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Zheng C, Chen Q, Wong MHG, Marx N, Khotpathoom T, Wang H, Yang F, Rao X, Chan BPL, Liu Y. Whole-Genome Analyses Reveal the Distinct Taxonomic Status of the Hainan Population of Endangered Rucervus eldii and Its Conservation Implications. Evol Appl 2024; 17:e70010. [PMID: 39286763 PMCID: PMC11403188 DOI: 10.1111/eva.70010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Revised: 08/14/2024] [Accepted: 08/22/2024] [Indexed: 09/19/2024] Open
Abstract
Eld's deer Rucervus eldii (McClelland, 1842) is an ungulate that lives in tropical lowland forests in several countries of Indochina and Hainan Island of China. Its remaining population is small and scattered, and the species is listed as an Endangered species on the IUCN Red List. The debate over the taxonomic status of the Hainan population has persisted for over a century-as an island-endemic subspecies R. e. hainanus, or an insular population of the subspecies R. e. siamensis, would have significant conservation implications. And, given the Hainan population had experienced both population bottleneck and multiple translocations in the past, conservation genomics would be a powerful tool to evaluate the genetic impacts of these events. In this study, we used conservation genomics assessment to study population differentiation and genetic diversity of R. e. siamensis in Cambodia and three Eld's deer subpopulations on Hainan Island. Based on the unique genetic profile and demographic analysis, this study corroborated previous studies using genetic markers that the Hainan Eld's deer warrants the taxonomic status of a distinct subspecies. The Hainan population exhibits a reduction in genetic diversity and an increase in the level of inbreeding when compared to the population of Cambodia. The signs of purifying selection were found against homozygous loss-of-function mutations to decrease the deleterious burden in the Hainan population. However, there was an accumulation of more deleterious missense mutations. Furthermore, significant differences in genetic diversity and level of inbreeding found among the three Hainan subpopulations indicated population isolation and suboptimal translocation strategies, which calls for urgent, coordinated, and science-based genetic management to ensure the long-term viability of the endemic subspecies hainanus. This study provides guidance for the conservation and management of Eld's deer.
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Affiliation(s)
- Chenqing Zheng
- State Key Laboratory of Biocontrol, School of Life Sciences Sun Yat-Sen University Guangzhou China
- School of Ecology Shenzhen Campus of Sun Yat-Sen University Shenzhen China
| | - Qing Chen
- School of Ecology Shenzhen Campus of Sun Yat-Sen University Shenzhen China
| | | | - Nick Marx
- Wildlife Alliance Phnom Penh Cambodia
| | - Thananh Khotpathoom
- Faculty of Forestry National University of Laos Vientiane Capital City Lao PDR
| | - Hesheng Wang
- Hainan Datian National Nature Reserve Dongfang City Hainan Province China
| | - Feng Yang
- Kadoorie Farm and Botanic Garden Tai Po, New Territories Hong Kong China
| | - Xiaodong Rao
- School of Tropical Agriculture and Forestry Hainan University Danzhou China
- Haikou Key Laboratory of Intelligent Forestry Haikou China
| | - Bosco Pui Lok Chan
- Kadoorie Farm and Botanic Garden Tai Po, New Territories Hong Kong China
- WWF-Hong Kong Kwai Chung New Territories Hong Kong
| | - Yang Liu
- State Key Laboratory of Biocontrol, School of Life Sciences Sun Yat-Sen University Guangzhou China
- School of Ecology Shenzhen Campus of Sun Yat-Sen University Shenzhen China
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Chen Y, Dong L, Yi H, Kidner C, Kang M. Genomic divergence and mutation load in the Begonia masoniana complex from limestone karsts. PLANT DIVERSITY 2024; 46:575-584. [PMID: 39290887 PMCID: PMC11403149 DOI: 10.1016/j.pld.2024.04.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Revised: 04/01/2024] [Accepted: 04/03/2024] [Indexed: 09/19/2024]
Abstract
Understanding genome-wide diversity, inbreeding, and the burden of accumulated deleterious mutations in small and isolated populations is essential for predicting and enhancing population persistence and resilience. However, these effects are rarely studied in limestone karst plants. Here, we re-sequenced the nuclear genomes of 62 individuals of the Begonia masoniana complex (B. liuyanii, B. longgangensis, B. masoniana and B. variegata) and investigated genomic divergence and genetic load for these four species. Our analyses revealed four distinct clusters corresponding to each species within the complex. Notably, there was only limited admixture between B. liuyanii and B. longgangensis occurring in overlapping geographic regions. All species experienced historical bottlenecks during the Pleistocene, which were likely caused by glacial climate fluctuations. We detected an asymmetric historical gene flow between group pairs within this timeframe, highlighting a distinctive pattern of interspecific divergence attributable to karst geographic isolation. We found that isolated populations of B. masoniana have limited gene flow, the smallest recent population size, the highest inbreeding coefficients, and the greatest accumulation of recessive deleterious mutations. These findings underscore the urgency to prioritize conservation efforts for these isolated population. This study is among the first to disentangle the genetic differentiation and specific demographic history of karst Begonia plants at the whole-genome level, shedding light on the potential risks associated with the accumulation of deleterious mutations over generations of inbreeding. Moreover, our findings may facilitate conservation planning by providing critical baseline genetic data and a better understanding of the historical events that have shaped current population structure of rare and endangered karst plants.
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Affiliation(s)
- Yiqing Chen
- Key Laboratory of National Forestry and Grassland Administration on Plant Conservation and Utilization in Southern China, Guangzhou 510650, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Lina Dong
- Guangxi Key Laboratory of Conservation and Restoration Ecology in Karst Terrain, Guangxi Institute of Botany, Guangxi Zhang Autonomous Region and the Chinese Academy of Sciences, Guilin 541006, China
| | - Huiqin Yi
- Key Laboratory of National Forestry and Grassland Administration on Plant Conservation and Utilization in Southern China, Guangzhou 510650, China
| | - Catherine Kidner
- Institute of Molecular Plant Sciences, University of Edinburgh, Daniel Rutherford Building Max Born Crescent, The King's Buildings, Edinburgh EH9 3BF, UK
- Royal Botanic Garden Edinburgh, 20a Inverleith Row, Edinburgh EH3 5LR, UK
| | - Ming Kang
- Key Laboratory of National Forestry and Grassland Administration on Plant Conservation and Utilization in Southern China, Guangzhou 510650, China
- State Key Laboratory of Plant Diversity and Specialty Crops, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
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Beer MA, Trumbo DR, Rautsaw RM, Kozakiewicz CP, Epstein B, Hohenlohe PA, Alford RA, Schwarzkopf L, Storfer A. Spatial variation in genomic signatures of local adaptation during the cane toad invasion of Australia. Mol Ecol 2024; 33:e17464. [PMID: 38994885 DOI: 10.1111/mec.17464] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Revised: 06/09/2024] [Accepted: 07/01/2024] [Indexed: 07/13/2024]
Abstract
Adaptive evolution can facilitate species' range expansions across environmentally heterogeneous landscapes. However, serial founder effects can limit the efficacy of selection, and the evolution of increased dispersal during range expansions may result in gene flow swamping local adaptation. Here, we study how genetic drift, gene flow and selection interact during the cane toad's (Rhinella marina) invasion across the heterogeneous landscape of Australia. Following its introduction in 1935, the cane toad colonised eastern Australia and established several stable range edges. The ongoing, more rapid range expansion in north-central Australia has occurred concomitant with an evolved increase in dispersal capacity. Using reduced representation genomic data of Australian cane toads from the expansion front and from two areas of their established range, we test the hypothesis that high gene flow constrains local adaptation at the expansion front relative to established areas. Genetic analyses indicate the three study areas are genetically distinct but show similar levels of allelic richness, heterozygosity and inbreeding. Markedly higher gene flow or recency of colonisation at the expansion front have likely hindered local adaptation at the time of sampling, as indicated by reduced slopes of genetic-environment associations (GEAs) estimated using a novel application of geographically weighted regression that accounts for allele surfing; GEA slopes are significantly steeper in established parts of the range. Our work bolsters evidence supporting adaptation of invasive species post-introduction and adds novel evidence for differing strengths of evolutionary forces among geographic areas with different invasion histories.
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Affiliation(s)
- Marc A Beer
- School of Biological Sciences, Washington State University, Pullman, Washington, USA
| | - Daryl R Trumbo
- Department of Biology, Colorado State University Pueblo, Pueblo, Colorado, USA
| | - Rhett M Rautsaw
- School of Biological Sciences, Washington State University, Pullman, Washington, USA
- Department of Integrative Biology, University of South Florida, Tampa, Florida, USA
| | - Christopher P Kozakiewicz
- W.K. Kellogg Biological Station, Department of Integrative Biology, Michigan State University, Hickory Corners, Michigan, USA
| | - Brendan Epstein
- Department of Plant and Microbial Biology, University of Minnesota, St Paul, Minnesota, USA
| | - Paul A Hohenlohe
- Department of Biological Sciences, University of Idaho, Moscow, Idaho, USA
| | - Ross A Alford
- College of Science and Engineering, James Cook University, Townsville, Queensland, Australia
| | - Lin Schwarzkopf
- College of Science and Engineering, James Cook University, Townsville, Queensland, Australia
| | - Andrew Storfer
- School of Biological Sciences, Washington State University, Pullman, Washington, USA
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Park KY, Lucas M, Chaulk A, Matter SF, Roland J, Keyghobadi N. Immigration allows population persistence and maintains genetic diversity despite an attempted experimental extinction. ROYAL SOCIETY OPEN SCIENCE 2024; 11:240557. [PMID: 39086829 PMCID: PMC11288673 DOI: 10.1098/rsos.240557] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/08/2024] [Revised: 07/07/2024] [Accepted: 07/08/2024] [Indexed: 08/02/2024]
Abstract
Widespread fragmentation and degradation of habitats make organisms increasingly vulnerable to declines in population size. Immigration is a key process potentially affecting the rescue and persistence of populations in the face of such pressures. Field research addressing severe demographic declines in the context of immigration among interconnected local populations is limited owing to difficulties in detecting such demographic events and the need for long-term monitoring of populations. In a 17-subpopulation metapopulation of the butterfly, Parnassius smintheus, all adults observed in two adjacent patches were removed over eight consecutive generations. Despite this severe and long-term reduction in survival and reproduction, the targeted populations did not go extinct. Here, we use genetic data to assess the role of immigration versus in situ reproduction in allowing the persistence of these populations. We genotyped 471 samples collected from the targeted populations throughout the removal experiment at 152 single nucleotide polymorphisms. We found no reduction in the genetic diversity of the targeted populations over time, but a decrease in the number of loci in Hardy-Weinberg equilibrium, consistent with a high level of immigration from multiple surrounding populations. Our results highlight the role of connectivity and movement in making metapopulations resilient to even severe and protracted localized population reductions.
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Affiliation(s)
- Keon Young Park
- Department of Biology, Western University, London, Ontario N6A 5B7, Canada
| | - Mel Lucas
- Department of Biology, Western University, London, Ontario N6A 5B7, Canada
| | - Andrew Chaulk
- Department of Biology, Western University, London, Ontario N6A 5B7, Canada
- Department of Biology, Memorial University of Newfoundland, St John's, Newfoundland A1C 5S7, Canada
| | - Stephen F Matter
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH 45221, USA
| | - Jens Roland
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta T6G 2E9, Canada
| | - Nusha Keyghobadi
- Department of Biology, Western University, London, Ontario N6A 5B7, Canada
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Yang Z, Liang L, Xiang W, Wang L, Ma Q, Wang Z. Conservation genomics provides insights into genetic resilience and adaptation of the endangered Chinese hazelnut, Corylus chinensis. PLANT DIVERSITY 2024; 46:294-308. [PMID: 38798732 PMCID: PMC11119545 DOI: 10.1016/j.pld.2024.03.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/20/2024] [Revised: 03/23/2024] [Accepted: 03/25/2024] [Indexed: 05/29/2024]
Abstract
Global climate change has increased concerns regarding biodiversity loss. However, many key conservation issues still required further research, including demographic history, deleterious mutation load, adaptive evolution, and putative introgression. Here we generated the first chromosome-level genome of the endangered Chinese hazelnut, Corylus chinensis, and compared the genomic signatures with its sympatric widespread C. kwechowensis-C. yunnanensis complex. We found large genome rearrangements across all Corylus species and identified species-specific expanded gene families that may be involved in adaptation. Population genomics revealed that both C. chinensis and the C. kwechowensis-C. yunnanensis complex had diverged into two genetic lineages, forming a consistent pattern of southwestern-northern differentiation. Population size of the narrow southwestern lineages of both species have decreased continuously since the late Miocene, whereas the widespread northern lineages have remained stable (C. chinensis) or have even recovered from population bottlenecks (C. kwechowensis-C. yunnanensis complex) during the Quaternary. Compared with C. kwechowensis-C. yunnanensis complex, C. chinensis showed significantly lower genomic diversity and higher inbreeding level. However, C. chinensis carried significantly fewer deleterious mutations than C. kwechowensis-C. yunnanensis complex, as more effective purging selection reduced the accumulation of homozygous variants. We also detected signals of positive selection and adaptive introgression in different lineages, which facilitated the accumulation of favorable variants and formation of local adaptation. Hence, both types of selection and exogenous introgression could have mitigated inbreeding and facilitated survival and persistence of C. chinensis. Overall, our study provides critical insights into lineage differentiation, local adaptation, and the potential for future recovery of endangered trees.
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Affiliation(s)
- Zhen Yang
- Key Laboratory of Tree Breeding and Cultivation, National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China
| | - Lisong Liang
- Key Laboratory of Tree Breeding and Cultivation, National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China
| | - Weibo Xiang
- National Engineering Research Center of Eco-Environment Protection for Yangtze River Economic Belt, China Three Gorges Corporation, Beijing 100083, China
- Rare Plants Research Institute of Yangtze River, China Three Gorges Corporation, Yichang 443133, China
| | - Lujun Wang
- Research Institute of Economic Forest Cultivation and Processing, Anhui Academy of Forestry, Hefei 230031, China
| | - Qinghua Ma
- Key Laboratory of Tree Breeding and Cultivation, National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China
| | - Zhaoshan Wang
- Key Laboratory of Tree Breeding and Cultivation, National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China
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Xia C, Zuo Y, Xue T, Kang M, Zhang H, Zhang X, Wang B, Zhang J, Deng H. The genetic structure and demographic history revealed by whole-genome resequencing provide insights into conservation of critically endangered Artocarpus nanchuanensis. FRONTIERS IN PLANT SCIENCE 2023; 14:1224308. [PMID: 37575939 PMCID: PMC10415164 DOI: 10.3389/fpls.2023.1224308] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Accepted: 07/12/2023] [Indexed: 08/15/2023]
Abstract
Introduction Whole-genome resequencing technology covers almost all nucleotide variations in the genome, which makes it possible to carry out conservation genomics research on endangered species at the whole-genome level. Methods In this study, based on the whole-genome resequencing data of 101 critically endangered Artocarpus nanchuanensis individuals, we evaluated the genetic diversity and population structure, inferred the demographic history and genetic load, predicted the potential distributions in the past, present and future, and classified conservation units to propose targeted suggestions for the conservation of this critically endangered species. Results Whole-genome resequencing for A. nanchuanensis generated approximately 2 Tb of data. Based on abundant mutation sites (25,312,571 single nucleotide polymorphisms sites), we revealed that the average genetic diversity (nucleotide diversity, π) of different populations of A. nanchuanensis was relatively low compared with other trees that have been studied. And we also revealed that the NHZ and QJT populations harboured unique genetic backgrounds and were significantly separated from the other five populations. In addition, positive genetic selective signals, significantly enriched in biological processes related to terpene synthesis, were identified in the NHZ population. The analysis of demographic history of A. nanchuanensis revealed the existence of three genetic bottleneck events. Moreover, abundant genetic loads (48.56% protein-coding genes) were identified in Artocarpus nanchuanensis, especially in genes related to early development and immune function of plants. The predication analysis of suitable habitat areas indicated that the past suitable habitat areas shifted from the north to the south due to global temperature decline. However, in the future, the actual distribution area of A. nanchuanensis will still maintain high suitability. Discussion Based on total analyses, we divided the populations of A. nanchuanensis into four conservation units and proposed a number of practical management suggestions for each conservation unit. Overall, our study provides meaningful guidance for the protection of A. nanchuanensis and important insight into conservation genomics research.
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Affiliation(s)
- Changying Xia
- Center for Biodiversity Conservation and Utilization, School of Life Sciences, Southwest University, Chongqing, China
| | - Youwei Zuo
- Center for Biodiversity Conservation and Utilization, School of Life Sciences, Southwest University, Chongqing, China
| | - Tiantian Xue
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Ming Kang
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - Huan Zhang
- Center for Biodiversity Conservation and Utilization, School of Life Sciences, Southwest University, Chongqing, China
| | - Xiaoxia Zhang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Binru Wang
- Center for Biodiversity Conservation and Utilization, School of Life Sciences, Southwest University, Chongqing, China
| | - Jiabin Zhang
- Center for Biodiversity Conservation and Utilization, School of Life Sciences, Southwest University, Chongqing, China
| | - Hongping Deng
- Center for Biodiversity Conservation and Utilization, School of Life Sciences, Southwest University, Chongqing, China
- Low Carbon and Ecological Environment Protection Research Center, Chongqing Academy of Science and Technology, Chongqing, China
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Prunier JG, Chevalier M, Raffard A, Loot G, Poulet N, Blanchet S. Genetic erosion reduces biomass temporal stability in wild fish populations. Nat Commun 2023; 14:4362. [PMID: 37474616 PMCID: PMC10359329 DOI: 10.1038/s41467-023-40104-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Accepted: 07/11/2023] [Indexed: 07/22/2023] Open
Abstract
Genetic diversity sustains species adaptation. However, it may also support key ecosystems functions and services, for example biomass production, that can be altered by the worldwide loss of genetic diversity. Despite extensive experimental evidence, there have been few attempts to empirically test whether genetic diversity actually promotes biomass and biomass stability in wild populations. Here, using long-term demographic wild fish data from two large river basins in southwestern France, we demonstrate through causal modeling analyses that populations with high genetic diversity do not reach higher biomasses than populations with low genetic diversity. Nonetheless, populations with high genetic diversity have much more stable biomasses over recent decades than populations having suffered from genetic erosion, which has implications for the provision of ecosystem services and the risk of population extinction. Our results strengthen the importance of adopting prominent environmental policies to conserve this important biodiversity facet.
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Affiliation(s)
- Jérôme G Prunier
- Centre National de la Recherche Scientifique (CNRS), Université Paul Sabatier (UPS); Station d'Ecologie Théorique et Expérimentale, UAR 2029, F-09200, Moulis, France.
| | - Mathieu Chevalier
- Department of Ecology and Evolution, University of Lausanne, Biophore, CH-1015, Lausanne, Switzerland
- Ifremer, DYNECO, F-29280, Plouzané, France
| | - Allan Raffard
- Centre National de la Recherche Scientifique (CNRS), Université Paul Sabatier (UPS); Station d'Ecologie Théorique et Expérimentale, UAR 2029, F-09200, Moulis, France
- Univ. Savoie Mont Blanc, INRAE, CARRTEL, 74200, Thonon-les-Bains, France
| | - Géraldine Loot
- CNRS, UPS, École Nationale de Formation Agronomique (ENFA), UMR 5174 EDB (Laboratoire Évolution & Diversité Biologique), 118 route de Narbonne, F-31062, Toulouse, cedex, 4, France
| | - Nicolas Poulet
- Pôle écohydraulique AFB-IMT, allée du Pr Camille Soula, 31400, Toulouse, France
| | - Simon Blanchet
- Centre National de la Recherche Scientifique (CNRS), Université Paul Sabatier (UPS); Station d'Ecologie Théorique et Expérimentale, UAR 2029, F-09200, Moulis, France.
- CNRS, UPS, École Nationale de Formation Agronomique (ENFA), UMR 5174 EDB (Laboratoire Évolution & Diversité Biologique), 118 route de Narbonne, F-31062, Toulouse, cedex, 4, France.
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Lehtinen RM. Empirical Evidence for the Rescue Effect from a Natural Microcosm. Animals (Basel) 2023; 13:1907. [PMID: 37370418 DOI: 10.3390/ani13121907] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Revised: 05/27/2023] [Accepted: 06/05/2023] [Indexed: 06/29/2023] Open
Abstract
Ecological theory predicts that populations which receive immigrants are less vulnerable to extinction than those that do not receive immigrants (the "rescue effect"). A parallel but opposite process may also exist, where emigration increases the risk of local extinction (the "abandon-ship effect"). Using a natural microcosm of plant-specialist frogs from Madagascar, empirical evidence for both processes is provided. Populations receiving immigrants were less extinction-prone than those without immigration, and those populations losing individuals through emigration were more extinction-prone than those in which no emigration occurred. The number of immigrants and emigrants was also elevated and depressed (respectively) in patches that did not go extinct. These data provide some of the first definitive empirical evidence for the rescue effect and provide suggestive initial data on the abandon-ship effect. Both of these processes may be important to understanding the dynamics of populations.
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Affiliation(s)
- Richard M Lehtinen
- Division of Reptiles and Amphibians, University of Michigan Museum of Zoology, Ann Arbor, MI 48109, USA
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Lloyd‐Jones LR, Brien ML, Feutry P, Lawrence E, Beri P, Booth S, Coulson S, Baylis SM, Villiers K, Taplin LE, Westcott DA. Implications of past and present genetic connectivity for management of the saltwater crocodile ( Crocodylus porosus). Evol Appl 2023; 16:911-935. [PMID: 37124084 PMCID: PMC10130557 DOI: 10.1111/eva.13545] [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: 08/17/2022] [Revised: 02/17/2023] [Accepted: 03/16/2023] [Indexed: 04/03/2023] Open
Abstract
Effective management of protected species requires information on appropriate evolutionary and geographic population boundaries and knowledge of how the physical environment and life-history traits combine to shape the population structure and connectivity. Saltwater crocodiles (Crocodylus porosus) are the largest and most widely distributed of living crocodilians, extending from Sri Lanka to Southeast Asia and down to northern Australia. Given the long-distance movement capabilities reported for C. porosus, management units are hypothesised to be highly connected by migration. However, the magnitude, scale, and consistency of connection across managed populations are not fully understood. Here we used an efficient genotyping method that combines DArTseq and sequence capture to survey≈ 3000 high-quality genome-wide single nucleotide polymorphisms from 1176 C. porosus sampled across nearly the entire range of the species in Queensland, Australia. We investigated historical and present-day connectivity patterns using fixation and diversity indices coupled with clustering methods and the spatial distribution of kin pairs. We inferred kinship using forward simulation coupled with a kinship estimation method that is robust to unspecified population structure. The results demonstrated that the C. porosus population has substantial genetic structure with six broad populations correlated with geographical location. The rate of gene flow was highly correlated with spatial distance, with greater differentiation along the east coast compared to the west. Kinship analyses revealed evidence of reproductive philopatry and limited dispersal, with approximately 90% of reported first and second-degree relatives showing a pairwise distance of <50 km between sampling locations. Given the limited dispersal, lack of suitable habitat, low densities of crocodiles and the high proportion of immature animals in the population, future management and conservation interventions should be considered at regional and state-wide scales.
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Affiliation(s)
- Luke R. Lloyd‐Jones
- Commonwealth Scientific and Industrial Research OrganisationData61BrisbaneQueensland4072Australia
| | - Matthew L. Brien
- Department of Environment and ScienceQueensland GovernmentCairnsQueensland4870Australia
| | - Pierre Feutry
- Commonwealth Scientific and Industrial Research OrganisationOceans and AtmosphereHobartTasmania7000Australia
| | - Emma Lawrence
- Commonwealth Scientific and Industrial Research OrganisationData61BrisbaneQueensland4072Australia
| | - Paul Beri
- Department of Environment and ScienceQueensland GovernmentCairnsQueensland4870Australia
| | - Simon Booth
- Department of Environment and ScienceQueensland GovernmentCairnsQueensland4870Australia
| | - Steven Coulson
- Department of Environment and ScienceQueensland GovernmentCairnsQueensland4870Australia
| | - Shane M. Baylis
- Commonwealth Scientific and Industrial Research OrganisationOceans and AtmosphereHobartTasmania7000Australia
| | - Kira Villiers
- Commonwealth Scientific and Industrial Research OrganisationData61BrisbaneQueensland4072Australia
| | - Laurence E. Taplin
- Department of Environment and ScienceQueensland GovernmentCairnsQueensland4870Australia
| | - David A. Westcott
- Commonwealth Scientific and Industrial Research OrganisationLand and WaterAthertonQueensland4883Australia
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Martínez-Gil H, Sánchez-Montes G, Montes-Gavilán P, Ugarte G, Martínez-Solano Í. Fine-scale functional connectivity of two syntopic pond-breeding amphibians with contrasting life-history traits: an integrative assessment of direct and indirect estimates of dispersal. CONSERV GENET 2023. [DOI: 10.1007/s10592-023-01506-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/27/2023]
Abstract
AbstractAssessing patterns of functional connectivity among amphibian demes is crucial to unravel their population dynamics and prevent their isolation and eventual extinction. Integrative studies based on direct (capture-mark-recapture) and indirect (genetic) estimates of dispersal provide robust, biologically realistic inferences on population structure and connectivity, with applications for conservation efforts. We focused on two pond-breeding amphibians with contrasting life-history traits: the short-lived, semi-arboreal Hyla molleri and the long-lived, fossorial Pelobates cultripes. We PIT-tagged 2150 individuals of both species in two ponds (Laguna and Gravera, separated by 700 m) and monitored them from 2009 to 2021 to document the frequency and spatial extent of dispersal events. In addition, we genotyped individuals from these and two additional breeding populations at a maximum distance of 5 km with 15–16 microsatellites to characterize fine-scale patterns of genetic structure. We detected dispersal events connecting Laguna and Gravera in both species, albeit at low frequencies (4.8% and 7.7% of recaptured individuals of H. molleri and P. cultripes, respectively). However, both species were capable of covering long distances, with individual accumulated displacements up to 3.5 km (Hyla) and 1.8 km (Pelobates). Breeding populations > 2 km apart were genetically differentiated, indicating lower connectivity at this spatial scale. Estimates of pairwise migration rates differed between species and were asymmetrical, with different ponds representing “source” populations contributing more migrants to other populations in each species. We discuss the role of differences in life history traits and ecological preferences in shaping population dynamics in the two species and highlight management implications of our results.
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Recent Changes in Genetic Diversity, Structure, and Gene Flow in a Passerine Experiencing a Rapid Population Decline, the Dupont’s Lark (Chersophilus duponti). DIVERSITY 2022. [DOI: 10.3390/d14121120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Monitoring temporal dynamics in genetic diversity is of great importance for conservation, especially for threatened species that are suffering a rapid population decline and increased fragmentation. Here, we investigate temporal variation in genetic diversity, structure, and gene flow in the Dupont’s lark (Chersophilus duponti) across most of its range. This species shows increasing levels of population fragmentation, substantial population declines, and severe range contraction, so temporal losses of genetic diversity, increasing differentiation, and decreasing gene flow are expected when comparing present day data with previous situations. To address this, we resampled sites (nine regions in two countries) after 12–15 years (five-to-seven generations) and assessed changes in genetic parameters using 11 microsatellite markers. We found no substantial loss in genetic diversity over time at the species level, but we detected considerable variation among regions in the amount of allelic diversity and heterozygosity lost over time. Temporal variation in allele frequencies (common, rare, and private alleles), and changes in genetic differentiation and gene flow over time suggest a major role of connectivity for the stability of the overall metapopulation. Our results agree with the hypothesis that connectivity rescues genetic diversity via immigration and gene flow. However, evidence of recent genetic bottleneck and the substantial changes detected in some regions are clear signs of genetic erosion and may be signalling a rapid decline of the populations. Urgent actions must be carried out to stop and reverse human impacts on this threatened lark and its habitat.
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Beet CR, Hogg ID, Cary SC, McDonald IR, Sinclair BJ. The Resilience of Polar Collembola (Springtails) in a Changing Climate. CURRENT RESEARCH IN INSECT SCIENCE 2022; 2:100046. [PMID: 36683955 PMCID: PMC9846479 DOI: 10.1016/j.cris.2022.100046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 08/30/2022] [Accepted: 09/08/2022] [Indexed: 06/17/2023]
Abstract
Assessing the resilience of polar biota to climate change is essential for predicting the effects of changing environmental conditions for ecosystems. Collembola are abundant in terrestrial polar ecosystems and are integral to food-webs and soil nutrient cycling. Using available literature, we consider resistance (genetic diversity; behavioural avoidance and physiological tolerances; biotic interactions) and recovery potential for polar Collembola. Polar Collembola have high levels of genetic diversity, considerable capacity for behavioural avoidance, wide thermal tolerance ranges, physiological plasticity, generalist-opportunistic feeding habits and broad ecological niches. The biggest threats to the ongoing resistance of polar Collembola are increasing levels of dispersal (gene flow), increased mean and extreme temperatures, drought, changing biotic interactions, and the arrival and spread of invasive species. If resistance capacities are insufficient, numerous studies have highlighted that while some species can recover from disturbances quickly, complete community-level recovery is exceedingly slow. Species dwelling deeper in the soil profile may be less able to resist climate change and may not recover in ecologically realistic timescales given the current rate of climate change. Ultimately, diverse communities are more likely to have species or populations that are able to resist or recover from disturbances. While much of the Arctic has comparatively high levels of diversity and phenotypic plasticity; areas of Antarctica have extremely low levels of diversity and are potentially much more vulnerable to climate change.
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Affiliation(s)
- Clare R. Beet
- Te Aka Mātuatua - School of Science, Te Whare Wānanga o Waikato - University of Waikato, Hamilton, New Zealand
- International Centre for Terrestrial Antarctic Research, University of Waikato, Hamilton, New Zealand
| | - Ian D. Hogg
- Te Aka Mātuatua - School of Science, Te Whare Wānanga o Waikato - University of Waikato, Hamilton, New Zealand
- Canadian High Arctic Research Station, Polar Knowledge Canada, Cambridge Bay, Nunavut, Canada
| | - S. Craig Cary
- Te Aka Mātuatua - School of Science, Te Whare Wānanga o Waikato - University of Waikato, Hamilton, New Zealand
- International Centre for Terrestrial Antarctic Research, University of Waikato, Hamilton, New Zealand
| | - Ian R. McDonald
- Te Aka Mātuatua - School of Science, Te Whare Wānanga o Waikato - University of Waikato, Hamilton, New Zealand
- International Centre for Terrestrial Antarctic Research, University of Waikato, Hamilton, New Zealand
| | - Brent J. Sinclair
- Department of Biology, University of Western Ontario, London, ON, Canada
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von Thaden A, Cocchiararo B, Mueller SA, Reiners TE, Reinert K, Tuchscherer I, Janke A, Nowak C. Informing conservation strategies with museum genomics: Long-term effects of past anthropogenic persecution on the elusive European wildcat. Ecol Evol 2021; 11:17932-17951. [PMID: 35003648 PMCID: PMC8717334 DOI: 10.1002/ece3.8385] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Revised: 11/04/2021] [Accepted: 11/09/2021] [Indexed: 12/13/2022] Open
Abstract
Like many carnivore species, European wildcats (Felis silvestris) have suffered severe anthropogenic population declines in the past, resulting in a strong population bottleneck at the beginning of the 20th century. In Germany, the species has managed to survive its near extinction in small isolated areas and is currently recolonizing former habitats owing to legal protection and concerted conservation efforts. Here, we SNP-genotyped and mtDNA-sequenced 56 historical and 650 contemporary samples to assess the impact of massive persecution on genetic diversity, population structure, and hybridization dynamics of wildcats. Spatiotemporal analyses suggest that the presumed postglacial differentiation between two genetically distinct metapopulations in Germany is in fact the result of the anthropogenic bottleneck followed by re-expansion from few secluded refugia. We found that, despite the bottleneck, populations experienced no severe genetic erosion, nor suffered from elevated inbreeding or showed signs of increased hybridization with domestic cats. Our findings have significant implications for current wildcat conservation strategies, as the data analyses show that the two presently recognized wildcat population clusters should be treated as a single conservation unit. Although current populations appear under no imminent threat from genetic factors, fostering connectivity through the implementation of forest corridors will facilitate the preservation of genetic diversity and promote long-term viability. The present study documents how museum collections can be used as essential resource for assessing long-term anthropogenic effects on natural populations, for example, regarding population structure and the delineation of appropriate conservation units, potentially informing todays' species conservation.
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Affiliation(s)
- Alina von Thaden
- Conservation Genetics GroupSenckenberg Research Institute and Natural History Museum FrankfurtGelnhausenGermany
- Institute of Ecology, Evolution & DiversityJohann Wolfgang Goethe‐University, BiologicumFrankfurt am MainGermany
| | - Berardino Cocchiararo
- Conservation Genetics GroupSenckenberg Research Institute and Natural History Museum FrankfurtGelnhausenGermany
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE‐TBG)Frankfurt am MainGermany
| | - Sarah Ashley Mueller
- Conservation Genetics GroupSenckenberg Research Institute and Natural History Museum FrankfurtGelnhausenGermany
- Institute of Ecology, Evolution & DiversityJohann Wolfgang Goethe‐University, BiologicumFrankfurt am MainGermany
| | - Tobias Erik Reiners
- Conservation Genetics GroupSenckenberg Research Institute and Natural History Museum FrankfurtGelnhausenGermany
| | - Katharina Reinert
- Conservation Genetics GroupSenckenberg Research Institute and Natural History Museum FrankfurtGelnhausenGermany
- Department of Physical GeographyJohann Wolfgang Goethe‐UniversityFrankfurt am MainGermany
| | - Iris Tuchscherer
- Conservation Genetics GroupSenckenberg Research Institute and Natural History Museum FrankfurtGelnhausenGermany
- Institute of Ecology, Evolution & DiversityJohann Wolfgang Goethe‐University, BiologicumFrankfurt am MainGermany
| | - Axel Janke
- Institute of Ecology, Evolution & DiversityJohann Wolfgang Goethe‐University, BiologicumFrankfurt am MainGermany
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE‐TBG)Frankfurt am MainGermany
- Senckenberg Biodiversity and Climate Research CentreSenckenberg Gesellschaft für NaturforschungFrankfurt am MainGermany
| | - Carsten Nowak
- Conservation Genetics GroupSenckenberg Research Institute and Natural History Museum FrankfurtGelnhausenGermany
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE‐TBG)Frankfurt am MainGermany
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Andrews AJ, Puncher GN, Bernal-Casasola D, Di Natale A, Massari F, Onar V, Toker NY, Hanke A, Pavey SA, Savojardo C, Martelli PL, Casadio R, Cilli E, Morales-Muñiz A, Mantovani B, Tinti F, Cariani A. Ancient DNA SNP-panel data suggests stability in bluefin tuna genetic diversity despite centuries of fluctuating catches in the eastern Atlantic and Mediterranean. Sci Rep 2021; 11:20744. [PMID: 34671077 PMCID: PMC8528830 DOI: 10.1038/s41598-021-99708-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Accepted: 09/25/2021] [Indexed: 11/10/2022] Open
Abstract
Atlantic bluefin tuna (Thunnus thynnus; BFT) abundance was depleted in the late 20th and early 21st century due to overfishing. Historical catch records further indicate that the abundance of BFT in the Mediterranean has been fluctuating since at least the 16th century. Here we build upon previous work on ancient DNA of BFT in the Mediterranean by comparing contemporary (2009–2012) specimens with archival (1911–1926) and archaeological (2nd century BCE–15th century CE) specimens that represent population states prior to these two major periods of exploitation, respectively. We successfully genotyped and analysed 259 contemporary and 123 historical (91 archival and 32 archaeological) specimens at 92 SNP loci that were selected for their ability to differentiate contemporary populations or their association with core biological functions. We found no evidence of genetic bottlenecks, inbreeding or population restructuring between temporal sample groups that might explain what has driven catch fluctuations since the 16th century. We also detected a putative adaptive response, involving the cytoskeletal protein synemin which may be related to muscle stress. However, these results require further investigation with more extensive genome-wide data to rule out demographic changes due to overfishing, and other natural and anthropogenic factors, in addition to elucidating the adaptive drivers related to these.
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Affiliation(s)
- Adam J Andrews
- Department of Biological, Geological and Environmental Sciences, University of Bologna, Ravenna, Italy. .,Department of Cultural Heritage, University of Bologna, Ravenna, Italy.
| | - Gregory N Puncher
- Department of Biological, Geological and Environmental Sciences, University of Bologna, Ravenna, Italy. .,Department of Biological Sciences, Canadian Rivers Institute, University of New Brunswick, Saint John, NB, Canada.
| | - Darío Bernal-Casasola
- Department of History, Geography and Philosophy, Faculty of Philosophy and Letters, University of Cádiz, Cádiz, Spain
| | | | - Francesco Massari
- Department of Biological, Geological and Environmental Sciences, University of Bologna, Ravenna, Italy
| | - Vedat Onar
- Osteoarcheology Practice and Research Centre and Faculty of Veterinary Medicine, Istanbul University-Cerrahpaşa, Avcılar, Istanbul, Turkey
| | - Nezir Yaşar Toker
- Osteoarcheology Practice and Research Centre and Faculty of Veterinary Medicine, Istanbul University-Cerrahpaşa, Avcılar, Istanbul, Turkey
| | - Alex Hanke
- St. Andrews Biological Station, Fisheries and Oceans Canada, St. Andrews, NB, Canada
| | - Scott A Pavey
- Department of Biological Sciences, Canadian Rivers Institute, University of New Brunswick, Saint John, NB, Canada
| | | | | | - Rita Casadio
- Biocomputing Group, University of Bologna, Bologna, Italy
| | - Elisabetta Cilli
- Department of Cultural Heritage, University of Bologna, Ravenna, Italy
| | | | - Barbara Mantovani
- Department of Biological, Geological and Environmental Sciences, University of Bologna, Bologna, Italy
| | - Fausto Tinti
- Department of Biological, Geological and Environmental Sciences, University of Bologna, Ravenna, Italy
| | - Alessia Cariani
- Department of Biological, Geological and Environmental Sciences, University of Bologna, Ravenna, Italy
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Ma H, Liu Y, Liu D, Sun W, Liu X, Wan Y, Zhang X, Zhang R, Yun Q, Wang J, Li Z, Ma Y. Chromosome-level genome assembly and population genetic analysis of a critically endangered rhododendron provide insights into its conservation. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 107:1533-1545. [PMID: 34189793 DOI: 10.1111/tpj.15399] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Accepted: 06/23/2021] [Indexed: 05/25/2023]
Abstract
Rhododendrons are woody plants, famous throughout the world as having high horticultural value. However, many wild species are currently threatened with extinction. Here, we report for the first time a high-quality, chromosome-level genome of Rhododendron griersonianum, which has contributed to approximately 10% of all horticultural rhododendron varieties but which in its wild form has been evaluated as critically endangered. The final genome assembly, which has a contig N50 size of approximately 34 M and a total length of 677 M, is the highest-quality genome sequenced within the genus to date, in part due to its low heterozygosity (0.18%). Identified repeats constitute approximately 57% of the genome, and 38 280 protein-coding genes were predicted with high support. We further resequenced 31 individuals of R. griersonianum as well as 30 individuals of its widespread relative R. delavayi, and performed additional conservation genomic analysis. The results showed that R. griersonianum had lower genetic diversity (θ = 2.58e-3; π = 1.94e-3) when compared not only to R. delavayi (θ = 11.61e-3, π = 12.97e-3), but also to most other woody plants. Furthermore, three severe genetic bottlenecks were detected using both the Stairway plot and fastsimcoal2 analysis, which are thought to have occurred in the late Middle Pleistocene and the Last Glacial Maximum (LGM) period. After these bottlenecks, R. griersonianum recovered and maintained a constant effective population size (>25 000) until now. Intriguingly, R. griersonianum has accumulated significantly more deleterious mutations in the homozygous state than R. delavayi, and several deleterious mutations (e.g., in genes involved in the response to heat stress) are likely to have harmed the adaptation of this plant to its surroundings. This high-quality, chromosome-level genome and the population genomic analysis of the critically endangered R. griersonianum will provide an invaluable resource as well as insights for future study in this species to facilitate conservation and in the genus Rhododendron in general.
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Affiliation(s)
- Hong Ma
- Research Institute of Resources Insects, Chinese Academy of Forestry, Kunming, 650233, China
| | - Yongbo Liu
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing, 100012, China
| | - Detuan Liu
- Yunnan Key Laboratory for Integrative Conservation of Plant Species with Extremely Small Populations, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
| | - Weibang Sun
- Yunnan Key Laboratory for Integrative Conservation of Plant Species with Extremely Small Populations, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
| | - Xiongfang Liu
- Research Institute of Resources Insects, Chinese Academy of Forestry, Kunming, 650233, China
| | - Youming Wan
- Research Institute of Resources Insects, Chinese Academy of Forestry, Kunming, 650233, China
| | - Xiujiao Zhang
- Research Institute of Resources Insects, Chinese Academy of Forestry, Kunming, 650233, China
| | - Rengang Zhang
- Beijing Ori-Gene Science and Technology Co. Ltd, Beijing, 102206, China
| | - Quanzheng Yun
- Beijing Ori-Gene Science and Technology Co. Ltd, Beijing, 102206, China
| | - Jihua Wang
- The Flower Research Institute, Yunnan Academy of Agricultural Sciences, Kunming, 650205, China
- National Engineering Research Center for Ornamental Horticulture, Kunming, 650205, China
| | - Zhenghong Li
- Research Institute of Resources Insects, Chinese Academy of Forestry, Kunming, 650233, China
| | - Yongpeng Ma
- Yunnan Key Laboratory for Integrative Conservation of Plant Species with Extremely Small Populations, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
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Yousefzadeh H, Raeisi S, Esmailzadeh O, Jalali G, Nasiri M, Walas Ł, Kozlowski G. Genetic Diversity and Structure of Rear Edge Populations of Sorbus aucuparia (Rosaceae) in the Hyrcanian Forest. PLANTS (BASEL, SWITZERLAND) 2021; 10:1471. [PMID: 34371674 PMCID: PMC8309350 DOI: 10.3390/plants10071471] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 06/19/2021] [Accepted: 06/23/2021] [Indexed: 11/16/2022]
Abstract
Sorbus aucuparia (Rosaceae) is a small tree species widely distributed in Eurasia. The Hyrcanian forest is the southernmost distribution limit of this species. Severe habitat degradation and inadequate human interventions have endangered the long-term survival of this species in this region, and it is necessary to develop and apply appropriate management methods to prevent the loss of its genetic diversity. In this study, we used 10 SSR markers in order to evaluate the genetic diversity of this taxon. Leaf samples were collected from five known populations of S. aucuparia throughout its distribution area in the Hyrcanian forest. Expected heterozygosity ranged from 0.61 (ASH) to 0.73, and according to the M-ratio, all populations showed a significant reduction in effective population size, indicating a genetic bottleneck. Global FST was not statistically significant and attained the same values with and without excluding null alleles (ENA) correction (FST = 0.12). Bayesian analysis performed with STRUCTURE defined two genetic clusters among the five known populations, while the results of discriminant analysis of principal components (DAPC) identified three distinct groups. The average proportion of migrants was 22. In general, the gene flow was asymmetrical, with the biggest differences between immigration and emigration in Barzekoh and Asbehriseh. The Mantel test showed that there was no significant correlation between genetic distance (FST) and geographic distance in S. aucuparia. The best pathway for theoretical gene flow is located across the coast of the Caspian Sea and significant spatial autocorrelation was observed in only one population. In order to reduce the extinction risk of very small and scattered populations of S. aucuparia in the Hyrcanian forest, it is very important to establish and/or enhance the connectivity through habitat restoration or genetic exchange.
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Affiliation(s)
- Hamed Yousefzadeh
- Department of Environmental Science, Faculty of Natural Resources, Tarbiat Modares University (TMU), Mazandaran 14115-111, Iran
| | - Shahla Raeisi
- Department of Forest Science and Engineering, Faculty of Natural Resources, Tarbiat Modares University (TMU), Mazandaran 14115-111, Iran; (S.R.); (O.E.); (G.J.)
| | - Omid Esmailzadeh
- Department of Forest Science and Engineering, Faculty of Natural Resources, Tarbiat Modares University (TMU), Mazandaran 14115-111, Iran; (S.R.); (O.E.); (G.J.)
| | - Gholamali Jalali
- Department of Forest Science and Engineering, Faculty of Natural Resources, Tarbiat Modares University (TMU), Mazandaran 14115-111, Iran; (S.R.); (O.E.); (G.J.)
| | - Malek Nasiri
- Department of Forestry, Faculty of Natural Resources, Tehran University (TU), Tehran 31587-77871, Iran;
| | - Łukasz Walas
- Department of Biogeography and Systematics, Institute of Dendrology, Polish Academy of Sciences, Parkowa 5, PL-62-035 Kornik, Poland;
| | - Gregor Kozlowski
- Department of Biology and Botanic Garden, University of Fribourg, Chemin du Musée 10, CH-1700 Fribourg, Switzerland;
- Natural History Museum Fribourg, Chemin du Musée 6, CH-1700 Fribourg, Switzerland
- Eastern China Conservation Centre for Wild Endangered Plant Resources, Shanghai Chenshan Botanical Garden, 3888 Chenhua Road, Songjiang, Shanghai 201602, China
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Filazzola A, Matter SF, MacIvor JS. The direct and indirect effects of extreme climate events on insects. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 769:145161. [PMID: 33486167 DOI: 10.1016/j.scitotenv.2021.145161] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Revised: 01/08/2021] [Accepted: 01/09/2021] [Indexed: 06/12/2023]
Abstract
Extreme climate events are predicted to increase in the future, which will have significant effects on insect biodiversity. Research into this area has been rapidly expanding, but knowledge gaps still exist. We conducted a review of the literature to provide a synthesis of extreme climate events on insects and identify future areas of research. In our review, we asked the following questions: 1) What are the direct and indirect mechanisms that extreme climate events affect individual insects? 2) What are the effects of extreme climate events on insect populations and demography? 3) What are the implications of the extreme climate events effects on insect communities? Drought was among the most frequently described type of extreme climate event affecting insects, as well as the effects of temperature extremes and extreme temperature variation. Our review explores the factors that determine the sensitivity or resilience to climate extremes for individuals, populations, and communities. We also identify areas of future research to better understand the role of extreme climate events on insects including effects on non-trophic interactions, alteration of population dynamics, and mediation of the functional the trait set of communities. Many insect species are under threat from global change and extreme climate events are a contributing factor. Biologists and policy makers should consider the role of extreme events in their work to mitigate the loss of biodiversity and delivery of ecosystem services by insects.
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Affiliation(s)
- Alessandro Filazzola
- Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada; Department of Biological Sciences, University of Toronto Scarborough, 1265 Military Trail, Canada.
| | - Stephen F Matter
- Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada; Department of Biological Sciences, University of Cincinnati, Cincinnati, OH 45221, United States of America
| | - J Scott MacIvor
- Department of Biological Sciences, University of Toronto Scarborough, 1265 Military Trail, Canada
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18
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Hardy BM, Pope KL, Latch EK. Genomic signatures of demographic declines in an imperiled amphibian inform conservation action. Anim Conserv 2021. [DOI: 10.1111/acv.12695] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- B. M. Hardy
- Behavioral and Molecular Ecology Research Group Department of Biological Sciences University of Wisconsin‐Milwaukee Milwaukee WI USA
- Graduate Degree Program in Ecology Colorado State University Fort Collins CO USA
| | - K. L. Pope
- United States Forest Service Pacific Southwest Research Station Arcata CA USA
| | - E. K. Latch
- Behavioral and Molecular Ecology Research Group Department of Biological Sciences University of Wisconsin‐Milwaukee Milwaukee WI USA
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Wang X, Bernhardsson C, Ingvarsson PK. Demography and Natural Selection Have Shaped Genetic Variation in the Widely Distributed Conifer Norway Spruce (Picea abies). Genome Biol Evol 2020; 12:3803-3817. [PMID: 31958121 PMCID: PMC7046165 DOI: 10.1093/gbe/evaa005] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/14/2020] [Indexed: 12/13/2022] Open
Abstract
Under the neutral theory, species with larger effective population size are expected to harbor higher genetic diversity. However, across a wide variety of organisms, the range of genetic diversity is orders of magnitude more narrow than the range of effective population size. This observation has become known as Lewontin’s paradox and although aspects of this phenomenon have been extensively studied, the underlying causes for the paradox remain unclear. Norway spruce (Picea abies) is a widely distributed conifer species across the northern hemisphere, and it consequently plays a major role in European forestry. Here, we use whole-genome resequencing data from 35 individuals to perform population genomic analyses in P. abies in an effort to understand what drives genome-wide patterns of variation in this species. Despite having a very wide geographic distribution and an corresponding enormous current population size, our analyses find that genetic diversity of P. abies is low across a number of populations (π = 0.0049 in Central-Europe, π = 0.0063 in Sweden-Norway, π = 0.0063 in Finland). To assess the reasons for the low levels of genetic diversity, we infer the demographic history of the species and find that it is characterized by several reoccurring bottlenecks with concomitant decreases in effective population size can, at least partly, provide an explanation for low polymorphism we observe in P. abies. Further analyses suggest that recurrent natural selection, both purifying and positive selection, can also contribute to the loss of genetic diversity in Norway spruce by reducing genetic diversity at linked sites. Finally, the overall low mutation rates seen in conifers can also help explain the low genetic diversity maintained in Norway spruce.
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Affiliation(s)
- Xi Wang
- Umeå Plant Science Centre, Department of Ecology and Environmental Science, Umeå University, Sweden.,Linnean Centre for Plant Biology, Department of Plant Biology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Carolina Bernhardsson
- Umeå Plant Science Centre, Department of Ecology and Environmental Science, Umeå University, Sweden.,Linnean Centre for Plant Biology, Department of Plant Biology, Swedish University of Agricultural Sciences, Uppsala, Sweden.,Department of Organismal Biology, Uppsala University, Uppsala, Sweden
| | - Pär K Ingvarsson
- Linnean Centre for Plant Biology, Department of Plant Biology, Swedish University of Agricultural Sciences, Uppsala, Sweden
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Transcribing molecular and climatic data into conservation management for the Himalayan endangered species, Taxus contorta (Griff.). CONSERV GENET 2020. [DOI: 10.1007/s10592-020-01319-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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21
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Minter M, Dasmahapatra KK, Thomas CD, Morecroft MD, Tonhasca A, Schmitt T, Siozios S, Hill JK. Past, current, and potential future distributions of unique genetic diversity in a cold-adapted mountain butterfly. Ecol Evol 2020; 10:11155-11168. [PMID: 33144956 PMCID: PMC7593187 DOI: 10.1002/ece3.6755] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Revised: 07/22/2020] [Accepted: 07/29/2020] [Indexed: 11/09/2022] Open
Abstract
AIM Climatic changes throughout the Pleistocene have strongly modified species distributions. We examine how these range shifts have affected the genetic diversity of a montane butterfly species and whether the genetic diversity in the extant populations is threatened by future climate change. LOCATION Europe. TAXON Erebia epiphron Lepidoptera: Nymphalidae. METHODS We analyzed mtDNA to map current genetic diversity and differentiation of E. epiphron across Europe to identify population refugia and postglacial range shifts. We used species distribution modeling (SDM) to hindcast distributions over the last 21,000 years to identify source locations of extant populations and to project distributions into the future (2070) to predict potential losses in genetic diversity. RESULTS We found substantial genetic diversity unique to specific regions within Europe (total number of haplotypes = 31, number of unique haplotypes = 27, H d = 0.9). Genetic data and SDM hindcasting suggest long-term separation and survival of discrete populations. Particularly, high rates of unique diversity in postglacially colonized sites in England (H d = 0.64) suggest this population was colonized from a now extinct cryptic refugium. Under future climate change, SDMs predict loss of climate suitability for E. epiphron, particularly at lower elevations (<1,000 meters above sea level) equating to 1 to 12 unique haplotypes being at risk under climate scenarios projecting 1°C and 2-3°C increases respectfully in global temperature by 2070. MAIN CONCLUSIONS Our results suggest that historical range expansion and retraction processes by a cold-adapted mountain species caused diversification between populations, resulting in unique genetic diversity which may be at risk if distributions of cold-adapted species shrink in future. Assisted colonizations of individuals from at-risk populations into climatically suitable unoccupied habitat might help conserve unique genetic diversity, and translocations into remaining populations might increase their genetic diversity and hence their ability to adapt to future climate change.
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Affiliation(s)
- Melissa Minter
- Leverhulme Centre for Anthropocene BiodiversityDepartment of BiologyUniversity of YorkYorkUK
| | - Kanchon K. Dasmahapatra
- Leverhulme Centre for Anthropocene BiodiversityDepartment of BiologyUniversity of YorkYorkUK
| | - Chris D. Thomas
- Leverhulme Centre for Anthropocene BiodiversityDepartment of BiologyUniversity of YorkYorkUK
| | | | | | - Thomas Schmitt
- Senckenberg Deutsches Entomologisches InstitutMünchebergGermany
| | - Stefanos Siozios
- Institute of Integrative BiologyUniversity of LiverpoolLiverpoolUK
| | - Jane K. Hill
- Leverhulme Centre for Anthropocene BiodiversityDepartment of BiologyUniversity of YorkYorkUK
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22
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Coleman MA, Minne AJP, Vranken S, Wernberg T. Genetic tropicalisation following a marine heatwave. Sci Rep 2020; 10:12726. [PMID: 32728196 PMCID: PMC7391769 DOI: 10.1038/s41598-020-69665-w] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Accepted: 07/08/2020] [Indexed: 11/14/2022] Open
Abstract
Extreme events are increasing globally with devastating ecological consequences, but the impacts on underlying genetic diversity and structure are often cryptic and poorly understood, hindering assessment of adaptive capacity and ecosystem vulnerability to future change. Using very rare "before" data we empirically demonstrate that an extreme marine heatwave caused a significant poleward shift in genetic clusters of kelp forests whereby alleles characteristic of cool water were replaced by those that predominated in warm water across 200 km of coastline. This "genetic tropicalisation" was facilitated by significant mortality of kelp and other co-occurring seaweeds within the footprint of the heatwave that opened space for rapid local proliferation of surviving kelp genotypes or dispersal and recruitment of spores from warmer waters. Genetic diversity declined and inbreeding increased in the newly tropicalised site, but these metrics were relative stable elsewhere within the footprint of the heatwave. Thus, extreme events such as marine heatwaves not only lead to significant mortality and population loss but can also drive significant genetic change in natural populations.
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Affiliation(s)
- Melinda A Coleman
- New South Wales Fisheries, National Marine Science Centre, 2 Bay Drive, Coffs Harbour, NSW, 2450, Australia.
- Southern Cross University, National Marine Science Centre, 2 Bay Drive, Coffs Harbour, NSW, 2450, Australia.
- Oceans Institute and School of Biological Sciences, University of Western Australia, 35 Stirling Highway, Crawley, WA, 6009, Australia.
| | - Antoine J P Minne
- Southern Cross University, National Marine Science Centre, 2 Bay Drive, Coffs Harbour, NSW, 2450, Australia
- Oceans Institute and School of Biological Sciences, University of Western Australia, 35 Stirling Highway, Crawley, WA, 6009, Australia
| | - Sofie Vranken
- Oceans Institute and School of Biological Sciences, University of Western Australia, 35 Stirling Highway, Crawley, WA, 6009, Australia
| | - Thomas Wernberg
- Oceans Institute and School of Biological Sciences, University of Western Australia, 35 Stirling Highway, Crawley, WA, 6009, Australia
- Department of Science and Environment, Roskilde University, 4000, Roskilde, Denmark
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23
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Valladares-Gómez A, Celis-Diez JL, Sepúlveda-Rodríguez C, Inostroza-Michael O, Hernández CE, Palma RE. Genetic Diversity, Population Structure, and Migration Scenarios of the Marsupial "Monito del Monte" in South-Central Chile. J Hered 2020; 110:651-661. [PMID: 31420661 DOI: 10.1093/jhered/esz049] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Accepted: 08/06/2019] [Indexed: 01/11/2023] Open
Abstract
In this study, we quantified the 3 pivotal genetic processes (i.e., genetic diversity, spatial genetic structuring, and migration) necessary for a better biological understanding and management of the singular "living-fossil" and near-threatened mouse opossum marsupial Dromiciops gliroides, the "Monito del Monte," in south-central Chile. We used 11 microsatellite loci to genotype 47 individuals distributed on the mainland and northern Chiloé Island. Allelic richness, observed and expected heterozygosity, inbreeding coefficient, and levels of genetic differentiation were estimated. The genetic structure was assessed based on Bayesian clustering methods. In addition, potential migration scenarios were evaluated based on a coalescent theory framework and Bayesian approach to parameter estimations. Microsatellites revealed moderate to high levels of genetic diversity across sampled localities. Moreover, such molecular markers suggested that at least 2 consistent genetic clusters could be identified along the D. gliroides distribution ("Northern" and "Southern" cluster). However, general levels of genetic differentiation observed among localities and between the 2 genetic clusters were relatively low. Migration analyses showed that the most likely routes of migration of D. gliroides occurred 1) from the Southern cluster to the Northern cluster and 2) from the Mainland to Chiloé Island. Our results could represent critical information for future conservation programs and for a recent proposal about the taxonomic status of this unique mouse opossum marsupial.
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Affiliation(s)
- Alejandro Valladares-Gómez
- Laboratorio de Biología Evolutiva, Departamento de Ecología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Casilla 114-D, Santiago, Chile
| | - Juan L Celis-Diez
- Escuela de Agronomía, Pontificia Universidad Católica de Valparaíso, Casilla 4-D, Quillota, Chile
| | - Constanza Sepúlveda-Rodríguez
- Laboratorio de Biología Evolutiva, Departamento de Ecología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Casilla 114-D, Santiago, Chile
| | - Oscar Inostroza-Michael
- Laboratorio de Ecología Evolutiva y Filoinformática, Facultad de Ciencias Naturales y Ocenográficas, Universidad de Concepción, Casilla 160-C, Concepción, Chile
| | - Cristián E Hernández
- Laboratorio de Ecología Evolutiva y Filoinformática, Facultad de Ciencias Naturales y Ocenográficas, Universidad de Concepción, Casilla 160-C, Concepción, Chile
| | - R Eduardo Palma
- Laboratorio de Biología Evolutiva, Departamento de Ecología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Casilla 114-D, Santiago, Chile
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24
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CapellÀ-Marzo B, SÁnchez-Montes G, MartÍnez-Solano I. Contrasting demographic trends and asymmetric migration rates in a spatially structured amphibian population. Integr Zool 2020; 15:482-497. [PMID: 32329558 DOI: 10.1111/1749-4877.12449] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Natural populations often persist at the landscape scale as metapopulations, with breeding units (subpopulations) experiencing temporal extinction and recolonization events. Important parameters to forecast population viability in these systems include the ratio of the effective number of breeders (Nb ) to the total number of adults (Na ) and migration rates among subpopulations. Here, we present the results of a 10-year integrative monitoring program of a metapopulation of the Iberian green frog (Pelophylax perezi) in central Spain. We characterized population dynamics at two main breeding ponds (Gravera and Laguna) using capture-mark-recapture data to estimate Na in each breeding season, and multilocus genotypes to estimate the effective population size (Ne ), Nb , individual breeding success, and migration rates. Both ponds experienced population decline after a dry season, with Gravera subsequently recovering and Laguna suffering a bottleneck associated with genetic impoverishment. In this subpopulation, average allelic richness and private alleles decreased from 2010 (10.87 and 1.67, respectively) to 2018 (8.0 and 0.20). The Nb /Na ratio in Laguna in 2018 was twice as high (0.95) than in Gravera (0.41) or in pre-bottleneck Laguna (0.50), suggesting plasticity or genetic compensation through increased individual breeding success. Migration rates were asymmetric between ponds, with a stronger contribution from Gravera to Laguna (29.9% vs. 16.2% in the opposite direction) that may result in a rescue effect. This study emphasizes the importance of integrative demographic approaches for the monitoring of natural populations based on a better understanding of their spatio-temporal dynamics, which provides valuable information for conservation actions.
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Affiliation(s)
- Berta CapellÀ-Marzo
- Department of Biodiversity and Evolutionary Biology, Museo Nacional de Ciencias Naturales, CSIC, Madrid, Spain
| | - Gregorio SÁnchez-Montes
- Department of Biodiversity and Evolutionary Biology, Museo Nacional de Ciencias Naturales, CSIC, Madrid, Spain
| | - Iñigo MartÍnez-Solano
- Department of Biodiversity and Evolutionary Biology, Museo Nacional de Ciencias Naturales, CSIC, Madrid, Spain
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25
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Gurgel CFD, Camacho O, Minne AJP, Wernberg T, Coleman MA. Marine Heatwave Drives Cryptic Loss of Genetic Diversity in Underwater Forests. Curr Biol 2020; 30:1199-1206.e2. [PMID: 32109397 DOI: 10.1016/j.cub.2020.01.051] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Revised: 11/21/2019] [Accepted: 01/15/2020] [Indexed: 11/19/2022]
Abstract
Extreme events have profound ecological impacts on species and ecosystems, including range contractions and collapse of entire ecosystems. Although theory predicts that extreme events cause loss of genetic diversity, empirical demonstrations are rare, obscuring implications for future adaptive capacity of species and populations. Here, we use rare genetic data from before an extreme event to empirically demonstrate massive and cryptic loss of genetic diversity across ∼800 km of underwater forests following the most severe marine heatwave on record. Two forest-forming seaweeds (Sargassum fallax and Scytothalia dorycarpa) lost ∼30%-65% of average genetic diversity within the 800-km footprint of the heatwave and up to 100% of diversity at some sites. Populations became dominated by single haplotypes that were often not dominant or present prior to the heatwave. Strikingly, these impacts were cryptic and not reflected in measures of forest cover used to determine ecological impact of the heatwave. Our results show that marine heatwaves can drive strong loss of genetic diversity, which may compromise adaptability to future climatic change.
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Affiliation(s)
- Carlos Frederico Deluqui Gurgel
- Centro de Ciências Biológicas, Departamento de Botânica, Laboratório de Ficologia, Universidade Federal de Santa Catarina, Florianópolis, Santa Catarina 99040-900, Brazil; State Herbarium of South Australia, Department for Environment and Natural Resources, SA State Government, GPO Box 1047, Adelaide, SA 5001, Australia.
| | - Olga Camacho
- Centro de Ciências Biológicas, Departamento de Botânica, Laboratório de Ficologia, Universidade Federal de Santa Catarina, Florianópolis, Santa Catarina 99040-900, Brazil
| | - Antoine J P Minne
- Oceans Institute and School of Biological Sciences, University of Western Australia, 35 Stirling Highway, Crawley, WA 6009, Australia; New South Wales Fisheries, National Marine Science Centre, 2 Bay Drive, Coffs Harbour, NSW 2450, Australia
| | - Thomas Wernberg
- Oceans Institute and School of Biological Sciences, University of Western Australia, 35 Stirling Highway, Crawley, WA 6009, Australia
| | - Melinda A Coleman
- Oceans Institute and School of Biological Sciences, University of Western Australia, 35 Stirling Highway, Crawley, WA 6009, Australia; New South Wales Fisheries, National Marine Science Centre, 2 Bay Drive, Coffs Harbour, NSW 2450, Australia; Southern Cross University, National Marine Science Centre, 2 Bay Drive, Coffs Harbour, NSW 2450, Australia.
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26
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Jangjoo M, Matter SF, Roland J, Keyghobadi N. Demographic fluctuations lead to rapid and cyclic shifts in genetic structure among populations of an alpine butterfly, Parnassius smintheus. J Evol Biol 2020; 33:668-681. [PMID: 32052525 DOI: 10.1111/jeb.13603] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Revised: 01/29/2020] [Accepted: 02/03/2020] [Indexed: 12/19/2022]
Abstract
Many populations, especially in insects, fluctuate in size, and periods of particularly low population size can have strong effects on genetic variation. Effects of demographic bottlenecks on genetic diversity of single populations are widely documented. Effects of bottlenecks on genetic structure among multiple interconnected populations are less studied, as are genetic changes across multiple cycles of demographic collapse and recovery. We take advantage of a long-term data set comprising demographic, genetic and movement data from a network of populations of the butterfly, Parnassius smintheus, to examine the effects of fluctuating population size on spatial genetic structure. We build on a previous study that documented increased genetic differentiation and loss of spatial genetic patterns (isolation by distance and by intervening forest cover) after a network-wide bottleneck event. Here, we show that genetic differentiation was reduced again and spatial patterns returned to the system extremely rapidly, within three years (i.e. generations). We also show that a second bottleneck had similar effects to the first, increasing differentiation and erasing spatial patterns. Thus, bottlenecks consistently drive random divergence of allele frequencies among populations in this system, but these effects are rapidly countered by gene flow during demographic recovery. Our results reveal a system in which the relative influence of genetic drift and gene flow continually shift as populations fluctuate in size, leading to cyclic changes in genetic structure. Our results also suggest caution in the interpretation of patterns of spatial genetic structure, and its association with landscape variables, when measured at only a single point in time.
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Affiliation(s)
- Maryam Jangjoo
- Department of Biology, Western University, London, ON, Canada
| | - Stephen F Matter
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH, USA.,Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada
| | - Jens Roland
- Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada
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27
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Phair NL, Toonen RJ, Knapp ISS, von der Heyden S. Anthropogenic pressures negatively impact genomic diversity of the vulnerable seagrass Zostera capensis. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2020; 255:109831. [PMID: 32063316 DOI: 10.1016/j.jenvman.2019.109831] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2019] [Revised: 11/03/2019] [Accepted: 11/05/2019] [Indexed: 06/10/2023]
Abstract
Zostera capensis is a keystone species providing essential ecosystem services to southern African coastal systems. Like most seagrasses globally, Z. capensis is declining and under threat from anthropogenic pressures, and indicators of seagrass health and resilience may be of interest in preventing further declines. As intraspecific diversity is an important component of resilience, we used a pooled RADseq approach to generate genome-wide measures of variation across the entire South African distribution of Z. capensis. Using nucleotide diversity, heterozygosity and allelic richness we tested for associations with fine-scale anthropogenic pressure data compiled by the South African National Biodiversity Assessment using generalised linear models. Increased fishing effort, habitat loss, sand mining and a change in estuary flow dynamics were found to play an important role in decreasing nucleotide diversity and expected heterozygosity, most likely due to the loss of less resilient genotypes as a result of direct physical damage or indirect consequences. As the building block for adaptation, nucleotide diversity is particularly important for resilience. Because of this, as well as the fact that nucleotide diversity displayed the most distinct difference between the west and east coast, and responded most strongly to anthropogenic pressures, we suggest that this may be a useful measure for monitoring genetic or genomic variation. As genomic diversity influences resilience and resistance to disturbances, the remaining diversity in South African seagrass beds urgently needs to be conserved through restoration efforts and careful management of pressures.
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Affiliation(s)
- Nikki Leanne Phair
- Evolutionary Genomics Group, Department of Botany and Zoology, University of Stellenbosch, Private Bag X1, Matieland, South Africa.
| | - Robert John Toonen
- Hawai'i Institute of Marine Biology, School of Ocean and Earth Science and Technology, University of Hawai'i at Mānoa, USA.
| | - Ingrid Sally Sigrid Knapp
- Hawai'i Institute of Marine Biology, School of Ocean and Earth Science and Technology, University of Hawai'i at Mānoa, USA.
| | - Sophie von der Heyden
- Evolutionary Genomics Group, Department of Botany and Zoology, University of Stellenbosch, Private Bag X1, Matieland, South Africa.
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28
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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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29
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Goff J, Yerke C, Keyghobadi N, Matter SF. Dispersing male Parnassius smintheus butterflies are more strongly affected by forest matrix than are females. INSECT SCIENCE 2019; 26:932-944. [PMID: 29575558 DOI: 10.1111/1744-7917.12592] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2017] [Revised: 03/07/2018] [Accepted: 03/14/2018] [Indexed: 06/08/2023]
Abstract
Dispersal is a central aspect of the ecology, evolution, and conservation of species. Predicting how species will respond to changing environmental conditions requires understanding factors that produce variation in dispersal. We explore one source of variation, differences between sexes within a spatial population network. Here, we compare the dispersal patterns of male and female Parnassius smintheus among 18 subpopulations over 8 years using the Virtual Migration Model. Estimated dispersal parameters differed between males and females, particularly with respect to movement through meadow and forest matrix habitat. The estimated dispersal distances of males through forest were much less than for females. Observations of female movement showed that, unlike males, females do not avoid forest nor does forest exert an edge effect. We explored whether further forest encroachment in this system would have different effects for males and females by fitting mean parameter estimates to the landscape configuration seen in 1993 and 2012. Despite differences in their dispersal due presumably to both habitat and physiological differences, males and females are predicted to respond in similar ways to reduced meadow area and increased forest isolation.
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Affiliation(s)
- Jennifer Goff
- Department of Biological Sciences, University of Cincinnati, Cincinnati, Ohio, USA
| | - Catherine Yerke
- Department of Biological Sciences, University of Cincinnati, Cincinnati, Ohio, USA
| | | | - Stephen F Matter
- Department of Biological Sciences, University of Cincinnati, Cincinnati, Ohio, USA
- Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada
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30
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Reynolds LK, Tiling KA, Digiantonio GB, Encomio VG, Morris LJ. Genetic diversity of Halodule wrightii is resistant to large scale dieback: a case study from the Indian River Lagoon. CONSERV GENET 2019. [DOI: 10.1007/s10592-019-01214-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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31
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Robertson EP, Fletcher RJ, Austin JD. The number of breeders explains genetic connectivity in an endangered bird. Mol Ecol 2019; 28:2746-2756. [DOI: 10.1111/mec.15109] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Revised: 04/13/2019] [Accepted: 04/15/2019] [Indexed: 01/25/2023]
Affiliation(s)
- Ellen P. Robertson
- Department of Wildlife Ecology and Conservation University of Florida Gainesville Florida USA
| | - Robert J. Fletcher
- Department of Wildlife Ecology and Conservation University of Florida Gainesville Florida USA
| | - James D. Austin
- Department of Wildlife Ecology and Conservation University of Florida Gainesville Florida USA
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32
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Hauenstein S, Fattebert J, Grüebler MU, Naef-Daenzer B, Pe'er G, Hartig F. Calibrating an individual-based movement model to predict functional connectivity for little owls. ECOLOGICAL APPLICATIONS : A PUBLICATION OF THE ECOLOGICAL SOCIETY OF AMERICA 2019; 29:e01873. [PMID: 30756457 DOI: 10.1002/eap.1873] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Revised: 12/19/2018] [Accepted: 02/01/2019] [Indexed: 06/09/2023]
Abstract
Dispersal is crucial for population viability and thus a popular target for conservation measures. However, the ability of individuals to move between habitat patches is notoriously difficult to estimate. One solution is to quantify functional connectivity via realistic individual-based movement models. Such simulation models, however, are difficult to build and even more difficult to parameterize. Here, we use the example of natal little owl (Athene noctua) dispersal to develop a new analysis chain for the calibration of individual-based dispersal models using a hybrid of statistical parameter estimation and Approximate Bayesian Computation (ABC). Specifically, we use locations of 126 radio-tracked juveniles to first estimate habitat utilization by generalized additive models (GAMs) and the biased random bridges (BRB) method. We then include the estimated parameters in a spatially explicit individual-based model (IBM) of little owl dispersal and calibrate further movement parameters using ABC. To derive efficient summary statistics, we use a new dimension reduction method based on random forest (RF) regression. Finally, we use the calibrated IBM to predict the dispersal potential of little owls from local populations in southwestern Germany to suitable habitat patches in northern Switzerland. We show that pre-calibrating habitat preference parameters while inferring movement behavioral parameters via ABC is a computationally efficient solution to obtain a plausible IBM parameterization. We also find that dimension reduction via RF regression outperforms the widely used least squares regression, which we applied as a benchmark approach. Estimated movement parameters for the individuals reveal plausible inter-individual and inter-sexual differences in movement behavior during natal dispersal. In agreement with a sex-biased dispersal distance in little owls, females show longer individual flights and higher directional persistence. Simulations from the fitted model indicate that a (re)colonization of northern Switzerland is generally possible, albeit restricted. We conclude that the presented analysis chain is a sensible work-flow to assess dispersal connectivity across species and ecosystems. It embraces species- and individual-specific behavioral responses to the landscape and allows likelihood-based calibration, despite an irregular sampling design. Our study highlights existing, yet narrow dispersal corridors, which may require enhancements to facilitate a recolonization of little owl habitat patches in northern Switzerland.
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Affiliation(s)
- Severin Hauenstein
- Department of Biometry and Environmental System Analysis, University of Freiburg, 79106, Freiburg, Germany
| | - Julien Fattebert
- Swiss Ornithological Institute, CH-6204 Sempach, Switzerland
- School of Life Sciences, University of KwaZulu-Natal, 4000 Durban, South Africa
| | | | | | - Guy Pe'er
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, 04103 Leipzig, Germany
- Department of Conservation Biology, UFZ-Helmholtz Centre for Environmental Research, Department of Economics and Department Ecosystem Services, 04318 Leipzig, Germany
- University of Leipzig, 04109 Leipzig, Germany
| | - Florian Hartig
- Department of Biometry and Environmental System Analysis, University of Freiburg, 79106, Freiburg, Germany
- Theoretical Ecology, University of Regensburg, 93053 Regensburg, Germany
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33
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Inglis GD, Duke GM, Goettel MS, Kabaluk JT, Ortega-Polo R. Biogeography and genotypic diversity of Metarhizium brunneum and Metarhizium robertsii in northwestern North American soils. Can J Microbiol 2019; 65:261-281. [DOI: 10.1139/cjm-2018-0297] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The biogeography and genotype diversity of Metarhizium species in northwestern North American soils was examined; 20 ecoregions were sampled, including 58 agricultural and 80 natural habitat subsites, and areas that were glaciated during the Pleistocene epoch. One hundred and twenty-nine isolates of M. brunneum, 26 isolates of M. robertsii, four isolates of M. guizhouense, one isolate of M. flavoviride, and 55 isolates of Beauveria were recovered. Metarhizium and Beauveria species were isolated in diverse ecoregions within the study area, but a trend for increased isolation of Metarhizium species in western regions of the study area was observed. Consistent with this observation, the prevalence of M. brunneum and M. robertsii decreased at higher elevations, and the opposite was true for Beauveria. Both M. brunneum and M. robertsii were more commonly isolated from agricultural and natural habitat subsites, and considerable genotypic diversity was observed in both habitats and within the same subsite. Metarhizium robertsii, but not M. brunneum, was more commonly isolated from nonglaciated locations; however, less diversity and richness was observed for M. brunneum recovered from glaciated versus nonglaciated locations consistent with insular biogeography. The study has implications for microbial control strategies in the region.
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Affiliation(s)
| | - Grant M. Duke
- Agriculture and Agri-Food Canada, Lethbridge, AB T1J 4B1, Canada
| | - Mark S. Goettel
- Agriculture and Agri-Food Canada, Lethbridge, AB T1J 4B1, Canada
| | - J. Todd Kabaluk
- Agriculture and Agri-Food Canada, Agassiz, BC V0M 1A0, Canada
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34
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Genetic heterogeneity of two bioeconomically important kelp species along the Norwegian coast. CONSERV GENET 2019. [DOI: 10.1007/s10592-019-01162-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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35
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Demastes JW, Hafner DJ, Hafner MS, Light JE, Spradling TA. Loss of genetic diversity, recovery and allele surfing in a colonizing parasite, Geomydoecus aurei. Mol Ecol 2019; 28:703-720. [PMID: 30589151 DOI: 10.1111/mec.14997] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2018] [Accepted: 12/17/2018] [Indexed: 02/07/2023]
Abstract
Understanding the genetic consequences of changes in species distributions has wide-ranging implications for predicting future outcomes of climate change, for protecting threatened or endangered populations and for understanding the history that has led to current genetic patterns within species. Herein, we examine the genetic consequences of range expansion over a 25-year period in a parasite (Geomydoecus aurei) that is in the process of expanding its geographic range via invasion of a novel host. By sampling the genetics of 1,935 G. aurei lice taken from 64 host individuals collected over this time period using 12 microsatellite markers, we test hypotheses concerning linear spatial expansion, genetic recovery time and allele surfing. We find evidence of decreasing allelic richness (AR) with increasing distance from the source population, supporting a linear, stepping stone model of spatial expansion that emphasizes the effects of repeated bottleneck events during colonization. We provide evidence of post-bottleneck genetic recovery, with average AR of infrapopulations increasing about 30% over the 225-generation span of time observed directly in this study. Our estimates of recovery rate suggest, however, that recovery has plateaued and that this population may not reach genetic diversity levels of the source population without further immigration from the source population. Finally, we employ a grid-based sampling scheme in the region of ongoing population expansion and provide empirical evidence for the power of allele surfing to impart genetic structure on a population, even under conditions of selective neutrality and in a place that lacks strong barriers to gene flow.
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Affiliation(s)
- James W Demastes
- Department of Biology, University of Northern Iowa, Cedar Falls, Iowa
| | - David J Hafner
- Museum of Southwestern Biology, University of New Mexico, Albuquerque, New Mexico
| | - Mark S Hafner
- Museum of Natural Science and Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana
| | - Jessica E Light
- Department of Wildlife and Fisheries Sciences, Texas A&M University, College Station, Texas
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Spencer PBS, Bain K, Hayward MW, Hillyer M, Friend JAT. Persistence of remnant patches and genetic loss at the distribution periphery in island and mainland populations of the quokka. AUST J ZOOL 2019. [DOI: 10.1071/zo19055] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Understanding the spatial structure of populations is important in developing effective management options for threatened species, and for managing habitat connectivity for metapopulation function, and for demographic and genetic heterogeneity. We used genetic information to investigate the structure of populations of the quokka, Setonix brachyurus, in south-west Western Australia. We hypothesised that movement between known populations would be relatively rare and result in significant genetic structuring. Genetic analyses from 412 adult individuals at 14 nuclear markers (microsatellite) from 33 sampling locations identified structure, diversity and spatial separation of quokkas across their mainland distribution and on two islands. We identified nine inferred (K = 9) populations of quokka that would be otherwise difficult to define with standard ecological techniques. The highest genetic diversity was evident in a large central population of quokka in the southern forest area and genetic diversity was lower at the peripheries of the distribution. The Rottnest Island population contained 70% of the genetic diversity of the mainland populations but the genetic diversity of animals on Bald Island was markedly lower. Populations of quokka in the northern jarrah forest were the only ones to show evidence of recent or long-term population bottlenecking. Of particular interest was the recently identified population at the Muddy Lakes area (the only remaining locality on the Swan Coastal Plain), which was identified as being genetically associated with the southern forest population. Overall, spatial and population cluster analysis showed small insular populations in the northern jarrah forest area, but in the southern forests there appears to be a large panmictic population.
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Mathieu-Bégné E, Loot G, Chevalier M, Paz-Vinas I, Blanchet S. Demographic and genetic collapses in spatially structured populations: insights from a long-term survey in wild fish metapopulations. OIKOS 2018. [DOI: 10.1111/oik.05511] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Eglantine Mathieu-Bégné
- Centre National de la Recherche Scientifique (CNRS), Univ. Paul Sabatier (UPS), Inst. de Recherche pour le Développement (IRD), Ecole Nationale Supérieure de Formation de l'Enseignement Agricole (ENSFEA); UMR5174, Evolution et Diversité Biologique, 118 route de Narbonne; FR-31062 Toulouse France
| | - Géraldine Loot
- Centre National de la Recherche Scientifique (CNRS), Univ. Paul Sabatier (UPS), Inst. de Recherche pour le Développement (IRD), Ecole Nationale Supérieure de Formation de l'Enseignement Agricole (ENSFEA); UMR5174, Evolution et Diversité Biologique, 118 route de Narbonne; FR-31062 Toulouse France
- Inst. Universitaire de France; Paris France
| | - Mathieu Chevalier
- Centre National de la Recherche Scientifique (CNRS), Univ. Paul Sabatier (UPS), Inst. de Recherche pour le Développement (IRD), Ecole Nationale Supérieure de Formation de l'Enseignement Agricole (ENSFEA); UMR5174, Evolution et Diversité Biologique, 118 route de Narbonne; FR-31062 Toulouse France
| | - Ivan Paz-Vinas
- Univ. de Lyon, Ecole Nationale des Travaux Publics de l'Etat (ENTPE), CNRS; UMR5023, Laboratoire d'Ecologie des Hydrosystèmes Naturels et Anthropisés; Villeurbanne France
- UPS, INP, CNRS, Univ. de Toulouse, UMR 5245 Laboratoire Écologie Fonctionnelle et Environnement; Ecolab Toulouse France
| | - Simon Blanchet
- Centre National de la Recherche Scientifique (CNRS), Univ. Paul Sabatier (UPS), Inst. de Recherche pour le Développement (IRD), Ecole Nationale Supérieure de Formation de l'Enseignement Agricole (ENSFEA); UMR5174, Evolution et Diversité Biologique, 118 route de Narbonne; FR-31062 Toulouse France
- CNRS, UPS; UMR5321, Station d'Ecologie Théorique et Expérimentale; Moulis France
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Baas P, van der Valk T, Vigilant L, Ngobobo U, Binyinyi E, Nishuli R, Caillaud D, Guschanski K. Population-level assessment of genetic diversity and habitat fragmentation in critically endangered Grauer's gorillas. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2018; 165:565-575. [PMID: 29313894 DOI: 10.1002/ajpa.23393] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Revised: 11/27/2017] [Accepted: 12/13/2017] [Indexed: 11/06/2022]
Abstract
OBJECTIVES The critically endangered Grauer's gorilla (Gorilla beringei graueri) has experienced an estimated 77% population decline within a single generation. Although crucial for informed conservation decisions, there is no clear understanding about population structure and distribution of genetic diversity across the species' highly fragmented range. We fill this gap by studying several core and peripheral Grauer's gorilla populations throughout their distribution range. MATERIALS AND METHODS We generated genetic profiles for a sampling of an unstudied population of Grauer's gorillas from within the species' core range at 13 autosomal microsatellite loci and combined them with previously published and newly generated data from four other Grauer's gorilla populations, two mountain gorilla populations, and one western lowland gorilla population. RESULTS In agreement with previous studies, the genetic diversity of Grauer's gorillas is intermediate, falling between western lowland and mountain gorillas. Among Grauer's gorilla populations, we observe lower genetic diversity and high differentiation in peripheral compared with central populations, indicating a strong effect of genetic drift and limited gene flow among small, isolated forest fragments. DISCUSSION Although genetically less diverse, peripheral populations are frequently essential for the long-term persistence of a species and migration between peripheral and core populations may significantly enrich the overall species genetic diversity. Thus, in addition to central Grauer's gorilla populations from the core of the distribution range that clearly deserve conservation attention, we argue that conservation strategies aiming to ensure long-term species viability should include preserving peripheral populations and enhancing habitat connectivity.
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Affiliation(s)
- Pauline Baas
- Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
| | - Tom van der Valk
- Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
| | - Linda Vigilant
- Primatology Department, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, Leipzig, Germany
| | - Urbain Ngobobo
- Dian Fossey Gorilla Fund International, 800 Cherokee Avenue, Atlanta, Georgia
| | - Escobar Binyinyi
- Dian Fossey Gorilla Fund International, 800 Cherokee Avenue, Atlanta, Georgia
| | - Radar Nishuli
- Institut Congolais pour la Conservation de la Nature, N4, Réserve de Faune à Okapis, Democratic Republic of Congo
| | - Damien Caillaud
- Dian Fossey Gorilla Fund International, 800 Cherokee Avenue, Atlanta, Georgia.,Department of Anthropology, University of California, Davis, One Shields Ave, Davis, California
| | - Katerina Guschanski
- Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
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Richmond JQ, Backlin AR, Galst-Cavalcante C, O'Brien JW, Fisher RN. Loss of dendritic connectivity in southern California's urban riverscape facilitates decline of an endemic freshwater fish. Mol Ecol 2017; 27:369-386. [PMID: 29193550 DOI: 10.1111/mec.14445] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Revised: 09/28/2017] [Accepted: 10/16/2017] [Indexed: 11/30/2022]
Abstract
Life history adaptations and spatial configuration of metapopulation networks allow certain species to persist in extreme fluctuating environments, yet long-term stability within these systems relies on the maintenance of linkage habitat. Degradation of such linkages in urban riverscapes can disrupt this dynamic in aquatic species, leading to increased extinction debt in local populations experiencing environment-related demographic flux. We used microsatellites and mtDNA to examine the effects of collapsed network structure in the endemic Santa Ana sucker Catostomus santaanae of southern California, a threatened species affected by natural flood-drought cycles, "boom-and-bust" demography, hybridization and presumed artificial transplantation. Our results show a predominance of drift-mediated processes in shaping population structure and that reverse mechanisms for counterbalancing the genetic effects of these phenomena have dissipated with the collapse of dendritic connectivity. We use approximate Bayesian models to support two cases of artificial transplantation and provide evidence that one of the invaded systems better represents the historic processes that maintained genetic variation within watersheds than any remaining drainages where C. santaanae is considered native. We further show that a stable dry gap in the northern range is preventing genetic dilution of pure C. santaanae persisting upstream of a hybrid assemblage involving a non-native sucker and that local accumulation of genetic variation in the same drainage is influenced by position within the network. This work has important implications for declining species that have historically relied on dendritic metapopulation networks to maintain source-sink dynamics in phasic environments, but no longer possess this capacity in urban-converted landscapes.
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Affiliation(s)
- Jonathan Q Richmond
- U.S. Geological Survey, Western Ecological Research Center, San Diego, CA, USA
| | - Adam R Backlin
- U.S. Geological Survey, Western Ecological Research Center, San Diego, CA, USA
| | | | - John W O'Brien
- California Department of Fish and Wildlife, Los Alamitos, CA, USA
| | - Robert N Fisher
- U.S. Geological Survey, Western Ecological Research Center, San Diego, CA, USA
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Sonsthagen SA, Wilson RE, Underwood JG. Genetic implications of bottleneck effects of differing severities on genetic diversity in naturally recovering populations: An example from Hawaiian coot and Hawaiian gallinule. Ecol Evol 2017; 7:9925-9934. [PMID: 29238526 PMCID: PMC5723630 DOI: 10.1002/ece3.3530] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2017] [Revised: 08/29/2017] [Accepted: 09/13/2017] [Indexed: 11/18/2022] Open
Abstract
The evolutionary trajectory of populations through time is influenced by the interplay of forces (biological, evolutionary, and anthropogenic) acting on the standing genetic variation. We used microsatellite and mitochondrial loci to examine the influence of population declines, of varying severity, on genetic diversity within two Hawaiian endemic waterbirds, the Hawaiian coot and Hawaiian gallinule, by comparing historical (samples collected in the late 1800s and early 1900s) and modern (collected in 2012–2013) populations. Population declines simultaneously experienced by Hawaiian coots and Hawaiian gallinules differentially shaped the evolutionary trajectory of these two populations. Within Hawaiian coot, large reductions (between −38.4% and −51.4%) in mitochondrial diversity were observed, although minimal differences were observed in the distribution of allelic and haplotypic frequencies between sampled time periods. Conversely, for Hawaiian gallinule, allelic frequencies were strongly differentiated between time periods, signatures of a genetic bottleneck were detected, and biases in means of the effective population size were observed at microsatellite loci. The strength of the decline appears to have had a greater influence on genetic diversity within Hawaiian gallinule than Hawaiian coot, coincident with the reduction in census size. These species exhibit similar life history characteristics and generation times; therefore, we hypothesize that differences in behavior and colonization history are likely playing a large role in how allelic and haplotypic frequencies are being shaped through time. Furthermore, differences in patterns of genetic diversity within Hawaiian coot and Hawaiian gallinule highlight the influence of demographic and evolutionary processes in shaping how species respond genetically to ecological stressors.
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Affiliation(s)
| | - Robert E Wilson
- Alaska Science Center U.S. Geological Survey Anchorage AK USA
| | - Jared G Underwood
- Pacific Reefs National Wildlife Refuge Complex U.S. Fish and Wildlife Service Honolulu HI USA
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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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