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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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2
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Machado-Aguilera MC, Lemus-Mejía L, Pérez-Torres J, Zárrate-Charry DA, Arias-Alzate A, González-Maya JF. Preserving the spots: Jaguar (Panthera onca) distribution and priority conservation areas in Colombia. PLoS One 2024; 19:e0300375. [PMID: 38517860 PMCID: PMC10959345 DOI: 10.1371/journal.pone.0300375] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Accepted: 02/26/2024] [Indexed: 03/24/2024] Open
Abstract
The jaguar (Panthera onca) is a charismatic species considered Vulnerable in Colombia but yet largely unknown in the country. The species is mostly threatened by the continuous decline in its habitats, mostly derived from deforestation and habitat loss, additional to hunting and conflicts with humans. Thus, the future of jaguars in Colombia depends on protecting and recovering existing habitats. The aims of this study were to 1) evaluate jaguar distribution and identify the remnant patches of habitat in Colombia, 2) define an ecological connectivity network within the country, and 3) propose a priority areas portfolio for the conservation and recovery of jaguars. We used a presence background model for estimating species potential distribution and subsequently identified remaining habitat patches across the country based on land cover and species-specific ecological attributes. We then created an ecological connectivity network based on circuit theory and following a multi-criteria approach identified jaguar priority areas for conservation (JPCA) and recovery (JPRA). Jaguar potential distribution comprises 1103122.43 km2, from which 56.71% maintain suitable patches of potential habitat. We identified 960 corridors between remnant patches of natural or semi-natural vegetation. Based on the criteria, JPCAs with greater importance were identified in each of the five Colombian regions. JPRAs were located mainly towards the Andean and Caribbean regions. These JPCAs and JPRAs could serve as a guide for designing and implementing management strategies for the long-term conservation and recovery of the species in Colombia.
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Affiliation(s)
- María Camila Machado-Aguilera
- Proyecto de Conservación de Aguas y Tierras – ProCAT Colombia, Bogotá, Colombia
- Laboratorio de Ecología Funcional, Unidad de Ecología y Sistemática (UNESIS), Depto. Biología, Pontificia Universidad Javeriana, Bogotá, Colombia
| | | | - Jairo Pérez-Torres
- Laboratorio de Ecología Funcional, Unidad de Ecología y Sistemática (UNESIS), Depto. Biología, Pontificia Universidad Javeriana, Bogotá, Colombia
| | - Diego A. Zárrate-Charry
- Proyecto de Conservación de Aguas y Tierras – ProCAT Colombia, Bogotá, Colombia
- WWF Colombia, Bogotá, Colombia
| | | | - José F. González-Maya
- Proyecto de Conservación de Aguas y Tierras – ProCAT Colombia, Bogotá, Colombia
- Departamento de Ciencias Ambientales, División de Ciencias Biológicas y de la Salud, Universidad Autónoma Metropolitana Unidad Lerma, Lerma de Villada, Estado de México, México
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3
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Zhao H, Wang N, Cheng H, Wang Y, Liu X, Qiao B, Zhao L. Mapping conservation priorities for wild yak (Bos mutus) habitats on the Tibetan Plateau, China. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 914:169803. [PMID: 38181949 DOI: 10.1016/j.scitotenv.2023.169803] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2023] [Revised: 09/23/2023] [Accepted: 12/29/2023] [Indexed: 01/07/2024]
Abstract
The wild yak (Bos mutus) is a cold-tolerant herbivore native to the Tibetan Plateau and has been categorized as vulnerable by the International Union for Conservation of Nature and Natural Resources. Low population densities within currently fragmented habitats and unclear landscape conservation priorities warrant attention. Herein, we employed the maximum entropy (MaxEnt) model using over 900 wild yak occurrence records to model wild yak habitat suitability. Our analysis revealed unprotected wild yak landscapes covering 30.79 % of the habitat area, indicating a conservation gap between protected areas (PAs) and wild yak habitats. To protect metapopulation dynamics and mitigate high risks of poaching, habitat degradation and fragmentation, resource competition, and degenerated genetic characterization of wild yaks in fragmented and degraded habitat, we identified eight habitat patches as landscape conservation units (LCUs) and 14 linkages among the LCUs, enhancing the connectivity between LCUs to decrease negative effects of genetic threats. A centrality analysis demonstrated that Changtang, Arjinshan, and Hoh Xil national nature reserves and their linkages are all critical for the maintenance of habitat connectivity. Here, we suggest that habitat- and LCU-specific conservation strategies should be highlighted during the establishment of PAs and transboundary cooperation. Ultimately, our results can assist conservationists and land managers in comprehending wild yak distribution, movement, and habitat requirements, as well as for the development of effective protection strategies. Furthermore, the combined modeling method (MaxEnt-Zonation-InVEST) could be utilized as a component for identifying conservation priorities and linkages between core patches for species and assessing the efficiency of PAs, core habitats, and corridors in achieving conservation goals. Our study can provide a framework in identifying priority conservation and connectivity between habitat patches to facilitate effectively conservation and genetic resilience for endangered species in fragmented habitats.
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Affiliation(s)
- Hang Zhao
- College of Earth and Environmental Sciences, Center for Glacier and Desert Research, Scientific Observing Station for Desert and Glacier, Lanzhou University, Lanzhou 730000, China.
| | - Nai'ang Wang
- College of Earth and Environmental Sciences, Center for Glacier and Desert Research, Scientific Observing Station for Desert and Glacier, Lanzhou University, Lanzhou 730000, China.
| | - Hongyi Cheng
- College of Earth and Environmental Sciences, Center for Glacier and Desert Research, Scientific Observing Station for Desert and Glacier, Lanzhou University, Lanzhou 730000, China.
| | - Yipeng Wang
- College of Earth and Environmental Sciences, Center for Glacier and Desert Research, Scientific Observing Station for Desert and Glacier, Lanzhou University, Lanzhou 730000, China.
| | - Xiao Liu
- College of Earth and Environmental Sciences, Center for Glacier and Desert Research, Scientific Observing Station for Desert and Glacier, Lanzhou University, Lanzhou 730000, China.
| | - Bin Qiao
- College of Earth and Environmental Sciences, Center for Glacier and Desert Research, Scientific Observing Station for Desert and Glacier, Lanzhou University, Lanzhou 730000, China.
| | - Liqiang Zhao
- College of Earth and Environmental Sciences, Center for Glacier and Desert Research, Scientific Observing Station for Desert and Glacier, Lanzhou University, Lanzhou 730000, China.
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Hui TCY, Tang Q, Ng EYX, Chong JL, Slade EM, Rheindt FE. Small-Mammal Genomics Highlights Viaducts as Potential Dispersal Conduits for Fragmented Populations. Animals (Basel) 2024; 14:426. [PMID: 38338069 PMCID: PMC10854910 DOI: 10.3390/ani14030426] [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: 12/27/2023] [Revised: 01/15/2024] [Accepted: 01/24/2024] [Indexed: 02/12/2024] Open
Abstract
Wildlife crossings are implemented in many countries to facilitate the dispersal of animals among habitats fragmented by roads. However, the efficacy of different types of habitat corridors remains poorly understood. We used a comprehensive sampling regime in two lowland dipterocarp forest areas in peninsular Malaysia to sample pairs of small mammal individuals in three treatment types: (1) viaduct sites, at which sampling locations were separated by a highway but connected by a vegetated viaduct; (2) non-viaduct sites, at which sampling locations were separated by a highway and not connected by a viaduct; and (3) control sites, at which there was no highway fragmenting the forest. For four small mammal species, the common tree shrew Tupaia glis, Rajah's spiny rat Maxomys rajah, Whitehead's spiny rat Maxomys whiteheadi and dark-tailed tree rat Niviventer cremoriventer, we used genome-wide markers to assess genetic diversity, gene flow and genetic structure. The differences in genetic distance across sampling settings among the four species indicate that they respond differently to the presence of highways and viaducts. Viaducts connecting forests separated by highways appear to maintain higher population connectivity than forest fragments without viaducts, at least in M. whiteheadi, but apparently not in the other species.
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Affiliation(s)
- Tabitha C. Y. Hui
- Asian School of the Environment, Nanyang Technological University, 50 Nanyang Avenue, Singapore 639798, Singapore
- Department of Biological Sciences, National University of Singapore, 16 Science Drive 4, Singapore 117558, Singapore; (Q.T.); (E.Y.X.N.); (F.E.R.)
| | - Qian Tang
- Department of Biological Sciences, National University of Singapore, 16 Science Drive 4, Singapore 117558, Singapore; (Q.T.); (E.Y.X.N.); (F.E.R.)
| | - Elize Y. X. Ng
- Department of Biological Sciences, National University of Singapore, 16 Science Drive 4, Singapore 117558, Singapore; (Q.T.); (E.Y.X.N.); (F.E.R.)
- Discipline of Biological Sciences, School of Natural Sciences, University of Tasmania, Hobart, TAS 7005, Australia
| | - Ju Lian Chong
- Faculty of Science and Marine Environment, Universiti Malaysia Terengganu, Kuala Terengganu 21030, Terengganu, Malaysia;
| | - Eleanor M. Slade
- Asian School of the Environment, Nanyang Technological University, 50 Nanyang Avenue, Singapore 639798, Singapore
| | - Frank E. Rheindt
- Department of Biological Sciences, National University of Singapore, 16 Science Drive 4, Singapore 117558, Singapore; (Q.T.); (E.Y.X.N.); (F.E.R.)
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de Carvalho DL, Silva SM, Sousa-Neves T, Gonçalves GSR, Silva DP, Santos MPD. Predicting the future of threatened birds from a Neotropical ecotone area. ENVIRONMENTAL MONITORING AND ASSESSMENT 2023; 196:61. [PMID: 38110623 DOI: 10.1007/s10661-023-12174-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Accepted: 11/22/2023] [Indexed: 12/20/2023]
Abstract
Climate change affects ecosystems in different ways. These effects are particularly worrying in the Neotropical region, where species are most vulnerable to these changes because they live closer to their thermal safety limits. Thus, establishing conservation priorities, particularly for the definition of protected areas (PAs), is a priority. However, some PA systems within the Neotropics are ineffective even under the present environmental conditions. Here, we test the effectiveness of a PA system, within an ecotone in northern Brazil, in protecting 24 endangered bird species under current and future (RCP8.5) climatic scenarios. We used species distribution modeling and dispersal corridor modeling to describe the priority areas for conservation of these species. Our results indicate that several threatened bird taxa are and will potentially be protected (i.e., occur within PAs). Nonetheless, the amount of protected area is insufficient to maintain the species in the ecotone. Moreover, most taxa will probably present drastic declines in their range sizes; some are even predicted to go globally extinct soon. Thus, we highlight the location of a potentially effective system of dispersal corridors that connects PAs in the ecotone. We reinforce the need to implement public policies and raise public awareness to maintain PAs and mitigate anthropogenic effects within them, corridors, and adjacent areas, aiming to conserve the richness and diversity of these already threatened species.
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Affiliation(s)
- Dorinny Lisboa de Carvalho
- Programa de Pós-Graduação em Zoologia, Universidade Federal do Pará, Museu Paraense Emílio Goeldi, Av. Augusto Corrêa 01, Guamá, Belém, PA, CEP 66075-110, Brazil.
| | - Sofia Marques Silva
- Coordenação em Zoologia, Museu Paraense Emílio Goeldi, Av. Perimetral, 1901, Terra Firme, Belém, PA, CEP 66077 830, Brazil
| | - Tiago Sousa-Neves
- Programa de Pós-Graduação em Zoologia, Universidade Federal do Pará, Museu Paraense Emílio Goeldi, Av. Augusto Corrêa 01, Guamá, Belém, PA, CEP 66075-110, Brazil
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Rua Padre Armando Quintas, 07, 4485-661, Vairão, Portugal
| | - Gabriela Silva Ribeiro Gonçalves
- Programa de Pós-Graduação em Zoologia, Universidade Federal do Pará, Museu Paraense Emílio Goeldi, Av. Augusto Corrêa 01, Guamá, Belém, PA, CEP 66075-110, Brazil
| | - Daniel Paiva Silva
- COBIMA Lab, Departamento de Ciências Biológicas, Instituto Federal Goiano, IF Goiano, Rodovia Geraldo Silva Nascimento, KM 2,5 Zona Rural, Urutaí, GO, CEP 75790-000, Brazil
| | - Marcos Pérsio Dantas Santos
- Programa de Pós-Graduação em Zoologia, Universidade Federal do Pará, Museu Paraense Emílio Goeldi, Av. Augusto Corrêa 01, Guamá, Belém, PA, CEP 66075-110, Brazil
- Instituto de Ciências Biológicas, Faculdade de Ciências Biológicas, Universidade Federal do Pará, Av. Augusto Corrêa 01, Guamá, Belém, PA, CEP 66075-110, Brazil
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Breitbart ST, Agrawal AA, Wagner HH, Johnson MTJ. Urbanization and a green corridor do not impact genetic divergence in common milkweed (Asclepias syriaca L.). Sci Rep 2023; 13:20437. [PMID: 37993590 PMCID: PMC10665382 DOI: 10.1038/s41598-023-47524-8] [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: 04/26/2023] [Accepted: 11/14/2023] [Indexed: 11/24/2023] Open
Abstract
Urbanization is altering landscapes globally at an unprecedented rate. While ecological differences between urban and rural environments often promote phenotypic divergence among populations, it is unclear to what degree these trait differences arise from genetic divergence as opposed to phenotypic plasticity. Furthermore, little is known about how specific landscape elements, such as green corridors, impact genetic divergence in urban environments. We tested the hypotheses that: (1) urbanization, and (2) proximity to an urban green corridor influence genetic divergence in common milkweed (Asclepias syriaca) populations for phenotypic traits. Using seeds from 52 populations along three urban-to-rural subtransects in the Greater Toronto Area, Canada, one of which followed a green corridor, we grew ~ 1000 plants in a common garden setup and measured > 20 ecologically-important traits associated with plant defense/damage, reproduction, and growth over four years. We found significant heritable variation for nine traits within common milkweed populations and weak phenotypic divergence among populations. However, neither urbanization nor an urban green corridor influenced genetic divergence in individual traits or multivariate phenotype. These findings contrast with the expanding literature demonstrating that urbanization promotes rapid evolutionary change and offer preliminary insights into the eco-evolutionary role of green corridors in urban environments.
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Affiliation(s)
- Sophie T Breitbart
- Department of Ecology and Evolutionary Biology, University of Toronto, 25 Willcocks Street, Toronto, ON, M5S 3B2, Canada.
- Department of Biology, University of Toronto Mississauga, 3359 Mississauga Road, Mississauga, ON, L5L 1C6, Canada.
- Centre for Urban Environments, University of Toronto Mississauga, 3359 Mississauga Road, Mississauga, ON, L5L 1C6, Canada.
| | - Anurag A Agrawal
- Department of Ecology and Evolutionary Biology, Cornell University, E145 Corson Hall, Ithaca, NY, 14853, USA
- Department of Entomology, Cornell University, 2126 Comstock Hall, Ithaca, NY, 14853, USA
| | - Helene H Wagner
- Department of Ecology and Evolutionary Biology, University of Toronto, 25 Willcocks Street, Toronto, ON, M5S 3B2, Canada
- Department of Biology, University of Toronto Mississauga, 3359 Mississauga Road, Mississauga, ON, L5L 1C6, Canada
- Centre for Urban Environments, University of Toronto Mississauga, 3359 Mississauga Road, Mississauga, ON, L5L 1C6, Canada
| | - Marc T J Johnson
- Department of Ecology and Evolutionary Biology, University of Toronto, 25 Willcocks Street, Toronto, ON, M5S 3B2, Canada
- Department of Biology, University of Toronto Mississauga, 3359 Mississauga Road, Mississauga, ON, L5L 1C6, Canada
- Centre for Urban Environments, University of Toronto Mississauga, 3359 Mississauga Road, Mississauga, ON, L5L 1C6, Canada
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Imron MA, Glass DM, Tafrichan M, Crego RD, Stabach JA, Leimgruber P. Beyond protected areas: The importance of mixed-use landscapes for the conservation of Sumatran elephants ( Elephas maximus sumatranus). Ecol Evol 2023; 13:e10560. [PMID: 37780084 PMCID: PMC10539044 DOI: 10.1002/ece3.10560] [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: 08/06/2023] [Accepted: 09/01/2023] [Indexed: 10/03/2023] Open
Abstract
Elephants were once widely distributed across the Indonesian island of Sumatra but now exist in small, isolated populations. Using the best data available on elephant occurrence, we aimed to (a) predict potential habitat suitability for elephants (Elephas maximus sumatranus) across the island of Sumatra and (b) model landscape connectivity among the extant elephant populations. We used direct sightings and indirect observations of elephant signs, as well as six remotely sensed proxies of surface ruggedness, vegetation productivity and structure, and human land use and disturbance, to model habitat suitability in a Google Earth Engine (GEE) environment. We validated the habitat suitability prediction using 10-fold spatial block cross validation and by calculating the area under the precision-recall curve (AUC-PR), sensitivity, and specificity for each model iteration. We also used a geolocation dataset collected from global positioning system (GPS) collars fitted on elephants as an independent validation dataset. Models showed good predictive performance with a mean AUC-PR of 0.73, sensitivity of 0.76, and specificity of 0.68. Greater than 83% of the independent GPS collar geolocations were located in predicted suitable habitat. We found human modification, surface ruggedness, and normalized difference vegetation index to be the most important variables for predicting suitable elephant habitat. Thirty-two percent, or 135,646 km2, of Sumatra's land area was predicted to be suitable habitat, with 43 patches of suitable habitat located across Sumatra. Areas with high connectivity were concentrated in the Riau and North Sumatra provinces. Though our analysis highlights the need to improve the quality of data collected on Sumatran elephants, more suitable habitat remains on Sumatra than is used by known populations. Targeted habitat conservation, especially of the suitable habitat in and around the Lamno, Balai Raja, Tesso Tenggara, Tesso Utara, Bukit Tigapuluh, Seblat, Padang Sugihan, and Bukit Barisan Selatan ranges, may improve the long-term viability of this critically endangered species.
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Affiliation(s)
| | - Danielle M. Glass
- Smithsonian National Zoo & Conservation Biology InstituteConservation Ecology CenterFront RoyalVirginiaUSA
| | | | - Ramiro D. Crego
- Smithsonian National Zoo & Conservation Biology InstituteConservation Ecology CenterFront RoyalVirginiaUSA
- School of Biological, Earth & Environmental SciencesUniversity College CorkCorkIreland
| | - Jared A. Stabach
- Smithsonian National Zoo & Conservation Biology InstituteConservation Ecology CenterFront RoyalVirginiaUSA
| | - Peter Leimgruber
- Smithsonian National Zoo & Conservation Biology InstituteConservation Ecology CenterFront RoyalVirginiaUSA
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8
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Dutcher KE, Nussear KE, Heaton JS, Esque TC, Vandergast AG. Move it or lose it: Predicted effects of culverts and population density on Mojave desert tortoise (Gopherus agassizii) connectivity. PLoS One 2023; 18:e0286820. [PMID: 37768995 PMCID: PMC10538755 DOI: 10.1371/journal.pone.0286820] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Accepted: 05/24/2023] [Indexed: 09/30/2023] Open
Abstract
Roadways and railways can reduce wildlife movements across landscapes, negatively impacting population connectivity. Connectivity may be improved by structures that allow safe passage across linear barriers, but connectivity could be adversely influenced by low population densities. The Mojave desert tortoise is threatened by habitat loss, fragmentation, and population declines. The tortoise continues to decline as disturbance increases across the Mojave Desert in the southwestern United States. While underground crossing structures, like hydrological culverts, have begun receiving attention, population density has not been considered in tortoise connectivity. Our work asks a novel question: How do culverts and population density affect connectivity and potentially drive genetic and demographic patterns? To explore the role of culverts and population density, we used agent-based spatially explicit forward-in-time simulations of gene flow. We constructed resistance surfaces with a range of barriers to movement and representative of tortoise habitat with anthropogenic disturbance. We predicted connectivity under variable population densities. Simulations were run for 200 non-overlapping generations (3400 years) with 30 replicates using 20 microsatellite loci. We evaluated population genetic structure and diversity and found that culverts would not entirely negate the effects of linear barriers, but gene flow improved. Our results also indicated that density is important for connectivity. Low densities resulted in declines regardless of the landscape barrier scenario (> 75% population census size, > 97% effective population size). Results from our simulation using current anthropogenic disturbance predicted decreased population connectivity over time. Genetic and demographic effects were detectable within five generations (85 years) following disturbance with estimated losses in effective population size of 69%. The pronounced declines in effective population size indicate this could be a useful monitoring metric. We suggest management strategies that improve connectivity, such as roadside fencing tied to culverts, conservation areas in a connected network, and development restricted to disturbed areas.
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Affiliation(s)
- Kirsten E. Dutcher
- Department of Geography, University of Nevada–Reno, Reno, Nevada, United States of America
| | - Kenneth E. Nussear
- Department of Geography, University of Nevada–Reno, Reno, Nevada, United States of America
| | - Jill S. Heaton
- Department of Geography, University of Nevada–Reno, Reno, Nevada, United States of America
| | - Todd C. Esque
- United States Geological Survey, Western Ecological Research Center, Boulder City, Nevada, United States of America
| | - Amy G. Vandergast
- United States Geological Survey, Western Ecological Research Center, San Diego, California, United States of America
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9
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Conservation genomics of an endangered arboreal mammal following the 2019-2020 Australian megafire. Sci Rep 2023; 13:480. [PMID: 36627361 PMCID: PMC9831986 DOI: 10.1038/s41598-023-27587-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Accepted: 01/04/2023] [Indexed: 01/11/2023] Open
Abstract
The impacts of a changing climate threaten species, populations and ecosystems. Despite these significant and large-scale impacts on threatened species, many remain understudied and have little to no genetic information available. The greater glider, Petauroides volans, is an endangered species highly sensitive to the predicted changes in temperature under a changing climate and was recently severely impacted by a megafire natural disaster (85% estimated population loss). Baseline genetic data is essential for conservation management and for detecting detrimental changes in fire-effected populations. We collected genetic samples within 2 years post the 2019-2020 catastrophic Australian bushfires to examine adaptive potential, baseline genetic diversity and population structure, across their southern range in the state of New South Wales. Population genomic analyses were conducted using 8493 genome-wide SNPs for 86 greater glider individuals across 14 geographic locations. Substantial genetic structure was detected across locations, with low genetic diversity and effective population sizes observed in isolated areas. Additionally, we found signals of putative adaptation in response to temperature in greater gliders using a genotype-environment association analysis. These findings have important implications for the management of greater glider populations by identifying at-risk populations and identifying adaptive potential. We demonstrate the importance of baseline genetic information for endangered species as a practical approach to conservation. This is particularly important given the threat that changes in temperatures and megafire events, as predicted under a changing climate, poses for this species.
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10
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Sparks MM, Kraft JC, Blackstone KMS, McNickle GG, Christie MR. Large genetic divergence underpins cryptic local adaptation across ecological and evolutionary gradients. Proc Biol Sci 2022; 289:20221472. [PMID: 36196546 PMCID: PMC9533007 DOI: 10.1098/rspb.2022.1472] [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] [Indexed: 11/24/2022] Open
Abstract
Environmentally covarying local adaptation is a form of cryptic local adaptation in which the covariance of the genetic and environmental effects on a phenotype obscures the divergence between locally adapted genotypes. Here, we systematically document the magnitude and drivers of the genetic effect (VG) for two forms of environmentally covarying local adaptation: counter- and cogradient variation. Using a hierarchical Bayesian meta-analysis, we calculated the overall effect size of VG as 1.05 and 2.13 for populations exhibiting countergradient or cogradient variation, respectively. These results indicate that the genetic contribution to phenotypic variation represents a 1.05 to 2.13 s.d. change in trait value between the most disparate populations depending on if populations are expressing counter- or cogradient variation. We also found that while there was substantial variance among abiotic and biotic covariates, the covariates with the largest mean effects were temperature (2.41) and gamete size (2.81). Our results demonstrate the pervasiveness and large genetic effects underlying environmentally covarying local adaptation in wild populations and highlight the importance of accounting for these effects in future studies.
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Affiliation(s)
- Morgan M Sparks
- Department of Biological Sciences, Purdue University, 915 West State Street, West Lafayette, IN 47907-2054, USA
| | - Joshua C Kraft
- Department of Botany and Plant Pathology, Purdue University, 915 West State Street, West Lafayette, IN 47907-2054, USA
| | - Kliffi M S Blackstone
- Department of Biological Sciences, Purdue University, 915 West State Street, West Lafayette, IN 47907-2054, USA
| | - Gordon G McNickle
- Department of Botany and Plant Pathology, Purdue University, 915 West State Street, West Lafayette, IN 47907-2054, USA.,Purdue Center for Plant Biology, Purdue University, 915 West State Street, West Lafayette, IN 47907-2054, USA
| | - Mark R Christie
- Department of Biological Sciences, Purdue University, 915 West State Street, West Lafayette, IN 47907-2054, USA.,Department of Forestry and Natural Resources, Purdue University, 715 West State Street, West Lafayette, IN 47907-2054, USA
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11
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Huang RM, van Aarde RJ, Pimm SL, Chase MJ, Leggett K. Mapping potential connections between Southern Africa's elephant populations. PLoS One 2022; 17:e0275791. [PMID: 36219597 PMCID: PMC9553058 DOI: 10.1371/journal.pone.0275791] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Accepted: 09/20/2022] [Indexed: 11/07/2022] Open
Abstract
Southern Africa spans nearly 7 million km2 and contains approximately 80% of the world’s savannah elephants (Loxodonta africana) mostly living in isolated protected areas. Here we ask what are the prospects for improving the connections between these populations? We combine 1.2 million telemetry observations from 254 elephants with spatial data on environmental factors and human land use across eight southern African countries. Telemetry data show what natural features limit elephant movement and what human factors, including fencing, further prevent or restrict dispersal. The resulting intersection of geospatial data and elephant presences provides a map of suitable landscapes that are environmentally appropriate for elephants and where humans allow elephants to occupy. We explore the environmental and anthropogenic constraints in detail using five case studies. Lastly, we review all the major potential connections that may remain to connect a fragmented elephant metapopulation and document connections that are no longer feasible.
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Affiliation(s)
- Ryan M. Huang
- Nicholas School of the Environment, Duke University, Durham, North Carolina, United States of America
- * E-mail: (RMH); (RJA)
| | - Rudi J. van Aarde
- Conservation Ecology Research Unit, Department of Zoology and Entomology, University of Pretoria, Hatfield, South Africa
- * E-mail: (RMH); (RJA)
| | - Stuart L. Pimm
- Nicholas School of the Environment, Duke University, Durham, North Carolina, United States of America
- Conservation Ecology Research Unit, Department of Zoology and Entomology, University of Pretoria, Hatfield, South Africa
| | | | - Keith Leggett
- Fowlers Gap Arid Zone Research Station, UNSW Sydney, Sydney, Fowlers Gap, Australia
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12
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Chai M, Tseng Y, Lu H, Luo M, Chang J, Liao P. Riding an escalator: upward range shift and patterns of genetic response to climate change in
Acer caudatifolium. DIVERS DISTRIB 2022. [DOI: 10.1111/ddi.13588] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
Affiliation(s)
- Min‐Wei Chai
- Department of Life Science National Taiwan Normal University Taipei Taiwan
| | - Yi‐Ting Tseng
- Department of Life Science National Taiwan Normal University Taipei Taiwan
- Metabolomics Core Laboratory, Healthy Aging Research Center Chang Gung University Taoyuan Taiwan
| | - Hsin‐Pei Lu
- Department of Life Science National Taiwan Normal University Taipei Taiwan
- Department of Life Science National Taiwan University Taipei Taiwan
| | - Min‐Xin Luo
- Department of Life Science National Taiwan Normal University Taipei Taiwan
| | - Jui‐Tse Chang
- Department of Life Science National Taiwan Normal University Taipei Taiwan
| | - Pei‐Chun Liao
- Department of Life Science National Taiwan Normal University Taipei Taiwan
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13
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Hohwieler KR, Villiers DL, Cristescu RH, Frere CH. Genetic erosion detected in a specialist mammal living in a fast‐developing environment. CONSERVATION SCIENCE AND PRACTICE 2022. [DOI: 10.1111/csp2.12738] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Affiliation(s)
- Katrin R. Hohwieler
- Global Change Ecology Research Group University of the Sunshine Coast, School of Science, Technology and Engineering Sippy Down Queensland Australia
| | | | - Romane H. Cristescu
- Global Change Ecology Research Group University of the Sunshine Coast, School of Science, Technology and Engineering Sippy Down Queensland Australia
| | - Celine H. Frere
- School of Biological Sciences University of Queensland St Lucia QLD Australia
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14
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Cooper BJ, Moore MJ, Douglas NA, Wagner WL, Johnson MG, Overson RP, Kinosian SP, McDonnell AJ, Levin RA, Raguso RA, Flores Olvera H, Ochoterena H, Fant JB, Skogen KA, Wickett NJ. Target enrichment and extensive population sampling help untangle the recent, rapid radiation of Oenothera sect. Calylophus. Syst Biol 2022:6588089. [PMID: 35583314 DOI: 10.1093/sysbio/syac032] [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: 03/16/2021] [Revised: 04/14/2022] [Accepted: 04/22/2022] [Indexed: 11/14/2022] Open
Abstract
Oenothera sect. Calylophus is a North American group of 13 recognized taxa in the evening primrose family (Onagraceae) with an evolutionary history that may include independent origins of bee pollination, edaphic endemism, and permanent translocation heterozygosity. Like other groups that radiated relatively recently and rapidly, taxon boundaries within Oenothera sect. Calylophus have remained challenging to circumscribe. In this study, we used target enrichment, flanking non-coding regions, gene tree/species tree methods, tests for gene flow modified for target-enrichment data, and morphometric analysis to reconstruct phylogenetic hypotheses, evaluate current taxon circumscriptions, and examine character evolution in Oenothera sect. Calylophus. Because sect. Calylophus comprises a clade with a relatively restricted geographic range, we were able to extensively sample across the range of geographic, edaphic and morphological diversity in the group. We found that the combination of exons and flanking non-coding regions led to improved support for species relationships. We reconstructed potential hybrid origins of some accessions and note that if processes such as hybridization are not taken into account, the number of inferred evolutionary transitions may be artificially inflated. We recovered strong evidence for multiple evolutionary origins of bee pollination from ancestral hawkmoth pollination, edaphic specialization on gypsum, and permanent translocation heterozygosity. This study applies newly emerging techniques alongside dense infraspecific sampling and morphological analyses to effectively reconstruct the recalcitrant history of a rapid radiation.
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Affiliation(s)
- Benjamin J Cooper
- The Negaunee Institute for Plant Conservation Science and Action, Chicago Botanic Garden, 1000 Lake Cook Rd., Glencoe, IL 60022, USA.,Northwestern University,Program in Plant Biology and Conservation,O.T. Hogan Hall, Room, 6-140B, 2205 Tech Drive, Evanston, IL 60208, USA
| | - Michael J Moore
- Oberlin College, Department of Biology, 119 Woodland St., Oberlin, OH 44074, USA
| | - Norman A Douglas
- Department of Biology, University of Florida, Gainesville, FL 32611, USA
| | - Warren L Wagner
- Department of Botany, MRC-166, Smithsonian Institution, PO Box 37012, Washington, DC 20013-7012, USA
| | - Matthew G Johnson
- The Negaunee Institute for Plant Conservation Science and Action, Chicago Botanic Garden, 1000 Lake Cook Rd., Glencoe, IL 60022, USA.,Department of Biological Sciences, Texas Tech University, Box 43131 Lubbock, TX 79409, USA
| | - Rick P Overson
- The Negaunee Institute for Plant Conservation Science and Action, Chicago Botanic Garden, 1000 Lake Cook Rd., Glencoe, IL 60022, USA.,School of Sustainability, Arizona State University, PO Box 875502, Tempe, AZ 85287-5502, USA
| | - Sylvia P Kinosian
- The Negaunee Institute for Plant Conservation Science and Action, Chicago Botanic Garden, 1000 Lake Cook Rd., Glencoe, IL 60022, USA
| | - Angela J McDonnell
- The Negaunee Institute for Plant Conservation Science and Action, Chicago Botanic Garden, 1000 Lake Cook Rd., Glencoe, IL 60022, USA
| | - Rachel A Levin
- Department of Biology, Amherst College, 25 East Drive, Amherst, MA, 01002, USA
| | - Robert A Raguso
- Department of Neurobiology and Behavior, Cornell University, 215 Tower Road, Ithaca, NY 14853, USA
| | - Hilda Flores Olvera
- Departamento de Botánica, Instituto de Biología, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Helga Ochoterena
- Departamento de Botánica, Instituto de Biología, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Jeremie B Fant
- The Negaunee Institute for Plant Conservation Science and Action, Chicago Botanic Garden, 1000 Lake Cook Rd., Glencoe, IL 60022, USA.,Northwestern University,Program in Plant Biology and Conservation,O.T. Hogan Hall, Room, 6-140B, 2205 Tech Drive, Evanston, IL 60208, USA
| | - Krissa A Skogen
- The Negaunee Institute for Plant Conservation Science and Action, Chicago Botanic Garden, 1000 Lake Cook Rd., Glencoe, IL 60022, USA.,Northwestern University,Program in Plant Biology and Conservation,O.T. Hogan Hall, Room, 6-140B, 2205 Tech Drive, Evanston, IL 60208, USA
| | - Norman J Wickett
- The Negaunee Institute for Plant Conservation Science and Action, Chicago Botanic Garden, 1000 Lake Cook Rd., Glencoe, IL 60022, USA.,Northwestern University,Program in Plant Biology and Conservation,O.T. Hogan Hall, Room, 6-140B, 2205 Tech Drive, Evanston, IL 60208, USA
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15
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Shafer CL. A greater yellowstone ecosystem grizzly bear case study: genetic reassessment for managers. CONSERV GENET RESOUR 2022. [DOI: 10.1007/s12686-022-01262-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
AbstractThere are five grizzly bear (Ursus arctos horribilis) populations in the lower 48 states of the United States. My goal in this Commentary was to ascertain whether genetic diversity is being lost from the isolated GYE grizzly bear population and to better understand any viability implications. I reviewed the scientific literature, including two key genetic studies that the US Fish and Wildlife Service (USFWS) relied upon for their 2007 and current 2017 GYE grizzly bear genetics policy. I discovered that some studies reveal a loss of heterozygosity in the GYE bear population, both historically and in recent decades. Some had a statistically significant depletion rate. My review took place periodically between 2010 and 2021 and indicates that the genome of the GYE grizzly bear population is too small for long-term adaptation. The paper includes a discussion about evolutionary adaptation which invokes time frames rarely considered by nature conservation planners. I also examined genetic statements in the USFWS’s 2017 GYE grizzly bear delisting regulations and highlighted those that seem incongruent with current scientific thought. If this paper is read by some scientists, land managers, administrators, environmentalists, and others with some genetics background, they will better understand some USFWS decisions and policy statements. This case study illustrates that land management agencies can provide a one-sided treatment of some science when writing regulations about genetics.
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16
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Diversity and Distribution of the Inland Water Decapods of Sicily (Crustacea, Malacostraca). DIVERSITY 2022. [DOI: 10.3390/d14040246] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The current knowledge of Sicilian inland water decapod malacostracans is scarce and an updated synopsis on species distribution is lacking. Therefore, we reviewed the checklist and recent distribution of Sicilian inland water decapods based on published and unpublished records and novel observations with the aim of providing an exhaustive repository, also to be used as a sound baseline for future surveys. Overall, five native decapod species occur in the study area, i.e., the atyid shrimp Atyaephyra desmarestii, the palaemonid shrimps Palaemon adspersus, P. antennarius, and P. elegans, and the freshwater crab Potamon fluviatile, and their current local distributions are described. In addition, three alien species were recorded: the common yabby Cherax destructor and the red swamp crayfish Procambarus clarkii, strictly linked to inland waters, and the Atlantic blue crab Callinectes sapidus, a mainly marine species that can also colonise the lower stretches of rivers and coastal brackish waters. The collected data suggest the existence of a partial segregation of native versus non-native species, with the latter currently confined to coastal water bodies and the lower stretches of rivers. Moreover, the exclusively freshwater caridean A. desmarestii and P. antennarius show a parapatric distribution in the study area, which may suggest the existence of mutual exclusion phenomena. The results obtained raise some concerns about the effects of alien species on the native biota, and dedicated monitoring and management strategies should be implemented in order to better understand and mitigate their impact.
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17
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Hudson J, Bourne SD, Seebens H, Chapman MA, Rius M. The reconstruction of invasion histories with genomic data in light of differing levels of anthropogenic transport. Philos Trans R Soc Lond B Biol Sci 2022; 377:20210023. [PMID: 35067090 PMCID: PMC8784929 DOI: 10.1098/rstb.2021.0023] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Unravelling the history of range shifts is key for understanding past, current and future species distributions. Anthropogenic transport of species alters natural dispersal patterns and directly affects population connectivity. Studies have suggested that high levels of anthropogenic transport homogenize patterns of genetic differentiation and blur colonization pathways. However, empirical evidence of these effects remains elusive. We compared two range-shifting species (Microcosmus squamiger and Ciona robusta) to examine how anthropogenic transport affects our ability to reconstruct colonization pathways using genomic data. We first investigated shipping networks from the 18th century onwards, cross-referencing these with regions where the species have records to infer how each species has potentially been affected by different levels of anthropogenic transport. We then genotyped thousands of single-nucleotide polymorphisms from 280 M. squamiger and 190 C. robusta individuals collected across their extensive species' ranges and reconstructed colonization pathways. Differing levels of anthropogenic transport did not preclude the elucidation of population structure, though specific inferences of colonization pathways were difficult to discern in some of the considered scenario sets. We conclude that genomic data in combination with information of underlying introduction drivers provide key insights into the historic spread of range-shifting species. This article is part of the theme issue ‘Species’ ranges in the face of changing environments (part I)’.
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Affiliation(s)
- J Hudson
- School of Ocean and Earth Science, University of Southampton, National Oceanography Centre, European Way, Southampton SO14 3ZH, UK
| | - S D Bourne
- School of Ocean and Earth Science, University of Southampton, National Oceanography Centre, European Way, Southampton SO14 3ZH, UK
| | - H Seebens
- Senckenberg Biodiversity and Climate Research Centre, Senckenberganlage 25, 60325 Frankfurt, Germany
| | - M A Chapman
- Department of Biological Sciences, University of Southampton, Life Sciences Building 85, Highfield Campus, Southampton SO17 1BJ, UK
| | - M Rius
- School of Ocean and Earth Science, University of Southampton, National Oceanography Centre, European Way, Southampton SO14 3ZH, UK.,Department of Zoology, Centre for Ecological Genomics and Wildlife Conservation, University of Johannesburg, Auckland Park 2006, South Africa.,Centre for Advanced Studies of Blanes (CEAB, CSIC), Accés a la Cala Sant Francesc 14, Blanes 17300, Spain
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18
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Dudney J, D'Antonio C, Hobbs RJ, Shackelford N, Standish RJ, Suding KN. Capacity for change: Three core attributes of adaptive capacity that bolster restoration efficacy. Restor Ecol 2022. [DOI: 10.1111/rec.13647] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Joan Dudney
- Department of Plant Sciences University of California, Davis Davis California USA
- Environmental Studies Program University of California, Santa Barbara Santa Barbara California USA
| | - Carla D'Antonio
- Environmental Studies Program University of California, Santa Barbara Santa Barbara California USA
- Department of Ecology, Evolution, and Marine Biology University of California, Santa Barbara Santa Barbara California USA
| | - Richard J. Hobbs
- School of Biological Sciences The University of Western Australia Crawley WA Australia
| | | | | | - Katharine N. Suding
- Department of Ecology and Evolutionary Biology University of Colorado at Boulder USA
- Institute of Arctic and Alpine Research University of Colorado at Boulder Boulder Colorado USA
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19
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Maciel EA, Oliveira-Filho AT, Sobral-Souza TS, Marimon BS, Cupertino-Eisenlohr MA, José-Silva L, Eisenlohr PV. Climate change forecasts suggest that the conservation area network in the Cerrado-Amazon transition zone needs to be expanded. ACTA OECOLOGICA 2021. [DOI: 10.1016/j.actao.2021.103764] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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20
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Searle CL, Christie MR. Evolutionary rescue in host-pathogen systems. Evolution 2021; 75:2948-2958. [PMID: 34018610 DOI: 10.1111/evo.14269] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Revised: 05/07/2021] [Accepted: 05/12/2021] [Indexed: 11/28/2022]
Abstract
Natural populations encounter a variety of threats that can increase their risk of extinction. Populations can avoid extinction through evolutionary rescue (ER), which occurs when an adaptive, genetic response to selection allows a population to recover from an environmental change that would otherwise cause extinction. While the traditional framework for ER was developed with abiotic risk factors in mind, ER may also occur in response to a biotic source of demographic change, such as the introduction of a novel pathogen. We first describe how ER in response to a pathogen differs from the traditional ER framework; density-dependent transmission, pathogen evolution, and pathogen extinction can change the strength of selection imposed by a pathogen and make host population persistence more likely. We also discuss several variables that affect traditional ER (abundance, genetic diversity, population connectivity, and community composition) that also directly affect disease risk resulting in diverse outcomes for ER in host-pathogen systems. Thus, generalizations developed in studies of traditional ER may not be relevant for ER in response to the introduction of a pathogen. Incorporating pathogens into the framework of ER will lead to a better understanding of how and when populations can avoid extinction in response to novel pathogens.
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Affiliation(s)
- Catherine L Searle
- Department of Biological Sciences, Purdue University, West Lafayette, Indiana, 47907
| | - Mark R Christie
- Department of Biological Sciences, Purdue University, West Lafayette, Indiana, 47907.,Department of Forestry and Natural Resources, Purdue University, West Lafayette, Indiana, 47907
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21
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Giallongo G, Douek J, Harbuzov Z, Galil BS, Rinkevich B. Long-term changes in population genetic features of a rapidly expanding marine invader: implication for invasion success. Biol Invasions 2021. [DOI: 10.1007/s10530-021-02521-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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22
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Corridors as a tool for linking habitats – Shortcomings and perspectives for plant conservation. J Nat Conserv 2021. [DOI: 10.1016/j.jnc.2021.125974] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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23
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Martin SA, Lipps GJ, Gibbs HL. Pedigree-based assessment of recent population connectivity in a threatened rattlesnake. Mol Ecol Resour 2021; 21:1820-1832. [PMID: 33738927 DOI: 10.1111/1755-0998.13383] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Accepted: 02/25/2021] [Indexed: 12/18/2022]
Abstract
Managing endangered species in fragmented landscapes requires estimating dispersal rates between populations over contemporary timescales. Here, we developed a new method for quantifying recent dispersal using genetic pedigree data for close and distant kin. Specifically, we describe an approach that infers missing shared ancestors between pairs of kin in habitat patches across a fragmented landscape. We then applied a stepping-stone model to assign unsampled individuals in the pedigree to probable locations based on minimizing the number of movements required to produce the observed locations in sampled kin pairs. Finally, we used all pairs of reconstructed parent-offspring sets to estimate dispersal rates between habitat patches under a Bayesian model. Our approach measures connectivity over the timescale represented by the small number of generations contained within the pedigree and so is appropriate for estimating the impacts of recent habitat changes due to human activity. We used our method to estimate recent movement between newly discovered populations of threatened Eastern Massasauga rattlesnakes (Sistrurus catenatus) using data from 2996 RAD-based genetic loci. Our pedigree analyses found no evidence for contemporary connectivity between five genetic groups, but, as validation of our approach, showed high dispersal rates between sample sites within a single genetic cluster. We conclude that these five genetic clusters of Eastern Massasauga rattlesnakes have small numbers of resident snakes and are demographically isolated conservation units. More broadly, our methodology can be widely applied to determine contemporary connectivity rates, independent of bias from shared genetic similarity due to ancestry that impacts other approaches.
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Affiliation(s)
- Scott A Martin
- Department of Evolution, Ecology, and Organismal Biology and Ohio Biodiversity Conservation Partnership, The Ohio State University, Columbus, OH, USA
| | - Gregory J Lipps
- Department of Evolution, Ecology, and Organismal Biology and Ohio Biodiversity Conservation Partnership, The Ohio State University, Columbus, OH, USA
| | - H Lisle Gibbs
- Department of Evolution, Ecology, and Organismal Biology and Ohio Biodiversity Conservation Partnership, The Ohio State University, Columbus, OH, USA
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24
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Corridor quality affects net movement, size of dispersers, and population growth in experimental microcosms. Oecologia 2021; 195:547-556. [PMID: 33423105 PMCID: PMC7882584 DOI: 10.1007/s00442-020-04834-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Accepted: 12/11/2020] [Indexed: 10/25/2022]
Abstract
Corridors are expected to increase species dispersal in fragmented habitats. However, it remains unclear how the quality of corridors influences the dispersal process, and how it interacts with corridor length and width. Here we investigate these factors using a small-scale laboratory system where we track the dispersal of the model organism Collembola Folsomia candida. Using this system, we study the effects of corridor length, width, and quality on the probability of dispersal, net movement, body size of dispersers, and the rate of change in population size after colonization. We show that corridor quality positively affected dispersal probability, net movement, and the rate of change in population size in colonised patches. Moreover, corridor quality significantly affected the size of dispersers, with only larger individuals dispersing through poor quality corridors. The length and width of corridors affected both the rate at which populations increased in colonised patches and the net number of individuals which dispersed, suggesting that these physical properties may be important in maintaining the flow of individuals in space. Our results thus suggest that corridor quality can have an important role in determining not only the probability of dispersal occurs but also the phenotypes of the individuals which disperse, with concomitant effects on the net movement of individuals and the rate of change in population size in the colonised patches.
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25
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Gagnaire PA. Comparative genomics approach to evolutionary process connectivity. Evol Appl 2020; 13:1320-1334. [PMID: 32684961 PMCID: PMC7359831 DOI: 10.1111/eva.12978] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Revised: 04/02/2020] [Accepted: 04/03/2020] [Indexed: 01/01/2023] Open
Abstract
The influence of species life history traits and historical demography on contemporary connectivity is still poorly understood. However, these factors partly determine the evolutionary responses of species to anthropogenic landscape alterations. Genetic connectivity and its evolutionary outcomes depend on a variety of spatially dependent evolutionary processes, such as population structure, local adaptation, genetic admixture, and speciation. Over the last years, population genomic studies have been interrogating these processes with increasing resolution, revealing a large diversity of species responses to spatially structured landscapes. In parallel, multispecies meta-analyses usually based on low-genome coverage data have provided fundamental insights into the ecological determinants of genetic connectivity, such as the influence of key life history traits on population structure. However, comparative studies still lack a thorough integration of macro- and micro-evolutionary scales to fully realize their potential. Here, I present how a comparative genomics framework may provide a deeper understanding of evolutionary process connectivity. This framework relies on coupling the inference of long-term demographic and selective history with an assessment of the contemporary consequences of genetic connectivity. Standardizing this approach across several species occupying the same landscape should help understand how spatial environmental heterogeneity has shaped the diversity of historical and contemporary connectivity patterns in different taxa with contrasted life history traits. I will argue that a reasonable amount of genome sequence data can be sufficient to resolve and connect complex macro- and micro-evolutionary histories. Ultimately, implementing this framework in varied taxonomic groups is expected to improve scientific guidelines for conservation and management policies.
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27
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Miu IV, Chisamera GB, Popescu VD, Iosif R, Nita A, Manolache S, Gavril VD, Cobzaru I, Rozylowicz L. Conservation priorities for terrestrial mammals in Dobrogea Region, Romania. Zookeys 2018:133-158. [PMID: 30402034 PMCID: PMC6215976 DOI: 10.3897/zookeys.792.25314] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Accepted: 08/30/2018] [Indexed: 11/26/2022] Open
Abstract
Based on species occurrence records of museum collections, published literature, and unpublished records shared by mammalian experts, we compiled a distribution database for 59 terrestrial mammals populating the extensively protected Dobrogea Region of Romania. The spatial patterns of mammal distribution and diversity was evaluated and systematic conservation planning applied to identify priority areas for their conservation. The spatial analyses revealed that intensive sampling was not directly correlated to mammal diversity but rather to accessibility for inventory. The spatial prioritisation analysis indicated a relatively aggregated pattern of areas with a high or low conservation value with virtually no connecting corridors between them. The significant overlap between Natura 2000 sites and national protected areas induced an over-optimistic vision of the effectiveness and representativeness of existing Natura 2000 network for species found in Annexes II and IV of the Habitats Directive. These results represent a key step in identifying core areas for the protection of mammal diversity and dispersal corridors for improved connectivity, and to guide future conservation efforts in increasing the effectiveness of the existing protected areas in the context of environmental changes.
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Affiliation(s)
- Iulia V Miu
- University of Bucharest, Center for Environmental Research and Impact Studies, 1 N. Balcescu, 010041, Bucharest, Romania
| | - Gabriel B Chisamera
- National Museum of Natural History Grigore Antipa, 1 Kiseleff Blvd., 011341, Bucharest, Romania
| | - Viorel D Popescu
- University of Bucharest, Center for Environmental Research and Impact Studies, 1 N. Balcescu, 010041, Bucharest, Romania.,Department of Biological Sciences, Ohio University, Athens, OH, USA
| | - Ruben Iosif
- University Ovidius Constanţa, Faculty of Natural Sciences and Agricultural Sciences, 1 Al. Universităţii, corp B, 900470, Constanţa, Romania
| | - Andreea Nita
- University of Bucharest, Center for Environmental Research and Impact Studies, 1 N. Balcescu, 010041, Bucharest, Romania
| | - Steluta Manolache
- University of Bucharest, Center for Environmental Research and Impact Studies, 1 N. Balcescu, 010041, Bucharest, Romania
| | - Viorel D Gavril
- University of Bucharest, Faculty of Biology, 91-95 Splaiul Independenței, 050095, Bucharest, Romania.,Romanian Academy, Institute of Biology, 296 Splaiul Independentei, 060031 Bucharest, Romania
| | - Ioana Cobzaru
- Romanian Academy, Institute of Biology, 296 Splaiul Independentei, 060031 Bucharest, Romania
| | - Laurentiu Rozylowicz
- University of Bucharest, Center for Environmental Research and Impact Studies, 1 N. Balcescu, 010041, Bucharest, Romania
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28
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Laborda Á, Montes de Oca L, Pérez-Miles F, Useta G, Simó M. The spider fauna from Uruguay River islands: understanding its role in a biological corridor. Biodivers Data J 2018; 6:e27319. [PMID: 30271252 PMCID: PMC6160865 DOI: 10.3897/bdj.6.e27319] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Accepted: 08/21/2018] [Indexed: 11/26/2022] Open
Abstract
Biological corridors are connections which link habitats in a regional scale, allowing the gene flow between populations. The Uruguay River comprises riverside and insular riparian forests along subtropical to temperate zones passing through different biogeographic provinces. The aim of this study was to characterise the spider fauna from the Uruguay River islands highlighting their connection role for the spider community of riparian forest. Spiders were studied from surveys in a fluvial island of the southern course of the river with nine campaigns being carried out from September 2007 to September 2009. Three complementary collecting methods were used: G-Vac, night hand collecting and pitfall traps. A total of 58 samples were taken in each campaign. A total of 33 families, 145 species/morphospecies and 8 guilds were registered. Theridiidae and space web weavers showed the highest abundance and species richness. Web weavers were predominant in the spider community evidencing the importance of the forest vegetation heterogeneity in spider diversity. Fifteen species have been recorded for the first time for Uruguay. Additional data of previous surveys in the northern islands of the river were analysed and compared. Several species confirm the role of the Uruguay River as a biological corridor from the upper to lower course of the river. The riparian forests from the islands constitute a southernmost intromission of Paranaense biota between Chaco and Pampa regions along the river. The results obtained are an important input for the conservation of these areas. Knowing the biodiversity, as well as its dynamics and the flow of biota that exists in these environments, would allow planning the management from a regional point of view.
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Affiliation(s)
- Álvaro Laborda
- Sección Entomología, Facultad de Ciencias, Universidad de la República. Iguá 4225. CP 11400, Montevideo, UruguaySección Entomología, Facultad de Ciencias, Universidad de la República. Iguá 4225. CP 11400MontevideoUruguay
| | - Laura Montes de Oca
- Instituto de Investigaciones Biológicas Clemente Estable, Laboratorio de Etología, Ecología y Evolución. Av. Italia 3318. CP 11200, Montevideo, UruguayInstituto de Investigaciones Biológicas Clemente Estable, Laboratorio de Etología, Ecología y Evolución. Av. Italia 3318. CP 11200MontevideoUruguay
| | - Fernando Pérez-Miles
- Sección Entomología, Facultad de Ciencias, Universidad de la República. Iguá 4225. CP 11400, Montevideo, UruguaySección Entomología, Facultad de Ciencias, Universidad de la República. Iguá 4225. CP 11400MontevideoUruguay
| | - Gonzalo Useta
- Laboratorio Tecnológico del Uruguay. Av. Italia 6201. CP 11500, Montevideo, UruguayLaboratorio Tecnológico del Uruguay. Av. Italia 6201. CP 11500MontevideoUruguay
| | - Miguel Simó
- Sección Entomología, Facultad de Ciencias, Universidad de la República. Iguá 4225. CP 11400, Montevideo, UruguaySección Entomología, Facultad de Ciencias, Universidad de la República. Iguá 4225. CP 11400MontevideoUruguay
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Sgarlata GM, Salmona J, Aleixo-Pais I, Rakotonanahary A, Sousa AP, Kun-Rodrigues C, Ralantoharijaona T, Jan F, Zaranaina R, Rasolondraibe E, Zaonarivelo JR, Andriaholinirina NV, Chikhi L. Genetic Differentiation and Demographic History of the Northern Rufous Mouse Lemur (Microcebus tavaratra) Across a Fragmented Landscape in Northern Madagascar. INT J PRIMATOL 2018. [DOI: 10.1007/s10764-018-0015-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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Aavik T, Helm A. Restoration of plant species and genetic diversity depends on landscape-scale dispersal. Restor Ecol 2017. [DOI: 10.1111/rec.12634] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- Tsipe Aavik
- Institute of Ecology and Earth Sciences; University of Tartu, Lai 40; 51005, Tartu Estonia
| | - Aveliina Helm
- Institute of Ecology and Earth Sciences; University of Tartu, Lai 40; 51005, Tartu Estonia
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31
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Cleary KA, Waits LP, Finegan B. Comparative landscape genetics of two frugivorous bats in a biological corridor undergoing agricultural intensification. Mol Ecol 2017; 26:4603-4617. [PMID: 28672105 DOI: 10.1111/mec.14230] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2016] [Accepted: 06/05/2017] [Indexed: 01/18/2023]
Abstract
Agricultural intensification in tropical landscapes poses a new threat to the ability of biological corridors to maintain functional connectivity for native species. We use a landscape genetics approach to evaluate impacts of expanding pineapple plantations on two widespread and abundant frugivorous bats in a biological corridor in Costa Rica. We hypothesize that the larger, more mobile Artibeus jamaicensis will be less impacted by pineapple than the smaller Carollia castanea. In 2012 and 2013, we sampled 735 bats in 26 remnant forest patches surrounded by different proportions of forest, pasture, crops and pineapple. We used 10 microsatellite loci for A. jamaicensis and 16 microsatellite loci for C. castanea to estimate genetic diversity and gene flow. Canonical correspondence analyses indicate that land cover type surrounding patches has no impact on genetic diversity of A. jamaicensis. However, for C. castanea, both percentage forest and pineapple surrounding patches explained a significant proportion of the variation in genetic diversity. Least-cost transect analyses (LCTA) and pairwise G″st suggest that for A. jamaicensis, pineapple is more permeable to gene flow than expected, while as expected, forest is the most permeable land cover for gene flow of C. castanea. For both species, LCTA indicate that development may play a role in inhibiting gene flow. The current study answers the call for landscape genetic research focused on tropical and agricultural landscapes, highlights the value of comparative landscape genetics in biological corridor design and management and is one of the few studies of biological corridors in any ecosystem to implement a genetic approach to test corridor efficacy.
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Affiliation(s)
- Katherine A Cleary
- Department of Fish and Wildlife Sciences, University of Idaho, Moscow, ID, USA.,Department of Biology, Clarkson University, Potsdam, NY, USA
| | - Lisette P Waits
- Department of Fish and Wildlife Sciences, University of Idaho, Moscow, ID, USA
| | - Bryan Finegan
- Forests, Biodiversity and Climate Change Program, CATIE, Turrialba, Cartago, Costa Rica
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de Brito Martins A, de Aguiar MAM. Barriers to gene flow and ring species formation. Evolution 2016; 71:442-448. [PMID: 27861800 DOI: 10.1111/evo.13121] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2016] [Accepted: 10/20/2016] [Indexed: 11/30/2022]
Abstract
Ring species are groups of organisms that dispersed along a ring-shaped region in such a way that the two ends of the population that meet after many generations are reproductively isolated. They provide a rare opportunity to understand the role of spatial structuring in speciation. Here, we simulate the evolution of ring species assuming that individuals become sexually isolated if the genetic distance between them is above a certain threshold. The model incorporates two forms of dispersal limitation: exogenous geographic barriers that limit the population range and endogenous barriers that result in genetic structuring within the population range. As expected, species' properties that reduce gene flow within the population range facilitate the evolution of reproductive isolation and ring species formation. However, if populations are confined to narrow ranges by geographic barriers, ring species formation increases when local mating is less spatially restricted. Ring species are most likely to form if a population expands while confined to a quasi-unidimensional range but preserving high mobility in the direction of the range expansion. These conditions are unlikely to be met or persist in real populations and may explain why ring species are rare.
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Affiliation(s)
- Ayana de Brito Martins
- Depto. de Física da Matéria Condensada, Inst. de Física "Gleb Wataghin", Universidade Estadual de Campinas, Campinas, SP, Brazil.,Depto. de Ecologia, Inst. de Biociências, Universidade de São Paulo, São Paulo, SP, Brazil.,Department of Fish Ecology and Evolution, Center for Ecology, Evolution and Biogeochemistry, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, ZH, Switzerland
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Ridley CE, Alexander LC. Applying gene flow science to environmental policy needs: a boundary work perspective. Evol Appl 2016; 9:924-36. [PMID: 27468309 PMCID: PMC4947153 DOI: 10.1111/eva.12393] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2015] [Accepted: 05/09/2016] [Indexed: 11/27/2022] Open
Abstract
One application of gene flow science is the policy arena. In this article, we describe two examples in which the topic of gene flow has entered into the U.S. national environmental policymaking process: regulation of genetically engineered crops and clarification of the jurisdictional scope of the Clean Water Act. We summarize both current scientific understanding and the legal context within which gene flow science has relevance. We also discuss the process by which scientific knowledge has been synthesized and communicated to decision-makers in these two contexts utilizing the concept of 'boundary work'. Boundary organizations, the work they engage in to bridge the worlds of science, policy, and practice, and the boundary objects they produce to translate scientific knowledge existed in both examples. However, the specific activities and attributes of the objects produced varied based on the needs of the decision-makers. We close with suggestions for how scientists can contribute to or engage in boundary work with policymakers.
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Affiliation(s)
- Caroline E. Ridley
- National Center for Environmental AssessmentU.S. Environmental Protection Agency, Office of Research and DevelopmentWashingtonDCUSA
| | - Laurie C. Alexander
- National Center for Environmental AssessmentU.S. Environmental Protection Agency, Office of Research and DevelopmentWashingtonDCUSA
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Bartlett M, Hale R, Hale M. Habitat quality limits gene flow between populations of Bombus ruderatus in the South Island, New Zealand. CONSERV GENET 2016. [DOI: 10.1007/s10592-016-0816-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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35
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Thomaz AT, Christie MR, Knowles LL. The architecture of river networks can drive the evolutionary dynamics of aquatic populations. Evolution 2016; 70:731-9. [DOI: 10.1111/evo.12883] [Citation(s) in RCA: 65] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2015] [Accepted: 02/01/2016] [Indexed: 12/11/2022]
Affiliation(s)
- Andréa T. Thomaz
- Department of Ecology and Evolutionary Biology; University of Michigan; Ann Arbor Michigan 48109
| | - Mark R. Christie
- Department of Ecology and Evolutionary Biology; University of Michigan; Ann Arbor Michigan 48109
- Department of Biological Science; Purdue University; West Lafayette Indiana 47907
- Department of Forestry and Natural Resources; Purdue University; West Lafayette Indiana 47907
| | - L. Lacey Knowles
- Department of Ecology and Evolutionary Biology; University of Michigan; Ann Arbor Michigan 48109
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36
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Yao G, Zhu Y, Wan QH, Fang SG. Major histocompatibility complex class II genetic variation in forest musk deer (Moschus berezovskii) in China. Anim Genet 2015; 46:535-43. [PMID: 26370614 DOI: 10.1111/age.12336] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/26/2015] [Indexed: 01/18/2023]
Abstract
The major histocompatibility complex (MHC) plays an important role in the immune system of vertebrates. We used the second exon of four MHC class II genes (DRA, DQA1, DQA2 and DRB3) to assess the overall MHC variation in forest musk deer (Moschus berezovskii). We also compared the MHC variation in captive and wild populations. We observed 22 alleles at four loci (four at DRA, four at DQA1, four at DQA2 and 10 at DRB3), 15 of which were newly identified alleles. Results suggest that forest musk deer maintain relatively high MHC variation, which may result from balancing selection. Moreover, considerable diversity was observed at the DRA locus. We found a high frequency of Mobe-DRA*02, Mobe-DQA1*01 and Mobe-DQA2*05 alleles, which may be important for pathogen resistance. A Ewens-Watterson test showed that the DRB3 locus in the wild population had experienced recent balancing selection. We detected a small divergence at the DRA locus, suggesting the effect of weak positive selection on the DRA gene. Alternatively, this locus may be young and not yet adapted a wide spectrum of alleles for pathogen resistance. The significant heterozygosity deficit observed at the DQA1 and DRB3 loci in the captive population and at all four loci in the wild population may be the result of a population bottleneck. Additionally, MHC genetic diversity was higher in the wild population than in the captive, suggesting that the wild population may have the ability to respond to a wider range of pathogens.
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Affiliation(s)
- Gang Yao
- The Key Laboratory of Conservation Biology for Endangered Wildlife of the Ministry of Education, and State Conservation Centre for Gene Resources of Endangered Wildlife, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Ying Zhu
- The Key Laboratory of Conservation Biology for Endangered Wildlife of the Ministry of Education, and State Conservation Centre for Gene Resources of Endangered Wildlife, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Qiu-Hong Wan
- The Key Laboratory of Conservation Biology for Endangered Wildlife of the Ministry of Education, and State Conservation Centre for Gene Resources of Endangered Wildlife, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Sheng-Guo Fang
- The Key Laboratory of Conservation Biology for Endangered Wildlife of the Ministry of Education, and State Conservation Centre for Gene Resources of Endangered Wildlife, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
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