distance units. In contrast, genetic diversity was unrelated to island size. Our results highlight the potential for islands to contribute to both theoretical and applied conservation, provide strong evidence of the driving forces of population structure within undisturbed landscapes, and identify the islands most valuable for conservation based on their contributions to gene flow and genetic diversity.
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Affiliation(s)
- E L Harradine
- School of Veterinary and Life Sciences, Murdoch University, 90 South Street, Western Australia, 6150, Australia
| | - M E Andrew
- School of Veterinary and Life Sciences, Murdoch University, 90 South Street, Western Australia, 6150, Australia
| | - J W Thomas
- School of Veterinary and Life Sciences, Murdoch University, 90 South Street, Western Australia, 6150, Australia
| | - R A How
- School of Anatomy, Physiology & Human Biology, The University of Western Australia, Crawley, WA, 6009, Australia
| | - L H Schmitt
- School of Anatomy, Physiology & Human Biology, The University of Western Australia, Crawley, WA, 6009, Australia
| | - P B S Spencer
- School of Veterinary and Life Sciences, Murdoch University, 90 South Street, Western Australia, 6150, Australia
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Rutkowski R, Krofel M, Giannatos G, Ćirović D, Männil P, Volokh AM, Lanszki J, Heltai M, Szabó L, Banea OC, Yavruyan E, Hayrapetyan V, Kopaliani N, Miliou A, Tryfonopoulos GA, Lymberakis P, Penezić A, Pakeltytė G, Suchecka E, Bogdanowicz W. A European Concern? Genetic Structure and Expansion of Golden Jackals (Canis aureus) in Europe and the Caucasus. PLoS One 2015; 10:e0141236. [PMID: 26540195 PMCID: PMC4634961 DOI: 10.1371/journal.pone.0141236] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2015] [Accepted: 10/05/2015] [Indexed: 11/19/2022] Open
Abstract
In the first continent-wide study of the golden jackal (Canis aureus), we characterised its population genetic structure and attempted to identify the origin of European populations. This provided a unique insight into genetic characteristics of a native carnivore population with rapid large-scale expansion. We analysed 15 microsatellite markers and a 406 base-pair fragment of the mitochondrial control region. Bayesian-based and principal components methods were applied to evaluate whether the geographical grouping of samples corresponded with genetic groups. Our analysis revealed low levels of genetic diversity, reflecting the unique history of the golden jackal among Europe’s native carnivores. The results suggest ongoing gene flow between south-eastern Europe and the Caucasus, with both contributing to the Baltic population, which appeared only recently. The population from the Peloponnese Peninsula in southern Greece forms a common genetic cluster with samples from south-eastern Europe (ΔK approach in STRUCTURE, Principal Components Analysis [PCA]), although the results based on BAPS and the estimated likelihood in STRUCTURE indicate that Peloponnesian jackals may represent a distinct population. Moreover, analyses of population structure also suggest either genetic distinctiveness of the island population from Samos near the coast of Asia Minor (BAPS, most STRUCTURE, PCA), or possibly its connection with the Caucasus population (one analysis in STRUCTURE). We speculate from our results that ancient Mediterranean jackal populations have persisted to the present day, and have merged with jackals colonising from Asia. These data also suggest that new populations of the golden jackal may be founded by long-distance dispersal, and thus should not be treated as an invasive alien species, i.e. an organism that is “non-native to an ecosystem, and which may cause economic or environmental harm or adversely affect human health”. These insights into the genetic structure and ancestry of Baltic jackals have important implications for management and conservation of jackals in Europe. The golden jackal is listed as an Annex V species in the EU Habitats Directive and as such, considering also the results presented here, should be legally protected in all EU member states.
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Affiliation(s)
- Robert Rutkowski
- Museum and Institute of Zoology, Polish Academy of Sciences, Warszawa, Poland
| | - Miha Krofel
- Wildlife Ecology Research Group, Department of Forestry, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Giorgos Giannatos
- Department of Zoology - Marine Biology, School of Biology, University of Athens, Panepistimioupolis, Athens, Greece
| | - Duško Ćirović
- Institute of Zoology, Faculty of Biology, University of Belgrade, Belgrade, Serbia
| | | | | | - József Lanszki
- Department of Nature Conservation, University of Kaposvár, Kaposvár, Hungary
| | - Miklós Heltai
- Institute for Wildlife Conservation, Szent István University, Gödöllő, Hungary
| | - László Szabó
- Institute for Wildlife Conservation, Szent István University, Gödöllő, Hungary
| | | | - Eduard Yavruyan
- Scientific Centre of Zoology and Hydroecology, National Academy of Sciences of Armenia, Yerevan, Armenia
| | - Vahram Hayrapetyan
- Stepanakert Branch of the Armenian National Agrarian University, Stepanakert, Armenia
| | - Natia Kopaliani
- Institute of Ecology, Ilia State University, Tbilisi, Georgia
| | - Anastasia Miliou
- Archipelagos Institute of Marine Conservation, Mesokampos, Pythagorio, Samos, Greece
| | | | - Petros Lymberakis
- Natural History Museum of Crete, University of Crete, Heraklion, Crete, Greece
| | - Aleksandra Penezić
- Institute of Zoology, Faculty of Biology, University of Belgrade, Belgrade, Serbia
| | | | - Ewa Suchecka
- Museum and Institute of Zoology, Polish Academy of Sciences, Warszawa, Poland
| | - Wiesław Bogdanowicz
- Museum and Institute of Zoology, Polish Academy of Sciences, Warszawa, Poland
- * E-mail:
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Ferrando A, Manunza A, Jordana J, Capote J, Pons A, Pais J, Delgado T, Atoche P, Cabrera B, Martínez A, Landi V, Delgado JV, Argüello A, Vidal O, Lalueza-Fox C, Ramírez O, Amills M. A mitochondrial analysis reveals distinct founder effect signatures in Canarian and Balearic goats. Anim Genet 2015; 46:452-6. [DOI: 10.1111/age.12302] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/25/2015] [Indexed: 11/28/2022]
Affiliation(s)
- A. Ferrando
- Departament de Ciència Animal i dels Aliments; Universitat Autònoma de Barcelona; Bellaterra 08193 Spain
| | - A. Manunza
- Department of Animal Genetics; Center for Research in Agricultural Genomics (CSIC-IRTA-UAB-UB); Campus Universitat Autònoma de Barcelona; Bellaterra 08193 Spain
| | - J. Jordana
- Departament de Ciència Animal i dels Aliments; Universitat Autònoma de Barcelona; Bellaterra 08193 Spain
| | - J. Capote
- Instituto Canario de Investigaciones Agrarias; La Laguna 38108 Tenerife Spain
| | - A. Pons
- Àrea Tècnica Agrària; Servei de Millora Agrària i Pesquera (SEMILLA); Son Ferriol 07198 Spain
| | - J. Pais
- Museo Arqueológico Benahorita; Camino de Las Adelfas; 38760 Los Llanos de Aridane La Palma Spain
| | - T. Delgado
- Museo Canario; Doctor Verneau; 2, 35001 Las Palmas de Gran Canaria Spain
| | - P. Atoche
- Departamento de Ciencias Históricas; Universidad de Las Palmas de Gran Canaria; 35001 Las Palmas de Gran Canaria
| | - B. Cabrera
- Department of Animal Genetics; Center for Research in Agricultural Genomics (CSIC-IRTA-UAB-UB); Campus Universitat Autònoma de Barcelona; Bellaterra 08193 Spain
| | - A. Martínez
- Departamento de Genética; Universidad de Córdoba; Córdoba 14071 Spain
| | - V. Landi
- Departamento de Genética; Universidad de Córdoba; Córdoba 14071 Spain
| | - J. V. Delgado
- Departamento de Genética; Universidad de Córdoba; Córdoba 14071 Spain
| | - A. Argüello
- Department of Animal Science; Universidad de Las Palmas de Gran Canaria; Arucas 35413 Spain
| | - O. Vidal
- Departament de Biologia; Universitat de Girona; Girona 17071 Spain
| | - C. Lalueza-Fox
- Institut de Biologia Evolutiva (CSIC - Universitat Pompeu Fabra); Barcelona 08003 Spain
| | - O. Ramírez
- Institut de Biologia Evolutiva (CSIC - Universitat Pompeu Fabra); Barcelona 08003 Spain
| | - M. Amills
- Departament de Ciència Animal i dels Aliments; Universitat Autònoma de Barcelona; Bellaterra 08193 Spain
- Department of Animal Genetics; Center for Research in Agricultural Genomics (CSIC-IRTA-UAB-UB); Campus Universitat Autònoma de Barcelona; Bellaterra 08193 Spain
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Fünfstück T, Vigilant L. The geographic distribution of genetic diversity within gorillas. Am J Primatol 2015; 77:974-985. [DOI: 10.1002/ajp.22427] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2015] [Revised: 04/23/2015] [Accepted: 04/26/2015] [Indexed: 11/06/2022]
Affiliation(s)
| | - Linda Vigilant
- Max Planck Institute for Evolutionary Anthropology; Leipzig Germany
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A comparative study on genetic effects of artificial and natural habitat fragmentation on Loropetalum chinense (Hamamelidaceae) in Southeast China. Heredity (Edinb) 2014; 114:544-51. [PMID: 25515015 DOI: 10.1038/hdy.2014.114] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2014] [Revised: 11/06/2014] [Accepted: 11/10/2014] [Indexed: 11/08/2022] Open
Abstract
Elucidating the demographic and landscape features that determine the genetic effects of habitat fragmentation has become fundamental to research in conservation and evolutionary biology. Land-bridge islands provide ideal study areas for investigating the genetic effects of habitat fragmentation at different temporal and spatial scales. In this context, we compared patterns of nuclear microsatellite variation between insular populations of a shrub of evergreen broad-leaved forest, Loropetalum chinense, from the artificially created Thousand-Island Lake (TIL) and the Holocene-dated Zhoushan Archipelago of Southeast China. Populations from the TIL region harboured higher levels of genetic diversity than those from the Zhoushan Archipelago, but these differences were not significant. There was no correlation between genetic diversity and most island features, excepting a negative effect of mainland-island distance on allelic richness and expected heterozygosity in the Zhoushan Archipelago. In general, levels of gene flow among island populations were moderate to high, and tests of alternative models of population history strongly favoured a gene flow-drift model over a pure drift model in each region. In sum, our results showed no obvious genetic effects of habitat fragmentation due to recent (artificial) or past (natural) island formation. Rather, they highlight the importance of gene flow (most likely via seed) in maintaining genetic variation and preventing inter-population differentiation in the face of habitat 'insularization' at different temporal and spatial scales.
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Hartmann SA, Schaefer HM, Segelbacher G. Genetic depletion at adaptive but not neutral loci in an endangered bird species. Mol Ecol 2014; 23:5712-25. [DOI: 10.1111/mec.12975] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2014] [Revised: 10/09/2014] [Accepted: 10/17/2014] [Indexed: 12/01/2022]
Affiliation(s)
- Stefanie A. Hartmann
- Wildlife Ecology and Management; Faculty of Environment and Natural Resources; University of Freiburg; Tennenbacher Straße 4 79106 Freiburg Germany
- Department of Evolutionary Biology and Animal Ecology; Faculty of Biology; University of Freiburg; Hauptstr. 1 79104 Freiburg Germany
| | - H. Martin Schaefer
- Department of Evolutionary Biology and Animal Ecology; Faculty of Biology; University of Freiburg; Hauptstr. 1 79104 Freiburg Germany
| | - Gernot Segelbacher
- Wildlife Ecology and Management; Faculty of Environment and Natural Resources; University of Freiburg; Tennenbacher Straße 4 79106 Freiburg Germany
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39
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Xue HL, Xu JH, Chen L, Xu LX. Genetic variation of the striped hamster (Cricetulus barabensis) and the impact of population density and environmental factors. Zool Stud 2014. [DOI: 10.1186/s40555-014-0063-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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40
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Nyman T, Valtonen M, Aspi J, Ruokonen M, Kunnasranta M, Palo JU. Demographic histories and genetic diversities of Fennoscandian marine and landlocked ringed seal subspecies. Ecol Evol 2014; 4:3420-34. [PMID: 25535558 PMCID: PMC4228616 DOI: 10.1002/ece3.1193] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2014] [Revised: 07/21/2014] [Accepted: 07/22/2014] [Indexed: 11/18/2022] Open
Abstract
Island populations are on average smaller, genetically less diverse, and at a higher risk to go extinct than mainland populations. Low genetic diversity may elevate extinction probability, but the genetic component of the risk can be affected by the mode of diversity loss, which, in turn, is connected to the demographic history of the population. Here, we examined the history of genetic erosion in three Fennoscandian ringed seal subspecies, of which one inhabits the Baltic Sea 'mainland' and two the 'aquatic islands' composed of Lake Saimaa in Finland and Lake Ladoga in Russia. Both lakes were colonized by marine seals after their formation c. 9500 years ago, but Lake Ladoga is larger and more contiguous than Lake Saimaa. All three populations suffered dramatic declines during the 20th century, but the bottleneck was particularly severe in Lake Saimaa. Data from 17 microsatellite loci and mitochondrial control-region sequences show that Saimaa ringed seals have lost most of the genetic diversity present in their Baltic ancestors, while the Ladoga population has experienced only minor reductions. Using Approximate Bayesian computing analyses, we show that the genetic uniformity of the Saimaa subspecies derives from an extended founder event and subsequent slow erosion, rather than from the recent bottleneck. This suggests that the population has persisted for nearly 10,000 years despite having low genetic variation. The relatively high diversity of the Ladoga population appears to result from a high number of initial colonizers and a high post-colonization population size, but possibly also by a shorter isolation period and/or occasional gene flow from the Baltic Sea.
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Affiliation(s)
- Tommi Nyman
- Department of Biology, University of Eastern FinlandPO Box 111, Joensuu, FI-80101, Finland
- Institute for Systematic Botany, University of Zurich, Zollikerstrasse 107Zurich, CH-8008, Switzerland
| | - Mia Valtonen
- Department of Biology, University of Eastern FinlandPO Box 111, Joensuu, FI-80101, Finland
| | - Jouni Aspi
- Department of Biology, University of OuluPO Box 3000, Oulu, FI-90014, Finland
| | - Minna Ruokonen
- Department of Biology, University of OuluPO Box 3000, Oulu, FI-90014, Finland
| | - Mervi Kunnasranta
- Department of Biology, University of Eastern FinlandPO Box 111, Joensuu, FI-80101, Finland
| | - Jukka U Palo
- Laboratory of Forensic Biology, Hjelt Institute, University of HelsinkiPO Box 40, Helsinki, FI-00014, Finland
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