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Lamka GF, Willoughby JR. Habitat remediation followed by managed connectivity reduces unwanted changes in evolutionary trajectory of high extirpation risk populations. PLoS One 2024; 19:e0304276. [PMID: 38814889 PMCID: PMC11139274 DOI: 10.1371/journal.pone.0304276] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Accepted: 05/09/2024] [Indexed: 06/01/2024] Open
Abstract
As we continue to convert green spaces into roadways and buildings, connectivity between populations and biodiversity will continue to decline. In threatened and endangered species, this trend is particularly concerning because the cessation of immigration can cause increased inbreeding and loss of genetic diversity, leading to lower adaptability and higher extirpation probabilities in these populations. Unfortunately, monitoring changes in genetic diversity from management actions such as assisted migration and predicting the extent of introduced genetic variation that is needed to prevent extirpation is difficult and costly in situ. Therefore, we designed an agent-based model to link population-wide genetic variability and the influx of unique alleles via immigration to population stability and extirpation outcomes. These models showed that management of connectivity can be critical in restoring at-risk populations and reducing the effects of inbreeding depression. However, the rescued populations were more similar to the migrant source population (average FST range 0.05-0.10) compared to the historical recipient population (average FST range 0.23-0.37). This means that these management actions not only recovered the populations from the effects of inbreeding depression, but they did so in a way that changed the evolutionary trajectory that was predicted and expected for these populations prior to the population crash. This change was most extreme in populations with the smallest population sizes, which are representative of critically endangered species that could reasonably be considered candidates for restored connectivity or translocation strategies. Understanding how these at-risk populations change in response to varying management interventions has broad implications for the long-term adaptability of these populations and can improve future efforts for protecting locally adapted allele complexes when connectivity is restored.
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Affiliation(s)
- Gina F. Lamka
- College of Forestry, Wildlife, and Environment, Auburn University, Auburn, Alabama, United States of America
| | - Janna R. Willoughby
- College of Forestry, Wildlife, and Environment, Auburn University, Auburn, Alabama, United States of America
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Tackett M, Berg C, Simmonds T, Lopez O, Brown J, Ruggiero R, Weber J. Breeding system and geospatial variation shape the population genetics of Triodanis perfoliata. Ecol Evol 2022; 12:e9382. [PMID: 36248672 PMCID: PMC9547245 DOI: 10.1002/ece3.9382] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2022] [Revised: 08/25/2022] [Accepted: 09/09/2022] [Indexed: 11/21/2022] Open
Abstract
Both intrinsic and extrinsic forces work together to shape connectivity and genetic variation in populations across the landscape. Here we explored how geography, breeding system traits, and environmental factors influence the population genetic patterns of Triodanis perfoliata, a widespread mix‐mating annual plant in the contiguous US. By integrating population genomic data with spatial analyses and modeling the relationship between a breeding system and genetic diversity, we illustrate the complex ways in which these forces shape genetic variation. Specifically, we used 4705 single nucleotide polymorphisms to assess genetic diversity, structure, and evolutionary history among 18 populations. Populations with more obligately selfing flowers harbored less genetic diversity (π: R2 = .63, p = .01, n = 9 populations), and we found significant population structuring (FST = 0.48). Both geographic isolation and environmental factors played significant roles in predicting the observed genetic diversity: we found that corridors of suitable environments appear to facilitate gene flow between populations, and that environmental resistance is correlated with increased genetic distance between populations. Last, we integrated our genetic results with species distribution modeling to assess likely patterns of connectivity among our study populations. Our landscape and evolutionary genetic results suggest that T. perfoliata experienced a complex demographic and evolutionary history, particularly in the center of its distribution. As such, there is no singular mechanism driving this species' evolution. Together, our analyses support the hypothesis that the breeding system, geography, and environmental variables shape the patterns of diversity and connectivity of T. perfoliata in the US.
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Affiliation(s)
- Morgan Tackett
- Neuroscience Graduate ProgramUniversity of Oklahoma Health Sciences CenterOklahoma CityOklahomaUSA
| | - Colette Berg
- Division of Biological SciencesUniversity of MontanaMissoulaMontanaUSA
| | - Taylor Simmonds
- School of Biological SciencesSouthern Illinois University, CarbondaleCarbondaleIllinoisUSA
| | - Olivia Lopez
- Department of BiologySoutheast Missouri State UniversityCape GirardeauMissouriUSA
| | - Jason Brown
- School of Biological SciencesSouthern Illinois University, CarbondaleCarbondaleIllinoisUSA
| | - Robert Ruggiero
- Department of BiologySoutheast Missouri State UniversityCape GirardeauMissouriUSA
| | - Jennifer Weber
- School of Biological SciencesSouthern Illinois University, CarbondaleCarbondaleIllinoisUSA
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Wang Z, Pierce NE. Fine-scale genome-wide signature of Pleistocene glaciation in Thitarodes moths (Lepidoptera: Hepialidae), host of Ophiocordyceps fungus in the Hengduan Mountains. Mol Ecol 2022; 32:2695-2714. [PMID: 35377501 DOI: 10.1111/mec.16457] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Revised: 02/12/2022] [Accepted: 03/21/2022] [Indexed: 11/28/2022]
Abstract
The Hengduan Mountains region is a biodiversity hotspot known for its topologically complex, deep valleys and high mountains. While landscape and glacial refugia have been evoked to explain patterns of inter-species divergence, the accumulation of intra-species (i.e. population level) genetic divergence across the mountain-valley landscape in this region has received less attention. We used genome-wide restriction site-associated DNA sequencing (RADseq) to reveal signatures of Pleistocene glaciation in populations of Thitarodes shambalaensis (Lepidoptera: Hepialidae), the host moth of parasitic Ophiocordyceps sinensis (Hypocreales: Ophiocordycipitaceae) or "caterpillar fungus" endemic to the glacier of eastern Mt. Gongga. We used moraine history along the glacier valleys to model the distribution and environmental barriers to gene flow across populations of T. shambalaensis. We found that moth populations separated by less than 10 km exhibited valley-based population genetic clustering and isolation-by-distance (IBD), while gene flow among populations was best explained by models using information about their distributions at the local last glacial maximum (LGML , 58 kya), not their contemporary distribution. Maximum likelihood lineage history among populations, and among subpopulations as little as 500 meters apart, recapitulated glaciation history across the landscape. We also found signals of isolated population expansion following the retreat of LGML glaciers. These results reveal the fine-scale, long-term historical influence of landscape and glaciation on the genetic structuring of populations of an endangered and economically important insect species. Similar mechanisms, given enough time and continued isolation, could explain the contribution of glacier refugia to the generation of species diversity among the Hengduan Mountains.
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Affiliation(s)
- Zhengyang Wang
- Museum of Comparative Zoology and Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, 02138, USA
| | - Naomi E Pierce
- Museum of Comparative Zoology and Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, 02138, USA
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Nazareno AG, Knowles LL, Dick CW, Lohmann LG. By Animal, Water, or Wind: Can Dispersal Mode Predict Genetic Connectivity in Riverine Plant Species? FRONTIERS IN PLANT SCIENCE 2021; 12:626405. [PMID: 33643353 PMCID: PMC7907645 DOI: 10.3389/fpls.2021.626405] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Accepted: 01/06/2021] [Indexed: 05/08/2023]
Abstract
Seed dispersal is crucial to gene flow among plant populations. Although the effects of geographic distance and barriers to gene flow are well studied in many systems, it is unclear how seed dispersal mediates gene flow in conjunction with interacting effects of geographic distance and barriers. To test whether distinct seed dispersal modes (i.e., hydrochory, anemochory, and zoochory) have a consistent effect on the level of genetic connectivity (i.e., gene flow) among populations of riverine plant species, we used unlinked single-nucleotide polymorphisms (SNPs) for eight co-distributed plant species sampled across the Rio Branco, a putative biogeographic barrier in the Amazon basin. We found that animal-dispersed plant species exhibited higher levels of genetic diversity and lack of inbreeding as a result of the stronger genetic connectivity than plant species whose seeds are dispersed by water or wind. Interestingly, our results also indicated that the Rio Branco facilitates gene dispersal for all plant species analyzed, irrespective of their mode of dispersal. Even at a small spatial scale, our findings suggest that ecology rather than geography play a key role in shaping the evolutionary history of plants in the Amazon basin. These results may help improve conservation and management policies in Amazonian riparian forests, where degradation and deforestation rates are high.
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Affiliation(s)
- Alison G. Nazareno
- Departamentos de Botânica, Universidade de São Paulo, São Paulo, Brazil
- Department of Genetics, Ecology and Evolution, Federal University of Minas Gerais, Belo Horizonte, Brazil
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, United States
- *Correspondence: Alison G. Nazareno,
| | - L. Lacey Knowles
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, United States
| | - Christopher W. Dick
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, United States
- Smithsonian Tropical Research Institute, Panama City, Panama
| | - Lúcia G. Lohmann
- Departamentos de Botânica, Universidade de São Paulo, São Paulo, Brazil
- Lúcia G. Lohmann,
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Yaegashi S, Omura T, Watanabe K. Spatial genetic structure of the invasive tree Robinia pseudoacacia to determine migration patterns to inform best practices for riparian restoration. AOB PLANTS 2020; 12:plaa043. [PMID: 33133479 PMCID: PMC7586742 DOI: 10.1093/aobpla/plaa043] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Accepted: 08/18/2020] [Indexed: 06/11/2023]
Abstract
The black locust Robinia pseudoacacia (Robinieae, Fabaceae) is a common invasive riparian tree in Japan. There are less effective management strategies to remove the tree from the riparian area because of its quickly established high population. We investigated the expansion patterns of R. pseudoacacia through sympatric (i.e. between high- and low-water channel (HWC/LWC) within a study site) and allopatric (i.e. along river corridor) dispersal in the Tama River (Tokyo, Japan). Four microsatellites were used to examine the effects of gene flow on six populations in three sites. These subpopulations showed small genetic distance (i.e. no barrier or slightly limited) and genetically mixed population structure. It indicated that both sympatric and allopatric dispersals were active. Many migrants were younger individuals (i.e. <5 years old) and were found in the LWC area. Thus, the LWC could receive more migrants than the HWC through both types of dispersals. In addition, our age and genetic structure analyses reveal that recruited individuals likely settled immediately after the clearing project of R. pseudoacacia through sympatric dispersal. It appears that the migration by allopatric dispersal occurred following this. For the effective management of R. pseudoacacia, migrants should be removed regularly following initial removal of invaders during site restoration.
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Affiliation(s)
- Sakiko Yaegashi
- Department of Civil and Environmental Engineering, University of Yamanashi, Kofu, Yamanashi Prefecture, Japan
| | - Tatsuo Omura
- New Industry Creation Hatchery Center (NIChe), Tohoku University, Aoba-yama, Sendai, Japan
| | - Kozo Watanabe
- Center for Marine Environmental Studies (CMES), Ehime University, Bunkyo-cho, Matsuyama, Ehime, Japan
- Department of Civil and Environmental Engineering, Ehime University, Matsuyama, Ehime, Japan
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Byrne M, Krauss SL, Millar MA, Elliott CP, Coates DJ, Yates C, Binks RM, Nevill P, Nistelberger H, Wardell-Johnson G, Robinson T, Butcher R, Barrett M, Gibson N. Persistence and stochasticity are key determinants of genetic diversity in plants associated with banded iron formation inselbergs. Biol Rev Camb Philos Soc 2018; 94:753-772. [PMID: 30479069 DOI: 10.1111/brv.12477] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2018] [Revised: 10/02/2018] [Accepted: 10/08/2018] [Indexed: 01/19/2023]
Abstract
The high species endemism characteristic of many of the world's terrestrial island systems provides a model for studying evolutionary patterns and processes, yet there has been no synthesis of studies to provide a systematic evaluation of terrestrial island systems in this context. The banded iron formations (BIFs) of south-western Australia are ancient terrestrial island formations occurring within a mosaic of alluvial clay soils, sandplains and occasional granite outcropping, across an old, gently undulating, highly weathered, plateau. Notably, these BIFs display exceptionally high beta plant diversity. Here, we address the determinants and consequences of genetic diversity for BIF-associated plant species through a comprehensive review of all studies on species distribution modelling, phylogenetics, phylogeography, population genetics, life-history traits and ecology. The taxa studied are predominantly narrowly endemic to individual or a few BIF ranges, but some have more regional distributions occurring both on and off BIFs. We compared genetic data for these BIF-endemic species to other localised species globally to assess whether the unique history and ancestry of BIF landscapes has driven distinct genetic responses in plants restricted to this habitat. We also assessed the influence of life-history parameters on patterns of genetic diversity. We found that BIF-endemic species display similar patterns of genetic diversity and structure to other species with localised distributions. Despite often highly restricted distributions, large effective population size or clonal reproduction appears to provide these BIF-endemic species with ecological and evolutionary resilience to environmental stochasticity. We conclude that persistence and stochasticity are key determinants of genetic diversity and its spatial structure within BIF-associated plant species, and that these are key evolutionary processes that should be considered in understanding the biogeography of inselbergs worldwide.
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Affiliation(s)
- Margaret Byrne
- Biodiversity and Conservation Science, Department of Biodiversity, Conservation and Attractions, Locked Bag 104, Bentley Delivery Centre, Perth, WA, 6983, Australia.,School of Biological Sciences, The University of Western Australia, 35 Stirling Highway, Crawley, WA, 6009, Australia.,School of Molecular and Life Sciences, Curtin University, GPO Box U1987, Perth, WA, 6845, Australia
| | - Siegfried L Krauss
- School of Biological Sciences, The University of Western Australia, 35 Stirling Highway, Crawley, WA, 6009, Australia.,Kings Park Science, Department of Biodiversity, Conservation and Attractions, 2 Kattidj Close, Kings Park, Perth, WA, 6005, Australia
| | - Melissa A Millar
- Biodiversity and Conservation Science, Department of Biodiversity, Conservation and Attractions, Locked Bag 104, Bentley Delivery Centre, Perth, WA, 6983, Australia
| | - Carole P Elliott
- School of Biological Sciences, The University of Western Australia, 35 Stirling Highway, Crawley, WA, 6009, Australia.,Kings Park Science, Department of Biodiversity, Conservation and Attractions, 2 Kattidj Close, Kings Park, Perth, WA, 6005, Australia
| | - David J Coates
- Biodiversity and Conservation Science, Department of Biodiversity, Conservation and Attractions, Locked Bag 104, Bentley Delivery Centre, Perth, WA, 6983, Australia
| | - Colin Yates
- Biodiversity and Conservation Science, Department of Biodiversity, Conservation and Attractions, Locked Bag 104, Bentley Delivery Centre, Perth, WA, 6983, Australia
| | - Rachel M Binks
- Biodiversity and Conservation Science, Department of Biodiversity, Conservation and Attractions, Locked Bag 104, Bentley Delivery Centre, Perth, WA, 6983, Australia
| | - Paul Nevill
- ARC Centre for Mine Site Restoration, School of Molecular and Life Sciences, Curtin University, GPO Box U1987, Perth, WA, 6845, Australia
| | - Heidi Nistelberger
- Biodiversity and Conservation Science, Department of Biodiversity, Conservation and Attractions, Locked Bag 104, Bentley Delivery Centre, Perth, WA, 6983, Australia.,School of Biological Sciences, The University of Western Australia, 35 Stirling Highway, Crawley, WA, 6009, Australia
| | - Grant Wardell-Johnson
- ARC Centre for Mine Site Restoration, School of Molecular and Life Sciences, Curtin University, GPO Box U1987, Perth, WA, 6845, Australia
| | - Todd Robinson
- School of Earth and Planetary Sciences, Curtin University, GPO Box U1987, Perth, WA, 6845, Australia
| | - Ryonen Butcher
- Biodiversity and Conservation Science, Department of Biodiversity, Conservation and Attractions, Locked Bag 104, Bentley Delivery Centre, Perth, WA, 6983, Australia
| | - Matthew Barrett
- Kings Park Science, Department of Biodiversity, Conservation and Attractions, 2 Kattidj Close, Kings Park, Perth, WA, 6005, Australia
| | - Neil Gibson
- Biodiversity and Conservation Science, Department of Biodiversity, Conservation and Attractions, Locked Bag 104, Bentley Delivery Centre, Perth, WA, 6983, Australia.,School of Biological Sciences, The University of Western Australia, 35 Stirling Highway, Crawley, WA, 6009, Australia
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