1
|
Zhao J, Xiao Y, Zhang Y, Shao Y, Ma T, Kou X, Zhang Y, Sang W, Axmacher JC. Socioeconomic development shows positive links to the conservation efficiency of China's protected area network. GLOBAL CHANGE BIOLOGY 2023; 29:3433-3448. [PMID: 36946769 DOI: 10.1111/gcb.16691] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Accepted: 03/13/2023] [Indexed: 05/16/2023]
Abstract
While the protected area (PA) covers >15% of the planet's terrestrial land area and continues to expand, factors determining its effectiveness in conserving endangered species are being debated. We investigated the links between direct anthropogenic pressures, socioeconomic settings, and the coverage of vertebrate taxa by China's PA network, and indicated that high socioeconomic status and low levels of human pressure correlate with high species coverage, with threatened mammals more effectively conserved than reptiles or amphibians. Positive links between conservation outcomes and socioeconomic progress appear linked to local livelihood improvements triggering positive perceptions of local PAs-aided further by ecological compensation and tourism schemes introduced in wealthy areas and reinforced by continued positive conservation outcomes. Socioeconomic development of China's less developed regions might assist regional PA efficiency and achievement of the Kunming-Montreal Global Biodiversity Framework, while also addressing potential shortcomings from an insufficient past focus on socioeconomic impacts for biodiversity conservation.
Collapse
Affiliation(s)
- Jinqi Zhao
- Minzu University of China, 27 Zhongguancun South Avenue, Beijing, 100081, China
| | - Yi Xiao
- Minzu University of China, 27 Zhongguancun South Avenue, Beijing, 100081, China
| | - Yanliang Zhang
- Minzu University of China, 27 Zhongguancun South Avenue, Beijing, 100081, China
| | - Yuting Shao
- Minzu University of China, 27 Zhongguancun South Avenue, Beijing, 100081, China
| | - Tianxiao Ma
- Minzu University of China, 27 Zhongguancun South Avenue, Beijing, 100081, China
| | - Xiaojun Kou
- Beijing Normal University, No. 19, Xinjiekouwai St, Haidian District, Beijing, 100875, China
| | - Yuanyuan Zhang
- Beijing Milu Ecological Research Center, Beijing, 100076, China
| | - Weiguo Sang
- Minzu University of China, 27 Zhongguancun South Avenue, Beijing, 100081, China
| | - Jan Christoph Axmacher
- UCL Department of Geography, University College London, London, WC1E 6BT, UK
- Agricultural University of Iceland, Keldnaholt, Reykjavik, Iceland
| |
Collapse
|
2
|
Zhang T, Niu Z, He J, Pu P, Meng F, Xi L, Tang X, Ding L, Ma M, Chen Q. Potential Effects of High Temperature and Heat Wave on Nanorana pleskei Based on Transcriptomic Analysis. Curr Issues Mol Biol 2023; 45:2937-2949. [PMID: 37185716 PMCID: PMC10136961 DOI: 10.3390/cimb45040192] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 03/28/2023] [Accepted: 03/29/2023] [Indexed: 04/07/2023] Open
Abstract
In the context of climate change, understanding how indigenous amphibians of the Qinghai-Tibet plateau react to stresses and their coping mechanisms could be crucial for predicting their fate and successful conservation. A liver transcriptome for Nanorana pleskei was constructed using high-throughput RNA sequencing, and its gene expression was compared with frogs acclimated under either room temperature or high temperature and also heat wave exposed ones. A total of 126,465 unigenes were produced, with 66,924 (52.92%) of them being annotated. Up to 694 genes were found to be differently regulated as a result of abnormal temperature acclimatization. Notably, genes belonging to the heat shock protein (HSP) family were down-regulated in both treated groups. Long-term exposure to high-temperature stress may impair the metabolic rate of the frog and trigger the body to maintain a hypometabolic state in an effort to survive challenging times. During heat waves, unlike the high-temperature group, mitochondrial function was not impaired, and the energy supply was largely normal to support the highly energy-consuming metabolic processes. Genes were more transcriptionally suppressed when treated with high temperatures than heat waves, and the body stayed in low-energy states for combating these long-term adverse environments to survive. It might be strategic to preserve initiation to executive protein activity under heat wave stress. Under both stress conditions, compromising the protection of HSP and sluggish steroid activity occurred in frogs. Frogs were more affected by high temperatures than by heat waves.
Collapse
Affiliation(s)
- Tao Zhang
- Department of Animal and Biomedical Sciences, School of Life Science, Lanzhou University, Lanzhou 730000, China
| | - Zhiyi Niu
- Department of Animal and Biomedical Sciences, School of Life Science, Lanzhou University, Lanzhou 730000, China
| | - Jie He
- Department of Animal and Biomedical Sciences, School of Life Science, Lanzhou University, Lanzhou 730000, China
| | - Peng Pu
- Department of Animal and Biomedical Sciences, School of Life Science, Lanzhou University, Lanzhou 730000, China
| | - Fei Meng
- Department of Animal and Biomedical Sciences, School of Life Science, Lanzhou University, Lanzhou 730000, China
| | - Lu Xi
- Department of Animal and Biomedical Sciences, School of Life Science, Lanzhou University, Lanzhou 730000, China
| | - Xiaolong Tang
- Department of Animal and Biomedical Sciences, School of Life Science, Lanzhou University, Lanzhou 730000, China
| | - Li Ding
- Department of Animal Science, School of Life Sciences and Engineering, Southwest University of Science and Technology, Mianyang 621010, China
| | - Miaojun Ma
- State Key Laboratory of Grassland and Agro-Ecosystems, School of Life Sciences, Lanzhou University, Lanzhou 730000, China
| | - Qiang Chen
- Department of Animal and Biomedical Sciences, School of Life Science, Lanzhou University, Lanzhou 730000, China
| |
Collapse
|
3
|
Schavinski CR, Santos MBD, Londero JEL, Rocha MCD, Amaral AMBD, Ruiz NQ, Leandro GDS, Loro VL, Schuch AP. Effects of isolated and combined exposures of Boana curupi (Anura: Hylidae) tadpoles to environmental doses of trichlorfon and ultraviolet radiation. MUTATION RESEARCH. GENETIC TOXICOLOGY AND ENVIRONMENTAL MUTAGENESIS 2022; 883-884:503549. [PMID: 36462791 DOI: 10.1016/j.mrgentox.2022.503549] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Revised: 07/22/2022] [Accepted: 09/16/2022] [Indexed: 06/17/2023]
Abstract
The biodiversity collapse strongly affects the amphibian group and many factors have been pointed out as catalytic agents. It is estimated that several events in the amphibian population decline worldwide may have been caused by the interaction of multiple drivers. Thus, this study aimed to evaluate the stressful effects of the exposure to environmental doses of trichlorfon (TCF) pesticide (0.5 μg/L; and an additional 100-fold concentration of 50 µg/L) and ultraviolet radiation (UV) (184.0 kJ/m² of UVA and 3.4 kJ/m² of UVB, which correspond to 5% of the daily dose) in tadpoles of the Boana curupi species (Anura: Hylidae). The isolated and combined exposures to TCF happened within 24 h of acute treatments under laboratory-controlled conditions. In the combined treatments, we adopted three different moments (M) of tadpole irradiation from the beginning of the exposures to TCF (0 h - M1; 12 h - M2; and 24 h - M3). Then, we evaluated tadpole survival, change in morphological characters, induction of apoptotic cells, lipid peroxidation (LPO), protein carbonyl content (PCC), glutathione S-transferase (GST), non-protein thiols (NPSH), and acetylcholinesterase (AChE), as well as the induction of genomic DNA (gDNA) damage. UVB treatment alone resulted in high mortality, along with a high level of apoptosis induction. Both UVA, UVB, and TCF increased LPO, PC, and AChE, while decreased GST activity. Regarding co-exposures, the most striking effect was observed in the interaction between UVB and TCF, which surprisingly decreased UVB-induced tadpole mortality, apoptosis, and gDNA damage. These results reinforce the B. curupi sensitivity to solar UVB radiation and indicate a complex response in face of UVB interaction with TCF, which may be related to activation of DNA repair pathways and/or inhibition of apoptosis, decreasing UVB-induced tadpole mortality.
Collapse
Affiliation(s)
- Cassiano Ricardo Schavinski
- Post-Graduation Program in Biological Sciences: Toxicological Biochemistry, Department of Biochemistry and Molecular Biology, Federal University of Santa Maria, Santa Maria, RS, Brazil
| | - Maurício Beux Dos Santos
- Post-Graduation Program in Biological Sciences: Toxicological Biochemistry, Department of Biochemistry and Molecular Biology, Federal University of Santa Maria, Santa Maria, RS, Brazil
| | - James Eduardo Lago Londero
- Post-Graduation Program in Biological Sciences: Toxicological Biochemistry, Department of Biochemistry and Molecular Biology, Federal University of Santa Maria, Santa Maria, RS, Brazil
| | - Marcelo Carvalho da Rocha
- Post-Graduation Program in Animal Biodiversity, Department of Ecology and Evolution, Federal University of Santa Maria, Santa Maria, RS, Brazil
| | - Aline Monique Blank do Amaral
- Post-Graduation Program in Animal Biodiversity, Department of Ecology and Evolution, Federal University of Santa Maria, Santa Maria, RS, Brazil
| | - Nathalia Quintero Ruiz
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Giovana da Silva Leandro
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Vania Lucia Loro
- Post-Graduation Program in Biological Sciences: Toxicological Biochemistry, Department of Biochemistry and Molecular Biology, Federal University of Santa Maria, Santa Maria, RS, Brazil
| | - André Passaglia Schuch
- Post-Graduation Program in Biological Sciences: Toxicological Biochemistry, Department of Biochemistry and Molecular Biology, Federal University of Santa Maria, Santa Maria, RS, Brazil.
| |
Collapse
|
4
|
Limited gene flow and pronounced population genetic structure of Eastern Massasauga (Sistrurus catenatus) in a Midwestern prairie remnant. PLoS One 2022; 17:e0265666. [PMID: 35324968 PMCID: PMC8947261 DOI: 10.1371/journal.pone.0265666] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Accepted: 03/04/2022] [Indexed: 11/19/2022] Open
Abstract
As anthropogenic changes continue to ecologically stress wildlife, obtaining measures of gene flow and genetic diversity are crucial for evaluating population trends and considering management and conservation strategies for small, imperiled populations. In our study, we conducted a molecular assessment to expand on previous work to elucidate patterns of diversity and connectivity in the remaining disjunct Eastern Massasauga Rattlesnake (Sistrurus catenatus) hibernacula in Illinois. We assayed genetic data for 327 samples collected during 1999–2015 from the Carlyle Lake study area across 21 microsatellite loci. We found hibernacula formed distinct genetic clusters corresponding to the three main study areas (Dam Recreation Areas, Eldon Hazlet State Park, and South Shore State Park). Genetic structuring and low estimates of dispersal indicated that connectivity among these study areas is limited and each is demographically independent. Hibernacula exhibited moderate levels of heterozygosity (0.60–0.73), but estimates of effective population size (5.2–41.0) were low and track census sizes generated via long-term mark-recapture data. Hibernacula at Carlyle Lake, which represent the only Eastern Massasauga remaining in Illinois, are vulnerable to future loss of genetic diversity through lack of gene flow as well as demographic and environmental stochastic processes. Our work highlights the need to include population-level genetic data in recovery planning and suggests that recovery efforts should focus on managing the three major study areas as separate conservation units in order to preserve and maintain long-term adaptive potential of these populations. Specific management goals should include improving connectivity among hibernacula, maintaining existing wet grassland habitat, and minimizing anthropogenic sources of mortality caused by habitat management (e.g., mowing, prescribed fire) and recreational activities. Our molecular study provides additional details about demographic parameters and connectivity at Carlyle Lake that can be used to guide recovery of Eastern Massasauga in Illinois and throughout its range.
Collapse
|
5
|
Phylogeography and Genetic Structure of the Swimming Crabs Portunus sanguinolentus (Herbst, 1783) in East Asia. JOURNAL OF MARINE SCIENCE AND ENGINEERING 2022. [DOI: 10.3390/jmse10020281] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The three-spot swimming crab (Portunus sanguinolentus) is mainly distributed in South East Asia. An analysis of mitochondrial control region partial sequences allows us to determine the population genetic structure, phylogeography and historical demography of this species in East Asia. The seven populations, which included 110 individuals, were collected from mainland China (Shanghai, SH, Xiamen, XM and Hong Kong, HK), Taiwan (Yilan, YL, Taichung, TC, Donggang, DG) and Singapore (Singapore, SGP). The nucleotide diversity (π) of all individuals was 0.01149, with values ranging from 0.00372 (SGP) to 0.01345 (YL). In total, 90 haplotypes have been identified, which can be divided into two major lineages: lineage A consists of specimens from SH, YL, XM, TC and DG, and lineage B corresponds to specimen from SGP. From the second to the most recent interglacial period, population expansion was observed in each lineage. However, a low level of genetic differentiation was also observed in the three-spotted swimming crab, P. sanguinolentus, according to FST values. Our results suggest that several past and present habitat configurations have shaped the genetic patterns of P. sanguinolentus until now. During Pleistocene glaciations, when sea levels were low, this species may have moved along the coast from Southeast Asia to China. It first colonized the Hong Kong area during this era. After sea levels rose and shorelines receded, it subsequently spread to the coast of mainland China.
Collapse
|
6
|
Muraro M, Romagnoli S, Barzaghi B, Falaschi M, Manenti R, Ficetola GF. Invasive predators induce plastic and adaptive responses during embryo development in a threatened frog. NEOBIOTA 2021. [DOI: 10.3897/neobiota.70.65454] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Invasive predators can strongly affect native populations. If alien predator pressure is strong enough, it can induce anti-predator responses, including phenotypic plasticity of exposed individuals and local adaptations of impacted populations. Furthermore, maternal investment is an additional pathway that could provide resources and improve performance in the presence of alien predators. We investigated the potential responses to an alien predator crayfish (Procambarus clarkii) in a threatened frog (Rana latastei) by combining field observations with laboratory measurements of embryo development rate, to assess the importance of parental investment, origin and exposure to the crayfish cues. We detected a strong variation in parental investment amongst frog populations, but this variation was not related to the invasion status of the site of origin, suggesting that mothers did not modulate parental investment in relation to the presence of alien predators. However, cues of the invasive crayfish elicited plastic responses in clutches and tadpoles development: embryos developed faster when exposed to the predator. Furthermore, embryos from invaded sites reached Gosner’s development stage 25 faster than those from non-invaded sites. This ontogenetic shift can be interpreted as a local adaptation to the alien predator and suggests that frogs are able to recognise the predatory risk. If these plastic responses and local adaptation are effective escape strategies against the invasive predator, they may improve the persistence of native frog populations.
Collapse
|
7
|
Jin L, Liao WB, Merilä J. Genomic evidence for adaptive differentiation among
Microhyla fissipes
populations: Implications for conservation. DIVERS DISTRIB 2021. [DOI: 10.1111/ddi.13433] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Affiliation(s)
- Long Jin
- Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education) China West Normal University Nanchong China
| | - Wen Bo Liao
- Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education) China West Normal University Nanchong China
| | - Juha Merilä
- Ecological Genetics Research Unit, Organismal and Evolutionary Biology Programme Faculty of Biological and Environmental Sciences FI‐00014 University of Helsinki Helsinki Finland
- Research Division for Ecology and Biodiversity School Biological Sciences The University of Hong KongHong Kong SAR
| |
Collapse
|
8
|
Gauffre B, Boissinot A, Quiquempois V, Leblois R, Grillet P, Morin S, Picard D, Ribout C, Lourdais O. Agricultural intensification alters marbled newt genetic diversity and gene flow through density and dispersal reduction. Mol Ecol 2021; 31:119-133. [PMID: 34674328 DOI: 10.1111/mec.16236] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Revised: 10/08/2021] [Accepted: 10/18/2021] [Indexed: 11/30/2022]
Abstract
Recent agricultural intensification threatens global biodiversity with amphibians being one of the most impacted groups. Because of their biphasic life cycle, amphibians are particularly vulnerable to habitat loss and fragmentation that often result in small, isolated populations and loss of genetic diversity. Here, we studied how landscape heterogeneity affects genetic diversity, gene flow and demographic parameters in the marbled newt, Triturus marmoratus, over a hedgerow network landscape in Western France. While the northern part of the study area consists of preserved hedged farmland, the southern part was more profoundly converted for intensive arable crops production after WWII. Based on 67 sampled ponds and 10 microsatellite loci, we characterized regional population genetic structure and evaluated the correlation between landscape variables and (i) local genetic diversity using mixed models and (ii) genetic distance using multiple regression methods and commonality analysis. We identified a single genetic population characterized by a spatially heterogeneous isolation-by-distance pattern. Pond density in the surrounding landscape positively affected local genetic diversity while arable crop land cover negatively affected gene flow and connectivity. We used demographic inferences to quantitatively assess differences in effective population density and dispersal between the contrasted landscapes characterizing the northern and southern parts of the study area. Altogether, results suggest recent land conversion affected T. marmoratus through reduction in both effective population density and dispersal due to habitat loss and reduced connectivity.
Collapse
Affiliation(s)
- Bertrand Gauffre
- INRAE, UR 1115 PSH, Plantes et Systèmes de culture Horticoles, Avignon, France.,School of Biological Sciences, Monash University, Clayton, Vic., Australia
| | - Alexandre Boissinot
- CNRS, UMR 7372 CEBC - Université de La Rochelle, Villiers-en-Bois, France.,Réserve Naturelle Régionale du Bocage des Antonins - Deux-Sèvres Nature Environnement, Niort, France
| | | | - Raphael Leblois
- CBGP UMR 1062, INRAE, CIRAD, IRD, Montpellier SupAgro, Univ. Montpellier, Montpellier, France.,Institut de Biologie Computationnelle, Univ. Montpellier, Montpelier, France
| | - Pierre Grillet
- CNRS, UMR 7372 CEBC - Université de La Rochelle, Villiers-en-Bois, France
| | - Sophie Morin
- Office Français de la Biodiversité, Villiers-en-Bois, France
| | - Damien Picard
- Département de Biologie, UFR Sciences, Angers, France
| | - Cécile Ribout
- CNRS, UMR 7372 CEBC - Université de La Rochelle, Villiers-en-Bois, France
| | - Olivier Lourdais
- CNRS, UMR 7372 CEBC - Université de La Rochelle, Villiers-en-Bois, France.,School of Life Sciences, Arizona State University, Tempe, AZ, USA
| |
Collapse
|
9
|
Zheng Y, Zhang S, Lu Q, Zhang S, Wang L, Hong M, Nguyen T, Zhao J, Yao M. Population genetic patterns of a mangrove‐associated frog reveal its colonization history and habitat connectivity. DIVERS DISTRIB 2021. [DOI: 10.1111/ddi.13304] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Affiliation(s)
- Yitao Zheng
- School of Life Sciences Peking University Beijing China
- Institute of Ecology College of Urban and Environmental Sciences Peking University Beijing China
| | - Shan Zhang
- School of Life Sciences Peking University Beijing China
- Institute of Ecology College of Urban and Environmental Sciences Peking University Beijing China
| | - Qi Lu
- School of Life Sciences Peking University Beijing China
- Institute of Ecology College of Urban and Environmental Sciences Peking University Beijing China
| | - Siyu Zhang
- School of Life Sciences Peking University Beijing China
- Institute of Ecology College of Urban and Environmental Sciences Peking University Beijing China
| | - Lijun Wang
- College of Life Sciences Hainan Normal University Haikou China
| | - Meiling Hong
- College of Life Sciences Hainan Normal University Haikou China
| | - Truong Nguyen
- Institute of Ecology and Biological Resources Academy of Science and Technology Hanoi Vietnam
- Vietnam Academy of Science and Technology Graduate University of Science and Technology Hanoi Vietnam
| | - Jindong Zhao
- School of Life Sciences Peking University Beijing China
- Institute of Ecology College of Urban and Environmental Sciences Peking University Beijing China
| | - Meng Yao
- School of Life Sciences Peking University Beijing China
- Institute of Ecology College of Urban and Environmental Sciences Peking University Beijing China
| |
Collapse
|
10
|
De Cahsan B, Kiemel K, Westbury MV, Lauritsen M, Autenrieth M, Gollmann G, Schweiger S, Stenberg M, Nyström P, Drews H, Tiedemann R. Southern introgression increases adaptive immune gene variability in northern range margin populations of Fire-bellied toad. Ecol Evol 2021; 11:9776-9790. [PMID: 34306661 PMCID: PMC8293767 DOI: 10.1002/ece3.7805] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Revised: 05/14/2021] [Accepted: 05/28/2021] [Indexed: 11/20/2022] Open
Abstract
Northern range margin populations of the European fire-bellied toad (Bombina bombina) have rapidly declined during recent decades. Extensive agricultural land use has fragmented the landscape, leading to habitat disruption and loss, as well as eutrophication of ponds. In Northern Germany (Schleswig-Holstein) and Southern Sweden (Skåne), this population decline resulted in decreased gene flow from surrounding populations, low genetic diversity, and a putative reduction in adaptive potential, leaving populations vulnerable to future environmental and climatic changes. Previous studies using mitochondrial control region and nuclear transcriptome-wide SNP data detected introgressive hybridization in multiple northern B. bombina populations after unreported release of toads from Austria. Here, we determine the impact of this introgression by comparing the body conditions (proxy for fitness) of introgressed and nonintrogressed populations and the genetic consequences in two candidate genes for putative local adaptation (the MHC II gene as part of the adaptive immune system and the stress response gene HSP70 kDa). We detected regional differences in body condition and observed significantly elevated levels of within individual MHC allele counts in introgressed Swedish populations, associated with a tendency toward higher body weight, relative to regional nonintrogressed populations. These differences were not observed among introgressed and nonintrogressed German populations. Genetic diversity in both MHC and HSP was generally lower in northern than Austrian populations. Our study sheds light on the potential benefits of translocations of more distantly related conspecifics as a means to increase adaptive genetic variability and fitness of genetically depauperate range margin populations without distortion of local adaptation.
Collapse
Affiliation(s)
- Binia De Cahsan
- Unit of Evolutionary Biology/Systematic ZoologyInstitute of Biochemistry and BiologyUniversity of PotsdamPotsdamGermany
- GLOBE InstituteUniversity of CopenhagenCopenhagenDenmark
| | - Katrin Kiemel
- Unit of Evolutionary Biology/Systematic ZoologyInstitute of Biochemistry and BiologyUniversity of PotsdamPotsdamGermany
| | | | - Maike Lauritsen
- Unit of Evolutionary Biology/Systematic ZoologyInstitute of Biochemistry and BiologyUniversity of PotsdamPotsdamGermany
| | - Marijke Autenrieth
- Unit of Evolutionary Biology/Systematic ZoologyInstitute of Biochemistry and BiologyUniversity of PotsdamPotsdamGermany
| | - Günter Gollmann
- Department of Evolutionary BiologyUniversity of ViennaViennaAustria
| | - Silke Schweiger
- Herpetological CollectionNatural History Museum ViennaViennaAustria
| | | | | | - Hauke Drews
- Stiftung Naturschutz Schleswig‐HolsteinMolfseeGermany
| | - Ralph Tiedemann
- Unit of Evolutionary Biology/Systematic ZoologyInstitute of Biochemistry and BiologyUniversity of PotsdamPotsdamGermany
| |
Collapse
|
11
|
Krishnan A. Lessons Across Scales: Molecular Ecology and Wildlife Conservation. J Indian Inst Sci 2021. [DOI: 10.1007/s41745-021-00232-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
|
12
|
Pröhl H, Auffarth J, Bergmann T, Buschmann H, Balkenhol N. Conservation genetics of the yellow-bellied toad (Bombina variegata): population structure, genetic diversity and landscape effects in an endangered amphibian. CONSERV GENET 2021. [DOI: 10.1007/s10592-021-01350-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
AbstractRevealing patterns of genetic diversity and barriers for gene flow are key points for successful conservation in endangered species. Methods based on molecular markers are also often used to delineate conservation units such as evolutionary significant units and management units. Here we combine phylo-geographic analyses (based on mtDNA) with population and landscape genetic analyses (based on microsatellites) for the endangered yellow-bellied toad Bombina variegata over a wide distribution range in Germany. Our analyses show that two genetic clusters are present in the study area, a northern and a southern/central one, but that these clusters are not deeply divergent. The genetic data suggest high fragmentation among toad occurrences and consequently low genetic diversity. Genetic diversity and genetic connectivity showed a negative relationship with road densities and urban areas surrounding toad occurrences, indicating that these landscape features act as barriers to gene flow. To preserve a maximum of genetic diversity, we recommend considering both genetic clusters as management units, and to increase gene flow among toad occurrences with the aim of restoring and protecting functional meta-populations within each of the clusters. Several isolated populations with especially low genetic diversity and signs of inbreeding need particular short-term conservation attention to avoid extinction. We also recommend to allow natural gene flow between both clusters but not to use individuals from one cluster for translocation or reintroduction into the other. Our results underscore the utility of molecular tools for species conservation, highlight outcomes of habitat fragmentation onto the genetic structure of an endangered amphibian and reveal particularly threatened populations in need for urgent conservation efforts.
Collapse
|
13
|
Grismer LL, Wood, Jr. PL, Poyarkov NA, Le MD, Kraus F, Agarwal I, Oliver PM, Nguyen SN, Nguyen TQ, Karunarathna S, Welton LJ, Stuart BL, Luu VQ, Bauer AM, O’Connell KA, Quah ESH, Chan KO, Ziegler T, Ngo H, Nazarov RA, Aowphol A, Chomdej S, Suwannapoom C, Siler CD, Anuar S, Tri NV, Grismer JL. Phylogenetic partitioning of the third-largest vertebrate genus in the world, Cyrtodactylus Gray, 1827 (Reptilia; Squamata; Gekkonidae) and its relevance to taxonomy and conservation. VERTEBRATE ZOOLOGY 2021. [DOI: 10.3897/vz.71.e59307] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
The gekkonid genus Cyrtodactylus is the third most speciose vertebrate genus in the world, containing well over 300 species that collectively range from South Asia to Melanesia across some of the most diverse landscapes and imperiled habitats on the planet. A genus-wide phylogeny of the group has never been presented because researchers working on different groups were using different genetic markers to construct phylogenies that could not be integrated. We present here Maximum likelihood and Bayesian inference mitochondrial and mito-nuclear phylogenies incorporating of 310 species that include dozens of species that had never been included in a genus-wide analysis. Based on the mitochondrial phylogeny, we partition Cyrtodactylus into 31 well-supported monophyletic species groups which, if used as recommended herein, will increase the information content of future integrative taxonomic analyses that continue to add new species to this genus at an ever-increasing annual rate. Data presented here reiterate the outcome of several previous studies indicating that Cyrtodactylus comprises an unprecedented number of narrow-range endemics restricted to single mountain tops, small islands, or karst formations that still remain unprotected. This phylogeny can provide a platform for various comparative ecological studies that can be integrated with conservation management programs across the broad diversity of landscapes and habitats occupied by this genus. Additionally, these data indicate that the true number of Cyrtodactylus remains substantially underrepresented.
Collapse
|
14
|
Grismer LL, Wood, Jr. PL, Poyarkov NA, Le MD, Kraus F, Agarwal I, Oliver PM, Nguyen SN, Nguyen TQ, Karunarathna S, Welton LJ, Stuart BL, Luu VQ, Bauer AM, O’Connell KA, Quah ESH, Chan KO, Ziegler T, Ngo H, Nazarov RA, Aowphol A, Chomdej S, Suwannapoom C, Siler CD, Anuar S, Tri NV, Grismer JL. Phylogenetic partitioning of the third-largest vertebrate genus in the world, Cyrtodactylus Gray, 1827 (Reptilia; Squamata; Gekkonidae) and its relevance to taxonomy and conservation. VERTEBRATE ZOOLOGY 2021. [DOI: 10.3897/vertebrate-zoology.71.e59307] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
The gekkonid genus Cyrtodactylus is the third most speciose vertebrate genus in the world, containing well over 300 species that collectively range from South Asia to Melanesia across some of the most diverse landscapes and imperiled habitats on the planet. A genus-wide phylogeny of the group has never been presented because researchers working on different groups were using different genetic markers to construct phylogenies that could not be integrated. We present here Maximum likelihood and Bayesian inference mitochondrial and mito-nuclear phylogenies incorporating of 310 species that include dozens of species that had never been included in a genus-wide analysis. Based on the mitochondrial phylogeny, we partition Cyrtodactylus into 31 well-supported monophyletic species groups which, if used as recommended herein, will increase the information content of future integrative taxonomic analyses that continue to add new species to this genus at an ever-increasing annual rate. Data presented here reiterate the outcome of several previous studies indicating that Cyrtodactylus comprises an unprecedented number of narrow-range endemics restricted to single mountain tops, small islands, or karst formations that still remain unprotected. This phylogeny can provide a platform for various comparative ecological studies that can be integrated with conservation management programs across the broad diversity of landscapes and habitats occupied by this genus. Additionally, these data indicate that the true number of Cyrtodactylus remains substantially underrepresented.
Collapse
|
15
|
Covarrubias S, González C, Gutiérrez‐Rodríguez C. Effects of natural and anthropogenic features on functional connectivity of anurans: a review of landscape genetics studies in temperate, subtropical and tropical species. J Zool (1987) 2020. [DOI: 10.1111/jzo.12851] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Affiliation(s)
- S. Covarrubias
- Instituto de Investigaciones sobre los Recursos Naturales Universidad Michoacana de San Nicolás de Hidalgo Morelia Michoacán México
| | - C. González
- Instituto de Investigaciones sobre los Recursos Naturales Universidad Michoacana de San Nicolás de Hidalgo Morelia Michoacán México
| | | |
Collapse
|
16
|
Pabijan M, Palomar G, Antunes B, Antoł W, Zieliński P, Babik W. Evolutionary principles guiding amphibian conservation. Evol Appl 2020; 13:857-878. [PMID: 32431739 PMCID: PMC7232768 DOI: 10.1111/eva.12940] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Revised: 02/05/2020] [Accepted: 02/18/2020] [Indexed: 12/18/2022] Open
Abstract
The Anthropocene has witnessed catastrophic amphibian declines across the globe. A multitude of new, primarily human-induced drivers of decline may lead to extinction, but can also push species onto novel evolutionary trajectories. If these are recognized by amphibian biologists, they can be engaged in conservation actions. Here, we summarize how principles stemming from evolutionary concepts have been applied for conservation purposes, and address emerging ideas at the vanguard of amphibian conservation science. In particular, we examine the consequences of increased drift and inbreeding in small populations and their implications for practical conservation. We then review studies of connectivity between populations at the landscape level, which have emphasized the limiting influence of anthropogenic structures and degraded habitat on genetic cohesion. The rapid pace of environmental changes leads to the central question of whether amphibian populations can cope either by adapting to new conditions or by shifting their ranges. We gloomily conclude that extinction seems far more likely than adaptation or range shifts for most species. That said, conservation strategies employing evolutionary principles, such as selective breeding, introduction of adaptive variants through translocations, ecosystem interventions aimed at decreasing phenotype-environment mismatch, or genetic engineering, may effectively counter amphibian decline in some areas or for some species. The spread of invasive species and infectious diseases has often had disastrous consequences, but has also provided some premier examples of rapid evolution with conservation implications. Much can be done in terms of setting aside valuable amphibian habitat that should encompass both natural and agricultural areas, as well as designing protected areas to maximize the phylogenetic and functional diversity of the amphibian community. We conclude that an explicit consideration and application of evolutionary principles, although certainly not a silver bullet, should increase effectiveness of amphibian conservation in both the short and long term.
Collapse
Affiliation(s)
- Maciej Pabijan
- Institute of Zoology and Biomedical ResearchFaculty of BiologyJagiellonian UniversityKrakówPoland
| | - Gemma Palomar
- Institute of Environmental SciencesFaculty of BiologyJagiellonian UniversityKrakówPoland
| | - Bernardo Antunes
- Institute of Environmental SciencesFaculty of BiologyJagiellonian UniversityKrakówPoland
| | - Weronika Antoł
- Institute of Environmental SciencesFaculty of BiologyJagiellonian UniversityKrakówPoland
| | - Piotr Zieliński
- Institute of Environmental SciencesFaculty of BiologyJagiellonian UniversityKrakówPoland
| | - Wiesław Babik
- Institute of Environmental SciencesFaculty of BiologyJagiellonian UniversityKrakówPoland
| |
Collapse
|
17
|
Novikova PY, Brennan IG, Booker W, Mahony M, Doughty P, Lemmon AR, Moriarty Lemmon E, Roberts JD, Yant L, Van de Peer Y, Keogh JS, Donnellan SC. Polyploidy breaks speciation barriers in Australian burrowing frogs Neobatrachus. PLoS Genet 2020; 16:e1008769. [PMID: 32392206 PMCID: PMC7259803 DOI: 10.1371/journal.pgen.1008769] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2019] [Revised: 05/29/2020] [Accepted: 04/08/2020] [Indexed: 01/13/2023] Open
Abstract
Polyploidy has played an important role in evolution across the tree of life but it is still unclear how polyploid lineages may persist after their initial formation. While both common and well-studied in plants, polyploidy is rare in animals and generally less understood. The Australian burrowing frog genus Neobatrachus is comprised of six diploid and three polyploid species and offers a powerful animal polyploid model system. We generated exome-capture sequence data from 87 individuals representing all nine species of Neobatrachus to investigate species-level relationships, the origin and inheritance mode of polyploid species, and the population genomic effects of polyploidy on genus-wide demography. We describe rapid speciation of diploid Neobatrachus species and show that the three independently originated polyploid species have tetrasomic or mixed inheritance. We document higher genetic diversity in tetraploids, resulting from widespread gene flow between the tetraploids, asymmetric inter-ploidy gene flow directed from sympatric diploids to tetraploids, and isolation of diploid species from each other. We also constructed models of ecologically suitable areas for each species to investigate the impact of climate on differing ploidy levels. These models suggest substantial change in suitable areas compared to past climate, which correspond to population genomic estimates of demographic histories. We propose that Neobatrachus diploids may be suffering the early genomic impacts of climate-induced habitat loss, while tetraploids appear to be avoiding this fate, possibly due to widespread gene flow. Finally, we demonstrate that Neobatrachus is an attractive model to study the effects of ploidy on the evolution of adaptation in animals.
Collapse
Affiliation(s)
- Polina Yu. Novikova
- VIB-UGent Center for Plant Systems Biology, Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
| | - Ian G. Brennan
- Division of Ecology & Evolution, Research School of Biology, The Australian National University, Canberra, Australia
| | - William Booker
- Department of Biological Science, Florida State University, Tallahassee, Florida, United States of America
| | - Michael Mahony
- School of Environmental and Life Sciences, University of Newcastle, Callaghan, Australia
| | - Paul Doughty
- Western Australian Museum, Welshpool, Perth, Australia
| | - Alan R. Lemmon
- Department of Scientific Computing, Florida State University, Tallahassee, Florida, United States of America
| | - Emily Moriarty Lemmon
- Department of Biological Science, Florida State University, Tallahassee, Florida, United States of America
| | - J. Dale Roberts
- School of Biological Sciences, and, Centre for Evolutionary Biology, University of Western Australia, Albany, Western Australia, Australia
| | - Levi Yant
- School of Life Sciences and Future Food Beacon, University of Nottingham, Nottingham, United Kingdom
| | - Yves Van de Peer
- VIB-UGent Center for Plant Systems Biology, Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Bioinformatics Institute Ghent, Ghent University, Ghent, Belgium
- Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
| | - J. Scott Keogh
- Division of Ecology & Evolution, Research School of Biology, The Australian National University, Canberra, Australia
| | - Stephen C. Donnellan
- South Australian Museum, North Terrace, Adelaide, Australia
- School of Biological Sciences, University of Adelaide, North Terrace, Adelaide, Australia
| |
Collapse
|
18
|
|
19
|
Arntzen JW, van Belkom J. 'Mainland-island' population structure of a terrestrial salamander in a forest-bocage landscape with little evidence for in situ ecological speciation. Sci Rep 2020; 10:1700. [PMID: 32015401 PMCID: PMC6997349 DOI: 10.1038/s41598-020-58551-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Accepted: 01/09/2020] [Indexed: 12/17/2022] Open
Abstract
Adaptation to different ecological environments can, through divergent selection, generate phenotypic and genetic differences between populations, and eventually give rise to new species. The fire salamander (Salamandra salamandra) has been proposed to represent an early stage of ecological speciation, driven by differential habitat adaptation through the deposition and development of larvae in streams versus ponds in the Kottenforst near Bonn (Germany). We set out to test this hypothesis of ecological speciation in an area different from the one where it was raised and we took the opportunity to explore for drivers of genetic differentiation at a landscape scale. A survey over 640 localities demonstrated the species' presence in ponds and streams across forests, hilly terrain and areas with hedgerows ('bocage'). Genetic variation at 14 microsatellite loci across 41 localities in and around two small deciduous forests showed that salamander effective population sizes were higher in forests than in the bocage, with panmixia in the forests (Fst < 0.010) versus genetic drift or founder effects in several of the small and more or less isolated bocage populations (Fst > 0.025). The system fits the 'mainland-island' metapopulation model rather than indicating adaptive genetic divergence in pond versus stream larval habitats. A reanalysis of the Kottenforst data indicated that microsatellite genetic variation fitted a geographical rather than an environmental axis, with a sharp transition from a western pond-breeding to an eastern, more frequently stream-breeding group of populations. A parallel changeover in mitochondrial DNA exists but remains to be well documented. The data support the existence of a hybrid zone following secondary contact of differentiated lineages, more so than speciation in situ.
Collapse
Affiliation(s)
- Jan W Arntzen
- Naturalis Biodiversity Center, Leiden, The Netherlands.
| | | |
Collapse
|
20
|
Peek RA, Bedwell M, O'Rourke SM, Goldberg C, Wengert GM, Miller MR. Hybridization between two parapatric ranid frog species in the northern Sierra Nevada, California, USA. Mol Ecol 2019; 28:4636-4647. [DOI: 10.1111/mec.15236] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Revised: 08/19/2019] [Accepted: 08/27/2019] [Indexed: 01/05/2023]
Affiliation(s)
- Ryan A. Peek
- Center for Watershed Sciences University of California Davis CA USA
- Department of Animal Science University of California Davis CA USA
| | - Mallory Bedwell
- School of the Environment Washington State University Pullman WA USA
| | - Sean M. O'Rourke
- Department of Animal Science University of California Davis CA USA
| | - Caren Goldberg
- School of the Environment Washington State University Pullman WA USA
| | | | - Michael R. Miller
- Center for Watershed Sciences University of California Davis CA USA
- Department of Animal Science University of California Davis CA USA
| |
Collapse
|
21
|
Ward A, Hide G, Jehle R. Skin swabs with FTA® cards as a dry storage source for amphibian DNA. CONSERV GENET RESOUR 2019. [DOI: 10.1007/s12686-018-1018-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
|
22
|
Linking effective population size dynamics to phenotypic traits in the common toad (Bufo bufo). CONSERV GENET 2019. [DOI: 10.1007/s10592-019-01185-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
|
23
|
von Takach Dukai B, Jack C, Borevitz J, Lindenmayer DB, Banks SC. Pervasive admixture between eucalypt species has consequences for conservation and assisted migration. Evol Appl 2019; 12:845-860. [PMID: 30976314 PMCID: PMC6439489 DOI: 10.1111/eva.12761] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Revised: 12/05/2018] [Accepted: 12/21/2018] [Indexed: 01/12/2023] Open
Abstract
Conservation management often uses information on genetic population structure to assess the importance of local provenancing for ecological restoration and reintroduction programs. For species that do not exhibit complete reproductive isolation, the estimation of population genetic parameters may be influenced by the extent of admixture. Therefore, to avoid perverse outcomes for conservation, genetically informed management strategies must determine whether hybridization between species is relevant, and the extent to which observed population genetic patterns are shaped by interspecific versus intraspecific gene flow. We used genotyping by sequencing to identify over 2,400 informative single nucleotide polymorphisms across 18 populations of Eucalyptus regnans F. Muell., a foundation tree species of montane forests in south-eastern Australia. We used these data to determine the extent of hybridization with another species, Eucalyptus obliqua L'Hér., and investigate how admixture influences genetic diversity parameters, by estimating metrics of genetic diversity and examining population genetic structure in datasets with and without admixed individuals. We found hybrid individuals at all sites and two highly introgressed populations. Hybrid individuals were not distributed evenly across environmental gradients, with logistic regression identifying hybrids as being associated with temperature. Removal of hybrids resulted in increases in genetic differentiation (F ST), expected heterozygosity, observed heterozygosity and the inbreeding coefficient, and different patterns of isolation by distance. After removal of hybrids and introgressed populations, mountain ash showed very little population genetic structure, with a small effect of isolation by distance, and very low global F ST(0.03). Our study shows that, in plants, decisions around provenancing of individuals for restoration depend on knowledge of whether hybridization is influencing population genetic structure. For species in which most genetic variation is held within populations, there may be little benefit in planning conservation strategies around environmental adaptation of seed sources. The possibility for adaptive introgression may also be relevant when species regularly hybridize.
Collapse
Affiliation(s)
- Brenton von Takach Dukai
- Fenner School of Environment and SocietyThe Australian National UniversityCanberraAustralian Capital TerritoryAustralia
| | - Cameron Jack
- ANU Bioinformatics Consultancy, John Curtin School of Medical ResearchAustralian National UniversityCanberraAustralian Capital TerritoryAustralia
| | - Justin Borevitz
- Research School of BiologyThe Australian National UniversityCanberraAustralian Capital TerritoryAustralia
- Centre of Excellence in Plant Energy BiologyThe Australian National UniversityCanberraAustralian Capital TerritoryAustralia
| | - David B. Lindenmayer
- Fenner School of Environment and SocietyThe Australian National UniversityCanberraAustralian Capital TerritoryAustralia
| | - Sam C. Banks
- Research Institute for the Environment and LivelihoodsCharles Darwin UniversityDarwinNorthwest TerritoriesAustralia
| |
Collapse
|
24
|
McCartney-Melstad E, Vu JK, Shaffer HB. Genomic data recover previously undetectable fragmentation effects in an endangered amphibian. Mol Ecol 2018; 27:4430-4443. [PMID: 30307076 DOI: 10.1111/mec.14892] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2018] [Revised: 08/17/2018] [Accepted: 10/01/2018] [Indexed: 12/30/2022]
Abstract
A critical consideration when using molecular ecological methods to detect trends and parameterize models at very fine spatial and temporal scales has always been the technical limits of resolution. Key landscape features, including most anthropogenic modifications, can cause biologically important, but very recent changes in gene flow that require substantial statistical power to detect. The problem is one of temporal scale: Human change is rapid and recent, while genetic changes accumulate slowly. We generated SNPs from thousands of nuclear loci to characterize the population structure of New York-endangered eastern tiger salamanders (Ambystoma tigrinum) on Long Island and quantify the impacts of roads on population fragmentation. In stark contrast to a recent microsatellite study, we uncovered highly structured populations over an extremely small spatial scale (approximately 40 km2 ) in an increasingly human-modified landscape. Geographic distance and the presence of roads between ponds were both strong predictors of genetic divergence, suggesting that both natural and anthropogenic factors contribute to the observed patterns of genetic variation. All ponds supported small to modest effective breeding populations, and pond surface area showed a strong positive correlation with population size. None of these patterns emerged in an earlier study of the same system using microsatellite loci, and we determined that at least 300-400 SNPs were needed to recover the fine-scale population structure present in this system. Conservation assessments using earlier genetic techniques in other species may similarly lack the statistical power for small-scale inferences and benefit from reassessments using genomic tools.
Collapse
Affiliation(s)
- Evan McCartney-Melstad
- Department of Ecology and Evolutionary Biology, La Kretz Center for California Conservation Science, and Institute of the Environment and Sustainability,, University of California, Los Angeles, Los Angeles, California
| | - Jannet K Vu
- Department of Ecology and Evolutionary Biology, La Kretz Center for California Conservation Science, and Institute of the Environment and Sustainability,, University of California, Los Angeles, Los Angeles, California.,Department of Ecology and Evolution, Stony Brook University, Stony Brook, New York
| | - H Bradley Shaffer
- Department of Ecology and Evolutionary Biology, La Kretz Center for California Conservation Science, and Institute of the Environment and Sustainability,, University of California, Los Angeles, Los Angeles, California
| |
Collapse
|
25
|
McCartney-Melstad E, Gidiş M, Shaffer HB. Population genomic data reveal extreme geographic subdivision and novel conservation actions for the declining foothill yellow-legged frog. Heredity (Edinb) 2018; 121:112-125. [PMID: 29941996 PMCID: PMC6039490 DOI: 10.1038/s41437-018-0097-7] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Revised: 04/17/2018] [Accepted: 05/13/2018] [Indexed: 12/25/2022] Open
Abstract
Genomic data have the potential to inform high resolution landscape genetic and biological conservation studies that go far beyond recent mitochondrial and microsatellite analyses. We characterize the relationships of populations of the foothill yellow-legged frog, Rana boylii, a declining, "sentinel" species for stream ecosystems throughout its range in California and Oregon. We generated RADseq data and applied phylogenetic methods, hierarchical Bayesian clustering, PCA and population differentiation with admixture analyses to characterize spatial genetic structure across the species range. To facilitate direct comparison with previous analyses, we included many localities and individuals from our earlier work based on mitochondrial DNA. The results are striking, and emphasize the power of our landscape genomic approach. We recovered five extremely differentiated primary clades that indicate that R. boylii may be the most genetically differentiated anuran yet studied. Our results provide better resolution and more spatially consistent patterns than our earlier work, confirming the increased resolving power of genomic data compared to single-locus studies. Genomic structure is not equal across the species distribution. Approximately half the range of R. boylii consists of a single, relatively uniform population, while Sierra Nevada and coastal California clades are deeply, hierarchically substructured with biogeographic breaks observed in other codistributed taxa. Our results indicate that clades should serve as management units for R. boylii rather than previously suggested watershed boundaries, and that the near-extinct population from southwestern California is particularly diverged, exhibits the lowest genetic diversity, and is a critical conservation target for species recovery.
Collapse
Affiliation(s)
- Evan McCartney-Melstad
- Department of Ecology and Evolutionary Biology, La Kretz Center for California Conservation Science, and Institute of the Environment and Sustainability, University of California, Los Angeles, CA, USA.
| | - Müge Gidiş
- Department of Ecology and Evolutionary Biology, La Kretz Center for California Conservation Science, and Institute of the Environment and Sustainability, University of California, Los Angeles, CA, USA
- Kütahya School of Health, Dumlupınar University, Kütahya, Turkey
| | - H Bradley Shaffer
- Department of Ecology and Evolutionary Biology, La Kretz Center for California Conservation Science, and Institute of the Environment and Sustainability, University of California, Los Angeles, CA, USA
| |
Collapse
|
26
|
Kobayashi S, Abe S, Tomita M, Matsuki R. Fine-scale Genetic Structure and Estimation of Gene Flow of the Japanese Brown Frog Rana japonica in a Satoyama Landscape on the Western Side of Inba Lake, Eastern Japan. CURRENT HERPETOLOGY 2018. [DOI: 10.5358/hsj.37.11] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Soh Kobayashi
- Environmental Science Research Laboratory, Central Research Institute of Electric Power Industry, 1646 Abiko, Chiba 270-1194, JAPAN
| | - Seiya Abe
- Environmental Science Research Laboratory, Central Research Institute of Electric Power Industry, 1646 Abiko, Chiba 270-1194, JAPAN
| | - Motoshi Tomita
- Environmental Science Research Laboratory, Central Research Institute of Electric Power Industry, 1646 Abiko, Chiba 270-1194, JAPAN
| | - Rikyu Matsuki
- Environmental Science Research Laboratory, Central Research Institute of Electric Power Industry, 1646 Abiko, Chiba 270-1194, JAPAN
| |
Collapse
|
27
|
Advancing Understanding of Amphibian Evolution, Ecology, Behavior, and Conservation with Massively Parallel Sequencing. POPULATION GENOMICS 2018. [DOI: 10.1007/13836_2018_61] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
|
28
|
Rhoads EA, Williams PK, Krane CM. High inbreeding and low connectivity among Ambystoma texanum populations in fragmented Ohio forests. Ecol Evol 2017; 7:11135-11147. [PMID: 29299288 PMCID: PMC5743690 DOI: 10.1002/ece3.3637] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2017] [Revised: 10/15/2017] [Accepted: 10/18/2017] [Indexed: 11/10/2022] Open
Abstract
Habitat loss and fragmentation negatively impact the size and diversity of many natural populations. Woodland amphibians require connected aquatic and terrestrial habitats to complete their life cycle, and often rely on metapopulation structure for long-term persistence. Wetland loss and deforestation fragment amphibian populations, which may result in population isolation and its negative effects. The aim of this research was to analyze the population genetic structure of small-mouthed salamanders (Ambystoma texanum) in western Ohio, where agriculture is now the dominant land use. Salamander tail tissue was collected from eight breeding pools. Three pools occur in the same forest; the other five are in forest patches at distances ranging from 250 m to 20 km from one another. Eight microsatellite loci were amplified by PCR and genotyped for allele size. Observed heterozygosities were lower than expected in all sampled populations; the two most isolated sites (Ha1, Ha2) had the highest inbreeding coefficients. Ha2 also had the lowest mean number of alleles and was found to be genetically differentiated from populations to which our data analysis indicates it was historically connected by gene flow. The most distant site (Ha1) had the highest number of private alleles and showed genetic differentiation from other populations both historically and currently. Geographic distance between pools was strongly correlated with the number of private alleles in a population. The results suggest that population isolation results in decreased genetic diversity and that a breakdown of metapopulation structure due to landscape change may contribute to differentiation between once-connected populations.
Collapse
|
29
|
Faucher L, Hénocq L, Vanappelghem C, Rondel S, Quevillart R, Gallina S, Godé C, Jaquiéry J, Arnaud JF. When new human-modified habitats favour the expansion of an amphibian pioneer species: Evolutionary history of the natterjack toad (Bufo calamita) in a coal basin. Mol Ecol 2017; 26:4434-4451. [PMID: 28667796 DOI: 10.1111/mec.14229] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Revised: 05/17/2017] [Accepted: 06/05/2017] [Indexed: 11/29/2022]
Abstract
Human activities affect microevolutionary dynamics by inducing environmental changes. In particular, land cover conversion and loss of native habitats decrease genetic diversity and jeopardize the adaptive ability of populations. Nonetheless, new anthropogenic habitats can also promote the successful establishment of emblematic pioneer species. We investigated this issue by examining the population genetic features and evolutionary history of the natterjack toad (Bufo [Epidalea] calamita) in northern France, where populations can be found in native coastal habitats and coalfield habitats shaped by European industrial history, along with an additional set of European populations located outside this focal area. We predicted contrasting patterns of genetic structure, with newly settled coalfield populations departing from migration-drift equilibrium. As expected, coalfield populations showed a mosaic of genetically divergent populations with short-range patterns of gene flow, and native coastal populations indicated an equilibrium state with an isolation-by-distance pattern suggestive of postglacial range expansion. However, coalfield populations exhibited (i) high levels of genetic diversity, (ii) no evidence of local inbreeding or reduced effective population size and (iii) multiple maternal mitochondrial lineages, a genetic footprint depicting independent colonization events. Furthermore, approximate Bayesian computations suggested several evolutionary trajectories from ancient isolation in glacial refugia during the Pleistocene, with biogeographical signatures of recent expansion probably confounded by human-mediated mixing of different lineages. From an evolutionary and conservation perspective, this study highlights the ecological value of industrial areas, provided that ongoing regional gene flow is ensured within the existing lineage boundaries.
Collapse
Affiliation(s)
- Leslie Faucher
- Univ. Lille, CNRS, UMR 8198 - Evo-Eco-Paleo, Lille, France
| | - Laura Hénocq
- Univ. Lille, CNRS, UMR 8198 - Evo-Eco-Paleo, Lille, France
| | - Cédric Vanappelghem
- Univ. Lille, CNRS, UMR 8198 - Evo-Eco-Paleo, Lille, France.,Conservatoire d'espaces naturels du Nord et du Pas de Calais, Lillers, France
| | - Stéphanie Rondel
- Centre Permanent d'Initiatives pour l'Environnement - Chaîne des Terrils, Loos-en-Gohelle, France
| | - Robin Quevillart
- Groupe ornithologique et naturaliste du Nord - Pas-de-Calais, Lille, France
| | - Sophie Gallina
- Univ. Lille, CNRS, UMR 8198 - Evo-Eco-Paleo, Lille, France
| | - Cécile Godé
- Univ. Lille, CNRS, UMR 8198 - Evo-Eco-Paleo, Lille, France
| | - Julie Jaquiéry
- UMR CNRS 6553 - ECOBIO, Université de Rennes 1, Rennes Cedex, France
| | | |
Collapse
|
30
|
|
31
|
Poorten TJ, Knapp RA, Rosenblum EB. Population genetic structure of the endangered Sierra Nevada yellow-legged frog (Rana sierrae) in Yosemite National Park based on multi-locus nuclear data from swab samples. CONSERV GENET 2017. [DOI: 10.1007/s10592-016-0923-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
|
32
|
Genetic diversity and divergence in the endangered Cape Verde warbler Acrocephalus brevipennis. CONSERV GENET 2016. [DOI: 10.1007/s10592-016-0909-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
|
33
|
Development of Nuclear Microsatellite Loci and Mitochondrial Single Nucleotide Polymorphisms for the Natterjack Toad,Bufo(Epidalea)calamita(Bufonidae), Using Next Generation Sequencing and Competitive Allele Specific PCR (KASPar): Table 1. J Hered 2016; 107:660-665. [DOI: 10.1093/jhered/esw068] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2016] [Accepted: 09/14/2016] [Indexed: 11/14/2022] Open
|
34
|
Hinkson KM, Henry NL, Hensley NM, Richter SC. Initial founders of captive populations are genetically representative of natural populations in critically endangered dusky gopher frogs, Lithobates sevosus. Zoo Biol 2016; 35:378-384. [PMID: 27383748 DOI: 10.1002/zoo.21309] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2015] [Revised: 03/11/2016] [Accepted: 06/28/2016] [Indexed: 11/11/2022]
Abstract
The rapid rate of decline in amphibian populations has urged many researchers and conservationists to establish captive, or ex situ, populations. Such populations are guarded against effects of habitat loss and degradation, and if actively managed, can serve as a reservoir for rare alleles that might be lost in the wild. Without proper management, ex situ population sizes can dwindle and will no longer perform this function. The dusky gopher frog, Lithobates sevosus, is a critically endangered species, imperiled by habitat loss and population isolation. To assist in recovery of the species and prevent further genetic erosion, a captive breeding program was initiated. We investigated how well natural genetic variation was captured within the ex situ population and determined relatedness within each ex situ population. We genotyped individuals from two natural populations and two founding, captive populations to compare metrics of genetic variation and relatedness. The data show the initial founder populations are genetically representative of the natural populations, although variation is low in each, and that relatedness values are similar. Therefore, founding captive populations were successful at capturing genetic variation in the wild. Future research should continue to compare genetic variation of captive and natural populations to monitor efficacy of their management programs. Zoo Biol. 35:378-384, 2016. © 2016 Wiley Periodicals, Inc.
Collapse
Affiliation(s)
- Kristin M Hinkson
- Department of Biological Sciences, Eastern Kentucky University, Richmond, Kentucky
| | - Natochia L Henry
- Department of Biological Sciences, Eastern Kentucky University, Richmond, Kentucky
| | - Nina M Hensley
- Department of Biological Sciences, Eastern Kentucky University, Richmond, Kentucky
| | - Stephen C Richter
- Department of Biological Sciences, Eastern Kentucky University, Richmond, Kentucky. .,Division of Natural Areas, Eastern Kentucky University, Richmond, Kentucky.
| |
Collapse
|
35
|
Wayne RK, Shaffer HB. Hybridization and endangered species protection in the molecular era. Mol Ecol 2016; 25:2680-9. [DOI: 10.1111/mec.13642] [Citation(s) in RCA: 100] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2016] [Revised: 04/03/2016] [Accepted: 04/08/2016] [Indexed: 01/05/2023]
Affiliation(s)
- Robert K. Wayne
- Department of Ecology and Evolutionary Biology 610 Charles E. Young Dr. South University of California Los Angeles CA 90095 USA
| | - H. Bradley Shaffer
- Department of Ecology and Evolutionary Biology 610 Charles E. Young Dr. South University of California Los Angeles CA 90095 USA
- La Kretz Center for California Conservation Science Institute of the Environment and Sustainability 619 Charles E. Young Dr. South University of California Los Angeles CA 90095 USA
| |
Collapse
|