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Luo S, Wang M, Ma W, Gu D, Jin Z, Yang R, Qian Z, Song C, Wang Z, Jin S. Environment DNA Reveals Fish Diversity in a Canyon River within the Upper Pearl River Drainage. Animals (Basel) 2024; 14:2433. [PMID: 39199966 PMCID: PMC11350740 DOI: 10.3390/ani14162433] [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: 06/21/2024] [Revised: 08/03/2024] [Accepted: 08/20/2024] [Indexed: 09/01/2024] Open
Abstract
Investigating fish diversity in canyon rivers through conventional fish surveys is challenging due to precipitous conditions, including steep slopes, rapid water flow, and complex habitats. Additionally, intensive construction of dams has further complicated the understanding of contemporary fish diversity in these rivers. In this study, we used the environmental DNA (eDNA) technique to assess fish diversity and examine the effects of dams on fish diversity in the Mabiehe River, a canyon river in the upper reaches of the Pearl River drainage. Water samples from 15 sampling sites were collected, yielding 9,356,148 valid sequences. Utilizing the NCBI public database, a total of 60 freshwater fish species were identified, with Carassius auratus, Cyprinus carpio, and Pelteobagrus fulvidraco being the most dominant species in the Mabiehe River. We also detected one nationally protected fish species, three provincially protected fish species, and six exotic species in this river. Furthermore, eDNA analyses demonstrated that the lotic river sections harbor more species and greater diversity than dammed sections, suggesting that dams might exert significant impacts on local fish diversity. Overall, this study supports the effectiveness of the eDNA technique as a complementary tool to traditional field surveys for monitoring fish biodiversity in canyon rivers.
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Affiliation(s)
- Si Luo
- School of Life Science and Food Engineering, Huaiyin Institute of Technology, Huai’an 223003, China; (S.L.); (R.Y.); (Z.Q.); (C.S.); (Z.W.)
| | - Meng Wang
- Power China Guiyang Engineering Corporation Limited, Guiyang 550081, China; (M.W.); (W.M.); (Z.J.)
| | - Weizhong Ma
- Power China Guiyang Engineering Corporation Limited, Guiyang 550081, China; (M.W.); (W.M.); (Z.J.)
| | - Dangen Gu
- Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, China;
| | - Zhijun Jin
- Power China Guiyang Engineering Corporation Limited, Guiyang 550081, China; (M.W.); (W.M.); (Z.J.)
| | - Ruiqi Yang
- School of Life Science and Food Engineering, Huaiyin Institute of Technology, Huai’an 223003, China; (S.L.); (R.Y.); (Z.Q.); (C.S.); (Z.W.)
| | - Zhen Qian
- School of Life Science and Food Engineering, Huaiyin Institute of Technology, Huai’an 223003, China; (S.L.); (R.Y.); (Z.Q.); (C.S.); (Z.W.)
| | - Chengwen Song
- School of Life Science and Food Engineering, Huaiyin Institute of Technology, Huai’an 223003, China; (S.L.); (R.Y.); (Z.Q.); (C.S.); (Z.W.)
| | - Zexin Wang
- School of Life Science and Food Engineering, Huaiyin Institute of Technology, Huai’an 223003, China; (S.L.); (R.Y.); (Z.Q.); (C.S.); (Z.W.)
| | - Shiyu Jin
- School of Life Science and Food Engineering, Huaiyin Institute of Technology, Huai’an 223003, China; (S.L.); (R.Y.); (Z.Q.); (C.S.); (Z.W.)
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2
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Masto NM, Keever AC, Highway CJ, Blake-Bradshaw AG, Feddersen JC, Hagy HM, Cohen BS. Proximity among protected area networks promotes functional connectivity for wintering waterfowl. Sci Rep 2024; 14:17527. [PMID: 39080395 PMCID: PMC11289371 DOI: 10.1038/s41598-024-68175-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2024] [Accepted: 07/22/2024] [Indexed: 08/02/2024] Open
Abstract
The equilibrium theorem provided a fundamental framework for understanding species' distributions and movement in fragmented ecosystems. Wetland-dependent avian species are model organisms to test insular predictions within protected area networks because their mobility allows surveillance of isolated patches without landscape barriers. We hypothesized size and isolation would influence functional connectivity of sanctuaries by GPS-marked wintering mallards (Anas platyrhynchos) within a mesocosm protected sanctuary area network. We evaluated functional connectivity and sanctuary use, measured by movements between sanctuaries, using a multistate modeling framework. Proximity drove connectivity, underscoring that patch isolation-not size-influenced connectivity, even for an avian species with no ascertainable landscape resistance or barriers. We also found that sanctuary use increased overwintering survival by reducing harvest mortality. Our test of equilibrium theory predictions demonstrated that isolation of protected sanctuary areas supersedes their size in determining functional connectivity for mallards and access to these areas may have direct fitness consequences. Our findings could refine land acquisition, restoration, and management practices with equal or greater emphasis on adjacency in protected area network design, especially for wetland-dependent migratory gamebirds.
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Affiliation(s)
- Nicholas M Masto
- Tennessee Technological University, College of Arts and Sciences, Cookeville, TN, USA.
- Cornell Lab of Ornithology, Ithaca, NY, USA.
| | - Allison C Keever
- Tennessee Technological University, College of Arts and Sciences, Cookeville, TN, USA
| | - Cory J Highway
- Tennessee Technological University, College of Arts and Sciences, Cookeville, TN, USA
| | | | - Jamie C Feddersen
- Tennessee Wildlife Resources Agency, Migratory Gamebird Program, Nashville, TN, USA
| | - Heath M Hagy
- United States Fish and Wildlife Service, Refuge System, Southeast Region, Stanton, TN, USA.
- United States Fish and Wildlife Service, Habitat and Population Evaluation Team, Bismarck, ND, USA.
| | - Bradley S Cohen
- Tennessee Technological University, College of Arts and Sciences, Cookeville, TN, USA
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3
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Cheng R, Zhou X, Zhang Y, Li Q, Zhang J, Luo Y, Chen Q, Liu Z, Li Y, Shen Y. eDNA reveals spatial homogenization of fish diversity in a mountain river affected by a reservoir cascade. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2024; 361:121248. [PMID: 38820798 DOI: 10.1016/j.jenvman.2024.121248] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Revised: 05/05/2024] [Accepted: 05/25/2024] [Indexed: 06/02/2024]
Abstract
One of the main reasons for the decline in global freshwater biodiversity can be attributed to alterations in hydrological conditions resulting from dam construction. However, the majority of current research has focused on single or limited numbers of dams. Here, we carried out a seasonal fish survey, using environmental DNA (eDNA) method, on the Wujiang River mainstream (Tributaries of the Yangtze River, China) to investigate the impact of large-scale cascade hydropower development on changes in fish diversity patterns. eDNA survey revealed that native fish species have decreased in contrast to alien fish. There was also a shift in fish community structure, with declines of the dominant rheophilic fish species, an increase of the small-size fish species, and homogenization of species composition across reservoirs. Additionally, environmental factors, such as temperature, dissolved oxygen and reservoir age, had a significant effect on fish community diversity. This study provides basic information for the evaluation of the impact of cascade developments on fish diversity patterns.
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Affiliation(s)
- Ruli Cheng
- Laboratory of Water Ecological Health and Environmental Safety, Chongqing Key Laboratory of Conservation and Utilization of Freshwater Fishes, Animal Biology Key Laboratory of Chongqing Education Commission, Chongqing Normal University, Chongqing, 401331, China
| | - Xinxin Zhou
- Laboratory of Water Ecological Health and Environmental Safety, Chongqing Key Laboratory of Conservation and Utilization of Freshwater Fishes, Animal Biology Key Laboratory of Chongqing Education Commission, Chongqing Normal University, Chongqing, 401331, China
| | - Yufeng Zhang
- Laboratory of Water Ecological Health and Environmental Safety, Chongqing Key Laboratory of Conservation and Utilization of Freshwater Fishes, Animal Biology Key Laboratory of Chongqing Education Commission, Chongqing Normal University, Chongqing, 401331, China
| | - Qinghua Li
- Laboratory of Water Ecological Health and Environmental Safety, Chongqing Key Laboratory of Conservation and Utilization of Freshwater Fishes, Animal Biology Key Laboratory of Chongqing Education Commission, Chongqing Normal University, Chongqing, 401331, China
| | - Jiaming Zhang
- Laboratory of Water Ecological Health and Environmental Safety, Chongqing Key Laboratory of Conservation and Utilization of Freshwater Fishes, Animal Biology Key Laboratory of Chongqing Education Commission, Chongqing Normal University, Chongqing, 401331, China
| | - Yang Luo
- Laboratory of Water Ecological Health and Environmental Safety, Chongqing Key Laboratory of Conservation and Utilization of Freshwater Fishes, Animal Biology Key Laboratory of Chongqing Education Commission, Chongqing Normal University, Chongqing, 401331, China
| | - Qiliang Chen
- Laboratory of Water Ecological Health and Environmental Safety, Chongqing Key Laboratory of Conservation and Utilization of Freshwater Fishes, Animal Biology Key Laboratory of Chongqing Education Commission, Chongqing Normal University, Chongqing, 401331, China
| | - Zhihao Liu
- Laboratory of Water Ecological Health and Environmental Safety, Chongqing Key Laboratory of Conservation and Utilization of Freshwater Fishes, Animal Biology Key Laboratory of Chongqing Education Commission, Chongqing Normal University, Chongqing, 401331, China
| | - Yingwen Li
- Laboratory of Water Ecological Health and Environmental Safety, Chongqing Key Laboratory of Conservation and Utilization of Freshwater Fishes, Animal Biology Key Laboratory of Chongqing Education Commission, Chongqing Normal University, Chongqing, 401331, China
| | - Yanjun Shen
- Laboratory of Water Ecological Health and Environmental Safety, Chongqing Key Laboratory of Conservation and Utilization of Freshwater Fishes, Animal Biology Key Laboratory of Chongqing Education Commission, Chongqing Normal University, Chongqing, 401331, China.
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4
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Thomas L, Şahin D, Adam AS, Grimaldi CM, Ryan NM, Duffy SL, Underwood JN, Kennington WJ, Gilmour JP. Resilience to periodic disturbances and the long-term genetic stability in Acropora coral. Commun Biol 2024; 7:410. [PMID: 38575730 PMCID: PMC10995172 DOI: 10.1038/s42003-024-06100-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Accepted: 03/22/2024] [Indexed: 04/06/2024] Open
Abstract
Climate change is restructuring natural ecosystems. The direct impacts of these events on biodiversity and community structure are widely documented, but the impacts on the genetic variation of populations remains largely unknown. We monitored populations of Acropora coral on a remote coral reef system in northwest Australia for two decades and through multiple cycles of impact and recovery. We combined these demographic data with a temporal genetic dataset of a common broadcast spawning corymbose Acropora to explore the spatial and temporal patterns of connectivity underlying recovery. Our data show that broad-scale dispersal and post-recruitment survival drive recovery from recurrent disturbances, including mass bleaching and mortality. Consequently, genetic diversity and associated patterns of connectivity are maintained through time in the broader metapopulation. The results highlight an inherent resilience in these globally threatened species of coral and showcase their ability to cope with multiple disturbances, given enough time to recover is permitted.
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Affiliation(s)
- L Thomas
- Australian Institute of Marine Science, Indian Ocean Marine Research Centre, Crawley, Australia.
- UWA Oceans Institute, The University of Western Australia, Crawley, Australia.
| | - D Şahin
- Australian Institute of Marine Science, Indian Ocean Marine Research Centre, Crawley, Australia
- UWA Oceans Institute, The University of Western Australia, Crawley, Australia
| | - A S Adam
- Australian Institute of Marine Science, Indian Ocean Marine Research Centre, Crawley, Australia
| | - C M Grimaldi
- Australian Institute of Marine Science, Indian Ocean Marine Research Centre, Crawley, Australia
- UWA Oceans Institute, The University of Western Australia, Crawley, Australia
| | - N M Ryan
- Australian Institute of Marine Science, Indian Ocean Marine Research Centre, Crawley, Australia
| | - S L Duffy
- Australian Institute of Marine Science, Indian Ocean Marine Research Centre, Crawley, Australia
- UWA Oceans Institute, The University of Western Australia, Crawley, Australia
| | - J N Underwood
- Australian Institute of Marine Science, Indian Ocean Marine Research Centre, Crawley, Australia
| | - W J Kennington
- UWA Oceans Institute, The University of Western Australia, Crawley, Australia
- Centre for Evolutionary Biology, School of Animal Biology, The University of Western Australia, Perth, Australia
| | - J P Gilmour
- Australian Institute of Marine Science, Indian Ocean Marine Research Centre, Crawley, Australia
- UWA Oceans Institute, The University of Western Australia, Crawley, Australia
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5
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Segura-García I, Olson JB, Gochfeld DJ, Brandt ME, Chaves-Fonnegra A. Severe hurricanes increase recruitment and gene flow in the clonal sponge Aplysina cauliformis. Mol Ecol 2024; 33:e17307. [PMID: 38444224 DOI: 10.1111/mec.17307] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Revised: 01/24/2024] [Accepted: 01/30/2024] [Indexed: 03/07/2024]
Abstract
Upright branching sponges, such as Aplysina cauliformis, provide critical three-dimensional habitat for other organisms and assist in stabilizing coral reef substrata, but are highly susceptible to breakage during storms. Breakage can increase sponge fragmentation, contributing to population clonality and inbreeding. Conversely, storms could provide opportunities for new genotypes to enter populations via larval recruitment, resulting in greater genetic diversity in locations with frequent storms. The unprecedented occurrence of two Category 5 hurricanes in close succession during 2017 in the U.S. Virgin Islands (USVI) provided a unique opportunity to evaluate whether recolonization of newly available substrata on coral reefs was due to local (e.g. re-growth of remnants, fragmentation, larval recruitment) or remote (e.g. larval transport and immigration) sponge genotypes. We sampled A. cauliformis adults and juveniles from four reefs around St. Thomas and two in St. Croix (USVI). Using a 2bRAD protocol, all samples were genotyped for single-nucleotide polymorphisms (SNPs). Results showed that these major storm events favoured sponge larval recruitment but did not increase the genetic diversity of A. cauliformis populations. Recolonization of substratum post-storms via clonality was lower (15%) than expected and instead was mainly due to sexual reproduction (85%) via local larval recruitment. Storms did enhance gene flow among and within reef sites located south of St. Thomas and north of St. Croix. Therefore, populations of clonal marine species with low pelagic dispersion, such as A. cauliformis, may benefit from increased frequency and magnitude of hurricanes for the maintenance of genetic diversity and to combat inbreeding, enhancing the resilience of Caribbean sponge communities to extreme storm events.
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Affiliation(s)
- Iris Segura-García
- Harbor Branch Oceanographic Institution, Florida Atlantic University, Fort Pierce, Florida, USA
| | - Julie B Olson
- Department of Biological Sciences, University of Alabama, Tuscaloosa, Alabama, USA
| | - Deborah J Gochfeld
- National Center for Natural Products Research, University of Mississippi, Oxford, Mississippi, USA
| | - Marilyn E Brandt
- Center for Marine and Environmental Studies, University of the Virgin Islands, St. Thomas, Virgin Islands, USA
| | - Andia Chaves-Fonnegra
- Harbor Branch Oceanographic Institution, Florida Atlantic University, Fort Pierce, Florida, USA
- Harriet L. Wilkes Honors College, Florida Atlantic University, Jupiter, Florida, USA
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6
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Ruggiero MV, Buffoli M, Wolf KKE, D'Alelio D, Di Tuccio V, Lombardi E, Manfellotto F, Vitale L, Margiotta F, Sarno D, John U, Ferrante MI, Montresor M. Multiannual patterns of genetic structure and mating type ratios highlight the complex bloom dynamics of a marine planktonic diatom. Sci Rep 2024; 14:6028. [PMID: 38472358 DOI: 10.1038/s41598-024-56292-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Accepted: 03/05/2024] [Indexed: 03/14/2024] Open
Abstract
Understanding the genetic structure of populations and the processes responsible for its spatial and temporal dynamics is vital for assessing species' adaptability and survival in changing environments. We investigate the genetic fingerprinting of blooming populations of the marine diatom Pseudo-nitzschia multistriata in the Gulf of Naples (Mediterranean Sea) from 2008 to 2020. Strains were genotyped using microsatellite fingerprinting and natural samples were also analysed with Microsatellite Pool-seq Barcoding based on Illumina sequencing of microsatellite loci. Both approaches revealed a clonal expansion event in 2013 and a more stable genetic structure during 2017-2020 compared to previous years. The identification of a mating type (MT) determination gene allowed to assign MT to strains isolated over the years. MTs were generally at equilibrium with two notable exceptions, including the clonal bloom of 2013. The populations exhibited linkage equilibrium in most blooms, indicating that sexual reproduction leads to genetic homogenization. Our findings show that P. multistriata blooms exhibit a dynamic genetic and demographic composition over time, most probably determined by deeper-layer cell inocula. Occasional clonal expansions and MT imbalances can potentially affect the persistence and ecological success of planktonic diatoms.
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Affiliation(s)
| | - Marina Buffoli
- Department of Integrative Marine Ecology, Stazione Zoologica Anton Dohrn, Naples, Italy
| | - Klara K E Wolf
- Institut für Marine Ökosystem- und Fischereiwissenschaften, Universität Hamburg, Hamburg, Germany
- Limnological Institute, Environmental Genomics, University of Konstanz, Konstanz, Germany
| | - Domenico D'Alelio
- Department of Integrative Marine Ecology, Stazione Zoologica Anton Dohrn, Naples, Italy
| | - Viviana Di Tuccio
- Department of Integrative Marine Ecology, Stazione Zoologica Anton Dohrn, Naples, Italy
| | - Ernestina Lombardi
- Department of Integrative Marine Ecology, Stazione Zoologica Anton Dohrn, Naples, Italy
| | - Francesco Manfellotto
- Department of Integrative Marine Ecology, Stazione Zoologica Anton Dohrn, Naples, Italy
| | - Laura Vitale
- Department of Integrative Marine Ecology, Stazione Zoologica Anton Dohrn, Naples, Italy
| | - Francesca Margiotta
- Department of Research Infrastructures for Marine Biological Resources, Stazione Zoologica Anton Dohrn, Naples, Italy
| | - Diana Sarno
- Department of Research Infrastructures for Marine Biological Resources, Stazione Zoologica Anton Dohrn, Naples, Italy
| | - Uwe John
- Alfred-Wegener-Institute, Helmholtz Centre for Polar and Marine Research, Bremerhaven, Germany
- Helmholtz Institute for Functional Marine Biodiversity, Oldenburg, Germany
| | - Maria Immacolata Ferrante
- Department of Integrative Marine Ecology, Stazione Zoologica Anton Dohrn, Naples, Italy
- Oceanography Section, National Institute of Oceanography and Applied Geophysics, Trieste, Italy
| | - Marina Montresor
- Department of Integrative Marine Ecology, Stazione Zoologica Anton Dohrn, Naples, Italy.
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7
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Haugen H, Dervo BK, Østbye K, Heggenes J, Devineau O, Linløkken A. Genetic diversity, gene flow, and landscape resistance in a pond-breeding amphibian in agricultural and natural forested landscapes in Norway. Evol Appl 2024; 17:e13633. [PMID: 38283603 PMCID: PMC10810167 DOI: 10.1111/eva.13633] [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: 07/05/2023] [Revised: 11/23/2023] [Accepted: 12/07/2023] [Indexed: 01/30/2024] Open
Abstract
Genetic diversity is a key part of biodiversity, threatened by human activities that lead to loss of gene flow and reduction of effective population sizes. Gene flow is a result of both landscape connectivity and demographic processes determining the number of dispersing individuals in space and time. Thus, the effect of human impact on processes determining the level of genetic diversity must be interpreted in the context of basic ecological conditions affecting survival and recruitment. When the intensity of human impact and habitat suitability correlate, the effect on genetic diversity and gene flow may be challenging to predict. We compared genetic diversity, gene flow and landscape resistance in two contrasting landscapes in Norway for the pond-breeding amphibian Triturus cristatus: a highly human-impacted, agricultural landscape with ecologically productive habitats, and a forested landscape with less productive habitats and lower levels of human impact. Our results show that genetic diversity was higher and gene flow lower within the forested landscape. Microclimatic moisture conditions and vegetation cover were important determinants of landscape resistance to gene flow within both landscapes. There were indications that landscape resistance was increased by minor roads in the forested landscape, which was not the case for the agricultural landscape, suggesting a higher vulnerability to human interference within the landscape matrix for the populations in less productive habitats. Our findings suggest that the effect of human impact on genetic diversity may not be straightforward but modulated by the ecological conditions underlying local demographic processes. Populations within both landscapes seem to be vulnerable to loss of genetic diversity, but due to different mechanisms. This has implications for the choice of relevant management actions, that is, increasing population stability may be more relevant within an agricultural landscape still permeable for dispersal, while conserving dispersal corridors may be more appropriate in the forested landscape, to avoid isolation and increased genetic drift.
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Affiliation(s)
- Hanne Haugen
- Department of Forestry and Wildlife ManagementInland Norway University of Applied SciencesHamarNorway
| | - Børre K. Dervo
- Norwegian Institute for Nature Research (NINA)OsloNorway
| | - Kjartan Østbye
- Department of Forestry and Wildlife ManagementInland Norway University of Applied SciencesHamarNorway
- Department of BiosciencesCenter for Ecological and Evolutionary Synthesis (CEES)University of OsloOsloNorway
| | - Jan Heggenes
- Department of Natural Sciences and Environmental HealthUniversity of South‐Eastern NorwayUniversity of South‐Eastern NorwayNotoddenNorway
| | - Olivier Devineau
- Department of Forestry and Wildlife ManagementInland Norway University of Applied SciencesHamarNorway
| | - Arne Linløkken
- Department of Forestry and Wildlife ManagementInland Norway University of Applied SciencesHamarNorway
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8
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Ngeve MN, Engelhardt KAM, Gray M, Neel MC. Calm after the storm? Similar patterns of genetic variation in a riverine foundation species before and after severe disturbance. Ecol Evol 2023; 13:e10670. [PMID: 37920773 PMCID: PMC10618894 DOI: 10.1002/ece3.10670] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Revised: 08/28/2023] [Accepted: 10/16/2023] [Indexed: 11/04/2023] Open
Abstract
In summer 2011, Tropical storms Lee and Irene caused an estimated 90% decline of the submersed aquatic plant Vallisneria americana Michx. (Hydrocharitaceae) in the Hudson River of New York (USA). To understand the genetic impact of such large-scale demographic losses, we compared diversity at 10 microsatellite loci in 135 samples collected from five sites just before the storms with 239 shoots collected from nine sites 4 years after. Although 80% of beds sampled in 2011 lacked V. americana in 2015, we found similar genotypic and genetic diversity and effective population sizes in pre-storm versus post-storm sites. These similarities suggest that despite local extirpations concentrated at the upstream end of the sampling area, V. americana was regionally resistant to genetic losses. Similar geographically based structure among sites in both sampling periods suggested that cryptic local refugia at previously occupied sites facilitated re-expansion after the storms. However, this apparent resistance to disturbance may lead to a false sense of security. Low effective population sizes and high clonality in both time periods suggest that V. americana beds were already small and had high frequency of asexual reproduction before the storms. Dispersal was not sufficient to recolonize more isolated sites that had been extirpated. Chronic low diversity and reliance on asexual reproduction for persistence can be risky when more frequent and intense storms are paired with ongoing anthropogenic stressors. Monitoring genetic diversity along with extent and abundance of V. americana will give a more complete picture of long-term potential for resilience.
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Affiliation(s)
- Magdalene N. Ngeve
- Department of Plant Science and Landscape ArchitectureUniversity of MarylandCollege ParkMarylandUSA
- Department of EntomologyUniversity of MarylandCollege ParkMarylandUSA
| | | | - Michelle Gray
- Department of Plant Science and Landscape ArchitectureUniversity of MarylandCollege ParkMarylandUSA
- Department of EntomologyUniversity of MarylandCollege ParkMarylandUSA
| | - Maile C. Neel
- Department of Plant Science and Landscape ArchitectureUniversity of MarylandCollege ParkMarylandUSA
- Department of EntomologyUniversity of MarylandCollege ParkMarylandUSA
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9
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Jones GM, Goldberg JF, Wilcox TM, Buckley LB, Parr CL, Linck EB, Fountain ED, Schwartz MK. Fire-driven animal evolution in the Pyrocene. Trends Ecol Evol 2023; 38:1072-1084. [PMID: 37479555 DOI: 10.1016/j.tree.2023.06.003] [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: 02/17/2023] [Revised: 06/02/2023] [Accepted: 06/06/2023] [Indexed: 07/23/2023]
Abstract
Fire regimes are a major agent of evolution in terrestrial animals. Changing fire regimes and the capacity for rapid evolution in wild animal populations suggests the potential for rapid, fire-driven adaptive animal evolution in the Pyrocene. Fire drives multiple modes of evolutionary change, including stabilizing, directional, disruptive, and fluctuating selection, and can strongly influence gene flow and genetic drift. Ongoing and future research in fire-driven animal evolution will benefit from further development of generalizable hypotheses, studies conducted in highly responsive taxa, and linking fire-adapted phenotypes to their underlying genetic basis. A better understanding of evolutionary responses to fire has the potential to positively influence conservation strategies that embrace evolutionary resilience to fire in the Pyrocene.
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Affiliation(s)
- Gavin M Jones
- USDA Forest Service, Rocky Mountain Research Station, Albuquerque, NM 87102, USA.
| | - Joshua F Goldberg
- USDA Forest Service, Rocky Mountain Research Station, Albuquerque, NM 87102, USA
| | - Taylor M Wilcox
- National Genomics Center for Fish and Wildlife Conservation, USDA Forest Service, Rocky Mountain Research Station, Missoula, MT 59801, USA
| | - Lauren B Buckley
- Department of Biology, University of Washington, Seattle, WA 98195, USA
| | - Catherine L Parr
- Department of Earth, Ocean and Ecological Sciences, University of Liverpool, Liverpool, L3 5TR, UK; Department of Zoology and Entomology, University of Pretoria, Pretoria 0028, South Africa; School of Animal, Plant and Environmental Sciences, University of the Witwatersrand, Wits 2050, South Africa
| | - Ethan B Linck
- Department of Zoology and Physiology, University of Wyoming, Laramie, WY 82071, USA
| | - Emily D Fountain
- Department of Forest and Wildlife Ecology, University of Wisconsin, Madison, WI 53706, USA
| | - Michael K Schwartz
- National Genomics Center for Fish and Wildlife Conservation, USDA Forest Service, Rocky Mountain Research Station, Missoula, MT 59801, USA
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10
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Zhao YJ, Yin GS, Gong X. RAD-sequencing improves the genetic characterization of a threatened tree peony ( Paeonia ludlowii) endemic to China: Implications for conservation. PLANT DIVERSITY 2023; 45:513-522. [PMID: 37936813 PMCID: PMC10625974 DOI: 10.1016/j.pld.2022.07.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Revised: 06/06/2022] [Accepted: 07/12/2022] [Indexed: 11/09/2023]
Abstract
Compared with traditional genetic markers, genomic approaches have proved valuable to the conservation of endangered species. Paeonia ludlowii having rarely and pure yellow flowers, is one of the world's most famous tree peonies. However, only several wild populations remain in the Yarlung Zangbo Valley (Nyingchi and Shannan regions, Xizang) in China due to increasing anthropogenic impact on the natural habitats. We used genome-wide single nucleotide polymorphisms to elucidate the spatial pattern of genetic variation, population structure and demographic history of P. ludlowii from the fragmented region comprising the entire range of this species, aiming to provide a basis for conserving the genetic resources of this species. Unlike genetic uniformity among populations revealed in previous studies, we found low but varied levels of intra-population genetic diversity, in which lower genetic diversity was detected in the population in Shannan region compared to those in Nyingzhi region. These spatial patterns may be likely associated with different population sizes caused by micro-environment differences in these two regions. Additionally, low genetic differentiation among populations (Fst = 0.0037) were detected at the species level. This line of evidence, combined with the result of significant genetic differentiation between the two closest populations and lack of isolation by distance, suggested that shared ancestry among now remnant populations rather than contemporary genetic connectivity resulted in subtle population structure. Demographic inference suggested that P. ludlowii probably experienced a temporal history of sharp population decline during the period of Last Glacial Maximum, and a subsequent bottleneck event resulting from prehistoric human activities on the Qinghai-Tibet Plateau. All these events, together with current habitat fragment and excavation might contribute to the endangered status of P. ludlowii. Our study improved the genetic characterization of the endangered tree peony (P. ludlowii) in China, and these genetic inferences should be considered when making different in situ and ex situ conservation actions for P. ludlowii in this evolutionary hotspot region.
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Affiliation(s)
- Yu-Juan Zhao
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, Yunnan, China
- Key Laboratory of Economic Plants and Biotechnology, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, Yunnan, China
- Yunnan Key Laboratory for Wild Plant Resources, Kunming 650201, Yunnan, China
| | - Gen-Shen Yin
- Kunming University, Institute of Agriculture and Life Sciences, Kunming 650214, Yunnan, China
| | - Xun Gong
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, Yunnan, China
- Key Laboratory of Economic Plants and Biotechnology, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, Yunnan, China
- Yunnan Key Laboratory for Wild Plant Resources, Kunming 650201, Yunnan, China
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11
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Shi L, Yang X, Cha M, Lyu T, Wang L, Zhou S, Dong Y, Dou H, Zhang H. Genetic diversity and structure of mongolian gazelle (Procapra gutturosa) populations in fragmented habitats. BMC Genomics 2023; 24:507. [PMID: 37648967 PMCID: PMC10469424 DOI: 10.1186/s12864-023-09574-0] [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: 08/13/2022] [Accepted: 08/10/2023] [Indexed: 09/01/2023] Open
Abstract
BACKGROUND The Mongolian gazelle (Procapra gutturosa) population has shown a considerable range of contractions and local extinctions over the last century, owing to habitat fragmentation and poaching. A thorough understanding of the genetic diversity and structure of Mongolian gazelle populations in fragmented habitats is critical for planning effective conservation strategies. RESULT In this study, we used eight microsatellite loci and mitochondrial cytochrome b (Cytb) to compare the levels of genetic diversity and genetic structure of Mongolian gazelle populations in the Hulun Lake National Nature Reserve (HLH) with those in the China-Mongolia border area (BJ). The results showed that the nucleotide diversity and observed heterozygosity of the HLH population were lower than those of the BJ population. Moreover, the HLH and BJ populations showed genetic differentiation. We concluded that the HLH population had lower genetic diversity and a distinct genetic structure compared with the BJ population. CONCLUSION The genetic diversity of fragmented Mongolian gazelle populations, can be improved by protecting these populations while reinforcing their gene exchange with other populations. For example, attempts can be made to introduce new individuals with higher genetic diversity from other populations to reduce inbreeding.
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Affiliation(s)
- Lupeng Shi
- College of Life Sciences, Qufu Normal University, Qufu, Shandong Province, China
| | - Xiufeng Yang
- College of Life Sciences, Qufu Normal University, Qufu, Shandong Province, China
| | - Muha Cha
- Hulunbuir Academy of Inland Lakes in Northern Cold & Arid Areas, Hulunbuir, China
| | - Tianshu Lyu
- College of Life Sciences, Qufu Normal University, Qufu, Shandong Province, China
| | - Lidong Wang
- College of Life Sciences, Qufu Normal University, Qufu, Shandong Province, China
| | - Shengyang Zhou
- College of Life Sciences, Qufu Normal University, Qufu, Shandong Province, China
| | - Yuehuan Dong
- College of Life Sciences, Qufu Normal University, Qufu, Shandong Province, China
| | - Huashan Dou
- Hulunbuir Academy of Inland Lakes in Northern Cold & Arid Areas, Hulunbuir, China
| | - Honghai Zhang
- College of Life Sciences, Qufu Normal University, Qufu, Shandong Province, China.
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12
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Ramsay MS, Sgarlata GM, Barratt CD, Salmona J, Andriatsitohaina B, Kiene F, Manzi S, Ramilison ML, Rakotondravony R, Chikhi L, Lehman SM, Radespiel U. Effects of Forest Fragmentation on Connectivity and Genetic Diversity in an Endemic and an Invasive Rodent in Northwestern Madagascar. Genes (Basel) 2023; 14:1451. [PMID: 37510355 PMCID: PMC10378931 DOI: 10.3390/genes14071451] [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: 06/02/2023] [Revised: 07/07/2023] [Accepted: 07/13/2023] [Indexed: 07/30/2023] Open
Abstract
Habitat loss and fragmentation are of concern to conservation biologists worldwide. However, not all organisms are affected equally by these processes; thus, it is important to study the effects of living in fragmented habitats on species that differ in lifestyle and habitat requirements. In this study, we examined the dispersal and connectivity patterns of rodents, one endemic (Eliurus myoxinus) and one invasive (Rattus rattus), in two landscapes containing forest fragments and adjacent continuous forest patches in northwestern Madagascar. We generated genetic (RADseq) data for 66 E. myoxinus and 81 R. rattus individuals to evaluate differences in genetic diversity as well as inbreeding and connectivity in two landscapes. We found higher levels of inbreeding and lower levels of genetic diversity in E. myoxinus compared with R. rattus. We observed related dyads both within and between habitat patches and positive spatial autocorrelation at lower distance classes for both species, with a stronger pattern of spatial autocorrelation in R. rattus. Across each site, we identified contrasting migration rates for each species, but these did not correspond to habitat-matrix dichotomies. The relatively low genetic diversity in the endemic E. myoxinus suggests ecological constraints that require further investigation.
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Affiliation(s)
- Malcolm S Ramsay
- Department of Anthropology, University of Toronto, Toronto, ON M5S 2S2, Canada
- Institute of Zoology, University of Veterinary Medicine Hannover, Foundation, 30559 Hannover, Germany
| | | | - Christopher D Barratt
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, 04103 Leipzig, Germany
| | - Jordi Salmona
- CNRS-UPS-IRD, UMR5174, Laboratoire Évolution & Diversité Biologique, Université Paul Sabatier, 31062 Toulouse, France
| | - Bertrand Andriatsitohaina
- Planet Madagascar, Antananarivo 101, Madagascar
- Faculté des Sciences, de Technologies et de l'Environnement, Université de Mahajanga, Mahajanga 401, Madagascar
| | - Frederik Kiene
- Institute of Zoology, University of Veterinary Medicine Hannover, Foundation, 30559 Hannover, Germany
| | - Sophie Manzi
- CNRS-UPS-IRD, UMR5174, Laboratoire Évolution & Diversité Biologique, Université Paul Sabatier, 31062 Toulouse, France
| | - Miarisoa L Ramilison
- Faculté des Sciences, de Technologies et de l'Environnement, Université de Mahajanga, Mahajanga 401, Madagascar
- Department of Primate Behavior and Ecology, Central Washington University, Ellensburg, WA 98926, USA
| | - Romule Rakotondravony
- Faculté des Sciences, de Technologies et de l'Environnement, Université de Mahajanga, Mahajanga 401, Madagascar
| | - Lounès Chikhi
- Instituto Gulbenkian de Ciência, 2780-156 Oeiras, Portugal
- CNRS-UPS-IRD, UMR5174, Laboratoire Évolution & Diversité Biologique, Université Paul Sabatier, 31062 Toulouse, France
| | - Shawn M Lehman
- Department of Anthropology, University of Toronto, Toronto, ON M5S 2S2, Canada
| | - Ute Radespiel
- Institute of Zoology, University of Veterinary Medicine Hannover, Foundation, 30559 Hannover, Germany
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13
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Cheng R, Luo Y, Zhang Y, Li Q, Li Y, Shen Y. eDNA metabarcoding reveals differences in fish diversity and community structure in heterogeneous habitat areas shaped by cascade hydropower. Ecol Evol 2023; 13:e10275. [PMID: 37424941 PMCID: PMC10326610 DOI: 10.1002/ece3.10275] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Revised: 06/14/2023] [Accepted: 06/25/2023] [Indexed: 07/11/2023] Open
Abstract
Freshwater ecosystems are under great threat from humans, among which habitat heterogeneity is the most obvious, being one of the important reasons for the decline of fish diversity. This phenomenon is particularly prominent in the Wujiang River, where the continuous rapids of the mainstream have been divided into 12 mutually isolated sections by 11 cascade hydropower reservoirs. Based on the fact that conventional survey methods are more harmful to the ecological environment, the efficient and noninvasive environmental DNA metabarcoding (eDNA) approach was used in this study to conduct an aquatic ecological survey of the 12 river sections of the mainstream of the Wujiang River. A total of 2299 operational taxonomic units (OTUs) were obtained, corresponding to 97 species, including four nationally protected fish species and 12 alien species. The results indicate that the fish community structure of the Wujiang River mainstream, which was originally dominated by rheophilic fish species, has been changed. And there are differences in fish species diversity and species composition among the reservoir areas of the mainstream of the Wujiang River. The fish species in the area have gradually declined under the influence of anthropogenic factors such as terraced hydropower and overfishing. The fish populations consequently have demonstrated a tendency to be species miniaturized, and the indigenous fish are severely threatened. In addition, the fish composition monitored by the eDNA approach was found to be close to the fish composition of historical information on the Wujiang River, indicating that eDNA approach may be used as a complementary tool to conventional methods in this basin.
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Affiliation(s)
- Ruli Cheng
- Laboratory of Water Ecological Health and Environmental Safety, School of Life SciencesChongqing Normal UniversityChongqingChina
| | - Yang Luo
- Laboratory of Water Ecological Health and Environmental Safety, School of Life SciencesChongqing Normal UniversityChongqingChina
| | - Yufeng Zhang
- Laboratory of Water Ecological Health and Environmental Safety, School of Life SciencesChongqing Normal UniversityChongqingChina
| | - Qinghua Li
- Laboratory of Water Ecological Health and Environmental Safety, School of Life SciencesChongqing Normal UniversityChongqingChina
| | - Yingwen Li
- Laboratory of Water Ecological Health and Environmental Safety, School of Life SciencesChongqing Normal UniversityChongqingChina
| | - Yanjun Shen
- Laboratory of Water Ecological Health and Environmental Safety, School of Life SciencesChongqing Normal UniversityChongqingChina
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14
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Stevens BS, Roberts SB, Conway CJ, Englestead DK. Effects of large-scale disturbance on animal space use: Functional responses by greater sage-grouse after megafire. Ecol Evol 2023; 13:e9933. [PMID: 37038512 PMCID: PMC10082181 DOI: 10.1002/ece3.9933] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 02/10/2023] [Accepted: 03/02/2023] [Indexed: 04/12/2023] Open
Abstract
Global change has altered the nature of disturbance regimes, and megafire events are increasingly common. Megafires result in immediate changes to habitat available to terrestrial wildlife over broad landscapes, yet we know surprisingly little about how such changes shape space use of sensitive species in habitat that remains. Functional responses provide a framework for understanding and predicting changes in space use following habitat alteration, but no previous studies have assessed functional responses as a consequence of megafire. We studied space use and tested for functional responses in habitat use by breeding greater sage-grouse (Centrocercus urophasianus) before and after landscape-level changes induced by a >40,000 ha, high-intensity megafire that burned sagebrush steppe in eastern Idaho, USA. We also incorporated functional responses into predictive resource selection functions (RSFs) to map breeding habitat before and after the fire. Megafire had strong effects on the distribution of available resources and resulted in context-dependent habitat use that was heterogeneous across different components of habitat. We observed functional responses in the use and selection of a variety of resources (shrubs and herbaceous vegetation) for both nesting and brood rearing. Functional responses in the use of nesting habitat were influenced by the overarching effect of megafire on vegetation, whereas responses during brood rearing appeared to be driven by individual variation in available resources that were conditional on nest locations. Importantly, RSFs built using data collected prior to the burn also had poor transferability for predicting space use in a post-megafire landscape. These results have strong implications for understanding and predicting how animals respond to a rapidly changing environment, given that increased severity, frequency, and extent of wildfire are consequences of global change with the capacity to reshape ecosystems. We therefore demonstrate a conceptual framework to better understand space use and aid habitat conservation for wildlife in a rapidly changing world.
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Affiliation(s)
- Bryan S. Stevens
- Idaho Cooperative Fish and Wildlife Research Unit, Department of Fish and Wildlife SciencesUniversity of IdahoMoscowIdahoUSA
| | | | - Courtney J. Conway
- U.S. Geological Survey, Idaho Cooperative Fish and Wildlife Research UnitUniversity of IdahoMoscowIdahoUSA
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15
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Peres PA, Mantelatto FL. Demographic changes and life-history strategies predict the genetic diversity in crabs. J Evol Biol 2023; 36:432-443. [PMID: 36537369 DOI: 10.1111/jeb.14138] [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: 06/22/2022] [Revised: 10/15/2022] [Accepted: 10/24/2022] [Indexed: 12/24/2022]
Abstract
Uncovering what predicts genetic diversity (GD) within species can help us access the status of populations and their evolutionary potential. Traits related to effective population size show a proportional association to GD, but evidence supports life-history strategies and habitat as the drivers of GD variation. Instead of investigating highly divergent taxa, focusing on one group could help to elucidate the factors influencing the GD. Additionally, most empirical data is based on vertebrate taxa; therefore, we might be missing novel patterns of GD found in neglected invertebrate groups. Here, we investigated the predictors of the GD in crabs (Brachyura) by compiling the most comprehensive cytochrome c oxidase subunit I (COI) available. Eight predictor variables were analysed across 150 species (16 992 sequences) using linear models (multiple linear regression) and comparative methods (PGLS). Our results indicate that population size fluctuation represents the most critical trait predicting GD, with species that have undergone bottlenecks followed by population expansion showing lower GD. Egg size, pelagic larval duration and habitat might play a role probably because of their association with how species respond to disturbances. Ultimately, K-strategists that have undergone bottlenecks are the species showing lower GD. Some variables do not show an association with GD as expected, most likely due to the taxon-specific role of some predictors, which should be considered in further investigations and generalizations. This work highlights the complexity underlying the predictors of GD and adds results from a marine invertebrate group to the current understanding of this topic.
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Affiliation(s)
- Pedro A Peres
- Faculty of Philosophy, Sciences and Letters at Ribeirão Preto (FFCLRP), Laboratory of Bioecology and Crustacean Systematics (LBSC), Ribeirão Preto, University of São Paulo (USP), Ribeirão Preto, São Paulo, Brazil
| | - Fernando L Mantelatto
- Faculty of Philosophy, Sciences and Letters at Ribeirão Preto (FFCLRP), Laboratory of Bioecology and Crustacean Systematics (LBSC), Ribeirão Preto, University of São Paulo (USP), Ribeirão Preto, São Paulo, Brazil
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16
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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.
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17
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Macagno H, González-Reyes A, Corronca J, Rodríguez-Artigas S, Flores G. How do assemblages of epigeal Araneae and Coleoptera respond to changes in habitat structure caused by sugar cane crops in Northern Argentina? NEOTROPICAL BIODIVERSITY 2022. [DOI: 10.1080/23766808.2022.2131311] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Affiliation(s)
- Hb Macagno
- CONICET-CCT-Salta. Facultad de Ciencias Naturales-Universidad Nacional de Salta (FCN-UNSa), Salta, Argentina
| | - Ax González-Reyes
- Instituto para el Estudio de la Biodiversidad de Invertebrados, Facultad de Ciencias Naturales, Universidad Nacional de Salta, Salta, Argentina
| | - Ja Corronca
- CONICET-CCT-Salta. Facultad de Ciencias Naturales-Universidad Nacional de Salta (FCN-UNSa), Salta, Argentina
| | - Sm Rodríguez-Artigas
- Instituto para el Estudio de la Biodiversidad de Invertebrados, Facultad de Ciencias Naturales, Universidad Nacional de Salta, Salta, Argentina
| | - Ge Flores
- Laboratorio de Entomología, Instituto Argentino de Investigaciones de las Zonas Áridas (IADIZA), Centro Científico Tecnológico CONICET Mendoza, Mendoza, Argentina
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18
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Leonhardt F, Arranz Aveces C, Müller A, Angin B, Jegu M, Haynes P, Ernst R. Low genetic diversity in a widespread whistling alien: A comparison of Eleutherodactylus johnstonei Barbour, 1914 (Eleutherodactylidae) and congeners in native and introduced ranges. NEOBIOTA 2022. [DOI: 10.3897/neobiota.79.86778] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
There is no clear empirical evidence to support the general assumption that genetic diversity favours successful invasions. Many invading species disperse and establish successfully despite low genetic diversity, a phenomenon known as the genetic paradox of biological invasion. Model systems that allow comparison of genetic patterns between exotic and native source populations are still scarce. This is particularly true for amphibians. Here we compare genetic patterns of the widely introduced Johnstone’s Whistling Frog, Eleutherodactylus johnstonei, with its successful alien congener E. antillensis and the single island endemic E. portoricensis. Genetic diversity and population differentiation in native and introduced populations of the three taxa were inferred from mitochondrial D-loop sequences (235 bp). Our results reveal that exotic populations of the two alien taxa, E. johnstonei and E. antillensis, are not only genetically impoverished due to founder effects, but that, moreover, their native range source-populations exhibit low genetic diversity and inter-population differentiation in the first place. Populations of the endemic E. portoricensis, on the other hand, are genetically more diverse and show marked inter-population differentiation. These observed genetic patterns are consistent with geological processes and invasion histories. We argue that the establishment success of the alien taxa in our model system is better explained by ecological factors and anthropogenic drivers than by genetic diversity. As these factors provide more parsimonious explanations, they should be given priority in management decisions. However, molecular studies with higher resolution are needed to fully test possible genetic and epigenetic components that could promote the invasion process.
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19
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Hemraj DA, Bishop MJ, Hancock B, Minuti JJ, Thurstan RH, Zu Ermgassen PSE, Russell BD. Oyster reef restoration fails to recoup global historic ecosystem losses despite substantial biodiversity gain. SCIENCE ADVANCES 2022; 8:eabp8747. [PMID: 36417529 PMCID: PMC9683697 DOI: 10.1126/sciadv.abp8747] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Accepted: 10/11/2022] [Indexed: 06/16/2023]
Abstract
Human activities have led to degradation of ecosystems globally. The lost ecosystem functions and services accumulate from the time of disturbance to the full recovery of the ecosystem and can be quantified as a "recovery debt," providing a valuable tool to develop better restoration practices that accelerate recovery and limit losses. Here, we quantified the recovery of faunal biodiversity and abundance toward a predisturbed state following structural restoration of oyster habitats globally. We found that while restoration initiates a rapid increase in biodiversity and abundance of reef-associated species within 2 years, recovery rate then decreases substantially, leaving a global shortfall in recovery of 35% below a predisturbed state. While efficient restoration methods boost recovery and minimize recovery shortfalls, the time to full recovery is yet to be quantified. Therefore, potential future coastal development should weigh up not only the instantaneous damage to ecosystem functions but also the potential for generational loss of services.
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Affiliation(s)
- Deevesh A. Hemraj
- The Swire Institute of Marine Science and Area of Ecology and Biodiversity, School of Biological Sciences, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, China
- Institute for Climate and Carbon Neutrality, The University of Hong Kong, Hong Kong SAR, China
| | - Melanie J. Bishop
- School of Natural Sciences, Macquarie University, Sydney, NSW, Australia
| | - Boze Hancock
- The Nature Conservancy, C/O URI Graduate School of Oceanography, 215 South Ferry Rd., Narragansett, RI, USA
| | - Jay J. Minuti
- The Swire Institute of Marine Science and Area of Ecology and Biodiversity, School of Biological Sciences, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, China
- Institute for Climate and Carbon Neutrality, The University of Hong Kong, Hong Kong SAR, China
| | - Ruth H. Thurstan
- Centre for Ecology and Conservation, College of Life and Environmental Sciences, The University of Exeter, Cornwall TR10 9FE, UK
| | - Philine S. E. Zu Ermgassen
- Changing Oceans Group, School of Geosciences, University of Edinburgh, James Hutton Rd, King’s Buildings, Edinburgh EH9 3FE, UK
| | - Bayden D. Russell
- The Swire Institute of Marine Science and Area of Ecology and Biodiversity, School of Biological Sciences, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, China
- Institute for Climate and Carbon Neutrality, The University of Hong Kong, Hong Kong SAR, China
- The Dove Marine Laboratory, School of Natural and Environmental Sciences, Newcastle University, Newcastle-upon-Tyne, UK
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20
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Effect of Life-History Traits and Habitat Condition on Genetic Diversity between Invasive and Native Plant Populations. DIVERSITY 2022. [DOI: 10.3390/d14121025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Plant invasions have a huge impact on the health of ecosystems and human well-being. The invasion risk varies with the introduction pathway, the propagule pressure, and the genetic diversity of the founding population. We performed a systematic review and meta-analysis of 30 studies reporting the genetic diversity of 31 plant species in their invasive and native ranges. We evaluated if patterns of genetic diversity differ between ranges and whether these responses are influenced by life-history traits, hybridization, polyploidization, and habitat condition. We found that invasive populations had significantly lower genetic diversity and higher inbreeding than native populations. In fragmented and degraded habitats, the genetic diversity of invaders was lower, but inbreeding was not affected. Polyploid invaders with hybrid capacity also showed lower genetic diversity. Invasive herbs with vegetative propagation were more sensitive to the loss of genetic diversity and had higher levels of inbreeding. Our synthesis showed that the genetic response in the invaded range could result from historical processes, such as founder and bottleneck events. Traits such as selfing are more likely to preserve the signatures of founder events and influence the genetic diversity in invasive populations. Additionally, clonality seems to be the predominant reproduction system in the invaded range.
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21
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Analysis of genome and methylation changes in Chinese indigenous chickens over time provides insight into species conservation. Commun Biol 2022; 5:952. [PMID: 36097156 PMCID: PMC9467985 DOI: 10.1038/s42003-022-03907-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Accepted: 08/26/2022] [Indexed: 11/08/2022] Open
Abstract
Conservation of natural resources is a vital and challenging task. Numerous animal genetic resources have been effectively conserved worldwide. However, the effectiveness of conservation programmes and the variation information of species have rarely been evaluated. Here, we performed whole-genome and whole-genome bisulfite sequencing of 90 Chinese indigenous chickens, which belonged to the Tibetan, Wenchang and Bian chicken breeds, and have been conserved under different conservation programmes. We observed that low genetic diversity and high DNA methylation variation occurs during ex situ in vivo conservation, while higher genetic diversity and differentiation occurs during in situ conservation. Further analyses revealed that most DNA methylation signatures are unique within ex situ in vivo conservation. Moreover, a high proportion of differentially methylated regions is found in genomic selection regions, suggesting a link between the effects of genomic variation and DNA methylation. Altogether our findings provide valuable information about genetic and DNA methylation variations during different conservation programmes, and hold practical relevance for species conservation. Comparisons of genomic and methylomic changes during the conservation of indigenous chicken breeds in China provide insight into conservation programmes for these breeds and their adaptations to unique environments.
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22
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Rauschkolb R, Li Z, Godefroid S, Dixon L, Durka W, Májeková M, Bossdorf O, Ensslin A, Scheepens JF. Evolution of plant drought strategies and herbivore tolerance after two decades of climate change. THE NEW PHYTOLOGIST 2022; 235:773-785. [PMID: 35357713 DOI: 10.1111/nph.18125] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Accepted: 03/24/2022] [Indexed: 06/14/2023]
Abstract
Ongoing global warming, coupled with increased drought frequencies, together with other biotic drivers may have resulted in complex evolutionary adaptation. The resurrection approach, comparing ancestors raised from stored seeds with their contemporary descendants under common conditions, is a powerful method to test for recent evolution in plant populations. We used 21-26-yr-old seeds of four European plant species - Matthiola tricuspidata, Plantago crassifolia, Clinopodium vulgare and Leontodon hispidus - stored in seed banks together with re-collected seeds from their wild populations. To test for evolutionary changes, we conducted a glasshouse experiment that quantified heritable changes in plant responses to drought and simulated insect herbivory. In three out of the four studied species, we found evidence that descendants had evolved shorter life cycles through faster growth and flowering. Shifts in the osmotic potential and leaf dry matter content indicated that descendants also evolved increased drought tolerance. A comparison of quantitative genetic differentiation (QST ) vs neutral molecular differentiation (FST ) values, using double digest restriction-site associated DNA (ddRAD) genotyping data, suggested that directional selection, and therefore adaptive evolution, was underlying some of the observed phenotypic changes. In summary, our study revealed evolutionary changes in plant populations over the last decades that are consistent with adaptation of drought escape and tolerance as well as herbivory avoidance.
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Affiliation(s)
- Robert Rauschkolb
- Plant Evolutionary Ecology, Institute of Evolution and Ecology, University of Tübingen, Auf der Morgenstelle 5, 72076, Tübingen, Germany
- Department of Plant Biodiversity, Institute of Ecology and Evolution with Herbarium Haussknecht and Botanical Garden, Friedrich Schiller University Jena, Germany, Philosophenweg 16, 07743, Jena, Germany
| | - Zixin Li
- Plant Evolutionary Ecology, Institute of Evolution and Ecology, University of Tübingen, Auf der Morgenstelle 5, 72076, Tübingen, Germany
| | | | - Lara Dixon
- Conservatoire Botanique National Méditerranéen de Porquerolles, 34 avenue Gambetta, 83400, Hyères, France
| | - Walter Durka
- Department of Community Ecology, Helmholtz Centre for Environmental Research - UFZ, Theodor-Lieser-Straße 4, 06120, Halle, Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, 04103, Leipzig, Germany
| | - Maria Májeková
- Plant Ecology, Institute of Evolution and Ecology, University of Tübingen, Auf der Morgenstelle 5, 72076, Tübingen, Germany
| | - Oliver Bossdorf
- Plant Evolutionary Ecology, Institute of Evolution and Ecology, University of Tübingen, Auf der Morgenstelle 5, 72076, Tübingen, Germany
| | - Andreas Ensslin
- Conservatory and Botanic Garden of the City of Geneva, 1296, Chambésy, Geneva, Switzerland
| | - J F Scheepens
- Plant Evolutionary Ecology, Faculty of Biological Sciences, Institute of Ecology, Evolution and Diversity, Goethe University Frankfurt, Max-von-Laue-Str. 13, 60438, Frankfurt am Main, Germany
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23
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Santos JL, Hradsky BA, Keith DA, Rowe KC, Senior KL, Sitters H, Kelly LT. Beyond inappropriate fire regimes: A synthesis of fire‐driven declines of threatened mammals in Australia. Conserv Lett 2022. [DOI: 10.1111/conl.12905] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Affiliation(s)
- Julianna L. Santos
- School of Ecosystem and Forest Sciences The University of Melbourne Parkville Australia
| | - Bronwyn A. Hradsky
- School of Ecosystem and Forest Sciences The University of Melbourne Parkville Australia
| | - David A. Keith
- Centre for Ecosystem Science, School of Biological, Earth and Environmental Sciences The University of New South Wales Sydney Australia
- New South Wales Department of Planning Infrastructure and Environment Parramatta Australia
| | - Kevin C. Rowe
- Sciences Department Museums Victoria Melbourne Australia
- School of BioSciences The University of Melbourne Parkville Australia
| | - Katharine L. Senior
- School of Ecosystem and Forest Sciences The University of Melbourne Parkville Australia
| | - Holly Sitters
- School of Ecosystem and Forest Sciences The University of Melbourne Parkville Australia
| | - Luke T. Kelly
- School of Ecosystem and Forest Sciences The University of Melbourne Parkville Australia
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24
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Dalongeville A, Nielsen ES, Teske PR, Heyden S. Comparative phylogeography in a marine biodiversity hotspot provides novel insights into evolutionary processes across the Atlantic‐Indian Ocean transition. DIVERS DISTRIB 2022. [DOI: 10.1111/ddi.13534] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Affiliation(s)
| | - Erica S. Nielsen
- Department of Evolution and Ecology University of California, Davis Davis California USA
| | - Peter R. Teske
- Department of Zoology Centre for Ecological Genomics and Wildlife Conservation University of Johannesburg Auckland Park South Africa
| | - Sophie Heyden
- Department of Botany and Zoology Evolutionary Genomics Group Stellenbosch University Stellenbosch South Africa
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25
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Mendonça HC, Pereira LFP, Maldonado dos Santos JV, Meda AR, Sant’ Ana GC. Genetic Diversity and Selection Footprints in the Genome of Brazilian Soybean Cultivars. FRONTIERS IN PLANT SCIENCE 2022; 13:842571. [PMID: 35432410 PMCID: PMC9006619 DOI: 10.3389/fpls.2022.842571] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Accepted: 02/14/2022] [Indexed: 06/14/2023]
Abstract
Although Brazil is currently the largest soybean producer in the world, only a small number of studies have analyzed the genetic diversity of Brazilian soybean. These studies have shown the existence of a narrow genetic base. The objectives of this work were to analyze the population structure and genetic diversity, and to identify selection signatures in the genome of soybean germplasms from different companies in Brazil. A panel consisting of 343 soybean lines from Brazil, North America, and Asia was genotyped using genotyping by sequencing (GBS). Population structure was assessed by Bayesian and multivariate approaches. Genetic diversity was analyzed using metrics such as the fixation index, nucleotide diversity, genetic dissimilarity, and linkage disequilibrium. The software BayeScan was used to detect selection signatures between Brazilian and Asian accessions as well as among Brazilian germplasms. Region of origin, company of origin, and relative maturity group (RMG) all had a significant influence on population structure. Varieties belonging to the same company and especially to the same RMG exhibited a high level of genetic similarity. This result was exacerbated among early maturing accessions. Brazilian soybean showed significantly lower genetic diversity when compared to Asian accessions. This was expected, because the crop's region of origin is its main genetic diversity reserve. We identified 7 genomic regions under selection between the Brazilian and Asian accessions, and 27 among Brazilian varieties developed by different companies. Associated with these genomic regions, we found 96 quantitative trait loci (QTLs) for important soybean breeding traits such as flowering, maturity, plant architecture, productivity components, pathogen resistance, and seed composition. Some of the QTLs associated with the markers under selection have genes of great importance to soybean's regional adaptation. The results reported herein allowed to expand the knowledge about the organization of the genetic variability of the Brazilian soybean germplasm. Furthermore, it was possible to identify genomic regions under selection possibly associated with the adaptation of soybean to Brazilian environments.
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Affiliation(s)
| | - Luiz Filipe Protasio Pereira
- Centro de Ciências Biológicas, State University of Londrina, Londrina, Brazil
- Laboratório de Biotecnologia, Instituto de Desenvolvimento Rural do Paraná, Embrapa Café, Londrina, Brazil
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26
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Di B, Firn J, Buckley YM, Lomas K, Pausas JG, Smith AL. The impact of roadside burning on genetic diversity in a high‐biomass invasive grass. Evol Appl 2022; 15:790-803. [PMID: 35603028 PMCID: PMC9108304 DOI: 10.1111/eva.13369] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Revised: 12/06/2021] [Accepted: 02/23/2022] [Indexed: 11/28/2022] Open
Affiliation(s)
- Binyin Di
- School of Agriculture and Food Sciences University of Queensland Gatton 4343 Australia
| | - Jennifer Firn
- School of Biology & Environmental Science Queensland University of Technology Brisbane 4000 Australia
| | - Yvonne M. Buckley
- School of Natural Sciences, Zoology Trinity College Dublin The University of Dublin Dublin 2 Ireland
| | - Kate Lomas
- School of Biology & Environmental Science Queensland University of Technology Brisbane 4000 Australia
| | - Juli G. Pausas
- Centro de Investigaciones sobre Desertificación (CIDE‐CSIC) 46113 Montcada, Valencia Spain
| | - Annabel L. Smith
- School of Agriculture and Food Sciences University of Queensland Gatton 4343 Australia
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27
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Roman J. The benefits of disturbance. Science 2021; 374:256-257. [PMID: 34648323 DOI: 10.1126/science.abm2257] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
[Figure: see text].
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Affiliation(s)
- Joe Roman
- Gund Institute for Environment, University of Vermont, Burlington, VT 05477, USA
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28
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Foster E, Watson J, Lemay MA, Tinker MT, Estes JA, Piercey R, Henson L, Ritland C, Miscampbell A, Nichol L, Hessing-Lewis M, Salomon AK, Darimont CT. Physical disturbance by recovering sea otter populations increases eelgrass genetic diversity. Science 2021; 374:333-336. [PMID: 34648338 DOI: 10.1126/science.abf2343] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
[Figure: see text].
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Affiliation(s)
- Erin Foster
- Hakai Institute, Heriot Bay, BC V0P 1H0, Canada.,Department of Geography, University of Victoria, Victoria, BC V8W 2Y2, Canada
| | - Jane Watson
- Department of Biology, Vancouver Island University, Nanaimo, BC V9R 5S5, Canada
| | | | - M Tim Tinker
- Nhydra Ecological Consulting, St. Margaret's Bay, NS B3Z 2G6, Canada.,Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, CA 95060, USA
| | - James A Estes
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, CA 95060, USA
| | | | - Lauren Henson
- Department of Geography, University of Victoria, Victoria, BC V8W 2Y2, Canada.,Raincoast Conservation Foundation, Bella Bella, BC V0T 1Z0, Canada
| | - Carol Ritland
- Genetic Data Centre, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Allyson Miscampbell
- Genetic Data Centre, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Linda Nichol
- Cetacean Research Program, Pacific Biological Station, Fisheries and Oceans Canada, Nanaimo, BC V9T 6N7, Canada
| | | | - Anne K Salomon
- School of Resource and Environmental Management, Simon Fraser University, Burnaby, BC V5A 1S6, Canada
| | - Chris T Darimont
- Hakai Institute, Heriot Bay, BC V0P 1H0, Canada.,Department of Geography, University of Victoria, Victoria, BC V8W 2Y2, Canada.,Raincoast Conservation Foundation, Bella Bella, BC V0T 1Z0, Canada
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29
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Lampert S, Ingle RA, Jackson JA, Gopal K, Plön S. Low mitochondrial genetic diversity in the Indian Ocean humpback dolphin Sousa plumbea in South African waters. ENDANGER SPECIES RES 2021. [DOI: 10.3354/esr01147] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
The Indian Ocean humpback dolphin Sousa plumbea has been described as South Africa’s most endangered marine mammal due to its low abundance, reliance on coastal habitats with increasing anthropogenic threats and high rates of mortality from bycatch in bather protection nets (BPNs). Although the species has been well studied in South Africa, only a single study has examined its molecular ecology to date, and its population structure remains poorly understood. However, understanding population structure is vital for the conservation and management of a species. To address these research gaps for S. plumbea in South African waters, we analysed the mitochondrial D-loop of 157 museum skin and tooth samples collected between 1963 and 2017 from across the species’ geographic range in South Africa. Our data show that the humpback dolphin has extremely low mitochondrial diversity (haplotype diversity, HD = 0.47; nucleotide diversity, π = 0.2%) with only 3 haplotypes identified, which is comparable to the Critically Endangered Māui dolphin Cephalorhynchus hectori maui and the Critically Endangered Mekong population of Irrawaddy dolphin Orcaella brevirostris. Mitochondrial genetic diversity has not changed significantly in the last 50 yr, despite the high levels of bycatch in BPNs over this time period. Furthermore, we found no evidence of differentiation between dolphins from the KwaZulu-Natal Coast and the Cape South Coast (Western Cape and Eastern Cape). The extremely low mitochondrial diversity we found adds to the growing body of evidence that the humpback dolphin is becoming increasingly vulnerable and that urgent conservation efforts are required for the survival of the species.
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Affiliation(s)
- S Lampert
- Department of Molecular and Cell Biology, University of Cape Town, Rondebosch 7700, South Africa
| | - RA Ingle
- Department of Molecular and Cell Biology, University of Cape Town, Rondebosch 7700, South Africa
| | - JA Jackson
- British Antarctic Survey, Cambridge CB3 0ET, UK
| | - K Gopal
- Natural Science Collections Facility (South African National Biodiversity Institute), Pretoria 0186, South Africa
- Department of Natural History, Iziko South African Museums, Cape Town 8001, South Africa
| | - S Plön
- Bayworld Centre for Research and Education (BCRE), Port Elizabeth 6013, South Africa
- Division of Medical Virology, Department of Pathology, Stellenbosch University, Cape Town 7505, South Africa
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30
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Díaz-Moreno DM, Hernández-Gonzalez F, Moncada-Jimenez JF, Mora C, Prada C, Jiménez-Alonso G, Balaguera-Reina SA. Molecular characterization of the spectacled caiman (Caiman crocodilus) in the upper Magdalena River basin, Colombia: Demographic and phylogeographic insights. SYST BIODIVERS 2021. [DOI: 10.1080/14772000.2021.1968975] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- Diana M. Díaz-Moreno
- Programa de Biología, Facultad de Ciencias, Universidad de Tolima, Calle 42 #1B-1 Barrio Santa Helena, Ibagué, 730001, Colombia
| | - Felipe Hernández-Gonzalez
- Programa de Biología, Facultad de Ciencias, Universidad de Tolima, Calle 42 #1B-1 Barrio Santa Helena, Ibagué, 730001, Colombia
| | - Juan F. Moncada-Jimenez
- Programa de Biología, Facultad de Ciencias, Universidad de Tolima, Calle 42 #1B-1 Barrio Santa Helena, Ibagué, 730001, Colombia
| | - Cristina Mora
- Grupo de Investigaciín en Biodiversidad y Dinámica de Ecosistemas Tropicales, Universidad de Tolima, Ibaguí, 730001, Colombia
| | - Carlos Prada
- Programa de Biología, Facultad de Ciencias, Universidad de Tolima, Calle 42 #1B-1 Barrio Santa Helena, Ibagué, 730001, Colombia
| | - Gonzalo Jiménez-Alonso
- Grupo Biodiversidad y Conservación Genética, Instituto de Genética, Universidad Nacional de Colombia, Carrera 30 #45-03 Edificio 426, Bogotá, 111321, DC, Colombia
- Programa de Zootecnia, Facultad de Zootecnia, Fundación Universitaria Agraria de Colombia, Calle 170 #54a-10, Bogoté, 111166, DC, Colombia
| | - Sergio A. Balaguera-Reina
- Programa de Biología Ambiental, Facultad de Ciencias Naturales y Matemáticas, Universidad de Ibagué, Carrera 22 Calle 67, Ibagué, 730001, Colombia
- Department of Wildlife Ecology and Conservation, Fort Lauderdale Research and Education Center, University of Florida, Fort Lauderdale, Florida, USA
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31
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Gates D, Jackson B, Schoville SD. Impacts of Fire on Butterfly Genetic Diversity and Connectivity. J Hered 2021; 112:367-376. [PMID: 34009382 DOI: 10.1093/jhered/esab027] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Accepted: 04/26/2021] [Indexed: 11/14/2022] Open
Abstract
How do novel fire regimes and a long history of fire suppression influence species genetic diversity? Genetic diversity provides the raw materials for sustaining viable populations and for allowing adaptation to novel environmental challenges, and at present, few studies address the genetic responses of animals to fire management. Here we study the genetic responses of 2 butterfly species to a landscape gradient of fire timing and severity in Yosemite National Park using a large set of genome-wide single nucleotide polymorphisms (SNPs). Butterflies are important bio-indicators of invertebrate diversity and play important roles in both bottom-up and top-down ecosystem processes, and typically increase in abundance following wildfires, due to an increase in abundance of flowering plants. However, it is not clear how genetic diversity and genetic connectivity of butterflies respond to landscape change following fire, and whether fire management has positive or negative effects. We found evidence to suggest that fire increases genetic diversity and reduces isolation in 2 butterfly species, but that aspects of the fire regime (severity, extent, timing, and frequency) differ in importance depending on the ecology of the specific species. This research is the first study to address fire management impacts on genetic diversity in invertebrates, and the results will allow fire managers to predict that fire reintroduction in protected areas will generally benefit butterfly populations.
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Affiliation(s)
- Daisy Gates
- Department of Entomology, University of Wisconsin-Madison, Madison, WI, USA
| | - Breeanne Jackson
- Division of Resources Management and Science, Yosemite National Park, El Portal, CA, USA
| | - Sean D Schoville
- Department of Entomology, University of Wisconsin-Madison, Madison, WI, USA
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32
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Giglio RM, Rocke TE, Osorio JE, Latch EK. Characterizing patterns of genomic variation in the threatened Utah prairie dog: Implications for conservation and management. Evol Appl 2021; 14:1036-1051. [PMID: 33897819 PMCID: PMC8061279 DOI: 10.1111/eva.13179] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2020] [Revised: 11/04/2020] [Accepted: 11/05/2020] [Indexed: 11/30/2022] Open
Abstract
Utah prairie dogs (Cynomys parvidens) are federally threatened due to eradication campaigns, habitat destruction, and outbreaks of plague. Today, Utah prairie dogs exist in small, isolated populations, making them less demographically stable and more susceptible to erosion of genetic variation by genetic drift. We characterized patterns of genetic structure at neutral and putatively adaptive loci in order to evaluate the relative effects of genetic drift and local adaptation on population divergence. We sampled individuals across the Utah prairie dog species range and generated 2955 single nucleotide polymorphisms using double digest restriction site-associated DNA sequencing. Genetic diversity was lower in low-elevation sites compared to high-elevation sites. Population divergence was high among sites and followed an isolation-by-distance model. Our results indicate that genetic drift plays a substantial role in the population divergence of the Utah prairie dog, and colonies would likely benefit from translocation of individuals between recovery units, which are characterized by distinct elevations, despite the detection of environmental associations with outlier loci. By understanding the processes that shape genetic structure, better informed decisions can be made with respect to the management of threatened species to ensure that adaptation is not stymied.
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Affiliation(s)
- Rachael M. Giglio
- Department of Biological SciencesUniversity of Wisconsin‐MilwaukeeMilwaukeeWIUSA
| | | | - Jorge E. Osorio
- Department of Pathobiological SciencesSchool of Veterinary MedicineUniversity of Wisconsin‐MadisonMadisonWIUSA
| | - Emily K. Latch
- Department of Biological SciencesUniversity of Wisconsin‐MilwaukeeMilwaukeeWIUSA
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33
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Influence of Environmental Factors on the Genetic and Chemical Diversity of Brickellia veronicifolia Populations Growing in Fragmented Shrublands from Mexico. PLANTS 2021; 10:plants10020325. [PMID: 33567633 PMCID: PMC7915050 DOI: 10.3390/plants10020325] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Revised: 02/01/2021] [Accepted: 02/05/2021] [Indexed: 12/31/2022]
Abstract
Brickellia veronicifolia is a native Asteraceae from Mexico that persists in fragmented habitats. This investigation reports the genetic and chemical diversity of B. veronicifolia. The diversity analysis based on iPBS markers showed an averaged Shannon index (S) of 0.3493, a Nei genetic diversity (h) of 0.2256, and a percentage of polymorphic loci average (P) of 80.7867%. The population structure obtained by AMOVA revealed that the highest variation found within populations was 94.58%. GC-MS profiling of six populations indicated that major volatiles were β–caryophyllene (11.63%), spathulenol (12.85%), caryophyllene oxide (13.98%), α–cadinol (7.04%), cubedol (6.72%) and tau-muurolol (4.81%). Mantel tests suggested a statistically significant relationship between minor volatiles and geographical distance (r = 0.6163; p = 0.0470; p ˂ 0.05). Likewise, major volatiles showed a significant correlation with the soil pH (r = 0.6862; p = 0.0230) and maximum temperature (r = 0.4999; p = 0.0280). Our study suggests that the variation and genetic divergence of B. veronicifolia has no relationship with climatic parameters, whereas the volatiles are probably influenced by environmental factors and not by the genotype per se. Based on the characteristics of B. veronicifolia, this plant could be considered as a candidate for restoring fragmented shrublands in Mexico.
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34
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Ghazi MG, Sharma SP, Tuboi C, Angom S, Gurumayum T, Nigam P, Hussain SA. Population genetics and evolutionary history of the endangered Eld's deer (Rucervus eldii) with implications for planning species recovery. Sci Rep 2021; 11:2564. [PMID: 33510319 PMCID: PMC7844053 DOI: 10.1038/s41598-021-82183-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Accepted: 01/18/2021] [Indexed: 01/30/2023] Open
Abstract
Eld's deer (Rucervus eldii) with three recognised subspecies (R. e. eldii, R. e. thamin, and R. e. siamensis) represents one of the most threatened cervids found in Southeast Asia. The species has experienced considerable range contractions and local extinctions owing to habitat loss and fragmentation, hunting, and illegal trade across its distribution range over the last century. Understanding the patterns of genetic variation is crucial for planning effective conservation strategies. This study investigated the phylogeography, divergence events and systematics of Eld's deer subspecies using the largest mtDNA dataset compiled to date. We also analysed the genetic structure and demographic history of R. e. eldii using 19 microsatellite markers. Our results showed that R. e. siamensis exhibits two divergent mtDNA lineages (mainland and Hainan Island), which diverged around 0.2 Mya (95% HPD 0.1-0.2), possibly driven by the fluctuating sea levels of the Early Holocene period. The divergence between R. e. eldii and R. e. siamensis occurred around 0.4 Mya (95% HPD 0.3-0.5), potentially associated with the adaptations to warm and humid climate with open grassland vegetation that predominated the region. Furthermore, R. e. eldii exhibits low levels of genetic diversity and small contemporary effective population size (median = 7, 4.7-10.8 at 95% CI) with widespread historical genetic bottlenecks which accentuates its vulnerability to inbreeding and extinction. Based on the observed significant evolutionary and systematic distance between Eld's deer and other species of the genus Rucervus, we propose to classify Eld's deer (Cervus eldii) in the genus Cervus, which is in congruent with previous phylogenetic studies. This study provides important conservation implications required to direct the ongoing population recovery programs and planning future conservation strategies.
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Affiliation(s)
| | - Surya Prasad Sharma
- Wildlife Institute of India, Chandrabani, Post Box #18, Dehra Dun, Uttarakhand, 248002, India
| | - Chongpi Tuboi
- Wildlife Institute of India, Chandrabani, Post Box #18, Dehra Dun, Uttarakhand, 248002, India
| | - Sangeeta Angom
- Wildlife Institute of India, Chandrabani, Post Box #18, Dehra Dun, Uttarakhand, 248002, India
| | - Tennison Gurumayum
- Wildlife Institute of India, Chandrabani, Post Box #18, Dehra Dun, Uttarakhand, 248002, India
| | - Parag Nigam
- Wildlife Institute of India, Chandrabani, Post Box #18, Dehra Dun, Uttarakhand, 248002, India
| | - Syed Ainul Hussain
- Wildlife Institute of India, Chandrabani, Post Box #18, Dehra Dun, Uttarakhand, 248002, India.
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35
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Blondel L, Paterson IG, Bentzen P, Hendry AP. Resistance and resilience of genetic and phenotypic diversity to "black swan" flood events: A retrospective analysis with historical samples of guppies. Mol Ecol 2021; 30:1017-1028. [PMID: 33346935 DOI: 10.1111/mec.15782] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Revised: 12/04/2020] [Accepted: 12/14/2020] [Indexed: 01/05/2023]
Abstract
Rare extreme "black swan" disturbances can impact ecosystems in many ways, such as destroying habitats, depleting resources, and causing high mortality. In rivers, for instance, exceptional floods that occur infrequently (e.g., so-called "50-year floods") can strongly impact the abundance of fishes and other aquatic organisms. Beyond such ecological effects, these floods could also impact intraspecific diversity by elevating genetic drift or dispersal and by imposing strong selection, which could then influence the population's ability to recover from disturbance. And yet, natural systems might be resistant (show little change) or resilient (show rapid recovery) even to rare extreme events - perhaps as a result of selection due to past events. We considered these possibilities in two rivers where native guppies experienced two extreme floods - one in 2005 and another in 2016. For each river, we selected four sites and used archived "historical" samples to compare levels of genetic and phenotypic diversity before vs. after floods. Genetic diversity was represented by 33 neutral microsatellite markers, and phenotypic diversity was represented by body length and male melanic (black) colour. We found that genetic diversity and population structure was mostly "resistant" to even these extreme floods; whereas the larger impacts on phenotypic diversity were short-lived, suggesting additional "resilience". We discuss the determinants of these two outcomes for guppies facing floods, and then consider the general implications for the resistance and resilience of intraspecific variation to black swan disturbances.
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Affiliation(s)
- Léa Blondel
- Redpath Museum and Department of Biology, McGill University, Montreal, QC, Canada
| | - Ian G Paterson
- Department of Biology, Dalhousie University, Halifax, NS, Canada
| | - Paul Bentzen
- Department of Biology, Dalhousie University, Halifax, NS, Canada
| | - Andrew P Hendry
- Redpath Museum and Department of Biology, McGill University, Montreal, QC, Canada
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36
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Reisch C, Sattler J. Impact of river dynamics on the genetic variation of Gypsophila repens (Caryophyllaceae): a comparison of heath forest and more dynamic gravel bank populations along an alpine river. PLANT BIOLOGY (STUTTGART, GERMANY) 2021; 23:205-211. [PMID: 33058499 DOI: 10.1111/plb.13195] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Accepted: 09/22/2020] [Indexed: 06/11/2023]
Abstract
Alpine rivers are, despite anthropogenic water flow regulation, still often highly dynamic ecosystems. Plant species occurring along these rivers are subject to ecological disturbance, mainly caused by seasonal flooding. Gypsophila repens typically grows at higher altitudes in the Alps, but also occurs at lower altitudes on gravel banks directly along the river and in heath forests at larger distances from the river. Populations on gravel banks are considered non-permanent and it is assumed that new individuals originate from seed periodically washed down from higher altitudes. Populations in heath forests are, in contrast, permanent and not regularly provided with seeds from higher altitudes through flooding. If the genetic structure of this plant species is strongly affected by gene flow via seed dispersal, then higher levels of genetic diversity in populations but less differentiation among populations on gravel banks than in heath forests can be expected. In this study, we analysed genetic diversity within and differentiation among 15 populations of G. repens from gravel banks and heath forests along the alpine River Isar using amplified fragment length polymorphisms (AFLP). Genetic diversity was, as assumed, slightly higher in gravel bank than in heath forest populations, but genetic differentiation was, in contrast to our expectations, comparable among populations in both habitat types. Our study provides evidence for increased genetic diversity under conditions of higher ecological disturbance and increased seed dispersal on gravel banks. Similar levels of genetic differentiation among populations in both habitat types can be attributed to the species' long lifetime, a permanent soil seed bank and gene flow by pollinators among different habitats/locations.
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Affiliation(s)
- C Reisch
- Institute of Plant Sciences, University of Regensburg, Regensburg, Germany
| | - J Sattler
- Institute of Plant Sciences, University of Regensburg, Regensburg, Germany
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37
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Dane M, Anderson NJ, Osburn CL, Colbourne JK, Frisch D. Centennial clonal stability of asexual Daphnia in Greenland lakes despite climate variability. Ecol Evol 2020; 10:14178-14188. [PMID: 33391708 PMCID: PMC7771157 DOI: 10.1002/ece3.7012] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Revised: 10/12/2020] [Accepted: 10/14/2020] [Indexed: 12/12/2022] Open
Abstract
Climate and environmental condition drive biodiversity at many levels of biological organization, from populations to ecosystems. Combined with paleoecological reconstructions, palaeogenetic information on resident populations provides novel insights into evolutionary trajectories and genetic diversity driven by environmental variability. While temporal observations of changing genetic structure are often made of sexual populations, little is known about how environmental change affects the long-term fate of asexual lineages. Here, we provide information on obligately asexual, triploid Daphnia populations from three Arctic lakes in West Greenland through the past 200-300 years to test the impact of environmental change on the temporal and spatial population genetic structure. The contrasting ecological state of the lakes, specifically regarding salinity and habitat structure may explain the observed lake-specific clonal composition over time. Palaeolimnological reconstructions show considerable regional environmental fluctuations since 1,700 (the end of the Little Ice Age), but the population genetic structure in two lakes was almost unchanged with at most two clones per time period. Their local populations were strongly dominated by a single clone that has persisted for 250-300 years. We discuss possible explanations for the apparent population genetic stability: (a) persistent clones are general-purpose genotypes that thrive under broad environmental conditions, (b) clonal lineages evolved subtle genotypic differences unresolved by microsatellite markers, or (c) epigenetic modifications allow for clonal adaptation to changing environmental conditions. Our results motivate research into the mechanisms of adaptation in these populations, as well as their evolutionary fate in the light of accelerating climate change in the polar regions.
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Affiliation(s)
- Maison Dane
- School of BiosciencesUniversity of BirminghamBirminghamUK
| | | | - Christopher L. Osburn
- Department of Marine, Earth, and Atmospheric SciencesNorth Carolina State UniversityRaleighNCUSA
| | | | - Dagmar Frisch
- School of BiosciencesUniversity of BirminghamBirminghamUK
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38
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Millette KL, Gonzalez A, Cristescu ME. Breaking ecological barriers: Anthropogenic disturbance leads to habitat transitions, hybridization, and high genetic diversity. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 740:140046. [PMID: 32563876 DOI: 10.1016/j.scitotenv.2020.140046] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2020] [Revised: 06/01/2020] [Accepted: 06/05/2020] [Indexed: 06/11/2023]
Abstract
Genetic diversity is expected to erode in disturbed habitats through strong selection, local extinctions, and recolonization associated with genetic bottlenecks and restricted gene flow. Despite this general prediction and over three decades of population genetics studies, our understanding of the long-term effect of environmental disturbance on local and regional genetic diversity remains limited. We conducted a population genetic survey of the microcrustacean Daphnia across a landscape subject to anthropogenic stressors from a century of industrial mining. At the local scale we found moderate genetic diversity (i.e., low clonal diversity), characteristic of habitat-specific selective sweeps and local extinctions, but high diversity and strong genetic structure at the regional scale despite the shared watershed of many lakes and exceptional dispersal ability of daphniids. Many habitats experienced changes in species assemblages, with the obligate asexual Daphnia pulex lineages-known only to inhabit ponds-dominating disrupted urban lakes. This habitat transition (pond to lake) was likely facilitated by the disruption of ecological barriers maintaining the genomic separation of these young species. Thus, disrupted habitats can exhibit complex and unexpected genetic patterns of local extinctions and recolonizations, followed by habitat transitions, hybridization and potential speciation events that are difficult to predict and should not be underestimated.
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Affiliation(s)
- Katie L Millette
- Department of Biology, McGill University, Montreal, Quebec H3A 1B1, Canada; Quebec Centre for Biodiversity Science, Canada.
| | - Andrew Gonzalez
- Department of Biology, McGill University, Montreal, Quebec H3A 1B1, Canada; Quebec Centre for Biodiversity Science, Canada
| | - Melania E Cristescu
- Department of Biology, McGill University, Montreal, Quebec H3A 1B1, Canada; Quebec Centre for Biodiversity Science, Canada
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Kollars NM, DuBois K, Stachowicz JJ. Sequential disturbances alter the outcome of inter‐genotypic interactions in a clonal plant. Funct Ecol 2020. [DOI: 10.1111/1365-2435.13690] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Affiliation(s)
- Nicole M. Kollars
- Center for Population Biology University of California Davis CA USA
- Department of Evolution and Ecology University of California Davis CA USA
| | - Katherine DuBois
- Department of Evolution and Ecology University of California Davis CA USA
- Bodega Marine Laboratory Bodega Bay CA USA
| | - John J. Stachowicz
- Center for Population Biology University of California Davis CA USA
- Department of Evolution and Ecology University of California Davis CA USA
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Lemos ASM, Azevedo-Silva M, Gonçalves-Neto S, Souza AP, Oliveira PS. Microsatellites for the Neotropical Ant, Odontomachus chelifer (Hymenoptera: Formicidae). JOURNAL OF INSECT SCIENCE (ONLINE) 2020; 20:5937568. [PMID: 33098430 PMCID: PMC7585319 DOI: 10.1093/jisesa/ieaa117] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Indexed: 05/01/2023]
Abstract
Odontomachus chelifer (Latreille) (Ponerinae) is a ground-dwelling, predominantly carnivorous ant whose colonies may contain multiple egg-laying queens and are potentially susceptible to border effects in the Brazilian savanna known as Cerrado. The ecology and natural history of O. chelifer is well studied, but very little is known about the genetic diversity of O. chelifer colonies. In this study, we developed microsatellite markers for the study of genetic variation in O. chelifer. We created a microsatellite-enriched library that resulted in the development and characterization of 22 markers, of which 18 were found to be polymorphic in the population studied. The mean expected heterozygosity was 0.59, whereas the mean rarified allelic richness was determined as 4.27 alleles per locus. The polymorphism level detected was similar to genetic diversity estimates found in other poneromorph ant species. The microsatellites developed here are likely to be useful for the investigation of colony structure, functional polygyny, breeding system, and population genetics in O. chelifer. Moreover, the description of O. chelifer's genetic diversity is crucial for its conservation and maintenance of its ecological role in the Cerrado savanna.
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Affiliation(s)
- Alessandra S M Lemos
- Graduação em Ciências Biológicas, Departamento de Biologia Animal, Universidade Estadual de Campinas, Campinas, SP, Brazil
| | - Marianne Azevedo-Silva
- Programa de Pós-Graduação em Ecologia, Departamento de Biologia Animal, Universidade Estadual de Campinas, Campinas, SP, Brazil
| | - Salatiel Gonçalves-Neto
- Graduação em Ciências Biológicas, Departamento de Biologia Animal, Universidade Estadual de Campinas, Campinas, SP, Brazil
| | - Anete P Souza
- Departamento de Biologia Vegetal, Centro de Biologia Molecular e Engenharia Genética, Universidade Estadual de Campinas, Campinas, SP, Brazil
| | - Paulo S Oliveira
- Departamento de Biologia Animal, Universidade Estadual de Campinas, Campinas, SP, Brazil
- Corresponding author, e-mail:
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41
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Attenuated phenotypic responses of lizard morphology to logging and fire-related forest disturbance. Evol Ecol 2020. [DOI: 10.1007/s10682-020-10067-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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42
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Genotyping-by-sequencing reveals the effects of riverscape, climate and interspecific introgression on the genetic diversity and local adaptation of the endangered Mexican golden trout (Oncorhynchus chrysogaster). CONSERV GENET 2020. [DOI: 10.1007/s10592-020-01297-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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43
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Unravelling effects of grazing intensity on genetic diversity and fitness of desert vegetation. Perspect Ecol Conserv 2020. [DOI: 10.1016/j.pecon.2020.06.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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Barga SC, Olwell P, Edwards F, Prescott L, Leger EA. Seeds of Success: A conservation and restoration investment in the future of U.S.lands. CONSERVATION SCIENCE AND PRACTICE 2020. [DOI: 10.1111/csp2.209] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Affiliation(s)
- Sarah C. Barga
- Department of BiologyUniversity of Nevada, Reno Reno Nevada USA
- United States Department of Agriculture Forest ServiceRocky Mountain Research Station Boise Idaho USA
| | - Peggy Olwell
- Plant Conservation and Restoration Program, Bureau of Land Management Washington District of Columbia USA
| | - Fred Edwards
- Plant Conservation and Restoration Program, Bureau of Land Management Washington District of Columbia USA
- Bureau of Land Management Reno Nevada USA
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Olarte Ó, SÁnchez-Montes G, MartÍnez-Solano Í. Integrative demographic study of the Iberian painted frog (Discoglossus galganoi): inter-annual variation in the effective to census population size ratio, with insights on mating system and breeding success. Integr Zool 2020; 15:498-510. [PMID: 32333629 DOI: 10.1111/1749-4877.12452] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
In the face of worldwide amphibian declines, integrative studies combining individual-based information and genetic data represent a powerful approach to produce robust, reliable, and comparable assessments of demographic dynamics. The Iberian painted frog (Discoglossus galganoi) is endemic to Spain and Portugal and shows decreasing population trends across its range, but few studies have attempted to estimate census sizes or assess genetic diversity in wild populations, and little is known about their reproductive biology. We applied an integrative approach based on the combination of capture-mark-recapture data and multilocus genotypes to monitor a breeding population of D. galganoi in central Spain during two consecutive breeding seasons, focusing on the estimation of demographic parameters and their temporal variation. Specifically, we estimated the number of adults (Na ), the effective population size (Ne ), and the effective number of breeders (Nb ), as well as survival and migration rates. We documented a >50% decrease in the estimated number of adults of both sexes between the breeding seasons of 2018 and 2019, probably associated with reduced rainfall in the latter. Estimates of Nb and the Nb /Na ratio were low in both seasons, with a 20-30% decrease in Nb and a 47% increase in the Nb /Na ratio in 2019. Based on the reconstruction of pedigrees from larval and adult genotypes, we provide the first genetic evidence of polygamy in males and females of D. galganoi and the first estimates of breeding success in the species.
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Affiliation(s)
- Óscar Olarte
- Department of Biodiversity and Evolutionary Biology, Museo Nacional de Ciencias Naturales (CSIC), c/ José Gutiérrez Abascal 2, Madrid, 28006, Spain
| | - Gregorio SÁnchez-Montes
- Department of Biodiversity and Evolutionary Biology, Museo Nacional de Ciencias Naturales (CSIC), c/ José Gutiérrez Abascal 2, Madrid, 28006, Spain
| | - Íñigo MartÍnez-Solano
- Department of Biodiversity and Evolutionary Biology, Museo Nacional de Ciencias Naturales (CSIC), c/ José Gutiérrez Abascal 2, Madrid, 28006, Spain
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Sitters H, Di Stefano J. Integrating functional connectivity and fire management for better conservation outcomes. CONSERVATION BIOLOGY : THE JOURNAL OF THE SOCIETY FOR CONSERVATION BIOLOGY 2020; 34:550-560. [PMID: 31777984 DOI: 10.1111/cobi.13446] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Revised: 11/11/2019] [Accepted: 11/22/2019] [Indexed: 06/10/2023]
Abstract
Globally, the mean abundance of terrestrial animals has fallen by 50% since 1970, and populations face ongoing threats associated with habitat loss, fragmentation, climate change, and disturbance. Climate change can influence the quality of remaining habitat directly and indirectly by precipitating increases in the extent, frequency, and severity of natural disturbances, such as fire. Species face the combined threats of habitat clearance, changing climates, and altered disturbance regimes, each of which may interact and have cascading impacts on animal populations. Typically, conservation agencies are limited in their capacity to mitigate rates of habitat clearance, habitat fragmentation, or climate change, yet fire management is increasingly used worldwide to reduce wildfire risk and achieve conservation outcomes. A popular approach to ecological fire management involves the creation of fire mosaics to promote animal diversity. However, this strategy has 2 fundamental limitations: the effect of fire on animal movement within or among habitat patches is not considered and the implications of the current fire regime for long-term population persistence are overlooked. Spatial and temporal patterns in fire history can influence animal movement, which is essential to the survival of individual animals, maintenance of genetic diversity, and persistence of populations, species, and ecosystems. We argue that there is rich potential for fire managers to manipulate animal movement patterns; enhance functional connectivity, gene flow, and genetic diversity; and increase the capacity of populations to persist under shifting environmental conditions. Recent methodological advances, such as spatiotemporal connectivity modeling, spatially explicit individual-based simulation, and fire-regime modeling can be integrated to achieve better outcomes for biodiversity in human-modified, fire-prone landscapes. Article impact statement: Land managers may conserve populations by using fire to sustain or enhance functional connectivity.
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Affiliation(s)
- Holly Sitters
- School of Ecosystem and Forest Sciences, The University of Melbourne, Creswick, Victoria, 3363, Australia
| | - Julian Di Stefano
- School of Ecosystem and Forest Sciences, The University of Melbourne, Creswick, Victoria, 3363, Australia
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Pagán JA, Veríssimo A, Sikkel PC, Xavier R. Hurricane-induced disturbance increases genetic diversity and population admixture of the direct-brooding isopod, Gnathia marleyi. Sci Rep 2020; 10:8649. [PMID: 32457295 PMCID: PMC7250855 DOI: 10.1038/s41598-020-64779-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Accepted: 03/31/2020] [Indexed: 11/19/2022] Open
Abstract
Severe disturbances can substantially alter eco-evolutionary processes and dynamics. While the impacts of catastrophic events on the biophysical attributes of communities are sometimes assessed, their effects on the genetic patterns of species remain poorly understood. To characterize how severe disturbances impact species at the molecular level, we examined the effects of the most energetic North Atlantic hurricane season in 50 years on the genetic diversity and structure of a dispersal-limited isopod, Gnathia marleyi. We sequenced a portion of the cytochrome oxidase I gene for 432 gnathiids, collected from six localities, ranging from western Puerto Rico to St John, US Virgin Islands. Importantly, multiple years of pre-hurricane sample collection allowed us to characterize temporal genetic patterns under undisturbed conditions and detect the changes subsequent to the 2017 hurricanes. Our results revealed no change to genetic diversity or structure for the years prior to the 2017 hurricanes, with genetic structure occurring at the local and regional levels, with three main clusters corresponding to Southwest Puerto Rico, East Puerto Rico, and the US Virgin Islands. However, directly following the 2017 hurricanes, genetic diversity increased at five of the six sampled localities. Additionally, we found a clear homogenizing effect prompted by increased shared genetic diversity among geographically distant regions and sites that resulted in substantially decreased among-region and among-site differentiation. Our work shows that severe disturbances caused by major tropical hurricanes facilitate gene-flow and increase overall genetic diversity and population admixture of dispersal limited coral reef species, potentially impacting the ecology and evolution of a key regional endemic.
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Affiliation(s)
- J Andrés Pagán
- CIBIO- Universidade do Porto, Centro de Investigção em Biodiversidade e Recursos Genéticos, Campus Agrário de Vairão, Rua Padre Armando Quintas, 4485-661, Vairão, Portugal
| | - Ana Veríssimo
- CIBIO- Universidade do Porto, Centro de Investigção em Biodiversidade e Recursos Genéticos, Campus Agrário de Vairão, Rua Padre Armando Quintas, 4485-661, Vairão, Portugal
| | - Paul C Sikkel
- Department of Biological Sciences and Environmental Sciences Program, Arkansas State University, PO Box 599, AR, 72467, State University, USA.
- Water Research Group, Unit for Environmental Sciences and Management, North-West University, Potchefstroom, South Africa.
| | - Raquel Xavier
- CIBIO- Universidade do Porto, Centro de Investigção em Biodiversidade e Recursos Genéticos, Campus Agrário de Vairão, Rua Padre Armando Quintas, 4485-661, Vairão, Portugal.
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Valenzuela‐Aguayo F, McCracken GR, Manosalva A, Habit E, Ruzzante DE. Human-induced habitat fragmentation effects on connectivity, diversity, and population persistence of an endemic fish, Percilia irwini, in the Biobío River basin (Chile). Evol Appl 2020; 13:794-807. [PMID: 32211068 PMCID: PMC7086057 DOI: 10.1111/eva.12901] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2019] [Revised: 10/14/2019] [Accepted: 11/05/2019] [Indexed: 01/15/2023] Open
Abstract
An understanding of how genetic variability is distributed in space is fundamental for the conservation and maintenance of diversity in spatially fragmented and vulnerable populations. While fragmentation can occur from natural barriers, it can also be exacerbated by anthropogenic activities such as hydroelectric power plant development. Whatever the source, fragmentation can have significant ecological effects, including disruptions of migratory processes and gene flow among populations. In Chile, the Biobío River basin exhibits a high degree of habitat fragmentation due to the numerous hydroelectric power plants in operation, the number of which is expected to increase following new renewable energy use strategies. Here, we assessed the effects of different kinds of barriers on the genetic structure of the endemic freshwater fish Percilia irwini, knowledge that is critically needed to inform conservation strategies in light of current and anticipated further fragmentation initiatives in the system. We identified eight genetic units throughout the entire Biobío system with high effective sizes. A reduced effective size estimate was, however, observed in a single population located between two impassable barriers. Both natural waterfalls and human-made dams were important drivers of population differentiation in this system; however, dams affect genetic diversity differentially depending on their mode of operation. Evidence of population extirpation was found in two river stretches limited by upstream and downstream dams. Significant gene flow in both directions was found among populations not separated by natural or anthropogenic barriers. Our results suggest a significant vulnerability of P. irwini populations to future dam development and demonstrate the importance of studying basin-wide data sets with genetic metrics to understand the strength and direction of anthropogenic impacts on fish populations.
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Affiliation(s)
- Francisca Valenzuela‐Aguayo
- Laboratorio de Ecología y Conservación de PecesDepartamento de Sistemas AcuáticosFacultad de Ciencias Ambientales y Centro EULAUniversidad de ConcepciónConcepciónChile
- Department of BiologyDalhousie UniversityHalifaxNSCanada
| | | | - Aliro Manosalva
- Laboratorio de Ecología y Conservación de PecesDepartamento de Sistemas AcuáticosFacultad de Ciencias Ambientales y Centro EULAUniversidad de ConcepciónConcepciónChile
| | - Evelyn Habit
- Laboratorio de Ecología y Conservación de PecesDepartamento de Sistemas AcuáticosFacultad de Ciencias Ambientales y Centro EULAUniversidad de ConcepciónConcepciónChile
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Huwe T, Prusty BK, Ray A, Lee S, Ravindran B, Michael E. Interactions between Parasitic Infections and the Human Gut Microbiome in Odisha, India. Am J Trop Med Hyg 2020; 100:1486-1489. [PMID: 30963988 DOI: 10.4269/ajtmh.18-0968] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Soil-transmitted helminth (STH) infections and malaria are parasitic diseases with enormous global health burdens. Research has demonstrated a relationship between each of these parasites and the gut microbiome, suggesting that the gut microbiota may be implicated in governing host susceptibility to diverse pathogens, and perhaps even coinfection by different pathogens, through similar microbiome-influenced pathways. Here, we have derived a first microbiome community profile associated with STH infections in Odisha, India, and tested the hypothesis that the gut microbiome can modulate host susceptibility to multiple parasite infections through the same pathways. This study revealed several bacterial taxa negatively associated with specific STH infections, including Lactobacillus and Lachnospiracaea. Our results also suggest that relative abundance of Lactobacillus is driven by the STH infection status more so than by the Plasmodium infection status. This study contributes to efforts to understand the effects of the microbiome on host susceptibility to parasitic infections in endemic communities.
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Affiliation(s)
- Tiffany Huwe
- Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana
| | | | - Aisurya Ray
- Institute of Life Sciences, Bhubaneswar, India
| | - Shaun Lee
- Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana
| | | | - Edwin Michael
- Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana
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50
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von Takach Dukai B, Peakall R, Lindenmayer DB, Banks SC. The influence of fire and silvicultural practices on the landscape-scale genetic structure of an Australian foundation tree species. CONSERV GENET 2019. [DOI: 10.1007/s10592-019-01245-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
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