1
|
Cai L, Liu D, Yang F, Zhang R, Yun Q, Dao Z, Ma Y, Sun W. The chromosome-scale genome of Magnolia sinica (Magnoliaceae) provides insights into the conservation of plant species with extremely small populations (PSESP). Gigascience 2024; 13:giad110. [PMID: 38206588 PMCID: PMC10999834 DOI: 10.1093/gigascience/giad110] [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: 03/06/2023] [Revised: 07/28/2023] [Accepted: 12/04/2023] [Indexed: 01/12/2024] Open
Abstract
Magnolia sinica (Magnoliaceae) is a highly threatened tree endemic to southeast Yunnan, China. In this study, we generated for the first time a high-quality chromosome-scale genome sequence from M. sinica, by combining Illumina and ONT data with Hi-C scaffolding methods. The final assembled genome size of M. sinica was 1.84 Gb, with a contig N50 of ca. 45 Mb and scaffold N50 of 92 Mb. Identified repeats constituted approximately 57% of the genome, and 43,473 protein-coding genes were predicted. Phylogenetic analysis shows that the magnolias form a sister clade with the eudicots and the order Ceratophyllales, while the monocots are sister to the other core angiosperms. In our study, a total of 21 individuals from the 5 remnant populations of M. sinica, as well as 22 specimens belonging to 8 related Magnoliaceae species, were resequenced. The results showed that M. sinica had higher genetic diversity (θw = 0.01126 and θπ = 0.01158) than other related species in the Magnoliaceae. However, population structure analysis suggested that the genetic differentiation among the 5 M. sinica populations was very low. Analyses of the demographic history of the species using different models consistently revealed that 2 bottleneck events occurred. The contemporary effective population size of M. sinica was estimated to be 10.9. The different patterns of genetic loads (inbreeding and numbers of deleterious mutations) suggested constructive strategies for the conservation of these 5 different populations of M. sinica. Overall, this high-quality genome will be a valuable genomic resource for conservation of M. sinica.
Collapse
Affiliation(s)
- Lei Cai
- Yunnan Key Laboratory for Integrative Conservation of Plant Species with Extremely Small Populations/Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
| | - Detuan Liu
- Yunnan Key Laboratory for Integrative Conservation of Plant Species with Extremely Small Populations/Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
- University of Chinese Academy of Sciences, 100049 Beijing, China
| | - Fengmao Yang
- Yunnan Key Laboratory for Integrative Conservation of Plant Species with Extremely Small Populations/Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
- University of Chinese Academy of Sciences, 100049 Beijing, China
| | - Rengang Zhang
- Yunnan Key Laboratory for Integrative Conservation of Plant Species with Extremely Small Populations/Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
- University of Chinese Academy of Sciences, 100049 Beijing, China
| | - Quanzheng Yun
- Department of Bioinformatics, Ori (Shandong) Gene Science and Technology Co., Ltd., Weifang, 261000, Shandong, China
| | - Zhiling Dao
- Yunnan Key Laboratory for Integrative Conservation of Plant Species with Extremely Small Populations/Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
| | - Yongpeng Ma
- Yunnan Key Laboratory for Integrative Conservation of Plant Species with Extremely Small Populations/Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
| | - Weibang Sun
- Yunnan Key Laboratory for Integrative Conservation of Plant Species with Extremely Small Populations/Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
| |
Collapse
|
2
|
Dutcher KE, Nussear KE, Heaton JS, Esque TC, Vandergast AG. Move it or lose it: Predicted effects of culverts and population density on Mojave desert tortoise (Gopherus agassizii) connectivity. PLoS One 2023; 18:e0286820. [PMID: 37768995 PMCID: PMC10538755 DOI: 10.1371/journal.pone.0286820] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Accepted: 05/24/2023] [Indexed: 09/30/2023] Open
Abstract
Roadways and railways can reduce wildlife movements across landscapes, negatively impacting population connectivity. Connectivity may be improved by structures that allow safe passage across linear barriers, but connectivity could be adversely influenced by low population densities. The Mojave desert tortoise is threatened by habitat loss, fragmentation, and population declines. The tortoise continues to decline as disturbance increases across the Mojave Desert in the southwestern United States. While underground crossing structures, like hydrological culverts, have begun receiving attention, population density has not been considered in tortoise connectivity. Our work asks a novel question: How do culverts and population density affect connectivity and potentially drive genetic and demographic patterns? To explore the role of culverts and population density, we used agent-based spatially explicit forward-in-time simulations of gene flow. We constructed resistance surfaces with a range of barriers to movement and representative of tortoise habitat with anthropogenic disturbance. We predicted connectivity under variable population densities. Simulations were run for 200 non-overlapping generations (3400 years) with 30 replicates using 20 microsatellite loci. We evaluated population genetic structure and diversity and found that culverts would not entirely negate the effects of linear barriers, but gene flow improved. Our results also indicated that density is important for connectivity. Low densities resulted in declines regardless of the landscape barrier scenario (> 75% population census size, > 97% effective population size). Results from our simulation using current anthropogenic disturbance predicted decreased population connectivity over time. Genetic and demographic effects were detectable within five generations (85 years) following disturbance with estimated losses in effective population size of 69%. The pronounced declines in effective population size indicate this could be a useful monitoring metric. We suggest management strategies that improve connectivity, such as roadside fencing tied to culverts, conservation areas in a connected network, and development restricted to disturbed areas.
Collapse
Affiliation(s)
- Kirsten E. Dutcher
- Department of Geography, University of Nevada–Reno, Reno, Nevada, United States of America
| | - Kenneth E. Nussear
- Department of Geography, University of Nevada–Reno, Reno, Nevada, United States of America
| | - Jill S. Heaton
- Department of Geography, University of Nevada–Reno, Reno, Nevada, United States of America
| | - Todd C. Esque
- United States Geological Survey, Western Ecological Research Center, Boulder City, Nevada, United States of America
| | - Amy G. Vandergast
- United States Geological Survey, Western Ecological Research Center, San Diego, California, United States of America
| |
Collapse
|
3
|
Hambálková L, Policht R, Cukor J, Hart V, Ševčík R. Black Grouse Hissing Calls Show Geographic Variability across the Distribution Area. Animals (Basel) 2023; 13:1844. [PMID: 37889765 PMCID: PMC10251829 DOI: 10.3390/ani13111844] [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: 05/08/2023] [Revised: 05/27/2023] [Accepted: 05/29/2023] [Indexed: 10/29/2023] Open
Abstract
The black grouse is a species whose population development requires constant monitoring due to a rapidly declining trend, especially in Central Europe. Variability in the voices of geographically separated populations can aid in counting within individual populations. This has been investigated with the black grouse. However, the variability of the acoustic behavior of black grouse between populations was investigated for the first time. In total, 82 male black grouse were recorded during the lekking season in four countries: the Czech Republic, Scotland, Finland, and Russia. We analyzed recordings of hissing calls, i.e., the non-vocal signal. DFA analysis correctly classified almost 70% of the recordings. The results indicate a certain degree of difference between the grouse populations from the four countries examined. The mean frequency of hissing calls for populations was 1410.71 ± 170.25 Hz, 1473.89 ± 167.59 Hz, 1544.38 ± 167.60 Hz, and 1826.34 ± 319.23 Hz in the Czech Republic, Finland, Russia, and Scotland, respectively. Populations from Scotland and Russia have greater intra-variability compared to grouse from the Czech Republic and Finland, indicating that population density is not the principal factor in the geographical variability of black grouse hissing calls. Range-level differences enhance knowledge and facilitate the assessment of species evolution.
Collapse
Affiliation(s)
- Lucie Hambálková
- Department of Game Management and Wildlife Biology, Faculty of Forestry, Czech University of Life Sciences, Kamýcká 129, Suchdol, 165 00 Praha, Czech Republic; (R.P.); (V.H.)
- Forestry and Game Management Research Institute, Strnady 136, 252 02 Jíloviště, Czech Republic;
| | - Richard Policht
- Department of Game Management and Wildlife Biology, Faculty of Forestry, Czech University of Life Sciences, Kamýcká 129, Suchdol, 165 00 Praha, Czech Republic; (R.P.); (V.H.)
| | - Jan Cukor
- Department of Game Management and Wildlife Biology, Faculty of Forestry, Czech University of Life Sciences, Kamýcká 129, Suchdol, 165 00 Praha, Czech Republic; (R.P.); (V.H.)
- Forestry and Game Management Research Institute, Strnady 136, 252 02 Jíloviště, Czech Republic;
| | - Vlastimil Hart
- Department of Game Management and Wildlife Biology, Faculty of Forestry, Czech University of Life Sciences, Kamýcká 129, Suchdol, 165 00 Praha, Czech Republic; (R.P.); (V.H.)
| | - Richard Ševčík
- Forestry and Game Management Research Institute, Strnady 136, 252 02 Jíloviště, Czech Republic;
| |
Collapse
|
4
|
Policht R, Hart V. Individual and Geographic Variation in Non-Harmonic Phases of Male Capercaillie ( Tetrao urogallus) Song. Animals (Basel) 2023; 13:ani13040765. [PMID: 36830551 PMCID: PMC9952776 DOI: 10.3390/ani13040765] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2022] [Revised: 02/12/2023] [Accepted: 02/13/2023] [Indexed: 02/22/2023] Open
Abstract
Individually distinct acoustic signals, produced mainly as tonal and harmonic sounds, have been recorded in many species; however, non-tonal 'noisy' signals have received little attention or have not been studied in detail. The capercaillies (Tetrao urogallus) produce complex courtship songs composed of non-tonal noisy signals in four discrete phases. We analyzed recordings from 24 captive male capercaillies in breeding centres in the Czech Republic, Poland, and Germany, and songs from wild males in Sweden, Norway, Finland, and Estonia to test whether a non-harmonic song can encode individual-specific information. We also analyzed the intra-population variation of the male song from three separate areas: Carpathian (Polish and Czech Beskid), Sumava, and Boreal (boreal range of species distribution). Temporal and frequency characteristics can reliably distinguish capercaillies at the individual level (91.7%). DFA model testing geographic variation assigned 91% of songs to the correct area (Carpathian, Sumava, Boreal). The cluster analysis revealed that males from the Boreal area formed a distinct cluster. Our analysis shows clear geographical patterns among our study males and may provide a valuable marker for identifying inter-population dynamics and could help to characterize the evolutionary histories of wood grouse. We discuss the potential use of this marker as a non-invasive monitoring tool for captive and free-roaming capercaillies.
Collapse
|
5
|
Genetic and demographic consequences of range contraction patterns during biological annihilation. Sci Rep 2023; 13:1691. [PMID: 36717685 PMCID: PMC9886963 DOI: 10.1038/s41598-023-28927-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Accepted: 01/27/2023] [Indexed: 01/31/2023] Open
Abstract
Species range contractions both contribute to, and result from, biological annihilation, yet do not receive the same attention as extinctions. Range contractions can lead to marked impacts on populations but are usually characterized only by reduction in extent of range. For effective conservation, it is critical to recognize that not all range contractions are the same. We propose three distinct patterns of range contraction: shrinkage, amputation, and fragmentation. We tested the impact of these patterns on populations of a generalist species using forward-time simulations. All three patterns caused 86-88% reduction in population abundance and significantly increased average relatedness, with differing patterns in declines of nucleotide diversity relative to the contraction pattern. The fragmentation pattern resulted in the strongest effects on post-contraction genetic diversity and structure. Defining and quantifying range contraction patterns and their consequences for Earth's biodiversity would provide useful and necessary information to combat biological annihilation.
Collapse
|
6
|
ENDOPARASITES IN WESTERN CAPERCAILLIES (TETRAO UROGALLUS) AND BLACK GROUSE (TETRAO TETRIX) KEPT IN VARIOUS TYPES OF AVIARIES. J Wildl Dis 2021; 58:114-121. [PMID: 34714912 DOI: 10.7589/jwd-d-21-00017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Accepted: 06/22/2021] [Indexed: 11/20/2022]
Abstract
Gallinaceous birds, including Western Capercaillies (Tetrao urogallus) and Black Grouse (Tetrao tetrix), are kept in aviaries and reintroduced to natural habitats as a part of ongoing measures to protect these endangered species. Although parasitic loads can immensely affect reintroduction success of these species, little is known about how the infestation level varies in birds reared with different methods. The aim of this study was to determine the prevalence of endoparasites in fecal samples collected from Galliformes kept in various types of aviaries and transported to reintroduction sites. Most parasitic infections in the examined birds were caused by protozoa of the genus Eimeria, including Eimeria lyruri and Eimeria procera in Western Capercaillies, and E. lyruri, Eimeria nadsoni, and Eimeria tetricis in Black Grouse, which also hosted nematodes of the Capillaria spp. and Ascaridia galli. The prevalence of parasites varied across different types of aviaries. In permanent aviaries, Eimeria spp. was detected in 36% and 35% of the fecal samples collected from Western Capercaillies and Black Grouse, whereas Capillaria spp. were identified in 41% and 69% of the samples, respectively. The prevalence of the identified parasites increased in permanent aviaries on the second sampling date. In contrast, birds kept in seminatural free-flight aviaries in line with the "born to be free" rearing method had a lower prevalence of these parasites. Galliformes housed in seminatural aviaries may be better prepared for reintroduction to their natural habitats.
Collapse
|
7
|
Hambálková L, Policht R, Horák J, Hart V. Acoustic individuality in the hissing calls of the male black grouse ( Lyrurus tetrix). PeerJ 2021; 9:e11837. [PMID: 34589291 PMCID: PMC8435199 DOI: 10.7717/peerj.11837] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Accepted: 07/01/2021] [Indexed: 11/20/2022] Open
Abstract
Acoustic individuality may well play a big role during the mating season of many birds. Black grouse (Lyrurus tetrix) produces two different long-distance calls during mating on leks: rookooing and hissing calls. The first one represents low frequency series of bubbling sounds and the second one represents hissing sound. This hissing represents a signal not produced by the syrinx. We analyzed 426 hissing calls from 24 individuals in Finland and Scotland. We conducted cross-validated discrimination analyses (DFA). The discrimination model classified each call with almost 78% accuracy (conventional result) and the validated DFA revealed 71% output, that is much higher than classification by chance (4%). The most important variables were Frequency 95%, 1st Quartile Frequency, Aggregate Entropy and Duration 90%. We also tested whether between individual variation is higher than within individual variation using PIC (Potential for individual coding) and we found that all acoustic parameters had PIC > 1. We confirmed that hissing call of black grouse is individually distinct. In comparison to the signals produced by the syrinx, non-vocal sounds have been studied rarely and according to our knowledge, this is the second evidence of vocal individuality in avian hissing sounds which are not produced by syrinx. Individuality in the vocalization of the male black grouse may aid females in mating partner selection, and for males it may enable competitor recognition and assessment. Individually distinct hissing calls could be of possible use to monitor individuals on leks. Such a method could overcome problems during traditional monitoring methods of this species, when one individual can be counted multiple times, because catching and traditional marking is problematic in this species.
Collapse
Affiliation(s)
- Lucie Hambálková
- Department of Game Management and Wildlife Biology, Faculty of Forestry and Wood Sciences, Czech University of Life Sciences, Prague, Czech Republic
| | - Richard Policht
- Department of Game Management and Wildlife Biology, Faculty of Forestry and Wood Sciences, Czech University of Life Sciences, Prague, Czech Republic
| | - Jiří Horák
- Department of Game Management and Wildlife Biology, Faculty of Forestry and Wood Sciences, Czech University of Life Sciences, Prague, Czech Republic
| | - Vlastimil Hart
- Department of Game Management and Wildlife Biology, Faculty of Forestry and Wood Sciences, Czech University of Life Sciences, Prague, Czech Republic
| |
Collapse
|
8
|
Effects of Forestry Intensification and Conservation on Green Infrastructures: A Spatio-Temporal Evaluation in Sweden. LAND 2021. [DOI: 10.3390/land10050531] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
There is a rivalry between policies on intensification of forest management to meet the demands of a growing bioeconomy, and policies on green infrastructure functionality. Evaluation of the net effects of different policy instruments on real-world outcomes is crucial. First, we present data on final felling rates in wood production landscapes and stand age distribution dynamic in two case study regions, and changes in dead wood amounts in Sweden. Second, the growth of formally protected areas was compiled and changes in functional connectivity analysed in these regions, and the development of dead wood and green tree retention in Sweden was described. The case studies were the counties Dalarna and Jämtland (77,000 km2) representing an expanding frontier of boreal forest transformation. In the wood production landscape, official final felling rates averaged 0.84%/year, extending the regional timber frontier. The amount of forest <60 years old increased from 27–34% in 1955 to 60–65% in 2017. The amounts of dead wood, a key forest naturalness indicator, declined from 1994 to 2016 in north Sweden, and increased in the south, albeit both at levels far below evidence-based biodiversity targets. Formal forest protection grew rapidly in the two counties from 1968 to 2020 but reached only 4% of productive forests. From 2000 to 2019, habitat network functionality for old Scots pine declined by 15–41%, and Norway spruce by 15–88%. There were mixed trends for dead wood and tree retention at the stand scale. The net result of the continued transformation of near-natural forest remnants and conservation efforts was negative at the regional and landscape levels, but partly positive at the stand scale. However, at all three scales, habitat amounts were far below critical thresholds for the maintenance of viable populations of species, let alone ecological integrity. Collaboration among stakeholder categories should reject opinionated narratives, and instead rely on evidence-based knowledge about green infrastructure pressures, responses, and states.
Collapse
|
9
|
Pârâu LG, Wink M. Common patterns in the molecular phylogeography of western palearctic birds: a comprehensive review. JOURNAL OF ORNITHOLOGY 2021; 162:937-959. [PMID: 34007780 PMCID: PMC8118378 DOI: 10.1007/s10336-021-01893-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/03/2020] [Revised: 04/26/2021] [Accepted: 05/02/2021] [Indexed: 06/12/2023]
Abstract
UNLABELLED A plethora of studies have offered crucial insights in the phylogeographic status of Western Palearctic bird species. However, an overview integrating all this information and analyzing the combined results is still missing. In this study, we compiled all published peer-reviewed and grey literature available on the phylogeography of Western Palearctic bird species. Our literature review indicates a total number of 198 studies, with the overwhelming majority published as journal articles (n = 186). In total, these literature items offer information on 145 bird species. 85 of these species are characterized by low genetic differentiation, 46 species indicate genetic variation but no geographic structuring i.e. panmixia, while 14 species show geographically distinct lineages and haplotypes. Majority of bird species inhabiting the Western Palearctic display genetic admixture. The glaciation cycles in the past few million years were pivotal factors in shaping this situation: during warm periods many species expanded their distribution range to the north over wide areas of Eurasia; whereas, during ice ages most areas were no longer suitable and species retreated to refugia, where lineages mixed. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s10336-021-01893-x.
Collapse
Affiliation(s)
- Liviu G. Pârâu
- Institute of Pharmacy and Molecular Biotechnology, Department Biology, Heidelberg University, Im Neuenheimer Feld 364, 4 OG, Heidelberg, Germany
- Present Address: SARS-CoV-2 Data Evaluation Office, Eurofins Genomics Europe Applied Genomics GmbH, Anzinger Straße 7a, 85560 Ebersberg, Germany
| | - Michael Wink
- Institute of Pharmacy and Molecular Biotechnology, Department Biology, Heidelberg University, Im Neuenheimer Feld 364, 4 OG, Heidelberg, Germany
| |
Collapse
|
10
|
Magota K, Sakaguchi S, Hirota SK, Tsunamoto Y, Suyama Y, Akai K, Setoguchi H. Comparative analysis of spatial genetic structures in sympatric populations of two riparian plants, Saxifraga acerifolia and Saxifraga fortunei. AMERICAN JOURNAL OF BOTANY 2021; 108:680-693. [PMID: 33881773 DOI: 10.1002/ajb2.1644] [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: 11/06/2019] [Accepted: 12/09/2020] [Indexed: 06/12/2023]
Abstract
PREMISE The genetic structure between plant populations is facilitated by the spatial population arrangement and limited dispersal of seed and pollen. Saxifraga acerifolia, a local endemic species in Japan, is a habitat specialist that is confined to waterfalls in riparian environments. Its sister species, Saxifraga fortunei, is a generalist that is widely distributed along riverbanks. Here, we examined sympatric populations of the two Saxifraga species to test whether the differences in habitat preference and colonization process influenced regional and local genetic structures. METHODS To reveal genetic structures, we examined chloroplast microsatellite variations and genome-wide nucleotide polymorphisms obtained by genotyping by sequencing. We also estimated the gene flow among and within populations and performed landscape genetic analyses to evaluate seed and pollen movement and the extent of genetic isolation related to geographic distance and/or habitat differences. RESULTS We found strong genetic structure in the specialist S. acerifolia, even on a small spatial scale (<1 km part); each population on a different waterfall in one river system had a completely different predominant haplotype. By contrast, the generalist S. fortunei showed no clear genetic differentiation. CONCLUSIONS Our findings suggest that the level of genetic isolation was increased in S. acerifolia by the spatially fragmented habitat and limited seed and pollen dispersal over waterfalls. Habitat differentiation between the sister taxa could have contributed to the different patterns of gene flow and then shaped the contrasting genetic structures.
Collapse
Affiliation(s)
- Kana Magota
- Graduate School of Human and Environmental Studies, Kyoto University, Yoshida Nihonmatsu-cho, Sakyo-ku, Kyoto, Kyoto, 606-8501, Japan
| | - Shota Sakaguchi
- Graduate School of Human and Environmental Studies, Kyoto University, Yoshida Nihonmatsu-cho, Sakyo-ku, Kyoto, Kyoto, 606-8501, Japan
| | - Shun K Hirota
- Kawatabi Field Science Center, Graduate School of Agricultural Science, Tohoku University, 232-3 Yomogida, Naruko-onsen, Osaki, Miyagi, 989-6711, Japan
| | - Yoshihiro Tsunamoto
- Tohoku Research Center, Forestry and Forest Products Research Institute, 92-25 Nabeyashiki, Shimo-kuriyagawa, Morioka, Iwate, 020-0123, Japan
| | - Yoshihisa Suyama
- Kawatabi Field Science Center, Graduate School of Agricultural Science, Tohoku University, 232-3 Yomogida, Naruko-onsen, Osaki, Miyagi, 989-6711, Japan
| | - Kensei Akai
- International Center for Island Studies Amami Station, Kagoshima University, Naze-Minatomachi 15-1, Amami, Kagoshima, 894-0026, Japan
| | - Hiroaki Setoguchi
- Graduate School of Human and Environmental Studies, Kyoto University, Yoshida Nihonmatsu-cho, Sakyo-ku, Kyoto, Kyoto, 606-8501, Japan
| |
Collapse
|
11
|
Kunz F, Kohnen A, Nopp-Mayr U, Coppes J. Past, present, future: tracking and simulating genetic differentiation over time in a closed metapopulation system. CONSERV GENET 2021. [DOI: 10.1007/s10592-021-01342-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
AbstractGenetic differentiation plays an essential role in the assessment of metapopulation systems of conservation concern. Migration rates affect the degree of genetic differentiation between subpopulations, with increasing genetic differentiation leading to increasing extinction risk. Analyses of genetic differentiation repeated over time together with projections into the future are therefore important to inform conservation. We investigated genetic differentiation in a closed metapopulation system of an obligate forest grouse, the Western capercaillie Tetrao urogallus, by comparing microsatellite population structure between a historic and a recent time period. We found an increase in genetic differentiation over a period of approximately 15 years. Making use of forward simulations accounting for population dynamics and genetics from both time periods, we explored future genetic differentiation by implementing scenarios of differing migration rates. Using migration rates derived from the recent dataset, simulations predicted further increase of genetic differentiation by 2050. We then examined effects of two realistic yet hypothetical migration scenarios on genetic differentiation. While isolation of a subpopulation led to overall increased genetic differentiation, the re-establishment of connectivity between two subpopulations maintained genetic differentiation at recent levels. Our results emphasize the importance of maintaining connectivity between subpopulations in order to prevent further genetic differentiation and loss of genetic variation. The simulation set-up we developed is highly adaptable and will aid researchers and conservationists alike in anticipating consequences of conservation strategies for metapopulation systems.
Collapse
|
12
|
Demography, genetics, and decline of a spatially structured population of lekking bird. Oecologia 2021; 195:117-129. [PMID: 33392789 DOI: 10.1007/s00442-020-04808-4] [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: 02/18/2020] [Accepted: 11/16/2020] [Indexed: 10/22/2022]
Abstract
Understanding the mechanisms underlying population decline is a critical challenge for conservation biologists. Both deterministic (e.g. habitat loss, fragmentation, and Allee effect) and stochastic (i.e. demographic and environmental stochasticity) demographic processes are involved in population decline. Simultaneously, a decrease of population size has far-reaching consequences for genetics of populations by increasing the risk of inbreeding and the strength of genetic drift, which together inevitably results in a loss of genetic diversity and a reduced effective population size ([Formula: see text]). These genetic factors may retroactively affect vital rates (a phenomenon coined 'inbreeding depression'), reduce population growth, and accelerate demographic decline. To date, most studies that have examined the demographic and genetic processes driving the decline of wild populations have neglected their spatial structure. In this study, we examined demographic and genetic factors involved in the decline of a spatially structured population of a lekking bird, the western capercaillie (Tetrao urogallus). To address this issue, we collected capture-recapture and genetic data over a 6-years period in the Vosges Mountains (France). Our study showed that the population of T. urogallus experienced a severe decline between 2010 and 2015. We did not detect any Allee effect on survival and recruitment. By contrast, individuals of both sexes dispersed to avoid small subpopulations, thus suggesting a potential behavioral response to a mate finding Allee effect. In parallel to this demographic decline, the population showed low levels of genetic diversity, high inbreeding and low effective population sizes at both subpopulation and population levels. Despite this, we did not detect evidence of inbreeding depression: neither adult survival nor recruitment were affected by individual inbreeding level. Our study underlines the benefit from combining demographic and genetic approaches to investigate processes that are involved in population decline.
Collapse
|
13
|
Effects of habitat fragment size and isolation on the density and genetics of urban red-backed salamanders (Plethodon cinereus). Urban Ecosyst 2020. [DOI: 10.1007/s11252-020-00958-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
|
14
|
DeSilva R, Dodd RS. Fragmented and isolated: limited gene flow coupled with weak isolation by environment in the paleoendemic giant sequoia (Sequoiadendron giganteum). AMERICAN JOURNAL OF BOTANY 2020; 107:45-55. [PMID: 31883111 DOI: 10.1002/ajb2.1406] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2019] [Accepted: 11/13/2019] [Indexed: 06/10/2023]
Abstract
PREMISE Patterns of genetic structure across a species' range reflect the long-term interplay between genetic drift, gene flow, and selection. Given the importance of gene flow in preventing the loss of diversity through genetic drift among spatially isolated populations, understanding the dynamics of gene flow and the factors that influence connectivity across a species' range is a major goal for conservation of genetic diversity. Here we present a detailed look at gene flow dynamics of Sequoiadendron giganteum, a paleoendemic tree species that will likely face numerous threats due to climate change. METHODS We used microsatellite markers to examine nineteen populations of S. giganteum for patterns of genetic structure and to estimate admixture and rates of gene flow between eight population pairs. Also, we used Generalized Dissimilarity Models to elucidate landscape factors that shape genetic differentiation among populations. RESULTS We found minimal gene flow between adjacent groves in the northern disjunct range. In most of the southern portion of the range, groves showed a signal of connectivity which degrades to isolation in the extreme south. Geographic distance was the most important predictor of genetic dissimilarity across the range, with environmental conditions related to precipitation and temperature explaining a small, but significant, portion of the genetic variance. CONCLUSIONS Due to their isolation and unique genetic composition, northern populations of S. giganteum should be considered a high conservation priority. In this region, we suggest germplasm conservation as well as restoration planting to enhance genetic diversity.
Collapse
Affiliation(s)
- Rainbow DeSilva
- Department of Environmental Science, Policy, and Management, University of California at Berkeley, Berkeley, California, USA
| | - Richard S Dodd
- Department of Environmental Science, Policy, and Management, University of California at Berkeley, Berkeley, California, USA
| |
Collapse
|
15
|
|
16
|
Thompson LM, Klütsch CFC, Manseau M, Wilson PJ. Spatial differences in genetic diversity and northward migration suggest genetic erosion along the boreal caribou southern range limit and continued range retraction. Ecol Evol 2019; 9:7030-7046. [PMID: 31380031 PMCID: PMC6662424 DOI: 10.1002/ece3.5269] [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: 12/12/2018] [Revised: 04/24/2019] [Accepted: 04/26/2019] [Indexed: 11/12/2022] Open
Abstract
With increasing human activities and associated landscape changes, distributions of terrestrial mammals become fragmented. These changes in distribution are often associated with reduced population sizes and loss of genetic connectivity and diversity (i.e., genetic erosion) which may further diminish a species' ability to respond to changing environmental conditions and lead to local population extinctions. We studied threatened boreal caribou (Rangifer tarandus caribou) populations across their distribution in Ontario/Manitoba (Canada) to assess changes in genetic diversity and connectivity in areas of high and low anthropogenic activity. Using data from >1,000 caribou and nine microsatellite loci, we assessed population genetic structure, genetic diversity, and recent migration rates using a combination of network and population genetic analyses. We used Bayesian clustering analyses to identify population genetic structure and explored spatial and temporal variation in those patterns by assembling networks based on R ST and F ST as historical and contemporary genetic edge distances, respectively. The Bayesian clustering analyses identified broad-scale patterns of genetic structure and closely aligned with the R ST network. The F ST network revealed substantial contemporary genetic differentiation, particularly in areas presenting contemporary anthropogenic disturbances and habitat fragmentation. In general, relatively lower genetic diversity and greater genetic differentiation were detected along the southern range limit, differing from areas in the northern parts of the distribution. Moreover, estimation of migration rates suggested a northward movement of animals away from the southern range limit. The patterns of genetic erosion revealed in our study suggest ongoing range retraction of boreal caribou in central Canada.
Collapse
Affiliation(s)
- Laura M. Thompson
- Natural Resources DNA Profiling and Forensic CentreTrent UniversityPeterboroughOntarioCanada
- Present address:
U.S. Geological SurveyNational Climate Adaptation Science CenterRestonVirginia
| | - Cornelya F. C. Klütsch
- Natural Resources DNA Profiling and Forensic CentreTrent UniversityPeterboroughOntarioCanada
- Present address:
Division of Environmental Research in the Barents RegionNorwegian Institute of Bioeconomy Research (NIBIO)SvanvikNorway
| | - Micheline Manseau
- Natural Resources DNA Profiling and Forensic CentreTrent UniversityPeterboroughOntarioCanada
- Natural Resources InstituteUniversity of ManitobaWinnipegManitobaCanada
- Landscape Science and TechnologyEnvironment and Climate Change CanadaOttawaOntarioCanada
| | - Paul J. Wilson
- Natural Resources DNA Profiling and Forensic CentreTrent UniversityPeterboroughOntarioCanada
| |
Collapse
|
17
|
Lamb CT, Ford AT, Proctor MF, Royle JA, Mowat G, Boutin S. Genetic tagging in the Anthropocene: scaling ecology from alleles to ecosystems. ECOLOGICAL APPLICATIONS : A PUBLICATION OF THE ECOLOGICAL SOCIETY OF AMERICA 2019; 29:e01876. [PMID: 30913353 DOI: 10.1002/eap.1876] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Revised: 01/04/2019] [Accepted: 02/01/2019] [Indexed: 06/09/2023]
Abstract
The Anthropocene is an era of marked human impact on the world. Quantifying these impacts has become central to understanding the dynamics of coupled human-natural systems, resource-dependent livelihoods, and biodiversity conservation. Ecologists are facing growing pressure to quantify the size, distribution, and trajectory of wild populations in a cost-effective and socially acceptable manner. Genetic tagging, combined with modern computational and genetic analyses, is an under-utilized tool to meet this demand, especially for wide-ranging, elusive, sensitive, and low-density species. Genetic tagging studies are now revealing unprecedented insight into the mechanisms that control the density, trajectory, connectivity, and patterns of human-wildlife interaction for populations over vast spatial extents. Here, we outline the application of, and ecological inferences from, new analytical techniques applied to genetically tagged individuals, contrast this approach with conventional methods, and describe how genetic tagging can be better applied to address outstanding questions in ecology. We provide example analyses using a long-term genetic tagging dataset of grizzly bears in the Canadian Rockies. The genetic tagging toolbox is a powerful and overlooked ensemble that ecologists and conservation biologists can leverage to generate evidence and meet the challenges of the Anthropocene.
Collapse
Affiliation(s)
- Clayton T Lamb
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, T6G 2E9, Canada
| | - Adam T Ford
- Department of Biology, University of British Columbia, Kelowna, British Columbia, V1V 1V7, Canada
| | | | - J Andrew Royle
- Patuxent Wildlife Research Center, U.S. Geological Survey, Laurel, Maryland, 20708, USA
| | - Garth Mowat
- Ministry of Forests, Lands and Natural Resource Operations, Nelson, British Columbia, V1L 4K3, Canada
- Earth and Environmental Sciences, University of British Columbia, Kelowna, British Columbia, V1V 1V7, Canada
| | - Stan Boutin
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, T6G 2E9, Canada
| |
Collapse
|
18
|
Bouchard C, Tessier N, Lapointe FJ. Watersheds influence the wood turtle’s (Glyptemys insculpta) genetic structure. CONSERV GENET 2019. [DOI: 10.1007/s10592-019-01169-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
|
19
|
Habibzadeh N, Storch I, Ludwig T. Differential habitat associations in peripheral populations of threatened species: The case of the Caucasian grouse. Ecol Res 2019. [DOI: 10.1111/1440-1703.1068] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Nader Habibzadeh
- Department of Environmental Science, Tabriz BranchIslamic Azad University Tabriz Iran
| | - Ilse Storch
- Chair of Wildlife Ecology and Management, Faculty of Environment and Natural ResourcesUniversity of Freiburg Freiburg Germany
| | - Tobias Ludwig
- Chair of Wildlife Ecology and Management, Faculty of Environment and Natural ResourcesUniversity of Freiburg Freiburg Germany
- Bavarian Regional Authority of Environment/Ornithological Station Garmisch‐Partenkirchen Garmisch‐Partenkirchen, Bavaria Germany
| |
Collapse
|
20
|
Jahner JP, Matocq MD, Malaney JL, Cox M, Wolff P, Gritts MA, Parchman TL. The genetic legacy of 50 years of desert bighorn sheep translocations. Evol Appl 2019; 12:198-213. [PMID: 30697334 PMCID: PMC6346675 DOI: 10.1111/eva.12708] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2018] [Revised: 08/16/2018] [Accepted: 08/18/2018] [Indexed: 12/20/2022] Open
Abstract
Conservation biologists have increasingly used translocations to mitigate population declines and restore locally extirpated populations. Genetic data can guide the selection of source populations for translocations and help evaluate restoration success. Bighorn sheep (Ovis canadensis) are a managed big game species that suffered widespread population extirpations across western North America throughout the early 1900s. Subsequent translocation programs have successfully re-established many formally extirpated bighorn herds, but most of these programs pre-date genetically informed management practices. The state of Nevada presents a particularly well-documented case of decline followed by restoration of extirpated herds. Desert bighorn sheep (O. c. nelsoni) populations declined to less than 3,000 individuals restricted to remnant herds in the Mojave Desert and a few locations in the Great Basin Desert. Beginning in 1968, the Nevada Department of Wildlife translocated ~2,000 individuals from remnant populations to restore previously extirpated areas, possibly establishing herds with mixed ancestries. Here, we examined genetic diversity and structure among remnant herds and the genetic consequences of translocation from these herds using a genotyping-by-sequencing approach to genotype 17,095 loci in 303 desert bighorn sheep. We found a signal of population genetic structure among remnant Mojave Desert populations, even across geographically proximate mountain ranges. Further, we found evidence of a genetically distinct, potential relict herd from a previously hypothesized Great Basin lineage of desert bighorn sheep. The genetic structure of source herds was clearly reflected in translocated populations. In most cases, herds retained genetic evidence of multiple translocation events and subsequent admixture when founded from multiple remnant source herds. Our results add to a growing literature on how population genomic data can be used to guide and monitor restoration programs.
Collapse
Affiliation(s)
| | - Marjorie D. Matocq
- Department of Natural Resources and Environmental Science, and Program in Ecology, Evolution, and Conservation BiologyUniversity of NevadaRenoNevada
| | - Jason L. Malaney
- Department of BiologyAustin Peay State UniversityClarksvilleTennessee
| | - Mike Cox
- Nevada Department of Wildlife, and Wild Sheep Working GroupWestern Association of Fish and Wildlife AgenciesRenoNevada
| | | | | | - Thomas L. Parchman
- Department of Biology, and Program in Ecology, Evolution, and Conservation BiologyUniversity of NevadaRenoNevada
| |
Collapse
|
21
|
Coppes J, Kämmerle JL, Willert M, Kohnen A, Palme R, Braunisch V. The importance of individual heterogeneity for interpreting faecal glucocorticoid metabolite levels in wildlife studies. J Appl Ecol 2018. [DOI: 10.1111/1365-2664.13140] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Joy Coppes
- Wildlife Ecology; Forest Research Institute of Baden-Wuerttemberg FVA; Freiburg Germany
| | - Jim-Lino Kämmerle
- Wildlife Ecology; Forest Research Institute of Baden-Wuerttemberg FVA; Freiburg Germany
- Wildlife Ecology and Wildlife Management; University of Freiburg; Freiburg Germany
| | - Mirjam Willert
- Wildlife Ecology; Forest Research Institute of Baden-Wuerttemberg FVA; Freiburg Germany
| | - Annette Kohnen
- Wildlife Ecology; Forest Research Institute of Baden-Wuerttemberg FVA; Freiburg Germany
| | - Rupert Palme
- Department of Biomedical Sciences; University of Veterinary Medicine; Vienna Austria
| | - Veronika Braunisch
- Wildlife Ecology; Forest Research Institute of Baden-Wuerttemberg FVA; Freiburg Germany
- Conservation Biology; Institute of Ecology and Evolution; University of Bern; Bern Switzerland
| |
Collapse
|
22
|
Floreana Island re-colonization potential of the Galápagos short-eared owl (Asio flammeus galapagoensis). CONSERV GENET 2017. [DOI: 10.1007/s10592-017-1007-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
|
23
|
Conservation in the southern edge of Tetrao urogallus distribution: Gene flow despite fragmentation in the stronghold of the Cantabrian capercaillie. EUR J WILDLIFE RES 2017. [DOI: 10.1007/s10344-017-1110-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
|
24
|
Rutkowski R, Zawadzka D, Suchecka E, Merta D. Conservation genetics of the capercaillie in Poland - Delineation of conservation units. PLoS One 2017; 12:e0174901. [PMID: 28376095 PMCID: PMC5380343 DOI: 10.1371/journal.pone.0174901] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2016] [Accepted: 03/17/2017] [Indexed: 12/03/2022] Open
Abstract
The capercaillie (Tetrao urogallus) is one of Poland's most endangered bird species, with an estimated population of 380-500 individuals in four isolated areas. To study these natural populations in Poland further, more than 900 non-invasive genetic samples were collected, along with samples from 59 birds representing large, continuous populations in Sweden and Russia; and from two centres in Poland breeding capercaillie. Microsatellite polymorphism at nine loci was then analysed to estimate within-population genetic diversity and genetic differentiation among populations. The results confirmed that isolation of populations and recent decreases in their sizes have reduced genetic diversity among capercaillie in Poland, with all the country's natural populations found to be experiencing the genetic after-effects of demographic bottlenecks. The results of analyses of genetic differentiation and structure further suggest the presence of a 'lowland' cluster (encompassing birds of the Augustowska and Solska Primaeval Forests in Poland, and of Sweden and Russia), and a Carpathian cluster. Capercaillie from Sweden and Russia are also found to differ markedly. The Polish lowland populations seem more closely related to birds from Scandinavia. Our genetic analysis also indicates that the stocks at breeding centres are of a high genetic diversity effectively reflecting the origins of founder individuals, though identification of ancestry requires further study in the case of some birds. Overall, the results sustain the conclusion that the Polish populations of capercaillie from the Carpathians and the lowlands should be treated as independent Management Units (MUs). This is to say that the breeding lines associated with these two sources should be maintained separately at breeding centres. The high level of genetic differentiation of birds from the Solska Primaeval Forest suggests that this population should also be assigned the status of independent MU.
Collapse
Affiliation(s)
- Robert Rutkowski
- Department of Molecular and Biometrical Techniques, Museum and Institute of Zoology Polish Academy of Sciences, Warsaw, Poland
| | - Dorota Zawadzka
- Institute of Forest Science, University of Łódź, Branch in Tomaszów Mazowiecki, Tomaszów Mazowiecki, Poland
| | - Ewa Suchecka
- Department of Molecular and Biometrical Techniques, Museum and Institute of Zoology Polish Academy of Sciences, Warsaw, Poland
| | - Dorota Merta
- Department of Ecology, Wildlife Research and Ecotourism, Pedagogical University of Cracow, Cracow, Poland
| |
Collapse
|
25
|
McDougall CA, Welsh AB, Gosselin T, Anderson WG, Nelson PA. Rethinking the influence of hydroelectric development on gene flow in a long-lived fish, the Lake Sturgeon Acipenser fulvescens. PLoS One 2017; 12:e0174269. [PMID: 28329005 PMCID: PMC5362236 DOI: 10.1371/journal.pone.0174269] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Accepted: 03/06/2017] [Indexed: 12/02/2022] Open
Abstract
Many hydroelectric dams have been in place for 50 - >100 years, which for most fish species means that enough generations have passed for fragmentation induced divergence to have accumulated. However, for long-lived species such as Lake Sturgeon, Acipenser fulvescens, it should be possible to discriminate between historical population structuring and contemporary gene flow and improve the broader understanding of anthropogenic influence. On the Winnipeg River, Manitoba, two hypotheses were tested: 1) Measureable quantities of former reservoir dwelling Lake Sturgeon now reside downstream of the Slave Falls Generating Station, and 2) genetically differentiated populations of Lake Sturgeon occur upstream and downstream, a result of historical structuring. Genetic methods based on ten microsatellite markers were employed, and simulations were conducted to provide context. With regards to contemporary upstream to downstream contributions, the inclusion of length-at-age data proved informative. Both pairwise relatedness and Bayesian clustering analysis substantiated that fast-growing outliers, apparently entrained after residing in the upstream reservoir for several years, accounted for ~15% of the Lake Sturgeon 525–750 mm fork length captured downstream. With regards to historical structuring, upstream and downstream populations were found to be differentiated (FST = 0.011, and 0.013–0.014 when fast-growing outliers were excluded), and heterozygosity metrics were higher for downstream versus upstream juveniles. Historical asymmetric (downstream) gene flow in the vicinity of the generating station was the most logical explanation for the observed genetic structuring. In this section of the Winnipeg River, construction of a major dam does not appear to have fragmented a previously panmictic Lake Sturgeon population, but alterations to habitat may be influencing upstream to downstream contributions in unexpected ways.
Collapse
Affiliation(s)
- Craig A. McDougall
- North/South Consultants Inc., Winnipeg, Manitoba, Canada
- Department of Biological Sciences, University of Manitoba, Winnipeg, Canada
- * E-mail:
| | - Amy B. Welsh
- Division of Forestry and Natural Resources, West Virginia University, Morgantown, West Virginia, United States of America
| | | | - W. Gary Anderson
- Department of Biological Sciences, University of Manitoba, Winnipeg, Canada
| | | |
Collapse
|
26
|
Johansson F, Halvarsson P, Mikolajewski D, Höglund J. Genetic differentiation in the boreal dragonfly Leucorrhinia dubia in the Palearctic region. Biol J Linn Soc Lond 2017. [DOI: 10.1093/biolinnean/blw033] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
|
27
|
Milanesi P, Holderegger R, Bollmann K, Gugerli F, Zellweger F. Three-dimensional habitat structure and landscape genetics: a step forward in estimating functional connectivity. Ecology 2017; 98:393-402. [DOI: 10.1002/ecy.1645] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/06/2016] [Revised: 10/19/2016] [Accepted: 10/21/2016] [Indexed: 11/07/2022]
Affiliation(s)
- P. Milanesi
- Swiss Ornithological Institute; Seerose 1 Sempach 6204 Switzerland
- WSL Swiss Federal Research Institute; Zürcherstrasse 111 Birmensdorf CH-8903 Switzerland
| | - R. Holderegger
- WSL Swiss Federal Research Institute; Zürcherstrasse 111 Birmensdorf CH-8903 Switzerland
- Department of Environmental Systems Science; ETH Zurich; Universitätsstrasse 16 Zurich 8092 Switzerland
| | - K. Bollmann
- WSL Swiss Federal Research Institute; Zürcherstrasse 111 Birmensdorf CH-8903 Switzerland
| | - F. Gugerli
- WSL Swiss Federal Research Institute; Zürcherstrasse 111 Birmensdorf CH-8903 Switzerland
| | - F. Zellweger
- WSL Swiss Federal Research Institute; Zürcherstrasse 111 Birmensdorf CH-8903 Switzerland
- Department of Environmental Systems Science; ETH Zurich; Universitätsstrasse 16 Zurich 8092 Switzerland
| |
Collapse
|
28
|
Mijangos JL, Pacioni C, Spencer PBS, Hillyer M, Craig MD. Characterizing the post-recolonization of Antechinus flavipes
and its genetic implications in a production forest landscape. Restor Ecol 2017. [DOI: 10.1111/rec.12493] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Jose L. Mijangos
- School of Veterinary and Life Sciences; Murdoch University; Murdoch Western Australia 6150 Australia
| | - Carlo Pacioni
- School of Veterinary and Life Sciences; Murdoch University; Murdoch Western Australia 6150 Australia
| | - Peter B. S. Spencer
- School of Veterinary and Life Sciences; Murdoch University; Murdoch Western Australia 6150 Australia
| | - Mia Hillyer
- School of Veterinary and Life Sciences; Murdoch University; Murdoch Western Australia 6150 Australia
- Molecular Systematics Unit/Terrestrial Zoology; Western Australian Museum; Welshpool Western Australia 6106 Australia
| | - Michael D. Craig
- School of Veterinary and Life Sciences; Murdoch University; Murdoch Western Australia 6150 Australia
- Centre of Excellence for Environmental Decisions, School of Plant Biology; University of Western Australia; Crawley Western Australia 6009 Australia
| |
Collapse
|
29
|
Limited Dispersal and Significant Fine - Scale Genetic Structure in a Tropical Montane Parrot Species. PLoS One 2016; 11:e0169165. [PMID: 28033364 PMCID: PMC5199109 DOI: 10.1371/journal.pone.0169165] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2015] [Accepted: 12/13/2016] [Indexed: 11/19/2022] Open
Abstract
Tropical montane ecosystems are biodiversity hotspots harbouring many endemics that are confined to specific habitat types within narrow altitudinal ranges. While deforestation put these ecosystems under threat, we still lack knowledge about how heterogeneous environments like the montane tropics promote population connectivity and persistence. We investigated the fine-scale genetic structure of the two largest subpopulations of the endangered El Oro parakeet (Pyrrhura orcesi) endemic to the Ecuadorian Andes. Specifically, we assessed the genetic divergence between three sites separated by small geographic distances but characterized by a heterogeneous habitat structure. Although geographical distances between sites are small (3-17 km), we found genetic differentiation between all sites. Even though dispersal capacity is generally high in parrots, our findings indicate that dispersal is limited even on this small geographic scale. Individual genotype assignment revealed similar genetic divergence across a valley (~ 3 km distance) compared to a continuous mountain range (~ 13 km distance). Our findings suggest that geographic barriers promote genetic divergence even on small spatial scales in this endangered endemic species. These results may have important implications for many other threatened and endemic species, particularly given the upslope shift of species predicted from climate change.
Collapse
|
30
|
Dool SE, Puechmaille SJ, Kelleher C, McAney K, Teeling EC. The Effects of Human-Mediated Habitat Fragmentation on a Sedentary Woodland-Associated Species (Rhinolophus hipposideros) at Its Range Margin. ACTA CHIROPTEROLOGICA 2016. [DOI: 10.3161/15081109acc2016.18.2.006] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Affiliation(s)
- Serena E. Dool
- School of Biology and Environmental Science, University College Dublin, Belfield, Dublin 4, Ireland
| | - Sébastien J. Puechmaille
- School of Biology and Environmental Science, University College Dublin, Belfield, Dublin 4, Ireland
| | - Conor Kelleher
- Spring Lane, Carrigagulla, Ballinagree, Macroom, County Cork, Ireland
| | - Kate McAney
- The Vincent Wildlife Trust, Donaghpatrick, Headford, County Galway, Ireland
| | - Emma C. Teeling
- School of Biology and Environmental Science, University College Dublin, Belfield, Dublin 4, Ireland
| |
Collapse
|
31
|
Khimoun A, Eraud C, Ollivier A, Arnoux E, Rocheteau V, Bely M, Lefol E, Delpuech M, Carpentier ML, Leblond G, Levesque A, Charbonnel A, Faivre B, Garnier S. Habitat specialization predicts genetic response to fragmentation in tropical birds. Mol Ecol 2016; 25:3831-44. [PMID: 27314987 DOI: 10.1111/mec.13733] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2015] [Revised: 06/06/2016] [Accepted: 06/07/2016] [Indexed: 01/19/2023]
Abstract
Habitat fragmentation is one of the most severe threats to biodiversity as it may lead to changes in population genetic structure, with ultimate modifications of species evolutionary potential and local extinctions. Nonetheless, fragmentation does not equally affect all species and identifying which ecological traits are related to species sensitivity to habitat fragmentation could help prioritization of conservation efforts. Despite the theoretical link between species ecology and extinction proneness, comparative studies explicitly testing the hypothesis that particular ecological traits underlies species-specific population structure are rare. Here, we used a comparative approach on eight bird species, co-occurring across the same fragmented landscape. For each species, we quantified relative levels of forest specialization and genetic differentiation among populations. To test the link between forest specialization and susceptibility to forest fragmentation, we assessed species responses to fragmentation by comparing levels of genetic differentiation between continuous and fragmented forest landscapes. Our results revealed a significant and substantial population structure at a very small spatial scale for mobile organisms such as birds. More importantly, we found that specialist species are more affected by forest fragmentation than generalist ones. Finally, our results suggest that even a simple habitat specialization index can be a satisfying predictor of genetic and demographic consequences of habitat fragmentation, providing a reliable practical and quantitative tool for conservation biology.
Collapse
Affiliation(s)
- Aurélie Khimoun
- UMR 6282 Biogéosciences, CNRS/Univ. Bourgogne Franche-Comté, Equipe BIOME, 6 bd Gabriel, 21000, Dijon, France
| | - Cyril Eraud
- Office National de la Chasse et de la Faune Sauvage, CNERA Avifaune Migratrice, Station biologique de Chizé, Carrefour de la Canauderie, 79360, Villiers en Bois, France
| | - Anthony Ollivier
- UMR 6282 Biogéosciences, CNRS/Univ. Bourgogne Franche-Comté, Equipe BIOME, 6 bd Gabriel, 21000, Dijon, France
| | - Emilie Arnoux
- UMR 6282 Biogéosciences, CNRS/Univ. Bourgogne Franche-Comté, Equipe BIOME, 6 bd Gabriel, 21000, Dijon, France
| | - Vincent Rocheteau
- UMR 6282 Biogéosciences, CNRS/Univ. Bourgogne Franche-Comté, Equipe BIOME, 6 bd Gabriel, 21000, Dijon, France
| | - Marine Bely
- Office National de la Chasse et de la Faune Sauvage, CNERA Avifaune Migratrice, Station biologique de Chizé, Carrefour de la Canauderie, 79360, Villiers en Bois, France
| | - Emilie Lefol
- Office National de la Chasse et de la Faune Sauvage, CNERA Avifaune Migratrice, Station biologique de Chizé, Carrefour de la Canauderie, 79360, Villiers en Bois, France
| | - Martin Delpuech
- Office National de la Chasse et de la Faune Sauvage, CNERA Avifaune Migratrice, Station biologique de Chizé, Carrefour de la Canauderie, 79360, Villiers en Bois, France
| | - Marie-Laure Carpentier
- Office National de la Chasse et de la Faune Sauvage, CNERA Avifaune Migratrice, Station biologique de Chizé, Carrefour de la Canauderie, 79360, Villiers en Bois, France
| | - Gilles Leblond
- SARL BIOS, 168 rue de Brindeau, 97190, Le Gosier, France
| | - Anthony Levesque
- Office National de la Chasse et de la Faune Sauvage, Cellule Technique des Antilles Françaises, Chemin de Boyer, Section Boisbert, 97129, Le Lamentin, France
| | - Anaïs Charbonnel
- Office National de la Chasse et de la Faune Sauvage, CNERA Avifaune Migratrice, Station biologique de Chizé, Carrefour de la Canauderie, 79360, Villiers en Bois, France
| | - Bruno Faivre
- UMR 6282 Biogéosciences, CNRS/Univ. Bourgogne Franche-Comté, Equipe BIOME, 6 bd Gabriel, 21000, Dijon, France
| | - Stéphane Garnier
- UMR 6282 Biogéosciences, CNRS/Univ. Bourgogne Franche-Comté, Equipe BIOME, 6 bd Gabriel, 21000, Dijon, France
| |
Collapse
|
32
|
Jahner JP, Gibson D, Weitzman CL, Blomberg EJ, Sedinger JS, Parchman TL. Fine-scale genetic structure among greater sage-grouse leks in central Nevada. BMC Evol Biol 2016; 16:127. [PMID: 27301494 PMCID: PMC4908695 DOI: 10.1186/s12862-016-0702-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2016] [Accepted: 06/07/2016] [Indexed: 01/07/2023] Open
Abstract
Background Mating systems that reduce dispersal and lead to non-random mating might increase the potential for genetic structure to arise at fine geographic scales. Greater sage-grouse (Centrocercus urophasianus) have a lek-based mating system and exhibit high site fidelity and skewed mating ratios. We quantified population structure by analyzing variation at 27,866 single-nucleotide polymorphisms in 140 males from ten leks (within five lek complexes) occurring in a small geographic region in central Nevada. Results Lek complexes, and to a lesser extent individual leks, formed statistically identifiable clusters in ordination analyses, providing evidence for fine-scale geographic genetic differentiation. Lek geography predicted genetic differentiation even at a small geographic scale, which could be sharpened by strong site fidelity. Relatedness was also higher among individuals within lek complexes (and leks), suggesting that reproductive skew, where few males participate in most of the successful matings, could also potentially contribute to genetic differentiation. Models incorporating a habitat resistance surface as a proxy for potentially reduced movement due to landscape features indicated that both geographic distance and habitat suitability (i.e. preferred habitat) predicted genetic structure, with no significant effect of man-made barriers to movement (i.e. power lines and roads). Finally, we illustrate how data sets containing fewer loci (<4000) had less statistical precision and failed to detect the full degree of genetic structure. Conclusion Our results suggest that habitat features and lek site geography of sage-grouse shape fine scale genetic structure, and highlight how larger data sets can have increased precision and accuracy for quantifying ecologically relevant genetic structure over small geographic scales. Electronic supplementary material The online version of this article (doi:10.1186/s12862-016-0702-4) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Joshua P Jahner
- Program in Ecology, Evolution, and Conservation Biology, University of Nevada, Reno, NV, 89557, USA. .,Department of Biology, University of Nevada, Reno, NV, 89557, USA.
| | - Daniel Gibson
- Program in Ecology, Evolution, and Conservation Biology, University of Nevada, Reno, NV, 89557, USA.,Department of Natural Resources and Environmental Science, University of Nevada, Reno, NV, 89557, USA
| | - Chava L Weitzman
- Program in Ecology, Evolution, and Conservation Biology, University of Nevada, Reno, NV, 89557, USA.,Department of Biology, University of Nevada, Reno, NV, 89557, USA
| | - Erik J Blomberg
- Program in Ecology, Evolution, and Conservation Biology, University of Nevada, Reno, NV, 89557, USA.,Department of Natural Resources and Environmental Science, University of Nevada, Reno, NV, 89557, USA.,Department of Wildlife, Fisheries, and Conservation Biology, University of Maine, Orono, ME, 04469, USA
| | - James S Sedinger
- Program in Ecology, Evolution, and Conservation Biology, University of Nevada, Reno, NV, 89557, USA.,Department of Natural Resources and Environmental Science, University of Nevada, Reno, NV, 89557, USA
| | - Thomas L Parchman
- Program in Ecology, Evolution, and Conservation Biology, University of Nevada, Reno, NV, 89557, USA.,Department of Biology, University of Nevada, Reno, NV, 89557, USA
| |
Collapse
|
33
|
Impacts of forest fragmentation and post-glacial colonization on the distribution of genetic diversity in the Polish population of the hazel grouse Terastes bonasia. EUR J WILDLIFE RES 2016. [DOI: 10.1007/s10344-016-1002-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
|
34
|
Barrowclough G, Schroeder M. Distribution of natal dispersal distances and the genetic structure of Spruce Grouse ( Falcipennis canadensis) populations. CAN J ZOOL 2016. [DOI: 10.1139/cjz-2016-0041] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Natal dispersal distances are difficult to measure, yet important for estimating the genetic structure and demographic connectedness of natural populations. Here we provide estimates of the distributions of male and female natal dispersal distances from a long-term study of Spruce Grouse (Falcipennis canadensis (L., 1758)) in southwestern Alberta, Canada, based on individuals marked as brood chicks and re-observed as adults during subsequent breeding seasons. The mean distance dispersed by females (2.33 km) was twice that of males (1.13 km), and both dispersal distributions were leptokurtic. Given estimates of population density and survivorship, we estimated the genetic effective neighborhood size of this population as approximately 541 individuals. We computed equivalent estimates for two additional long-term studies of this species, based on data available in the literature; mean natal dispersal distances, averaged across sexes, ranged from 1.73 to 2.73 km for the three populations; effective deme sizes ranged from 541 to 890. Consequently, three widespread populations of Spruce Grouse yielded roughly similar estimates of demographic and genetic structure.
Collapse
Affiliation(s)
- G.F. Barrowclough
- Department of Ornithology, American Museum of Natural History, Central Park West at 79th Street, New York, NY 10024, USA
| | - M.A. Schroeder
- Washington Department of Fish and Wildlife, P.O. Box 1077, Bridgeport, WA 98813, USA
| |
Collapse
|
35
|
Merta D, Kobielski J, Theuerkauf J, Gula R. Towards a successful reintroduction of capercaillies — activity, movements and diet of young released to the Lower Silesia Forest, Poland. WILDLIFE BIOLOGY 2016. [DOI: 10.2981/wlb.00208] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
|
36
|
Bonin MC, Harrison HB, Williamson DH, Frisch AJ, Saenz-Agudelo P, Berumen ML, Jones GP. The role of marine reserves in the replenishment of a locally impacted population of anemonefish on the Great Barrier Reef. Mol Ecol 2016; 25:487-99. [DOI: 10.1111/mec.13484] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2014] [Revised: 10/24/2015] [Accepted: 11/16/2015] [Indexed: 11/27/2022]
Affiliation(s)
- Mary C. Bonin
- Australian Research Council Centre of Excellence for Coral Reef Studies; James Cook University; Townsville QLD 4811 Australia
- College of Marine & Environmental Sciences; James Cook University; Townsville QLD 4811 Australia
| | - Hugo B. Harrison
- Australian Research Council Centre of Excellence for Coral Reef Studies; James Cook University; Townsville QLD 4811 Australia
| | - David H. Williamson
- Australian Research Council Centre of Excellence for Coral Reef Studies; James Cook University; Townsville QLD 4811 Australia
| | - Ashley J. Frisch
- Australian Research Council Centre of Excellence for Coral Reef Studies; James Cook University; Townsville QLD 4811 Australia
| | - Pablo Saenz-Agudelo
- Instituto de Ciencias Ambientales y Evolutivas; Facultad de Ciencias; Universidad Austral de Chile; Valdivia Chile
- Red Sea Research Center; Division of Biological and Environmental Science and Engineering; King Abdullah University of Science and Technology; Thuwal 23955 Saudi Arabia
| | - Michael L. Berumen
- Red Sea Research Center; Division of Biological and Environmental Science and Engineering; King Abdullah University of Science and Technology; Thuwal 23955 Saudi Arabia
| | - Geoffrey P. Jones
- Australian Research Council Centre of Excellence for Coral Reef Studies; James Cook University; Townsville QLD 4811 Australia
- College of Marine & Environmental Sciences; James Cook University; Townsville QLD 4811 Australia
| |
Collapse
|
37
|
Strzała T, Kowalczyk A, Łukaszewicz E. Reintroduction of the European Capercaillie from the Capercaillie Breeding Centre in Wisła Forest District: Genetic Assessments of Captive and Reintroduced Populations. PLoS One 2015; 10:e0145433. [PMID: 26682897 PMCID: PMC4684292 DOI: 10.1371/journal.pone.0145433] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2015] [Accepted: 12/03/2015] [Indexed: 11/18/2022] Open
Abstract
The Western capercaillie (Tetrao urogallus) is a specific bird species, which, despite its very broad distribution and large global population size, is highly endangered in many Western and Central European countries. According to the species situation, in many countries (including Poland), breeding and reintroduction programmes have been started. One of the most complex and large-scale reintroduction programmes was started in Bory Dolnośląskie Forest, and the Capercaillie Breeding Centre in Wisła Forest District was used as one of the sources of individuals for reintroduction. As genetic tools provide essential knowledge about species biodiversity, which is crucially important during the breeding process and reintroduction, both captive and reintroduced grouse populations were genetically analysed. We were particularly interested in genetic diversity of the individuals in both populations and the genetic relationship between them, as well as between them and other capercaillie representatives from their current range. To fulfil these goals we determined nine microsatellite loci along with a fragment of the mitochondrial control region. Genetic diversity parameters were moderate to high compared to populations from other Central and Western European countries. Both populations were clustered into three distinct genetic clades based on microsatellites. Phylogenetic analysis placed all mitochondrial haplotypes we revealed in the Eurasian clade. The present results will play an important role as they will help to preserve and maximize genetic diversity in captive populations, and will provide a basis for future monitoring of the reintroduction process.
Collapse
Affiliation(s)
- Tomasz Strzała
- Department of Genetics, Faculty of Biology, Wroclaw University of Environmental and Life Sciences, Wrocław, Poland
- * E-mail:
| | - Artur Kowalczyk
- Division of Poultry Breeding, Institute of Animal Breeding, Faculty of Biology, Wroclaw University of Environmental and Life Sciences, Wrocław, Poland
| | - Ewa Łukaszewicz
- Division of Poultry Breeding, Institute of Animal Breeding, Faculty of Biology, Wroclaw University of Environmental and Life Sciences, Wrocław, Poland
| |
Collapse
|
38
|
Klinga P, Mikoláš M, Zhelev P, Höglund J, Paule L. Genetic differentiation of western capercaillie in the Carpathian Mountains: the importance of post glacial expansions and habitat connectivity. Biol J Linn Soc Lond 2015. [DOI: 10.1111/bij.12643] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Peter Klinga
- Faculty of Forestry; Technical University; SK-96053 Zvolen Slovakia
| | - Martin Mikoláš
- Faculty of Forestry and Wood Sciences; Czech University of Life Sciences; Kamýcka cesta 1176 CZ-165 21 Praha 6-Suchdol Czech Republic
- PRALES; Odtrnovie 563 SK-013 22 Rosina Slovakia
| | - Petar Zhelev
- Faculty of Forestry; University of Forestry; Kliment Ohridski Blvd. 10 BG-17456 Sofia Bulgaria
| | - Jacob Höglund
- Department of Ecology and Genetics; Evolutionary Biology Centre; Uppsala University; Norbyvägen 18D SE-752 36 Uppsala Sweden
| | - Ladislav Paule
- Faculty of Forestry; Technical University; SK-96053 Zvolen Slovakia
| |
Collapse
|
39
|
Revealing the consequences of male-biased trophy hunting on the maintenance of genetic variation. CONSERV GENET 2015. [DOI: 10.1007/s10592-015-0747-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
|
40
|
Xenikoudakis G, Ersmark E, Tison JL, Waits L, Kindberg J, Swenson JE, Dalén L. Consequences of a demographic bottleneck on genetic structure and variation in the Scandinavian brown bear. Mol Ecol 2015; 24:3441-54. [PMID: 26042479 DOI: 10.1111/mec.13239] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2014] [Revised: 05/07/2015] [Accepted: 05/08/2015] [Indexed: 11/30/2022]
Abstract
The Scandinavian brown bear went through a major decline in population size approximately 100 years ago, due to intense hunting. After being protected, the population subsequently recovered and today numbers in the thousands. The genetic diversity in the contemporary population has been investigated in considerable detail, and it has been shown that the population consists of several subpopulations that display relatively high levels of genetic variation. However, previous studies have been unable to resolve the degree to which the demographic bottleneck impacted the contemporary genetic structure and diversity. In this study, we used mitochondrial and microsatellite DNA markers from pre- and postbottleneck Scandinavian brown bear samples to investigate the effect of the bottleneck. Simulation and multivariate analysis suggested the same genetic structure for the historical and modern samples, which are clustered into three subpopulations in southern, central and northern Scandinavia. However, the southern subpopulation appears to have gone through a marked change in allele frequencies. When comparing the mitochondrial DNA diversity in the whole population, we found a major decline in haplotype numbers across the bottleneck. However, the loss of autosomal genetic diversity was less pronounced, although a significant decline in allelic richness was observed in the southern subpopulation. Approximate Bayesian computations provided clear support for a decline in effective population size during the bottleneck, in both the southern and northern subpopulations. These results have implications for the future management of the Scandinavian brown bear because they indicate a recent loss in genetic diversity and also that the current genetic structure may have been caused by historical ecological processes rather than recent anthropogenic persecution.
Collapse
Affiliation(s)
- G Xenikoudakis
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, SE-10405, Stockholm, Sweden.,Department of Zoology, Stockholm University, SE-106 91, Stockholm, Sweden
| | - E Ersmark
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, SE-10405, Stockholm, Sweden.,Department of Zoology, Stockholm University, SE-106 91, Stockholm, Sweden
| | - J-L Tison
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, SE-10405, Stockholm, Sweden
| | - L Waits
- Department of Fish and Wildlife Sciences, University of Idaho, 875 Perimeter Drive MS 1136, Moscow, ID, 83844, USA
| | - J Kindberg
- Department of Wildlife, Fish, and Environmental Studies, Swedish University of Agricultural Sciences, SE-90183, Umeå, Sweden
| | - J E Swenson
- Department of Ecology and Natural Resource Management, Norwegian University of Life Sciences, NO-1432, Ås, Norway.,Norwegian Institute for Nature Research, PO Box 5685 Sluppen, NO-7485, Trondheim, Norway
| | - L Dalén
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, SE-10405, Stockholm, Sweden
| |
Collapse
|
41
|
de Flamingh A, Sole CL, van Aarde RJ. Genetic evidence for spatial structuring in a continuous African elephant (Loxodonta africana) population. CONSERV GENET 2014. [DOI: 10.1007/s10592-014-0686-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
|
42
|
Rösner S, Brandl R, Segelbacher G, Lorenc T, Müller J. Noninvasive genetic sampling allows estimation of capercaillie numbers and population structure in the Bohemian Forest. EUR J WILDLIFE RES 2014. [DOI: 10.1007/s10344-014-0848-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
|
43
|
Williford D, Deyoung RW, Honeycutt RL, Brennan LA, Hernández F, Wehland EM, Sands JP, Demaso SJ, Miller KS, Perez RM. Contemporary genetic structure of the northern bobwhite west of the Mississippi River. J Wildl Manage 2014. [DOI: 10.1002/jwmg.733] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Damon Williford
- Caesar Kleberg Wildlife Research Institute; Texas A&M University-Kingsville; Kingsville TX 78363 USA
| | - Randy W. Deyoung
- Caesar Kleberg Wildlife Research Institute; Texas A&M University-Kingsville; Kingsville TX 78363 USA
| | | | - Leonard A. Brennan
- Caesar Kleberg Wildlife Research Institute; Texas A&M University-Kingsville; Kingsville TX 78363 USA
| | - Fidel Hernández
- Caesar Kleberg Wildlife Research Institute; Texas A&M University-Kingsville; Kingsville TX 78363 USA
| | - Erin M. Wehland
- Caesar Kleberg Wildlife Research Institute; Texas A&M University-Kingsville; Kingsville TX 78363 USA
| | - Joseph P. Sands
- Caesar Kleberg Wildlife Research Institute; Texas A&M University-Kingsville; Kingsville TX 78363 USA
| | - Stephen J. Demaso
- Caesar Kleberg Wildlife Research Institute; Texas A&M University-Kingsville; Kingsville TX 78363 USA
| | - Katherine S. Miller
- Caesar Kleberg Wildlife Research Institute; Texas A&M University-Kingsville; Kingsville TX 78363 USA
| | - Robert M. Perez
- Texas Parks and Wildlife Department; 4200 Smith School Road Austin TX 78744 USA
| |
Collapse
|
44
|
Morán-Luis M, Fameli A, Blanco-Fontao B, Fernández-Gil A, Rodríguez-Muñoz R, Quevedo M, Mirol P, Bañuelos MJ. Demographic status and genetic tagging of endangered capercaillie in NW Spain. PLoS One 2014; 9:e99799. [PMID: 24926790 PMCID: PMC4057396 DOI: 10.1371/journal.pone.0099799] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2014] [Accepted: 05/17/2014] [Indexed: 11/18/2022] Open
Abstract
Counting rare and elusive animals and evaluating their demographic status, are fundamental yet challenging aspects of population ecology and conservation biology. We set out to estimate population size (Nc), genetic effective population size (Ne gen), sex ratio, and movements based on genetic tagging for the threatened Cantabrian capercaillie. We used 9 microsatellite loci to genotype 134 droppings collected at 34 display areas during the breeding season. Using genetic capture-mark-recapture, we estimated 93 individuals (Nc, 95% CI: 70-116) in an area of about 500 km2, with sex ratio biased towards males (1∶1.6). Estimated Ne gen (35.5) was 38% of Nc, notably higher than the published average in wild populations. This capercaillie population is small and well within concern in terms of population viability. By genetic tagging, we detected mostly short movements; just a few males were recaptured between contiguous display areas. Non-invasive surveys of endangered populations have a great potential, yet adequate sample size and location are key to obtain reliable information on conservation status.
Collapse
Affiliation(s)
- María Morán-Luis
- Research Unit of Biodiversity (UO-PA-CSIC), University of Oviedo, Mieres, Spain
- Ecology Unit, Department of Biology of Organisms and Systems, University of Oviedo, Oviedo, Spain
| | - Alberto Fameli
- Group of Biodiversity and Conservation Genetics (GECOBI), Argentinian Museum of Natural Sciences ‘Bernardino Rivadavia’, Buenos Aires, Argentina
| | - Beatriz Blanco-Fontao
- Ecology Unit, Department of Biology of Organisms and Systems, University of Oviedo, Oviedo, Spain
| | - Alberto Fernández-Gil
- Department of Conservation Biology, Doñana Biological Station (CSIC), Sevilla, Spain
| | - Rolando Rodríguez-Muñoz
- Centre for Ecology and Conservation, School of Biosciences, University of Exeter, Penryn, United Kingdom
| | - Mario Quevedo
- Research Unit of Biodiversity (UO-PA-CSIC), University of Oviedo, Mieres, Spain
- Ecology Unit, Department of Biology of Organisms and Systems, University of Oviedo, Oviedo, Spain
| | - Patricia Mirol
- Group of Biodiversity and Conservation Genetics (GECOBI), Argentinian Museum of Natural Sciences ‘Bernardino Rivadavia’, Buenos Aires, Argentina
| | - María-José Bañuelos
- Research Unit of Biodiversity (UO-PA-CSIC), University of Oviedo, Mieres, Spain
- Ecology Unit, Department of Biology of Organisms and Systems, University of Oviedo, Oviedo, Spain
| |
Collapse
|
45
|
Braunisch V, Coppes J, Arlettaz R, Suchant R, Zellweger F, Bollmann K. Temperate mountain forest biodiversity under climate change: compensating negative effects by increasing structural complexity. PLoS One 2014; 9:e97718. [PMID: 24823495 PMCID: PMC4019656 DOI: 10.1371/journal.pone.0097718] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2014] [Accepted: 04/22/2014] [Indexed: 11/30/2022] Open
Abstract
Species adapted to cold-climatic mountain environments are expected to face a high risk of range contractions, if not local extinctions under climate change. Yet, the populations of many endothermic species may not be primarily affected by physiological constraints, but indirectly by climate-induced changes of habitat characteristics. In mountain forests, where vertebrate species largely depend on vegetation composition and structure, deteriorating habitat suitability may thus be mitigated or even compensated by habitat management aiming at compositional and structural enhancement. We tested this possibility using four cold-adapted bird species with complementary habitat requirements as model organisms. Based on species data and environmental information collected in 300 1-km2 grid cells distributed across four mountain ranges in central Europe, we investigated (1) how species' occurrence is explained by climate, landscape, and vegetation, (2) to what extent climate change and climate-induced vegetation changes will affect habitat suitability, and (3) whether these changes could be compensated by adaptive habitat management. Species presence was modelled as a function of climate, landscape and vegetation variables under current climate; moreover, vegetation-climate relationships were assessed. The models were extrapolated to the climatic conditions of 2050, assuming the moderate IPCC-scenario A1B, and changes in species' occurrence probability were quantified. Finally, we assessed the maximum increase in occurrence probability that could be achieved by modifying one or multiple vegetation variables under altered climate conditions. Climate variables contributed significantly to explaining species occurrence, and expected climatic changes, as well as climate-induced vegetation trends, decreased the occurrence probability of all four species, particularly at the low-altitudinal margins of their distribution. These effects could be partly compensated by modifying single vegetation factors, but full compensation would only be achieved if several factors were changed in concert. The results illustrate the possibilities and limitations of adaptive species conservation management under climate change.
Collapse
Affiliation(s)
- Veronika Braunisch
- Forest Research Institute of Baden-Württemberg, Freiburg, Germany
- Conservation Biology, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
| | - Joy Coppes
- Forest Research Institute of Baden-Württemberg, Freiburg, Germany
| | - Raphaël Arlettaz
- Conservation Biology, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
- Swiss Ornithological Institute, Valais Field Station, Sion, Switzerland
| | - Rudi Suchant
- Forest Research Institute of Baden-Württemberg, Freiburg, Germany
| | - Florian Zellweger
- Swiss Federal Institute for Forest, Snow and Landscape Research, Birmensdorf, Switzerland
- Institute of Terrestrial Ecosystems, Swiss Federal Institute of Technology, Zürich, Switzerland
| | - Kurt Bollmann
- Swiss Federal Institute for Forest, Snow and Landscape Research, Birmensdorf, Switzerland
| |
Collapse
|
46
|
Fenderson LE, Kovach AI, Litvaitis JA, O'Brien KM, Boland KM, Jakubas WJ. A multiscale analysis of gene flow for the New England cottontail, an imperiled habitat specialist in a fragmented landscape. Ecol Evol 2014; 4:1853-75. [PMID: 24963381 PMCID: PMC4063480 DOI: 10.1002/ece3.1068] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2013] [Revised: 03/12/2014] [Accepted: 03/14/2014] [Indexed: 11/21/2022] Open
Abstract
Landscape features of anthropogenic or natural origin can influence organisms' dispersal patterns and the connectivity of populations. Understanding these relationships is of broad interest in ecology and evolutionary biology and provides key insights for habitat conservation planning at the landscape scale. This knowledge is germane to restoration efforts for the New England cottontail (Sylvilagus transitionalis), an early successional habitat specialist of conservation concern. We evaluated local population structure and measures of genetic diversity of a geographically isolated population of cottontails in the northeastern United States. We also conducted a multiscale landscape genetic analysis, in which we assessed genetic discontinuities relative to the landscape and developed several resistance models to test hypotheses about landscape features that promote or inhibit cottontail dispersal within and across the local populations. Bayesian clustering identified four genetically distinct populations, with very little migration among them, and additional substructure within one of those populations. These populations had private alleles, low genetic diversity, critically low effective population sizes (3.2-36.7), and evidence of recent genetic bottlenecks. Major highways and a river were found to limit cottontail dispersal and to separate populations. The habitat along roadsides, railroad beds, and utility corridors, on the other hand, was found to facilitate cottontail movement among patches. The relative importance of dispersal barriers and facilitators on gene flow varied among populations in relation to landscape composition, demonstrating the complexity and context dependency of factors influencing gene flow and highlighting the importance of replication and scale in landscape genetic studies. Our findings provide information for the design of restoration landscapes for the New England cottontail and also highlight the dual influence of roads, as both barriers and facilitators of dispersal for an early successional habitat specialist in a fragmented landscape.
Collapse
Affiliation(s)
- Lindsey E Fenderson
- 114 James Hall, Department of Natural Resources and the Environment, University of New Hampshire Durham, New Hampshire, 03824
| | - Adrienne I Kovach
- 114 James Hall, Department of Natural Resources and the Environment, University of New Hampshire Durham, New Hampshire, 03824
| | - John A Litvaitis
- 114 James Hall, Department of Natural Resources and the Environment, University of New Hampshire Durham, New Hampshire, 03824
| | - Kathleen M O'Brien
- United States Fish and Wildlife Service, Rachel Carson National Wildlife Refuge 321 Port Road, Wells, Maine, 04090
| | - Kelly M Boland
- United States Fish and Wildlife Service, Rachel Carson National Wildlife Refuge 321 Port Road, Wells, Maine, 04090
| | - Walter J Jakubas
- Maine Department of Inland Fisheries & Wildlife 650 State Street, Bangor, Maine, 04401
| |
Collapse
|
47
|
Genetic differentiation over a short water barrier in the Brazilian tanager, Ramphocelus bresilius (Passeriformes: Thraupidae) an endemic species of the Atlantic forest, Brazil. CONSERV GENET 2014. [DOI: 10.1007/s10592-014-0607-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
|
48
|
White NE, Bunce M, Mawson PR, Dawson R, Saunders DA, Allentoft ME. Identifying conservation units after large‐scale land clearing: a spatio‐temporal molecular survey of endangered white‐tailed black cockatoos (
Calyptorhynchus
spp.). DIVERS DISTRIB 2014. [DOI: 10.1111/ddi.12202] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Affiliation(s)
- Nicole E. White
- Trace and Environmental DNA Laboratory Department of Environment and Agriculture Curtin University Perth WA 6102 Australia
- School of Veterinary and Life Sciences Murdoch University Perth WA 6150 Australia
| | - Michael Bunce
- Trace and Environmental DNA Laboratory Department of Environment and Agriculture Curtin University Perth WA 6102 Australia
- School of Veterinary and Life Sciences Murdoch University Perth WA 6150 Australia
| | | | - Rick Dawson
- Department of Parks and Wildlife Locked Bag 104 Bentley D.C. Perth WA 6983 Australia
| | | | - Morten E. Allentoft
- School of Veterinary and Life Sciences Murdoch University Perth WA 6150 Australia
- Centre for GeoGenetics Natural History Museum University of Copenhagen Øster Voldgade 5‐7 1350 Copenhagen K Denmark
| |
Collapse
|
49
|
Genetic characterization of game bird island populations: The conservation of the black francolin (Francolinus francolinus) of Cyprus. J Nat Conserv 2014. [DOI: 10.1016/j.jnc.2013.07.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
|
50
|
Mondol S, Bruford MW, Ramakrishnan U. Demographic loss, genetic structure and the conservation implications for Indian tigers. Proc Biol Sci 2013; 280:20130496. [PMID: 23677341 PMCID: PMC3673047 DOI: 10.1098/rspb.2013.0496] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2013] [Accepted: 04/23/2013] [Indexed: 11/12/2022] Open
Abstract
India is home to approximately 60 per cent of the world's remaining wild tigers, a species that has declined in the last few centuries to occupy less than 7 per cent of its former geographical range. While Indian tiger numbers have somewhat stabilized in recent years, they remain low and populations are highly fragmented. Therefore, the application of evidence-based demographic and genetic management to enhance the remaining populations is a priority. In this context, and using genetic data from historical and modern tigers, we investigated anthropogenic impacts on genetic variation in Indian tigers using mitochondrial and nuclear genetic markers. We found a very high number of historical mitochondrial DNA variants, 93 per cent of which are not detected in modern populations. Population differentiation was higher in modern tigers. Simulations incorporating historical data support population decline, and suggest high population structure in extant populations. Decreased connectivity and habitat loss as a result of ongoing fragmentation in the Indian subcontinent has therefore resulted in a loss of genetic variants and increased genetic differentiation among tiger populations. These results highlight that anthropogenic fragmentation and species-specific demographic processes can interact to alter the partitioning of genetic variation over very short time scales. We conclude that ongoing strategies to maximize the size of some tiger populations, at the expense of losing others, is an inadequate conservation strategy, as it could result in a loss of genetic diversity that may be of adaptive significance for this emblematic species.
Collapse
Affiliation(s)
- Samrat Mondol
- National Centre for Biological Sciences, TIFR, GKVK Campus, Bellary Road, Bangalore 560065, India
| | | | - Uma Ramakrishnan
- National Centre for Biological Sciences, TIFR, GKVK Campus, Bellary Road, Bangalore 560065, India
| |
Collapse
|