1
|
Pearce DL, Edson JE, Jennelle CS, Walter WD. Evaluation of DNA yield from various tissue and sampling sources for use in single nucleotide polymorphism panels. Sci Rep 2024; 14:11340. [PMID: 38760358 PMCID: PMC11101418 DOI: 10.1038/s41598-024-56128-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Accepted: 03/01/2024] [Indexed: 05/19/2024] Open
Abstract
Genetics studies are used by wildlife managers and researchers to gain inference into a population of a species of interest. To gain these insights, microsatellites have been the primary method; however, there currently is a shift from microsatellites to single nucleotide polymorphisms (SNPs). With the different DNA requirements between microsatellites and SNPs, an investigation into which samples can provide adequate DNA yield is warranted. Using samples that were collected from previous genetic projects from regions in the USA from 2014 to 2021, we investigated the DNA yield of eight sample categories to gain insights into which provided adequate DNA to be used in ddRADseq or already developed high- or medium-density SNP panels. We found seven sample categories that met the DNA requirements for use in all three panels, and one sample category that did not meet any of the three panels requirements; however, DNA integrity was highly variable and not all sample categories that met panel DNA requirements could be considered high quality DNA. Additionally, we used linear random-effects models to determine which covariates would have the greatest influence on DNA yield. We determined that all covariates (tissue type, storage method, preservative, DNA quality, time until DNA extraction and time after DNA extraction) could influence DNA yield.
Collapse
Affiliation(s)
- David L Pearce
- Pennsylvania Cooperative Fish and Wildlife Research Unit, The Pennsylvania State University, 413 Forest Resources Building, University Park, PA, 16802, USA
- Department of Rangeland, Wildlife and Fisheries Management, Texas A&M University, College Station, TX, 77843, USA
| | - Jessie E Edson
- Pennsylvania Cooperative Fish and Wildlife Research Unit, The Pennsylvania State University, 413 Forest Resources Building, University Park, PA, 16802, USA
| | - Chris S Jennelle
- Minnesota Department of Natural Resources, 5463 West Broadway Ave., Forest Lake, MN, 55025, USA
- Minnesota Department of Natural Resources, Division of Ecological and Water Resources, Nongame Wildlife Program, St Paul, MN, 55155, USA
| | - W David Walter
- U.S. Geological Survey, Pennsylvania Cooperative Fish and Wildlife Research Unit, The Pennsylvania State University, 403 Forest Resources Building, University Park, PA, 16802, USA.
| |
Collapse
|
2
|
Morin E, Razafimbelo NT, Yengué JL, Guinard Y, Grandjean F, Bech N. Are human-induced changes good or bad to dynamic landscape connectivity? JOURNAL OF ENVIRONMENTAL MANAGEMENT 2024; 352:120009. [PMID: 38184871 DOI: 10.1016/j.jenvman.2023.120009] [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: 05/14/2023] [Revised: 12/30/2023] [Accepted: 12/30/2023] [Indexed: 01/09/2024]
Abstract
Land managers must find a compromise between rapidly changing landscapes and biodiversity conservation through ecological networks. Estimating ecological networks is a key approach to enhance or maintain functional connectivity by identifying the nodes and links of a graph, which represent habitats and their corresponding functional corridors, respectively. To understand the current state of biodiversity, it is necessary to consider dynamic landscape connectivity while relying on relevant land cover maps. Although a current land cover map is relatively easy to produce using existing data, this is challenging for past landscapes. Here we investigated the impact of changes in landscape connectivity in an urban landscape at a fine scale on the habitat availability of two bird species: the tree pipit Anthus trivialis and the short-toed treecreeper Certhia brachydactyla. These species, exhibiting different niche ecologies, have shown contrasting population trends at a medium-term scale. The occurrences of C. brachydactyla were better correlated with resistance values that maximise the use of corridors, whereas the occurrences of A. trivialis better fitted with intermediate resistance values. The statistical approach indirectly highlighted relevant information about the ecology the capacity of both species to use urban habitats. Landscape connectivity increased for both species over the 24-year study period and may have implications for local abundances, which could explain, at the national scale, the increase in populations of C. brachydactyla, but not the decrease in populations of A. trivialis. Thus, more attention must be paid on rural habitats and their associated species that are more impacted by human activities, but efforts could also be achieved in urban areas especially for highly corridor-dependent species. Studying dynamic landscape connectivity at a fine scale is essential for estimating past and future land cover changes and their associated impacts on ecological networks, to better reconcile human and biodiversity concerns in land management.
Collapse
Affiliation(s)
- Elie Morin
- Université de Poitiers, Laboratoire Ecologie et Biologie des Interactions (UMR CNRS 7267), 3 Rue Jacques Fort, 86000, Poitiers, France.
| | - Ny Tolotra Razafimbelo
- Université de Laval, Faculté de Foresterie et Géomatique Département des Sciences Géomatiques, 1055 Avenue Du Séminaire, Québec (Québec), G1V 0A6, Canada
| | - Jean-Louis Yengué
- Université de Poitiers, Laboratoire RURALITES, UR13823, MSHS, Bâtiment A5, 5 Rue Théodore Lefèbvre, TSA 21103, 86073, Poitiers, Cedex 9, France
| | - Yvonnick Guinard
- Grand Poitiers Communauté Urbaine, Hôtel Communautaire, 84 Rue des Carmélites, 86000, Poitiers, France
| | - Frédéric Grandjean
- Université de Poitiers, Laboratoire Ecologie et Biologie des Interactions (UMR CNRS 7267), 3 Rue Jacques Fort, 86000, Poitiers, France
| | - Nicolas Bech
- Université de Poitiers, Laboratoire Ecologie et Biologie des Interactions (UMR CNRS 7267), 3 Rue Jacques Fort, 86000, Poitiers, France
| |
Collapse
|
3
|
Le Tallec T, Hozer C, Perret M, Théry M. Light pollution and habitat fragmentation in the grey mouse lemur. Sci Rep 2024; 14:1662. [PMID: 38238414 PMCID: PMC10796386 DOI: 10.1038/s41598-024-51853-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Accepted: 01/10/2024] [Indexed: 01/22/2024] Open
Abstract
Light pollution, by changing organisms' behavior, affects locomotion, migration and can ultimately fragment the habitat. To investigate the effects of light pollution on habitat fragmentation, we conducted an experimental study on a nocturnal and photosensitive primate, the grey mouse lemur (Microcebus murinus). Twelve males were housed individually in an apparatus with two cages connected by two corridors, opaque and transparent. During 4 nights, the transparent corridor was illuminated by specific light intensities: 0 lx, 0.3 lx, 20 lx and 51.5 lx corresponding respectively to total darkness, full moon, minimal intensity recommended by the European standard EN-13201 on public lighting, and to light pollution recorded in an urban area. Each night, general activity, use of corridors and cage occupancy were recorded using an infrared camera. For the first time in a nocturnal primate, results demonstrate that light pollution changes the preference of use of corridors, modifies the locomotor pattern and limits the ability of animals to efficiently exploit their environment according to a light intensity-dependent relationship. However, results indicate that a dark corridor allows partial compensation partly preserving general activities. This study highlights the necessity to consider light pollution during the implementation of conservation plans and the relevance of nocturnal frames.
Collapse
Affiliation(s)
- Thomas Le Tallec
- UMR 7179 MECADEV, Centre National de la Recherche Scientifique, Muséum National d'Histoire Naturelle, 1 avenue du petit Château, 91800, Brunoy, France.
| | - Clara Hozer
- UMR 7179 MECADEV, Centre National de la Recherche Scientifique, Muséum National d'Histoire Naturelle, 1 avenue du petit Château, 91800, Brunoy, France
| | - Martine Perret
- UMR 7179 MECADEV, Centre National de la Recherche Scientifique, Muséum National d'Histoire Naturelle, 1 avenue du petit Château, 91800, Brunoy, France
| | - Marc Théry
- UMR 7179 MECADEV, Centre National de la Recherche Scientifique, Muséum National d'Histoire Naturelle, 1 avenue du petit Château, 91800, Brunoy, France
| |
Collapse
|
4
|
da Silveira JAG, Moreira SM, do Nascimento AF, de Oliveira MM, dos Santos HA, Estevam LGTDM, Pereira CR, Oliveira AGG, D’Elia ML, Araujo ADC, Silva JMM. Preparing Collared Peccary ( Pecari tajacu Linnaeus, 1758) for Reintroduction into the Wild: A Screening for Parasites and Hemopathogens of a Captive Population. Pathogens 2024; 13:47. [PMID: 38251354 PMCID: PMC10819336 DOI: 10.3390/pathogens13010047] [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: 12/06/2023] [Revised: 12/28/2023] [Accepted: 12/31/2023] [Indexed: 01/23/2024] Open
Abstract
The reintroduction of captive animals to the wild helps restore endangered species, but it risks pathogen transmission, harming wild populations. Such transmission can impact the genetic diversity and long-term viability of these populations. This study assessed parasite diversity and load in captive Pecari tajacu, a species native to the Americas and culturally significant to Brazilian indigenous culture, prior to reintroduction. Samples from 24 peccaries were analyzed for ectoparasites, hemopathogens, and stool parasites with direct and molecular analysis. Findings showed that various parasites were present. Two peccaries (8.3%) were infested by the adult tick Amblyomma sculptum. Six (25.0%) tested positive for Trypanosoma evansi, four (16.7%) for hemobacteria of the family Anaplasmataceae, twelve (50.0%) for hemotropic Mycoplasma, and seven (29.2%) for Leishmania braziliensis. Stool samples indicated multiple parasites, with sixteen (66.7%) peccaries infected by Strongylida order parasites, Spiruridae in three (12.5%), and Ascaris suum in one (4.2%) animal. Cysts of Balantidium sp. were found in twenty (83.3%), Entamoeba polecki in five (20.8%), and Iodamoeba bütschlii in two (8.3%) peccaries. To our current knowledge, this is the first global report of Leishmania braziliensis, Iodamoeba bütschlii, and Entamoeba polecki in P. tajacu, irrespective of the environment, including both captivity and wild conditions. Some of these parasites are common in domestic animals, and others are zoonotic, indicating potential interspecies pathogen transmission.
Collapse
Affiliation(s)
| | - Simone Magela Moreira
- Department of Agrarian Sciences, Federal Institute of Education, Science and Technology of Minas Gerais-Campus Bambuí, Bambuí 38900-000, MG, Brazil; (S.M.M.); (A.F.d.N.)
| | - Ariane Flávia do Nascimento
- Department of Agrarian Sciences, Federal Institute of Education, Science and Technology of Minas Gerais-Campus Bambuí, Bambuí 38900-000, MG, Brazil; (S.M.M.); (A.F.d.N.)
| | - Marco Miguel de Oliveira
- Biological Science, State University of Minas Gerais-Unit Ituiutaba, Ituiutaba 38302-192, MG, Brazil;
| | - Hudson Andrade dos Santos
- Department of Parasitology, Institute of Biological Science, Federal University of Minas Gerais, Belo Horizonte 31270-901, MG, Brazil; (H.A.d.S.); (A.d.C.A.)
| | | | | | - Anna Gabriela Guimarães Oliveira
- Department of Preventive Veterinary Medicine, Veterinary School, Federal University of Minas Gerais, Belo Horizonte 31270-901, MG, Brazil;
| | | | - Andreina de Carvalho Araujo
- Department of Parasitology, Institute of Biological Science, Federal University of Minas Gerais, Belo Horizonte 31270-901, MG, Brazil; (H.A.d.S.); (A.d.C.A.)
| | | |
Collapse
|
5
|
Xia Y, Chen L, Srivastava V, Parshad RD. Stability and bifurcation analysis of a two-patch model with the Allee effect and dispersal. MATHEMATICAL BIOSCIENCES AND ENGINEERING : MBE 2023; 20:19781-19807. [PMID: 38052624 DOI: 10.3934/mbe.2023876] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/07/2023]
Abstract
In the current manuscript, a two-patch model with the Allee effect and nonlinear dispersal is presented. We study both the ordinary differential equation (ODE) case and the partial differential equation (PDE) case here. In the ODE model, the stability of the equilibrium points and the existence of saddle-node bifurcation are discussed. The phase diagram and bifurcation curve of our model are also given as a results of numerical simulation. Besides, the corresponding linear dispersal case is also presented. We show that, when the Allee effect is large, high intensity of linear dispersal is not favorable to the persistence of the species. We further show when the Allee effect is large, nonlinear diffusion is more beneficial to the survival of the population than linear diffusion. Moreover, the results of the PDE model extend our findings from discrete patches to continuous patches.
Collapse
Affiliation(s)
- Yue Xia
- School of Mathematics and Statistics, Fuzhou University, Fuzhou, Fujian 350108, China
| | - Lijuan Chen
- School of Mathematics and Statistics, Fuzhou University, Fuzhou, Fujian 350108, China
| | | | - Rana D Parshad
- Department of Mathematics, Iowa State University, Ames, IA 50011, USA
| |
Collapse
|
6
|
Dolker S, Jabin G, Singh SK, Joshi BD, Singh VK, Dalui S, Chandra K, Sharma LK, Thakur M. Landscape genetics identified conservation priority areas for blue sheep (Pseudois nayaur) in the Indian Trans-Himalayan Region. Sci Rep 2023; 13:18152. [PMID: 37875501 PMCID: PMC10598060 DOI: 10.1038/s41598-023-44823-y] [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: 01/23/2023] [Accepted: 10/12/2023] [Indexed: 10/26/2023] Open
Abstract
The trans-Himalayan region of India, although have xeric features, still supports a unique assemblage of biodiversity, including some of the charismatic and endemic species. In the present study, we studied blue sheep (Pseudois nayaur) across the distribution range in the Western trans Himalayas of India and found about 18,775 km2 area suitable for blue sheep. The explicit Bayesian based spatial and non-spatial population structure analysis assigned blue sheep into two genetic populations, i.e., Ladakh and Lahaul-Spiti. We found relatively high genetic divergence in blue sheep which is also supported by the low current flow in Circuitscape model. With the multiple evidences, we explain landscape resistance facilitated by the landscape heterogeneity, and large patches of unsuitable habitats forced population divergence and poor functional connectivity. We found that blue sheep population has been demographically stable in the past, but showed a slight decline within the last few decades. This study is the first range-wide attempt to exhibit landscape features in shaping the spatial distribution, genetic structure and demography patterns of blue sheep in Western Himalayas, and will be of use in the conservation and management planning of blue sheep.
Collapse
Affiliation(s)
- Stanzin Dolker
- Zoological Survey of India, New Alipore, Kolkata, 700053, West Bengal, India
- Department of Zoology, University of Calcutta, Kolkata, 700019, West Bengal, India
| | - Gul Jabin
- Zoological Survey of India, New Alipore, Kolkata, 700053, West Bengal, India
- Department of Zoology, University of Calcutta, Kolkata, 700019, West Bengal, India
| | - Sujeet Kumar Singh
- Zoological Survey of India, New Alipore, Kolkata, 700053, West Bengal, India
- Amity Institute of Forestry and Wildlife, Amity University Campus, Sector-125, Noida, 201303, UP, India
| | - Bheem Dutt Joshi
- Zoological Survey of India, New Alipore, Kolkata, 700053, West Bengal, India
| | - Vinaya Kumar Singh
- Zoological Survey of India, New Alipore, Kolkata, 700053, West Bengal, India
| | - Supriyo Dalui
- Zoological Survey of India, New Alipore, Kolkata, 700053, West Bengal, India
- Department of Zoology, University of Calcutta, Kolkata, 700019, West Bengal, India
| | - Kailash Chandra
- Zoological Survey of India, New Alipore, Kolkata, 700053, West Bengal, India
| | - Lalit Kumar Sharma
- Zoological Survey of India, New Alipore, Kolkata, 700053, West Bengal, India
| | - Mukesh Thakur
- Zoological Survey of India, New Alipore, Kolkata, 700053, West Bengal, India.
| |
Collapse
|
7
|
Savary P, Foltête JC, Moal H, Vuidel G, Garnier S. Inferring landscape resistance to gene flow when genetic drift is spatially heterogeneous. Mol Ecol Resour 2023; 23:1574-1588. [PMID: 37332161 DOI: 10.1111/1755-0998.13821] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Revised: 05/12/2023] [Accepted: 05/24/2023] [Indexed: 06/20/2023]
Abstract
In connectivity models, land cover types are assigned cost values characterizing their resistance to species movements. Landscape genetic methods infer these values from the relationship between genetic differentiation and cost distances. The spatial heterogeneity of population sizes, and consequently genetic drift, is rarely included in this inference although it influences genetic differentiation. Similarly, migration rates and population spatial distributions potentially influence this inference. Here, we assessed the reliability of cost value inference under several migration rates, population spatial patterns and degrees of population size heterogeneity. Additionally, we assessed whether considering intra-population variables, here using gravity models, improved the inference when drift is spatially heterogeneous. We simulated several gene flow intensities between populations with varying local sizes and spatial distributions. We then fit gravity models of genetic distances as a function of (i) the 'true' cost distances driving simulations or alternative cost distances, and (ii) intra-population variables (population sizes, patch areas). We determined the conditions making the identification of the 'true' costs possible and assessed the contribution of intra-population variables to this objective. Overall, the inference ranked cost scenarios reliably in terms of similarity with the 'true' scenario (cost distance Mantel correlations), but this 'true' scenario rarely provided the best model goodness of fit. Ranking inaccuracies and failures to identify the 'true' scenario were more pronounced when migration was very restricted (<4 dispersal events/generation), population sizes were most heterogeneous and some populations were spatially aggregated. In these situations, considering intra-population variables helps identify cost scenarios reliably, thereby improving cost value inference from genetic data.
Collapse
Affiliation(s)
- Paul Savary
- ARP-Astrance, Paris, France
- UMR 6049 Thé MA, Université de Franche-Comté, CNRS, Besançon Cedex, France
- UMR 6282 Biogéosciences, Université Bourgogne Franche-Comté, CNRS, Dijon, France
| | | | | | - Gilles Vuidel
- UMR 6049 Thé MA, Université de Franche-Comté, CNRS, Besançon Cedex, France
| | - Stéphane Garnier
- UMR 6282 Biogéosciences, Université Bourgogne Franche-Comté, CNRS, Dijon, France
| |
Collapse
|
8
|
Ramsay MS, Sgarlata GM, Barratt CD, Salmona J, Andriatsitohaina B, Kiene F, Manzi S, Ramilison ML, Rakotondravony R, Chikhi L, Lehman SM, Radespiel U. Effects of Forest Fragmentation on Connectivity and Genetic Diversity in an Endemic and an Invasive Rodent in Northwestern Madagascar. Genes (Basel) 2023; 14:1451. [PMID: 37510355 PMCID: PMC10378931 DOI: 10.3390/genes14071451] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Revised: 07/07/2023] [Accepted: 07/13/2023] [Indexed: 07/30/2023] Open
Abstract
Habitat loss and fragmentation are of concern to conservation biologists worldwide. However, not all organisms are affected equally by these processes; thus, it is important to study the effects of living in fragmented habitats on species that differ in lifestyle and habitat requirements. In this study, we examined the dispersal and connectivity patterns of rodents, one endemic (Eliurus myoxinus) and one invasive (Rattus rattus), in two landscapes containing forest fragments and adjacent continuous forest patches in northwestern Madagascar. We generated genetic (RADseq) data for 66 E. myoxinus and 81 R. rattus individuals to evaluate differences in genetic diversity as well as inbreeding and connectivity in two landscapes. We found higher levels of inbreeding and lower levels of genetic diversity in E. myoxinus compared with R. rattus. We observed related dyads both within and between habitat patches and positive spatial autocorrelation at lower distance classes for both species, with a stronger pattern of spatial autocorrelation in R. rattus. Across each site, we identified contrasting migration rates for each species, but these did not correspond to habitat-matrix dichotomies. The relatively low genetic diversity in the endemic E. myoxinus suggests ecological constraints that require further investigation.
Collapse
Affiliation(s)
- Malcolm S Ramsay
- Department of Anthropology, University of Toronto, Toronto, ON M5S 2S2, Canada
- Institute of Zoology, University of Veterinary Medicine Hannover, Foundation, 30559 Hannover, Germany
| | | | - Christopher D Barratt
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, 04103 Leipzig, Germany
| | - Jordi Salmona
- CNRS-UPS-IRD, UMR5174, Laboratoire Évolution & Diversité Biologique, Université Paul Sabatier, 31062 Toulouse, France
| | - Bertrand Andriatsitohaina
- Planet Madagascar, Antananarivo 101, Madagascar
- Faculté des Sciences, de Technologies et de l'Environnement, Université de Mahajanga, Mahajanga 401, Madagascar
| | - Frederik Kiene
- Institute of Zoology, University of Veterinary Medicine Hannover, Foundation, 30559 Hannover, Germany
| | - Sophie Manzi
- CNRS-UPS-IRD, UMR5174, Laboratoire Évolution & Diversité Biologique, Université Paul Sabatier, 31062 Toulouse, France
| | - Miarisoa L Ramilison
- Faculté des Sciences, de Technologies et de l'Environnement, Université de Mahajanga, Mahajanga 401, Madagascar
- Department of Primate Behavior and Ecology, Central Washington University, Ellensburg, WA 98926, USA
| | - Romule Rakotondravony
- Faculté des Sciences, de Technologies et de l'Environnement, Université de Mahajanga, Mahajanga 401, Madagascar
| | - Lounès Chikhi
- Instituto Gulbenkian de Ciência, 2780-156 Oeiras, Portugal
- CNRS-UPS-IRD, UMR5174, Laboratoire Évolution & Diversité Biologique, Université Paul Sabatier, 31062 Toulouse, France
| | - Shawn M Lehman
- Department of Anthropology, University of Toronto, Toronto, ON M5S 2S2, Canada
| | - Ute Radespiel
- Institute of Zoology, University of Veterinary Medicine Hannover, Foundation, 30559 Hannover, Germany
| |
Collapse
|
9
|
Nguyen AM, Todd BD, Halstead BJ. Survival and establishment of captive‐reared and translocated giant gartersnakes after release. J Wildl Manage 2023. [DOI: 10.1002/jwmg.22374] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/19/2023]
Affiliation(s)
- Allison M. Nguyen
- U.S. Geological Survey 800 Business Park Drive Suite D Dixon CA 95620 USA
| | - Brian D. Todd
- University of California Davis, One Shields Avenue Davis CA 95616 USA
| | - Brian J. Halstead
- U.S. Geological Survey 800 Business Park Drive Suite D Dixon CA 95620 USA
| |
Collapse
|
10
|
Kim YR, Kim HR, Kim JY, Myeong HH, Kang JH, Kim BJ, Lee HJ. Spatio-temporal genetic structure of the striped field mouse (Apodemus agrarius) populations inhabiting national parks in South Korea: Implications for conservation and management of protected areas. Front Ecol Evol 2023. [DOI: 10.3389/fevo.2023.1038058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Population or habitat connectivity is a key component in maintaining species and community-level regional biodiversity as well as intraspecific genetic diversity. Ongoing human activities cause habitat destruction and fragmentation, which exacerbate the connectivity due to restricted animal movements across local habitats, eventually resulting in the loss of biodiversity. The Baekdudaegan Mountain Range (BMR) on the Korean Peninsula represents “biodiversity hotspots” and eight of the 22 Korean national parks are located within the BMR. Given the striped field mouse (Apodemus agrarius) is the most common and ecologically important small mammals in these protected areas, the population genetic assessment of this species will allow for identifying “genetic diversity hotspots” and also “genetic barriers” that may hinder gene flow, and will therefore inform on effective conservation and management efforts for the national park habitats. We collected samples from hair, tail, or buccal swabs for 252 A. agrarius individuals in 2015 and 2019. By using mitochondrial DNA cytochrome b (cyt b) sequences and nine microsatellite loci, we determined levels of genetic diversity, genetic differentiation, and gene flow among eight national park populations of A. agrarius along the BMR. We found high levels of genetic diversity but the occurrences of inbreeding for all the nine samples analyzed. Our results also indicated that there was detectable temporal genetic variation between the 2015 and 2019 populations in the Jirisan National Park, which is probably due to a short-term decline in genetic diversity caused by reduced population sizes. We also found a well-admixed shared gene pool among the national park populations. However, a significant positive correlation between geographic and genetic distances was detected only in mtDNA but not microsatellites, which might be attributed to different dispersal patterns between sexes. There was a genetic barrier to animal movements around the Woraksan National Park areas. The poor habitat connectivity surrounding these areas can be improved by establishing an ecological corridor. Our findings of the presence of genetic barriers in some protected areas provide insights into the conservation and management efforts to improve the population or habitat connectivity among the national parks.
Collapse
|
11
|
Informing Wildlife Corridor Creation through Population Genetics of an Arboreal Marsupial in a Fragmented Landscape. Genes (Basel) 2023; 14:genes14020349. [PMID: 36833276 PMCID: PMC9957349 DOI: 10.3390/genes14020349] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Revised: 01/18/2023] [Accepted: 01/19/2023] [Indexed: 01/31/2023] Open
Abstract
Habitat loss and fragmentation contribute significantly to the decline of arboreal mammal populations. As populations become fragmented and isolated, a reduction in gene flow can result in a loss of genetic diversity and have an overall impact upon long-term persistence. Creating wildlife corridors can mitigate such effects by increasing the movement and dispersal of animals, thus acting to reduce population isolation. To evaluate the success of a corridor, a before-after experimental research framework can be used. Here, we report the genetic diversity and structure of sugar glider (Petaurus breviceps) sampling locations within a fragmented landscape prior to the implementation of a wildlife corridor. This study used 5999 genome-wide SNPs from 94 sugar gliders caught from 8 locations in a fragmented landscape in south-eastern New South Wales, Australia. Overall genetic structure was limited, and gene flow was detected across the landscape. Our findings indicate that the study area contains one large population. A major highway dissecting the landscape did not act as a significant barrier to dispersal, though this may be because of its relatively new presence in the landscape (completed in 2018). Future studies may yet indicate its long-term impact as a barrier to gene flow. Future work should aim to repeat the methods of this study to examine the medium-to-long-term impacts of the wildlife corridor on sugar gliders, as well as examine the genetic structure of other native, specialist species in the landscape.
Collapse
|
12
|
Dugovich BS, Beechler BR, Dolan BP, Crowhurst RS, Gonzales BJ, Powers JG, Hughson DL, Vu RK, Epps CW, Jolles AE. Population connectivity patterns of genetic diversity, immune responses and exposure to infectious pneumonia in a metapopulation of desert bighorn sheep. J Anim Ecol 2023. [PMID: 36637333 DOI: 10.1111/1365-2656.13885] [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: 05/31/2022] [Accepted: 01/03/2023] [Indexed: 01/14/2023]
Abstract
Habitat fragmentation is an important driver of biodiversity loss and can be remediated through management actions aimed at maintenance of natural connectivity in metapopulations. Connectivity may protect populations from infectious diseases by preserving immunogenetic diversity and disease resistance. However, connectivity could exacerbate the risk of infectious disease spread across vulnerable populations. We tracked the spread of a novel strain of Mycoplasma ovipneumoniae in a metapopulation of desert bighorn sheep Ovis canadensis nelsoni in the Mojave Desert to investigate how variation in connectivity among populations influenced disease outcomes. M. ovipneumoniae was detected throughout the metapopulation, indicating that the relative isolation of many of these populations did not protect them from pathogen invasion. However, we show that connectivity among bighorn sheep populations was correlated with higher immunogenetic diversity, a protective immune response and lower disease prevalence. Variation in protective immunity predicted infection risk in individual bighorn sheep and was associated with heterozygosity at genetic loci linked to adaptive and innate immune signalling. Together, these findings may indicate that population connectivity maintains immunogenetic diversity in bighorn sheep populations in this system and has direct effects on immune responses in individual bighorn sheep and their susceptibility to infection by a deadly pathogen. Our study suggests that the genetic benefits of population connectivity could outweigh the risk of infectious disease spread and supports conservation management that maintains natural connectivity in metapopulations.
Collapse
Affiliation(s)
- Brian S Dugovich
- Department of Integrative Biology, Oregon State University, Corvallis, Oregon, USA
| | - Brianna R Beechler
- Carlson College of Veterinary Medicine, Oregon State University, Corvallis, Oregon, USA
| | - Brian P Dolan
- Carlson College of Veterinary Medicine, Oregon State University, Corvallis, Oregon, USA
| | - Rachel S Crowhurst
- Department of Fisheries, Wildlife, and Conservation Sciences, Oregon State University, Corvallis, Oregon, USA
| | - Ben J Gonzales
- California Department of Fish and Wildlife, Rancho Cordova, California, USA
| | - Jenny G Powers
- National Park Service, Biological Resources Division, Fort Collins, Colorado, USA
| | - Debra L Hughson
- National Park Service, Mojave National Preserve, Barstow, California, USA
| | - Regina K Vu
- California Department of Fish and Wildlife, Rancho Cordova, California, USA
| | - Clinton W Epps
- Department of Fisheries, Wildlife, and Conservation Sciences, Oregon State University, Corvallis, Oregon, USA
| | - Anna E Jolles
- Department of Integrative Biology, Oregon State University, Corvallis, Oregon, USA.,Carlson College of Veterinary Medicine, Oregon State University, Corvallis, Oregon, USA
| |
Collapse
|
13
|
Huang L, Feng G, Li D, Shang W, Zhang L, Yan R, Jiang Y, Li S. Genetic variation of endangered Jankowski’s Bunting (Emberiza jankowskii): High connectivity and a moderate history of demographic decline. Front Ecol Evol 2023. [DOI: 10.3389/fevo.2022.996617] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
IntroductionContinued discovery of “mismatch” patterns between population size and genetic diversity, involving wild species such as insects, amphibians, birds, mammals, and others, has raised issues about how population history, especially recent dynamics under human disturbance, affects currently standing genetic variation. Previous studies have revealed high genetic diversity in endangered Jankowski’s Bunting. However, it is unclear how the demographic history and recent habitat changes shape the genetic variation of Jankowski’s Bunting.MethodsTo explore the formation and maintenance of high genetic diversity in endangered Jankowski’s Bunting, we used a mitochondrial control region (partial mtDNA CR) and 15 nuclear microsatellite markers to explore the recent demographic history of Jankowski’s Bunting, and we compared the historical and contemporary gene flows between populations to reveal the impact of habitat change on population connectivity. Specifically, we aimed to test the following hypotheses: (1) Jankowski’s Bunting has a large historical Ne and a moderate demographic history; and (2) recent habitat change might have no significant impact on the species’ population connectivity.ResultsThe results suggested that large historical effective population size, as well as severe but slow population decline, may partially explain the high observable genetic diversity. Comparison of historical (over the past 4Ne generations) and contemporary (1–3 generations) gene flow indicated that the connectivity between five local populations was only marginally affected by landscape changes.DiscussionOur results suggest that high population connectivity and a moderate history of demographic decline are powerful explanations for the rich genetic variation in Jankowski’s Bunting. Although there is no evidence that the genetic health of Jankowski’s Bunting is threatened, the time-lag effects on the genetic response to recent environmental changes is a reminder to be cautious about the current genetic characteristics of this species. Where possible, factors influencing genetic variation should be integrated into a systematic framework for conducting robust population health assessments. Given the small contemporary population size, inbreeding, and ecological specialization, we recommend that habitat protection be maintained to maximize the genetic diversity and population connectivity of Jankowski’s Bunting.
Collapse
|
14
|
Zylinski S, Swan M, Sitters H. Contrasting responses of native and introduced mammal communities to fire mosaics in a modified landscape. ECOLOGICAL APPLICATIONS : A PUBLICATION OF THE ECOLOGICAL SOCIETY OF AMERICA 2022; 32:e2570. [PMID: 35167168 DOI: 10.1002/eap.2570] [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: 08/26/2021] [Revised: 11/24/2021] [Accepted: 12/16/2021] [Indexed: 06/14/2023]
Abstract
Planned fire is increasingly recognized as an important tool in conservation, but other factors such as land-use change may hinder the ability of land managers to use fire for the benefit of biodiversity. The mosaic of past fires in native vegetation may interact with the mosaic of other land-cover types in human-modified landscapes, yet the effects of these interactions on mammal communities are unknown. We investigated the responses of ground-dwelling mammal community composition and species richness to interactions between land cover and post-fire vegetation growth-stage mosaics in southern Australia. This fire-prone, human-modified landscape features a fine-scale fire mosaic in native vegetation patches surrounded by pasture, horticulture, and peri-urban environments. We measured the composition of land-cover types and fire mosaics (landscape structure) at multiple scales of up to 1257 ha surrounding 129 study sites, and considered native and introduced species together and separately. Land-cover composition was the primary driver of community composition: native species favored areas with a greater proportion of native heathy woodland, whereas introduced species were associated with landscapes comprising more cleared land. The fire mosaic also influenced community composition and species richness: greater growth-stage diversity was associated with native habitat-specialist communities and fewer introduced species. In areas with more cleared land, native species richness increased when there was a greater proportion of mid-successional vegetation, demonstrating that the effect of fire mosaics on mammal diversity depended on land-cover composition. The positive relationship between introduced species richness and cleared land extent was also stronger in recently burned sites than in other growth stages, suggesting that introduced species are well suited to more modified areas of the landscape. Land managers need to consider the underlying land-cover composition and the potential interactions it may have with fire mosaics and species composition. In this landscape a greater diversity of growth stages may disadvantage introduced species yet an increase in mid-successional vegetation in more modified areas would be likely to benefit native mammal communities. Our study highlights that fire management may need to be tailored depending on the context of land use and the species of interest.
Collapse
Affiliation(s)
- Simeon Zylinski
- School of Ecosystem and Forest Sciences, The University of Melbourne, Creswick, Victoria, Australia
| | - Matthew Swan
- School of Ecosystem and Forest Sciences, The University of Melbourne, Creswick, Victoria, Australia
| | - Holly Sitters
- School of Ecosystem and Forest Sciences, The University of Melbourne, Creswick, Victoria, Australia
| |
Collapse
|
15
|
Grether GF, Okamoto KW. Eco‐evolutionary dynamics of interference competition. Ecol Lett 2022; 25:2167-2176. [DOI: 10.1111/ele.14091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Revised: 07/21/2022] [Accepted: 07/24/2022] [Indexed: 11/29/2022]
Affiliation(s)
- Gregory F. Grether
- Department of Ecology and Evolutionary Biology University of California Los Angeles Los Angeles California USA
| | | |
Collapse
|
16
|
McManus J, Faraut L, Couldridge V, van Deventer J, Samuels I, Cilliers D, Devens C, Vorster P, Smuts B. Assessment of leopard translocations in South Africa. FRONTIERS IN CONSERVATION SCIENCE 2022. [DOI: 10.3389/fcosc.2022.943078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Translocations are commonly employed to mitigate human–carnivore conflict but rarely evaluated, resulting in conflicting reports of success, particularly for leopards (Panthera pardus). We evaluate the status of available leopard translocation data, the factors driving the intentional removal of leopards, and the potential causal factors associated with successful and failed translocation events. We obtained data on 60 leopard translocation events across five provinces in South Africa between 1994 and 2021. We considered a successful translocation outcome when (1) the animal was moved outside of its original home range, (2) the animal established a new home range away from the capture site, (3) no substantive livestock losses were linked to the translocated animal in the post-release monitoring period, and (4) the animal survived at least 6 months post-translocation. If mortality occurred due to factors that were equally likely to impact resident individuals and were unrelated to the translocation event (e.g., poaching), the event was not considered a failed effort. Most translocations were the result of human–carnivore conflict (HCC; 82%, n = 49), stressing the high prevalence of HCC and the importance of advocating preventative conflict mitigation efforts to conserve leopards. The leopards were moved distances from 2.5 to 196.3 km (63.3 ± 51.7km). Forty (67%) translocation events had unknown outcomes, indicating the limited data available on translocation outcomes. This also indicates the disparity in the objectives of translocations by various entities involved with translocations and suggests that monitoring be a prerequisite for future translocations. Twenty events offered reliable outcomes by means of post-event monitoring, with seven (12%) considered successful, with three (5%) as failures, and with four (7%) not moved beyond their original home ranges, while six (8%) ended in unrelated deaths. The failed events were attributed to inter/intra-specific competition, and one animal returned to its original home range after a translocation distance of 68 km. Translocation success was strongly explained by translocation distance. We found that damage-causing leopards were successfully translocated under specific conditions, and longer translocation distances increase success. Translocations are commonly employed but are still poorly monitored. We discuss basic standardized protocols to improve future leopard translocations (including pre- and post-monitoring) while advocating alternative non-lethal practices to reduce the prevalence of human–carnivore conflict.
Collapse
|
17
|
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
| |
Collapse
|
18
|
Mitochondrial genetic diversity, phylogeography and historical demography of Moroccan native freshwater fishes: a case study of the genus Luciobarbus Heckel, 1843. Biologia (Bratisl) 2022. [DOI: 10.1007/s11756-022-01107-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
|
19
|
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.
Collapse
|
20
|
Łopucki R, Mróz I, Nowak-Życzyńska Z, Perlińska-Teresiak M, Owadowska-Cornil E, Klich D. Genetic Structure of the Root Vole Microtus oeconomus: Resistance of the Habitat Specialist to the Natural Fragmentation of Preferred Moist Habitats. Genes (Basel) 2022; 13:genes13030434. [PMID: 35327989 PMCID: PMC8954809 DOI: 10.3390/genes13030434] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2022] [Revised: 02/11/2022] [Accepted: 02/22/2022] [Indexed: 11/16/2022] Open
Abstract
Climate-related changes have a severe impact on wetland ecosystems and pose a serious challenge for wetland-dependent animals as their preferred habitats decline, lose spatial continuity, and appear as isolated islands in the landscape. In this paper, we studied the effects of long-term habitat changes (drying out and fragmentation of wet non-forest habitats) on the genetic structure of the population of the root vole Microtus oeconomus, a species preferring moist habitats. We intended to check what barriers and what distances affected its genetic isolation on a local scale. The study was conducted in the area of Kampinoski National Park in central Poland (Europe). DNA variability of 218 root vole individuals was assessed by genotyping nine microsatellite loci. Despite its spatial fragmentation, the studied population did not seem to be highly structured, and isolation through distance was the main differentiating factor. Even a distance of several kilometres of unfavourable natural habitats and unfavourable terrain did not exclude the exchange of genes between subpopulations. Our results suggest that the genetic effects of the fragmentation of wetlands have been considerably compensated (delayed) due to the migratory abilities of this species. Our study does not provide clear results on the impact of anthropogenic barriers but suggests that such barriers may have a much stronger effect than natural barriers.
Collapse
Affiliation(s)
- Rafał Łopucki
- Centre for Interdisciplinary Research, The John Paul II Catholic University of Lublin, Konstantynów 1J, 20-708 Lublin, Poland;
- Department of Animal Genetics and Conservation, Warsaw University of Life Sciences-SGGW, Ciszewskiego 8, 02-786 Warsaw, Poland; (Z.N.-Ż.); (M.P.-T.)
| | - Iwona Mróz
- The John Paul II Catholic University of Lublin, Racławickie 14, 20-950 Lublin, Poland;
| | - Zuzanna Nowak-Życzyńska
- Department of Animal Genetics and Conservation, Warsaw University of Life Sciences-SGGW, Ciszewskiego 8, 02-786 Warsaw, Poland; (Z.N.-Ż.); (M.P.-T.)
| | - Magdalena Perlińska-Teresiak
- Department of Animal Genetics and Conservation, Warsaw University of Life Sciences-SGGW, Ciszewskiego 8, 02-786 Warsaw, Poland; (Z.N.-Ż.); (M.P.-T.)
| | - Edyta Owadowska-Cornil
- Science and Nature Monitoring Department, Kampinoski National Park, Tetmajera 38, 05-080 Izabelin, Poland;
| | - Daniel Klich
- Department of Animal Genetics and Conservation, Warsaw University of Life Sciences-SGGW, Ciszewskiego 8, 02-786 Warsaw, Poland; (Z.N.-Ż.); (M.P.-T.)
- Correspondence:
| |
Collapse
|
21
|
Delineating Functional Corridors Linking Leopard Habitat in the Eastern and Western Cape, South Africa. CONSERVATION 2022. [DOI: 10.3390/conservation2010009] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Natural landscapes are increasingly fragmented due to human activity. This contributes to isolation and inadequate gene flow among wildlife populations. These threats intensify where populations are already low, and gene flow is compromised. Ensuring habitat connectivity despite transformed landscapes can mitigate these risks. Leopards are associated with high levels of biodiversity and are the last widely occurring, free-roaming apex predator in South Africa. Although highly adaptable, leopard survival is reduced by human-caused mortality and habitat destruction. We aimed to assess the connectivity of leopard habitat in the Eastern Cape and Western Cape, South Africa. We predicted leopard habitat by correlating GPS data from 31 leopards to environmental features that included human-associated and natural landscapes. We used circuit theory to delineate corridors linking known leopard populations. Finally, using camera traps, we tested whether five predicted corridors were used by leopards. Leopard habitat was strongly correlated to moderate slopes and areas of natural land-cover and plantations, highlighting mountainous areas as important habitat with high connectivity probability. While most habitat patches showed some level of connectivity, leopards avoided highly transformed landscapes, potentially isolating some populations. Where corridors are not functional, active conservation measures for species connectivity becomes important.
Collapse
|
22
|
Strong population genetic structure and cryptic diversity in the Florida bonneted bat (Eumops floridanus). CONSERV GENET 2022. [DOI: 10.1007/s10592-022-01432-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
|
23
|
Mularo AJ, Bernal XE, DeWoody JA. Dominance can increase genetic variance after a population bottleneck: a synthesis of the theoretical and empirical evidence. J Hered 2022; 113:257-271. [PMID: 35143665 DOI: 10.1093/jhered/esac007] [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: 09/26/2021] [Accepted: 02/07/2022] [Indexed: 11/13/2022] Open
Abstract
Drastic reductions in population size, or population bottlenecks, can lead to a reduction in additive genetic variance and adaptive potential. Genetic variance for some quantitative genetic traits, however, can increase after a population reduction. Empirical evaluations of quantitative traits following experimental bottlenecks indicate that non-additive genetic effects, including both allelic dominance at a given locus and epistatic interactions among loci, may impact the additive variance contributed by alleles that ultimately influences phenotypic expression and fitness. The dramatic effects of bottlenecks on overall genetic diversity have been well studied, but relatively little is known about how dominance and demographic events like bottlenecks can impact additive genetic variance. Herein, we critically examine how the degree of dominance among alleles affects additive genetic variance after a bottleneck. We first review and synthesize studies that document the impact of empirical bottlenecks on dominance variance. We then extend earlier work by elaborating on two theoretical models that illustrate the relationship between dominance and the potential increase in additive genetic variance immediately following a bottleneck. Furthermore, we investigate the parameters that influence the maximum level of genetic variation (associated with adaptive potential) after a bottleneck, including the number of founding individuals. Finally, we validated our methods using forward-time population genetic simulations of loci with varying dominance and selection levels. The fate of non-additive genetic variation following bottlenecks could have important implications for conservation and management efforts in a wide variety of taxa, and our work should help contextualize future studies (e.g., epistatic variance) in population genomics.
Collapse
Affiliation(s)
- Andrew J Mularo
- Department of Biological Sciences, Purdue University, West Lafayette, Indiana, USA
| | - Ximena E Bernal
- Department of Biological Sciences, Purdue University, West Lafayette, Indiana, USA.,Smithsonian Tropical Research Institute, Balboa, Republic of Panamá
| | - J Andrew DeWoody
- Department of Biological Sciences, Purdue University, West Lafayette, Indiana, USA.,Department of Forestry and Natural Resources, Purdue University, West Lafayette, IN
| |
Collapse
|
24
|
Assessing the influence of the amount of reachable habitat on genetic structure using landscape and genetic graphs. Heredity (Edinb) 2022; 128:120-131. [PMID: 34963701 PMCID: PMC8814055 DOI: 10.1038/s41437-021-00495-w] [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: 07/05/2021] [Revised: 12/16/2021] [Accepted: 12/17/2021] [Indexed: 02/03/2023] Open
Abstract
Genetic structure, i.e. intra-population genetic diversity and inter-population genetic differentiation, is influenced by the amount and spatial configuration of habitat. Measuring the amount of reachable habitat (ARH) makes it possible to describe habitat patterns by considering intra-patch and inter-patch connectivity, dispersal capacities and matrix resistance. Complementary ARH metrics computed under various resistance scenarios are expected to reflect both drift and gene flow influence on genetic structure. Using an empirical genetic dataset concerning the large marsh grasshopper (Stethophyma grossum), we tested whether ARH metrics are good predictors of genetic structure. We further investigated (i) how the components of the ARH influence genetic structure and (ii) which resistance scenario best explains these relationships. We computed local genetic diversity and genetic differentiation indices in genetic graphs, and ARH metrics in the unified and flexible framework offered by landscape graphs, and we tested the relationships between these variables. ARH metrics were relevant predictors of the two components of genetic structure, providing an advantage over commonly used habitat metrics. Although allelic richness was significantly explained by three complementary ARH metrics in the best PLS regression model, private allelic richness and MIW indices were essentially related with the ARH measured outside the focal patch. Considering several matrix resistance scenarios was also key for explaining the different genetic responses. We thus call for further use of ARH metrics in landscape genetics to explain the influence of habitat patterns on the different components of genetic structure.
Collapse
|
25
|
Trense D, Hoffmann AA, Fischer K. Large- and small-scale geographic structures affecting genetic patterns across populations of an Alpine butterfly. Ecol Evol 2021; 11:14697-14714. [PMID: 34765135 PMCID: PMC8571576 DOI: 10.1002/ece3.8157] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 09/04/2021] [Accepted: 09/08/2021] [Indexed: 11/09/2022] Open
Abstract
Understanding factors influencing patterns of genetic diversity and the population genetic structure of species is of particular importance in the current era of global climate change and habitat loss. These factors include the evolutionary history of a species as well as heterogeneity in the environment it occupies, which in turn can change across time. Most studies investigating spatio-temporal genetic patterns have focused on patterns across wide geographic areas rather than local variation, but the latter can nevertheless be important particularly in topographically complex areas. Here, we consider these issues in the Sooty Copper butterfly (Lycaena tityrus) from the European Alps, using genome-wide SNPs identified through RADseq. We found strong genetic differentiation within the Alps with four genetic clusters, indicating western, central, and eastern refuges, and a strong reduction of genetic diversity from west to east. This reduction in diversity may suggest that the southwestern refuge was the largest one in comparison to other refuges. Also, the high genetic diversity in the west may result from (a) admixture of different western refuges, (b) more recent demographic changes, or (c) introgression of lowland L. tityrus populations. At small spatial scales, populations were structured by several landscape features and especially by high mountain ridges and large river valleys. We detected 36 outlier loci likely under altitudinal selection, including several loci related to membranes and cellular processes. We suggest that efforts to preserve alpine L. tityrus should focus on the genetically diverse populations in the western Alps, and that the dolomite populations should be treated as genetically distinct management units, since they appear to be currently more threatened than others. This study demonstrates the usefulness of SNP-based approaches for understanding patterns of genetic diversity, gene flow, and selection in a region that is expected to be particularly vulnerable to climate change.
Collapse
Affiliation(s)
- Daronja Trense
- Institute for Integrated Natural Sciences, ZoologyUniversity Koblenz‐LandauKoblenzGermany
| | - Ary A. Hoffmann
- Pest & Environmental Adaptation Research GroupSchool of BiosciencesBio21 InstituteParkvilleVic.Australia
| | - Klaus Fischer
- Institute for Integrated Natural Sciences, ZoologyUniversity Koblenz‐LandauKoblenzGermany
| |
Collapse
|
26
|
Dayananda SK, Mammides C, Liang D, Kotagama SW, Goodale E. A review of avian experimental translocations that measure movement through human-modified landscapes. Glob Ecol Conserv 2021. [DOI: 10.1016/j.gecco.2021.e01876] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
|
27
|
Nelson HV, Frankham GJ, Leo V, Anson JR, Eldridge MDB, de Bruyn M. Conservation genomics of the ‘Endangered’ long-nosed bandicoot (Perameles nasuta) population at North Head, Sydney, Australia. CONSERV GENET 2021. [DOI: 10.1007/s10592-021-01356-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
|
28
|
Modi S, Mondol S, Nigam P, Habib B. Genetic analyses reveal demographic decline and population differentiation in an endangered social carnivore, Asiatic wild dog. Sci Rep 2021; 11:16371. [PMID: 34385570 PMCID: PMC8361113 DOI: 10.1038/s41598-021-95918-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2020] [Accepted: 07/31/2021] [Indexed: 02/07/2023] Open
Abstract
Deforestation and agricultural intensification have resulted in an alarming change in the global land cover over the past 300 years, posing a threat to species conservation. Dhole is a monophyletic, social canid and, being an endangered and highly forest-dependent species, is more prone to the loss of favorable habitat in the Anthropocene. We determined the genetic differentiation and demographic history of dhole across the tiger reserves of Maharashtra using the microsatellite data of 305 individuals. Simulation-based analyses revealed a 77-85% decline in the major dhole sub-populations. Protected areas have provided refuge to the historically declining dhole population resulting in clustering with strong genetic structure in the remnant dhole population. The historical population decline coincides with the extreme events in the landscape over the past 300 years. The study highlights the pattern of genetic differentiation and diversity of a highly forest-dependent species which can be associated with the loss of forest cover outside tiger reserves. It also warrants attention to develop conservation plans for the remnant surviving population of dholes in India.
Collapse
Affiliation(s)
- Shrushti Modi
- Wildlife Institute of India, Chandrabani, Dehradun, 248001, India
| | - Samrat Mondol
- Wildlife Institute of India, Chandrabani, Dehradun, 248001, India
| | - Parag Nigam
- Wildlife Institute of India, Chandrabani, Dehradun, 248001, India
| | - Bilal Habib
- Wildlife Institute of India, Chandrabani, Dehradun, 248001, India.
| |
Collapse
|
29
|
Gehri RR, Gruenthal K, Larson WA. It's complicated: Heterogeneous patterns of genetic structure in five fish species from a fragmented river suggest multiple processes can drive differentiation. Evol Appl 2021; 14:2079-2097. [PMID: 34429750 PMCID: PMC8372089 DOI: 10.1111/eva.13268] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2020] [Accepted: 05/26/2021] [Indexed: 11/28/2022] Open
Abstract
Fragmentation of river systems by dams can have substantial genetic impacts on fish populations. However, genetic structure can exist naturally at small scales through processes other than isolation by physical barriers. We sampled individuals from five native fish species with varying life histories above and below a dam in the lower Boardman River, Michigan, USA, and used RADseq to investigate processes influencing genetic structure in this system. Species assessed were white sucker Catostomus commersonii, yellow perch Perca flavescens, walleye Sander vitreus, smallmouth bass Micropterus dolomieu, and rock bass Ambloplites rupestris. We detected significant differentiation within each species, but patterns of population structure varied substantially. Interestingly, genetic structure did not appear to be solely the result of fragmentation by the dam. While genetic structure in yellow perch and walleye generally coincided with "above dam" and "below dam" sampling locations, samples from our other three species did not. Specifically, samples from rock bass, smallmouth bass, and, to a much lesser extent, white sucker, aligned with a putative Great Lakes (GL) group that contained mostly individuals sampled below the dam and a putative Boardman River (BR) group that contained individuals sampled both above and below the dam, with some evidence of admixture among groups. We hypothesize that the GL and BR groups formed prior to dam construction and our samples largely represent a mixed stock that was sampled sympatrically outside of the spawning season. Support for this hypothesis is especially strong in smallmouth bass, where GL fish were 151 mm smaller than BR fish on average, suggesting a potential ontogenetic habitat shift of young GL fish into the lower river for feeding and/or refuge. Our study illuminates the complex dynamics shaping genetic structure in fragmented river systems and indicates that conclusions drawn for a single species cannot be generalized.
Collapse
Affiliation(s)
- Rebecca R. Gehri
- Wisconsin Cooperative Fishery Research UnitCollege of Natural ResourcesUniversity of Wisconsin‐Stevens PointStevens PointWIUSA
| | - Kristen Gruenthal
- Office of Applied ScienceWisconsin Department of Natural ResourcesCollege of Natural ResourcesUniversity of Wisconsin‐Stevens PointStevens PointWIUSA
- Alaska Department of Fish and GameGene Conservation LaboratoryJuneauAKUSA
| | - Wesley A. Larson
- U.S. Geological SurveyWisconsin Cooperative Fishery Research UnitCollege of Natural ResourcesUniversity of Wisconsin‐Stevens PointStevens PointWIUSA
- National Oceanographic and Atmospheric AdministrationNational Marine Fisheries ServiceAlaska Fisheries Science CenterAuke Bay LaboratoriesJuneauAKUSA
| |
Collapse
|
30
|
Byer NW, Holding ML, Crowell MM, Pierson TW, Dilts TE, Larrucea ES, Shoemaker KT, Matocq MD. Adaptive divergence despite low effective population size in a peripherally isolated population of the pygmy rabbit, Brachylagus idahoensis. Mol Ecol 2021; 30:4173-4188. [PMID: 34166550 DOI: 10.1111/mec.16040] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2020] [Revised: 06/01/2021] [Accepted: 06/18/2021] [Indexed: 11/30/2022]
Abstract
Local adaptation can occur when spatially separated populations are subjected to contrasting environmental conditions. Historically, understanding the genetic basis of adaptation has been difficult, but increased availability of genome-wide markers facilitates studies of local adaptation in non-model organisms of conservation concern. The pygmy rabbit (Brachylagus idahoensis) is an imperiled lagomorph that relies on sagebrush for forage and cover. This reliance has led to widespread population declines following reductions in the distribution of sagebrush, leading to geographic separation between populations. In this study, we used >20,000 single nucleotide polymorphisms, genotype-environment association methods, and demographic modeling to examine neutral genetic variation and local adaptation in the pygmy rabbit in Nevada and California. We identified 308 loci as outliers, many of which had functional annotations related to metabolism of plant secondary compounds. Likewise, patterns of spatial variation in outlier loci were correlated with landscape and climatic variables including proximity to streams, sagebrush cover, and precipitation. We found that populations in the Mono Basin of California probably diverged from other Great Basin populations during late Pleistocene climate oscillations, and that this region is adaptively differentiated from other regions in the southern Great Basin despite limited gene flow and low effective population size. Our results demonstrate that peripherally isolated populations can maintain adaptive divergence.
Collapse
Affiliation(s)
- Nathan W Byer
- Department of Natural Resources and Environmental Science, University of Nevada-Reno, Reno, Nevada, USA
| | - Matthew L Holding
- Department of Natural Resources and Environmental Science, University of Nevada-Reno, Reno, Nevada, USA
| | - Miranda M Crowell
- Department of Natural Resources and Environmental Science, University of Nevada-Reno, Reno, Nevada, USA
| | - Todd W Pierson
- Department of Ecology, Evolution, and Organismal Biology, Kennesaw State University, Kennesaw, Georgia, USA
| | - Thomas E Dilts
- Department of Natural Resources and Environmental Science, University of Nevada-Reno, Reno, Nevada, USA
| | | | - Kevin T Shoemaker
- Department of Natural Resources and Environmental Science, University of Nevada-Reno, Reno, Nevada, USA
| | - Marjorie D Matocq
- Department of Natural Resources and Environmental Science, University of Nevada-Reno, Reno, Nevada, USA
| |
Collapse
|
31
|
Dominguez JC, Calero-Riestra M, Olea PP, Malo JE, Burridge CP, Proft K, Illanas S, Viñuela J, García JT. Lack of detectable genetic isolation in the cyclic rodent Microtus arvalis despite large landscape fragmentation owing to transportation infrastructures. Sci Rep 2021; 11:12534. [PMID: 34131199 PMCID: PMC8206325 DOI: 10.1038/s41598-021-91824-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Accepted: 05/31/2021] [Indexed: 02/05/2023] Open
Abstract
Although roads are widely seen as dispersal barriers, their genetic consequences for animals that experience large fluctuations in population density are poorly documented. We developed a spatially paired experimental design to assess the genetic impacts of roads on cyclic voles (Microtus arvalis) during a high-density phase in North-Western Spain. We compared genetic patterns from 15 paired plots bisected by three different barrier types, using linear mixed models and computing effect sizes to assess the importance of each type, and the influence of road features like width or the age of the infrastructure. Evidence of effects by roads on genetic diversity and differentiation were lacking. We speculate that the recurrent (each 3-5 generations) episodes of massive dispersal associated with population density peaks can homogenize populations and mitigate the possible genetic impact of landscape fragmentation by roads. This study highlights the importance of developing spatially replicated experimental designs that allow us to consider the large natural spatial variation in genetic parameters. More generally, these results contribute to our understanding of the not well explored effects of habitat fragmentation on dispersal in species showing "boom-bust" dynamics.
Collapse
Affiliation(s)
- Julio C Dominguez
- IREC, Instituto de Investigación en Recursos Cinegéticos (CSIC-UCLM-JCCM), Ronda de Toledo, 12, 13071, Ciudad Real, Spain.
| | - María Calero-Riestra
- IREC, Instituto de Investigación en Recursos Cinegéticos (CSIC-UCLM-JCCM), Ronda de Toledo, 12, 13071, Ciudad Real, Spain
| | - Pedro P Olea
- Terrestrial Ecology Group (TEG-UAM), Departamento de Ecología, Facultad de Ciencias, Universidad Autónoma de Madrid, C/Darwin 2, 28049, Madrid, Spain
- Centro de Investigación en Biodiversidad y Cambio Global (CIBC-UAM), Universidad Autónoma de Madrid, C. Darwin 2, 28049, Madrid, Spain
| | - Juan E Malo
- Terrestrial Ecology Group (TEG-UAM), Departamento de Ecología, Facultad de Ciencias, Universidad Autónoma de Madrid, C/Darwin 2, 28049, Madrid, Spain
- Centro de Investigación en Biodiversidad y Cambio Global (CIBC-UAM), Universidad Autónoma de Madrid, C. Darwin 2, 28049, Madrid, Spain
| | - Christopher P Burridge
- Discipline of Biological Sciences, University of Tasmania, Private Bag 55, Hobart, TAS, 7001, Australia
| | - Kirstin Proft
- Discipline of Biological Sciences, University of Tasmania, Private Bag 55, Hobart, TAS, 7001, Australia
| | - Sonia Illanas
- IREC, Instituto de Investigación en Recursos Cinegéticos (CSIC-UCLM-JCCM), Ronda de Toledo, 12, 13071, Ciudad Real, Spain
| | - Javier Viñuela
- IREC, Instituto de Investigación en Recursos Cinegéticos (CSIC-UCLM-JCCM), Ronda de Toledo, 12, 13071, Ciudad Real, Spain
| | - Jesús T García
- IREC, Instituto de Investigación en Recursos Cinegéticos (CSIC-UCLM-JCCM), Ronda de Toledo, 12, 13071, Ciudad Real, Spain
| |
Collapse
|
32
|
Bauder JM, Peterman WE, Spear SF, Jenkins CL, Whiteley AR, McGarigal K. Multiscale assessment of functional connectivity: Landscape genetics of eastern indigo snakes in an anthropogenically fragmented landscape in central Florida. Mol Ecol 2021; 30:3422-3438. [PMID: 33978288 DOI: 10.1111/mec.15979] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Revised: 05/04/2021] [Accepted: 05/05/2021] [Indexed: 01/08/2023]
Abstract
Landscape features can strongly influence gene flow and the strength and direction of these effects may vary across spatial scales. However, few studies have evaluated methodological approaches for selecting spatial scales in landscape genetics analyses, in part because of computational challenges associated with optimizing landscape resistance surfaces (LRS). We used the federally threatened eastern indigo snake (Drymarchon couperi) in central Florida as a case study with which to compare the importance of landscape features and their scales of effect in influencing gene flow. We used genetic algorithms (ResistanceGA) to empirically optimize LRS using categorical land cover surfaces, multiscale resource selection surfaces (RSS), and four combinations of landscape covariates measured at multiple spatial scales (multisurface multiscale LRS). We compared LRS where scale was selected using pseudo- and full optimization. Multisurface multiscale LRS received more empirical support than LRS optimized from categorical land cover surfaces or RSS. Multiscale LRS with scale selected using full optimization generally outperformed those with scale selected using pseudo-optimization. Multiscale LRS with large spatial scales (1200-1800 m) received the most empirical support. Our results highlight the importance of considering landscape features across multiple spatial scales in landscape genetic analyses, particularly broad scales relative to species movement potential. Different effects of scale on home range-level movements and dispersal could explain weak associations between habitat suitability and gene flow in other studies. Our results also demonstrate the importance of large tracts of undeveloped upland habitat with heterogenous vegetation communities and low urbanization for promoting indigo snake connectivity.
Collapse
Affiliation(s)
- Javan M Bauder
- Department of Environmental Conservation, University of Massachusetts, Amherst, MA, USA.,Illinois Natural History Survey, Prairie Research Institute, University of Illinois, Champaign, IL, USA
| | - William E Peterman
- School of Environment and Natural Resources, The Ohio State University, Columbus, OH, USA
| | - Stephen F Spear
- The Orianne Society, Tiger, GA, USA.,Department of Fish and Wildlife Resources, University of Idaho, Moscow, ID, USA.,The Wilds, Cumberland, OH, USA.,Upper Midwest Environmental Sciences Center, U.S. Geological Survey, La Crosse, WI, USA
| | | | - Andrew R Whiteley
- Department of Ecosystems and Conservation Sciences and Wildlife Biology Program, University of Montana, Missoula, MT, USA
| | - Kevin McGarigal
- Department of Environmental Conservation, University of Massachusetts, Amherst, MA, USA
| |
Collapse
|
33
|
Minias P, Janiszewska A, Pikus E, Zadworny T, Anderwald D. MHC Reflects Fine-Scale Habitat Structure in White-Tailed Eagles, Haliaeetus albicilla. J Hered 2021; 112:335-345. [PMID: 33942876 DOI: 10.1093/jhered/esab026] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Accepted: 04/26/2021] [Indexed: 11/12/2022] Open
Abstract
The major histocompatibility complex (MHC) genes code for key immune receptors responsible for recognition of intra- and extracellular pathogens (MHC class I and class II, respectively). It was hypothesized that MHC polymorphism can be maintained via fluctuating selection resulting from between-habitat variation in pathogen regimes. We examined associations between MHC class I and class II genes and habitat structure in an apex avian predator, the white-tailed eagle, Haliaeetus albicilla. We genotyped MHC class I and class II genes in ca. 150 white-tailed eagle chicks from nearly 100 nesting territories distributed across 3 distinct populations in Poland. Habitat structure was quantified at the level of foraging territories and directly at the nest sites. We found strong support for associations of habitat traits with diversity and allelic composition at the MHC class II. Forest area within territory and forest productivity were identified as the major habitat predictors of MHC class II polymorphism, whereas other habitat traits (distance to nearest open water, grassland, and water area within territory or understory presence) showed fewer associations with class II alleles. In contrast, there was little support for associations between MHC class I genes and habitat structure. All significant associations were apparent at the within-population level rather than between populations. Our results suggest that extracellular (rather than intracellular) pathogens may exert much stronger selective pressure on the white-tailed eagle. Associations of habitat structure with MHC class II may reflect fluctuating (balancing) selection, which maintains MHC diversity within populations.
Collapse
Affiliation(s)
- Piotr Minias
- Department of Biodiversity Studies and Bioeducation, Faculty of Biology and Environmental Protection, University of Łódź, Banacha, Łódź, Poland
| | - Aleksandra Janiszewska
- Department of Biodiversity Studies and Bioeducation, Faculty of Biology and Environmental Protection, University of Łódź, Banacha, Łódź, Poland
| | - Ewa Pikus
- Department of Biodiversity Studies and Bioeducation, Faculty of Biology and Environmental Protection, University of Łódź, Banacha, Łódź, Poland
| | - Tomasz Zadworny
- Regional Directorate of Environmental Protection in Łódź, Traugutta, Łódź, Poland
| | | |
Collapse
|
34
|
Tassone EE, Miles LS, Dyer RJ, Rosenberg MS, Cowling RM, Verrelli BC. Evolutionary stability, landscape heterogeneity, and human land-usage shape population genetic connectivity in the Cape Floristic Region biodiversity hotspot. Evol Appl 2021; 14:1109-1123. [PMID: 33897824 PMCID: PMC8061270 DOI: 10.1111/eva.13185] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Revised: 12/03/2020] [Accepted: 12/08/2020] [Indexed: 01/06/2023] Open
Abstract
As human-induced change eliminates natural habitats, it impacts genetic diversity and population connectivity for local biodiversity. The South African Cape Floristic Region (CFR) is the most diverse extratropical area for plant biodiversity, and much of its habitat is protected as a UNESCO World Heritage site. There has long been great interest in explaining the underlying factors driving this unique diversity, especially as much of the CFR is endangered by urbanization and other anthropogenic activity. Here, we use a population and landscape genetic analysis of SNP data from the CFR endemic plant Leucadendron salignum or "common sunshine conebush" as a model to address the evolutionary and environmental factors shaping the vast CFR diversity. We found that high population structure, along with relatively deeper and older genealogies, is characteristic of the southwestern CFR, whereas low population structure and more recent lineage coalescence depict the eastern CFR. Population network analyses show genetic connectivity is facilitated in areas of lower elevation and higher seasonal precipitation. These population genetic signatures corroborate CFR species-level patterns consistent with high Pleistocene biome stability and landscape heterogeneity in the southwest, but with coincident instability in the east. Finally, we also find evidence of human land-usage as a significant gene flow barrier, especially in severely threatened lowlands where genetic connectivity has been historically the highest. These results help identify areas where conservation plans can prioritize protecting high genetic diversity threatened by contemporary human activities within this unique cultural UNESCO site.
Collapse
Affiliation(s)
| | - Lindsay S. Miles
- Center for the Study of Biological ComplexityVirginia Commonwealth UniversityRichmondVirginiaUSA
| | - Rodney J. Dyer
- Center for Environmental StudiesVirginia Commonwealth UniversityRichmondVirginiaUSA
| | - Michael S. Rosenberg
- School of Life SciencesArizona State UniversityTempeArizonaUSA
- Center for the Study of Biological ComplexityVirginia Commonwealth UniversityRichmondVirginiaUSA
| | - Richard M. Cowling
- African Centre for Coastal PalaeoscienceBotany DepartmentNelson Mandela UniversityPort ElizabethSouth Africa
| | - Brian C. Verrelli
- School of Life SciencesArizona State UniversityTempeArizonaUSA
- Center for the Study of Biological ComplexityVirginia Commonwealth UniversityRichmondVirginiaUSA
| |
Collapse
|
35
|
Dujon AM, Ujvari B, Thomas F. Cancer risk landscapes: A framework to study cancer in ecosystems. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 763:142955. [PMID: 33109371 DOI: 10.1016/j.scitotenv.2020.142955] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Revised: 10/06/2020] [Accepted: 10/08/2020] [Indexed: 06/11/2023]
Abstract
Cancer is a family of diseases that has been documented in most metazoan species and ecosystems. Human induced environmental changes are increasingly exposing wildlife to carcinogenic risk factors, and negative repercussions on ecosystems and on the conservation of endangered species are already been observed. It is therefore of key importance to understand the spatiotemporal variability of those risk factors and how they interact with the biosphere to mitigate their effects. Here we introduce the concept of cancer risk landscape that can be applied to understand how species are exposed to, interact with, and modify cancer risk factors. With this publication we aim to provide a framework in order to stimulate a discussion on how to mitigate cancer-causing risk factors.
Collapse
Affiliation(s)
- Antoine M Dujon
- Deakin University, Geelong, School of Life and Environmental Sciences, Centre for Integrative Ecology, Waurn Ponds, Vic 3216, Australia; CREEC, UMR IRD 224-CNRS 5290-Université de Montpellier, Montpellier, France; CANECEV-Centre de Recherches Ecologiques et Evolutives sur le cancer (CREEC), Montpellier 34090, France.
| | - Beata Ujvari
- Deakin University, Geelong, School of Life and Environmental Sciences, Centre for Integrative Ecology, Waurn Ponds, Vic 3216, Australia; CANECEV-Centre de Recherches Ecologiques et Evolutives sur le cancer (CREEC), Montpellier 34090, France
| | - Frédéric Thomas
- Deakin University, Geelong, School of Life and Environmental Sciences, Centre for Integrative Ecology, Waurn Ponds, Vic 3216, Australia; CREEC, UMR IRD 224-CNRS 5290-Université de Montpellier, Montpellier, France; CANECEV-Centre de Recherches Ecologiques et Evolutives sur le cancer (CREEC), Montpellier 34090, France
| |
Collapse
|
36
|
Backhouse F, Dalziell AH, Magrath RD, Rice AN, Crisologo TL, Welbergen JA. Differential geographic patterns in song components of male Albert's lyrebirds. Ecol Evol 2021; 11:2701-2716. [PMID: 33767830 PMCID: PMC7981226 DOI: 10.1002/ece3.7225] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Revised: 12/18/2020] [Accepted: 12/23/2020] [Indexed: 12/25/2022] Open
Abstract
Geographic variation in bird song has received much attention in evolutionary studies, yet few consider components within songs that may be subject to different constraints and follow different evolutionary trajectories. Here, we quantify patterns of geographic variation in the socially transmitted "whistle" song of Albert's lyrebirds (Menura alberti), an oscine passerine renowned for its remarkable vocal abilities. Albert's lyrebirds are confined to narrow stretches of suitable habitat in Australia, allowing us to map likely paths of cultural transmission using a species distribution model and least cost paths. We use quantitative methods to divide the songs into three components present in all study populations: the introductory elements, the song body, and the final element. We compare geographic separation between populations with variation in these components as well as the full song. All populations were distinguishable by song, and songs varied according to the geographic distance between populations. However, within songs, only the introductory elements and song body could be used to distinguish among populations. The song body and final element changed with distance, but the introductory elements varied independently of geographic separation. These differing geographic patterns of within-song variation are unexpected, given that the whistle song components are always produced in the same sequence and may be perceived as a temporally discrete unit. Knowledge of such spatial patterns of within-song variation enables further work to determine possible selective pressures and constraints acting on each song component and provides spatially explicit targets for preserving cultural diversity. As such, our study highlights the importance for science and conservation of investigating spatial patterns within seemingly discrete behavioral traits at multiple levels of organization.
Collapse
Affiliation(s)
- Fiona Backhouse
- The Hawkesbury Institute for the EnvironmentWestern Sydney UniversityRichmondNSWAustralia
| | - Anastasia H. Dalziell
- The Hawkesbury Institute for the EnvironmentWestern Sydney UniversityRichmondNSWAustralia
- Centre for Sustainable Ecosystem SolutionsSchool of Earth, Atmospheric and Life SciencesUniversity of WollongongWollongongNSWAustralia
- Fuller Evolutionary Biology ProgramCornell Lab of OrnithologyCornell UniversityIthacaNYUSA
- Macaulay LibraryCornell Lab of OrnithologyCornell UniversityIthacaNYUSA
- Center for Conservation BioacousticsCornell Lab of OrnithologyCornell UniversityIthacaNYUSA
| | - Robert D. Magrath
- Research School of Biologythe Australian National UniversityCanberraACTAustralia
| | - Aaron N. Rice
- Center for Conservation BioacousticsCornell Lab of OrnithologyCornell UniversityIthacaNYUSA
| | - Taylor L. Crisologo
- The Hawkesbury Institute for the EnvironmentWestern Sydney UniversityRichmondNSWAustralia
- Macaulay LibraryCornell Lab of OrnithologyCornell UniversityIthacaNYUSA
| | - Justin A. Welbergen
- The Hawkesbury Institute for the EnvironmentWestern Sydney UniversityRichmondNSWAustralia
| |
Collapse
|
37
|
Curry CJ, Davis BW, Bertola LD, White PA, Murphy WJ, Derr JN. Spatiotemporal Genetic Diversity of Lions Reveals the Influence of Habitat Fragmentation across Africa. Mol Biol Evol 2021; 38:48-57. [PMID: 32667997 PMCID: PMC8480188 DOI: 10.1093/molbev/msaa174] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Direct comparisons between historical and contemporary populations allow for detecting changes in genetic diversity through time and assessment of the impact of habitat fragmentation. Here, we determined the genetic architecture of both historical and modern lions to document changes in genetic diversity over the last century. We surveyed microsatellite and mitochondrial genome variation from 143 high-quality museum specimens of known provenance, allowing us to directly compare this information with data from several recently published nuclear and mitochondrial studies. Our results provide evidence for male-mediated gene flow and recent isolation of local subpopulations, likely due to habitat fragmentation. Nuclear markers showed a significant decrease in genetic diversity from the historical (HE = 0.833) to the modern (HE = 0.796) populations, whereas mitochondrial genetic diversity was maintained (Hd = 0.98 for both). Although the historical population appears to have been panmictic based on nDNA data, hierarchical structure analysis identified four tiers of genetic structure in modern populations and was able to detect most sampling locations. Mitogenome analyses identified four clusters: Southern, Mixed, Eastern, and Western and were consistent between modern and historically sampled haplotypes. Within the last century, habitat fragmentation caused lion subpopulations to become more geographically isolated as human expansion changed the African landscape. This resulted in an increase in fine-scale nuclear genetic structure and loss of genetic diversity as lion subpopulations became more differentiated, whereas mitochondrial structure and diversity were maintained over time.
Collapse
Affiliation(s)
- Caitlin J Curry
- Interdisciplinary Program in Genetics, Texas A&M University, College Station, TX
- Department of Veterinary Pathobiology, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX
| | - Brian W Davis
- Department of Veterinary Integrative Biosciences, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX
| | - Laura D Bertola
- Department of Biology, City College of New York, New York, NY
| | - Paula A White
- Center for Tropical Research, Institute of the Environment and Sustainability, University of California Los Angeles, Los Angeles, CA
| | - William J Murphy
- Interdisciplinary Program in Genetics, Texas A&M University, College Station, TX
- Department of Veterinary Integrative Biosciences, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX
| | - James N Derr
- Interdisciplinary Program in Genetics, Texas A&M University, College Station, TX
- Department of Veterinary Pathobiology, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX
| |
Collapse
|
38
|
Zupan S, Jugovic J, Čelik T, Buzan E. Population genetic structure of the highly endangered butterfly Coenonympha oedippus (Nymphalidae: Satyrinae) at its southern edge of distribution. Genetica 2021; 149:21-36. [PMID: 33389279 DOI: 10.1007/s10709-020-00108-0] [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: 08/17/2020] [Accepted: 11/06/2020] [Indexed: 10/22/2022]
Abstract
The Slovenian False Ringlet Coenonympha oedippus populations are under serious threat, as in the last two decades have witnessed a sharp decline in population distribution and size due to destruction, fragmentation and/or habitat quality degradation through intensive agriculture, abandonment of use and urbanization. We investigated the genetic diversity and structure of C. oedippus from the entire range of the species in Slovenia. Our results showed that the genetic variation in the Slovenian C. oedippus populations agrees with the geographical structure and the ecotypes previously determined by morphological and ecological data. We confirmed the existence of four genetically divergent and spatially non-overlapping geographical groups (Istria, Karst, Gorica, Ljubljansko barje) and two ecotypes ("wet" and "dry"). Despite small sample sizes due to critically threatened species, the results indicated significant nuclear and mitochondrial genetic diversity within the spatial groups. By gaining new insights into the evolutionary history of the C. oedippus population, we have recommended to consider the Slovenian population as one Evolutionary Significant Unit, and four spatial populations as Management Units for conservation purposes.
Collapse
Affiliation(s)
- Sara Zupan
- Department of Biodiversity, Faculty of Mathematics, Natural Sciences and Information Technologies, University of Primorska, Glagoljaška 8, 6000, Koper, Slovenia
| | - Jure Jugovic
- Department of Biodiversity, Faculty of Mathematics, Natural Sciences and Information Technologies, University of Primorska, Glagoljaška 8, 6000, Koper, Slovenia
| | - Tatjana Čelik
- Research Centre of the Slovenian Academy of Sciences and Arts, Novi trg 2, 1000, Ljubljana, Slovenia
| | - Elena Buzan
- Department of Biodiversity, Faculty of Mathematics, Natural Sciences and Information Technologies, University of Primorska, Glagoljaška 8, 6000, Koper, Slovenia. .,Environmental Protection College, Trg mladosti 7, 3320, Velenje, Slovenia.
| |
Collapse
|
39
|
Fusco NA, Pehek E, Munshi‐South J. Urbanization reduces gene flow but not genetic diversity of stream salamander populations in the New York City metropolitan area. Evol Appl 2021; 14:99-116. [PMID: 33519959 PMCID: PMC7819553 DOI: 10.1111/eva.13025] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Accepted: 05/12/2020] [Indexed: 12/12/2022] Open
Abstract
Natural landscape heterogeneity and barriers resulting from urbanization can reduce genetic connectivity between populations. The evolutionary, demographic, and ecological effects of reduced connectivity may lead to population isolation and ultimately extinction. Alteration to the terrestrial and aquatic environment caused by urban influence can affect gene flow, specifically for stream salamanders who depend on both landscapes for survival and reproduction. To examine how urbanization affects a relatively common stream salamander species, we compared genetic connectivity of Eurycea bislineata (northern two-lined salamander) populations within and between streams in an urban, suburban, and rural habitat around the New York City (NYC) metropolitan area. We report reduced genetic connectivity between streams within the urban landscape found to correspond with potential barriers to gene flow, that is, areas with more dense urbanization (roadways, industrial buildings, and residential housing). The suburban populations also exhibited areas of reduced connectivity correlated with areas of greater human land use and greater connectivity within a preserve protected from development. Connectivity was relatively high among neighboring rural streams, but a major roadway corresponded with genetic breaks even though the habitat contained more connected green space overall. Despite greater human disturbance across the landscape, urban and suburban salamander populations maintained comparable levels of genetic diversity to their rural counterparts. Yet small effective population size in the urban habitats yielded a high probability of loss of heterozygosity due to genetic drift in the future. In conclusion, urbanization impacted connectivity among stream salamander populations where its continual influence may eventually hinder population persistence for this native species in urban habitats.
Collapse
Affiliation(s)
| | - Ellen Pehek
- Natural Resources GroupNew York City Department of Parks & RecreationNew YorkNYUSA
| | | |
Collapse
|
40
|
Perrin A, Khimoun A, Faivre B, Ollivier A, de Pracontal N, Théron F, Loubon M, Leblond G, Duron O, Garnier S. Habitat fragmentation differentially shapes neutral and immune gene variation in a tropical bird species. Heredity (Edinb) 2021; 126:148-162. [PMID: 32934360 PMCID: PMC7853120 DOI: 10.1038/s41437-020-00366-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 08/30/2020] [Accepted: 08/30/2020] [Indexed: 01/11/2023] Open
Abstract
Habitat fragmentation is a major cause of biodiversity loss, responsible for an alteration of intraspecific patterns of neutral genetic diversity and structure. Although neutral genetic variation can be informative for demographic inferences, it may be a poor predictor of adaptive genetic diversity and thus of the consequences of habitat fragmentation on selective evolutionary processes. In this context, we contrasted patterns of genetic diversity and structure of neutral loci (microsatellites) and immune genes (i.e., toll-like receptors) in an understorey bird species, the wedge-billed woodcreeper Glyphorynchus spirurus. The objectives were (1) to investigate forest fragmentation effects on population genetic diversity, (2) to disentangle the relative role of demography (genetic drift and migration) and selection, and (3) to assess whether immunogenetic patterns could be associated with variation of ectoparasite (i.e., ticks) pressures. Our results revealed an erosion of neutral genetic diversity and a substantial genetic differentiation among fragmented populations, resulting from a decrease in landscape connectivity and leading to the divergence of distinct genetic pools at a small spatial scale. Patterns of genetic diversity observed for TLR4 and TLR5 were concordant with neutral genetic patterns, whereas those observed for TLR3 and TLR21 were discordant. This result underlines that the dominant evolutionary force shaping immunogenetic diversity (genetic drift vs. selection) may be different depending on loci considered. Finally, tick prevalence was higher in fragmented environments. We discussed the hypothesis that pathogen selective pressures may contribute to maintain adaptive genetic diversity despite the negative demographic effect of habitat fragmentation on neutral genetic diversity.
Collapse
Affiliation(s)
- Antoine Perrin
- Biogéosciences, UMR 6282 CNRS, Université Bourgogne Franche-Comté, 6 Boulevard Gabriel, 21000, Dijon, France.
| | - Aurélie Khimoun
- Biogéosciences, UMR 6282 CNRS, Université Bourgogne Franche-Comté, 6 Boulevard Gabriel, 21000, Dijon, France
| | - Bruno Faivre
- Biogéosciences, UMR 6282 CNRS, Université Bourgogne Franche-Comté, 6 Boulevard Gabriel, 21000, Dijon, France
| | - Anthony Ollivier
- Biogéosciences, UMR 6282 CNRS, Université Bourgogne Franche-Comté, 6 Boulevard Gabriel, 21000, Dijon, France
| | - Nyls de Pracontal
- Groupe d'Etude et de Protection des Oiseaux en Guyane, 431 route d'Attila Cabassou, 97354, Rémire-Montjoly, France
| | - Franck Théron
- Groupe d'Etude et de Protection des Oiseaux en Guyane, 431 route d'Attila Cabassou, 97354, Rémire-Montjoly, France
| | - Maxime Loubon
- Groupe d'Etude et de Protection des Oiseaux en Guyane, 431 route d'Attila Cabassou, 97354, Rémire-Montjoly, France
| | - Gilles Leblond
- SARL BIOS, Route de Davidon, Duzer, 97115, Sainte-Rose, France
| | - Olivier Duron
- Maladies Infectieuses et Vecteurs: Ecologie, Génétique, Evolution et Contrôle (MIVEGEC), Centre National de la Recherche Scientifique (CNRS), Institut pour la Recherche et le Développement (IRD), Université de Montpellier (UM), Montpellier, France
| | - Stéphane Garnier
- Biogéosciences, UMR 6282 CNRS, Université Bourgogne Franche-Comté, 6 Boulevard Gabriel, 21000, Dijon, France
| |
Collapse
|
41
|
Brauer CJ, Beheregaray LB. Recent and rapid anthropogenic habitat fragmentation increases extinction risk for freshwater biodiversity. Evol Appl 2020; 13:2857-2869. [PMID: 33294027 PMCID: PMC7691462 DOI: 10.1111/eva.13128] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Revised: 08/31/2020] [Accepted: 09/01/2020] [Indexed: 12/16/2022] Open
Abstract
Anthropogenic habitat fragmentation is often implicated as driving the current global extinction crisis, particularly in freshwater ecosystems. The genetic signal of recent population isolation can be confounded by the complex spatial arrangement of dendritic river systems. Consequently, many populations may presently be managed separately based on an incorrect assumption that they have evolved in isolation. Integrating landscape genomics data with models of connectivity that account for landscape structure, we show that the cumulative effects of multiple in-stream barriers have contributed to the recent decline of a freshwater fish from the Murray-Darling Basin, Australia. In addition, individual-based eco-evolutionary simulations further demonstrate that contemporary inferences about population isolation are consistent with the 160-year time frame since construction of in-stream barriers began in the region. Our findings suggest that the impact of very recent fragmentation may be often underestimated for freshwater biodiversity. We argue that proactive conservation measures to reconnect many riverine populations are urgently needed.
Collapse
Affiliation(s)
- Chris J. Brauer
- Molecular Ecology Laboratory, College of Science and EngineeringFlinders UniversityAdelaideSAAustralia
| | - Luciano B. Beheregaray
- Molecular Ecology Laboratory, College of Science and EngineeringFlinders UniversityAdelaideSAAustralia
| |
Collapse
|
42
|
Cruz-Salazar B, Ruiz-Montoya L. Population genetics of the common opossum, Didelphis marsupialis (Marsupialia: Didelphimorphia: Didelphidae), in southeastern Mexico. STUDIES ON NEOTROPICAL FAUNA AND ENVIRONMENT 2020. [DOI: 10.1080/01650521.2020.1844971] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Affiliation(s)
- Bárbara Cruz-Salazar
- Consejo Nacional de Ciencia y Tecnología-Universidad Autónoma de Tlaxcala, Centro Tlaxcala de Biología de la Conducta, La Loma de Xicohténcatl, Mexico
| | - Lorena Ruiz-Montoya
- Departamento de Conservación de la Biodiversidad, El Colegio de la Frontera Sur, San Cristóbal de Las Casas, Mexico
| |
Collapse
|
43
|
Effects of landscape heterogeneity on population genetic structure and demography of Amazonian phyllostomid bats. MAMMAL RES 2020. [DOI: 10.1007/s13364-020-00546-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
|
44
|
Kozakiewicz CP, Ricci L, Patton AH, Stahlke AR, Hendricks SA, Margres MJ, Ruiz-Aravena M, Hamilton DG, Hamede R, McCallum H, Jones ME, Hohenlohe PA, Storfer A. Comparative landscape genetics reveals differential effects of environment on host and pathogen genetic structure in Tasmanian devils (Sarcophilus harrisii) and their transmissible tumour. Mol Ecol 2020; 29:3217-3233. [PMID: 32682353 PMCID: PMC9805799 DOI: 10.1111/mec.15558] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2019] [Revised: 06/24/2020] [Accepted: 07/08/2020] [Indexed: 01/03/2023]
Abstract
Genetic structure in host species is often used to predict disease spread. However, host and pathogen genetic variation may be incongruent. Understanding landscape factors that have either concordant or divergent influence on host and pathogen genetic structure is crucial for wildlife disease management. Devil facial tumour disease (DFTD) was first observed in 1996 and has spread throughout almost the entire Tasmanian devil geographic range, causing dramatic population declines. Whereas DFTD is predominantly spread via biting among adults, devils typically disperse as juveniles, which experience low DFTD prevalence. Thus, we predicted little association between devil and tumour population structure and that environmental factors influencing gene flow differ between devils and tumours. We employed a comparative landscape genetics framework to test the influence of environmental factors on patterns of isolation by resistance (IBR) and isolation by environment (IBE) in devils and DFTD. Although we found evidence for broad-scale costructuring between devils and tumours, we found no relationship between host and tumour individual genetic distances. Further, the factors driving the spatial distribution of genetic variation differed for each. Devils exhibited a strong IBR pattern driven by major roads, with no evidence of IBE. By contrast, tumours showed little evidence for IBR and a weak IBE pattern with respect to elevation in one of two tumour clusters we identify herein. Our results warrant caution when inferring pathogen spread using host population genetic structure and suggest that reliance on environmental barriers to host connectivity may be ineffective for managing the spread of wildlife diseases. Our findings demonstrate the utility of comparative landscape genetics for identifying differential factors driving host dispersal and pathogen transmission.
Collapse
Affiliation(s)
| | - Lauren Ricci
- School of Biological Sciences, Washington State University, Pullman, Washington, USA
| | - Austin H. Patton
- School of Biological Sciences, Washington State University, Pullman, Washington, USA,Department of Integrative Biology, University of California, Berkeley, CA, USA
| | - Amanda R. Stahlke
- Department of Biological Sciences, Institute for Bioinformatics and Evolutionary Studies, University of Idaho, Moscow, Idaho, USA
| | - Sarah A. Hendricks
- Department of Biological Sciences, Institute for Bioinformatics and Evolutionary Studies, University of Idaho, Moscow, Idaho, USA
| | - Mark J. Margres
- School of Biological Sciences, Washington State University, Pullman, Washington, USA,Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, USA
| | - Manuel Ruiz-Aravena
- School of Natural Sciences, University of Tasmania, Hobart, Tasmania, Australia,Environmental Futures Research Institute, Griffith University, Nathan, Queensland, Australia
| | - David G. Hamilton
- School of Natural Sciences, University of Tasmania, Hobart, Tasmania, Australia
| | - Rodrigo Hamede
- School of Natural Sciences, University of Tasmania, Hobart, Tasmania, Australia
| | - Hamish McCallum
- Environmental Futures Research Institute, Griffith University, Nathan, Queensland, Australia
| | - Menna E. Jones
- School of Natural Sciences, University of Tasmania, Hobart, Tasmania, Australia
| | - Paul A. Hohenlohe
- Department of Biological Sciences, Institute for Bioinformatics and Evolutionary Studies, University of Idaho, Moscow, Idaho, USA
| | - Andrew Storfer
- School of Biological Sciences, Washington State University, Pullman, Washington, USA,corresponding author: Andrew Storfer, School of Biological Sciences, Washington State University, Pullman, WA, USA.
| |
Collapse
|
45
|
Latorre-Cardenas MC, Gutiérrez-Rodríguez C, Rico Y. Estimating genetic and demographic parameters relevant for the conservation of the Neotropical otter, Lontra longicaudis, in Mexico. CONSERV GENET 2020. [DOI: 10.1007/s10592-020-01283-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
|
46
|
Premier J, Fickel J, Heurich M, Kramer-Schadt S. The boon and bane of boldness: movement syndrome as saviour and sink for population genetic diversity. MOVEMENT ECOLOGY 2020; 8:16. [PMID: 32337047 PMCID: PMC7175569 DOI: 10.1186/s40462-020-00204-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Accepted: 04/07/2020] [Indexed: 05/05/2023]
Abstract
BACKGROUND Many felid species are of high conservation concern, and with increasing human disturbance the situation is worsening. Small isolated populations are at risk of genetic impoverishment decreasing within-species biodiversity. Movement is known to be a key behavioural trait that shapes both demographic and genetic dynamics and affects population survival. However, we have limited knowledge on how different manifestations of movement behaviour translate to population processes. In this study, we aimed to 1) understand the potential effects of movement behaviour on the genetic diversity of small felid populations in heterogeneous landscapes, while 2) presenting a simulation tool that can help inform conservation practitioners following, or considering, population management actions targeting the risk of genetic impoverishment. METHODS We developed a spatially explicit individual-based population model including neutral genetic markers for felids and applied this to the example of Eurasian lynx. Using a neutral landscape approach, we simulated reintroductions into a three-patch system, comprising two breeding patches separated by a larger patch of differing landscape heterogeneity, and tested for the effects of various behavioural movement syndromes and founder population sizes. We explored a range of movement syndromes by simulating populations with various movement model parametrisations that range from 'shy' to 'bold' movement behaviour. RESULTS We find that movement syndromes can lead to a higher loss of genetic diversity and an increase in between population genetic structure for both "bold" and "shy" movement behaviours, depending on landscape conditions, with larger decreases in genetic diversity and larger increases in genetic differentiation associated with bold movement syndromes, where the first colonisers quickly reproduce and subsequently dominate the gene pool. In addition, we underline the fact that a larger founder population can offset the genetic losses associated with subpopulation isolation and gene pool dominance. CONCLUSIONS We identified a movement syndrome trade-off for population genetic variation, whereby bold-explorers could be saviours - by connecting populations and promoting panmixia, or sinks - by increasing genetic losses via a 'founder takes all' effect, whereas shy-stayers maintain a more gradual genetic drift due to their more cautious behaviour. Simulations should incorporate movement behaviour to provide better projections of long-term population viability and within-species biodiversity, which includes genetic diversity. Simulations incorporating demographics and genetics have great potential for informing conservation management actions, such as population reintroductions or reinforcements. Here, we present such a simulation tool for solitary felids.
Collapse
Affiliation(s)
- Joseph Premier
- Chair of wildlife ecology and wildlife management, Faculty of Environment and Natural Resources, University of Freiburg, Tennenbacher Straße 4, 79106 Freiburg, Germany
- Leibniz Institute for Zoo and Wildlife Research (IZW), Alfred-Kowalke-Str. 17, 10315 Berlin, Germany
- Department of Visitor Management and National Park Monitoring, Bavarian Forest National Park, Freyunger Str. 2, 94481 Grafenau, Germany
| | - Jörns Fickel
- Leibniz Institute for Zoo and Wildlife Research (IZW), Alfred-Kowalke-Str. 17, 10315 Berlin, Germany
- Institute for Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Str. 24-25, 14476 Potsdam-Golm, Germany
| | - Marco Heurich
- Chair of wildlife ecology and wildlife management, Faculty of Environment and Natural Resources, University of Freiburg, Tennenbacher Straße 4, 79106 Freiburg, Germany
- Department of Visitor Management and National Park Monitoring, Bavarian Forest National Park, Freyunger Str. 2, 94481 Grafenau, Germany
| | - Stephanie Kramer-Schadt
- Leibniz Institute for Zoo and Wildlife Research (IZW), Alfred-Kowalke-Str. 17, 10315 Berlin, Germany
- Department of Ecology, Technical University Berlin, Rothenburg Str. 12, 12165 Berlin, Germany
| |
Collapse
|
47
|
Duncan SI, Robertson EP, Fletcher RJ, Austin JD. Urbanization and Population Genetic Structure of the Panama City crayfish (Procambarus econfinae). J Hered 2020; 111:204-215. [PMID: 31746328 DOI: 10.1093/jhered/esz072] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Accepted: 11/18/2019] [Indexed: 11/13/2022] Open
Abstract
For species with geographically restricted distributions, the impacts of habitat loss and fragmentation on long-term persistence may be particularly pronounced. We examined the genetic structure of Panama City crayfish (PCC), Procambarus econfinae, whose historical distribution is limited to an area approximately 145 km2, largely within the limits of Panama City and eastern Bay County, FL. Currently, PCC occupy approximately 28% of its historical range, with suitable habitat composed of fragmented patches in the highly urbanized western portion of the range and managed plantations in the more contiguous eastern portion of the range. We used 1640 anonymous single-nucleotide polymorphisms to evaluate the effects of anthropogenic habitat modification on the genetic diversity and population structure of 161 PCC sampled from across its known distribution. First, we examined urban habitat patches in the west compared with less-developed habitat patches in the east. Second, we used approximate Bayesian computation to model inferences on the demographic history of eastern and western populations. We found anthropogenic habitat modifications explain the genetic structure of PCC range-wide. Clustering analyses revealed significant genetic structure between and within eastern and western regions. Estimates of divergence between east and west were consistent with urban growth in the mid-20th century. PCC have low genetic diversity and high levels of inbreeding and relatedness, indicating populations are small and isolated. Our results suggest that PCC have been strongly affected by habitat loss and fragmentation and management strategies, including legal protection, translocations, or reintroductions, may be necessary to ensure long-term persistence.
Collapse
Affiliation(s)
| | - Ellen P Robertson
- Department of Wildlife Ecology and Conservation, University of Florida, Gainesville, FL
| | - Robert J Fletcher
- Department of Wildlife Ecology and Conservation, University of Florida, Gainesville, FL
| | - James D Austin
- Department of Wildlife Ecology and Conservation, University of Florida, Gainesville, FL
| |
Collapse
|
48
|
Vaeokhaw S, Ngoprasert D, Swatdipong A, Gale GA, Klinsawat W, Vichitsoonthonkul T. Effects of a highway on the genetic diversity of Asiatic black bears. URSUS 2020. [DOI: 10.2192/ursus-d-18-00013.2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Affiliation(s)
- Sakawrat Vaeokhaw
- Conservation Ecology Program, King Mongkut's University of Technology Thonburi, Bangkok, 10150, Thailand
| | - Dusit Ngoprasert
- Conservation Ecology Program, King Mongkut's University of Technology Thonburi, Bangkok, 10150, Thailand
| | - Akarapong Swatdipong
- Department of Genetics, Faculty of Science, Kasetsart University, Bangkok, 10900, Thailand
| | - George A. Gale
- Conservation Ecology Program, King Mongkut's University of Technology Thonburi, Bangkok, 10150, Thailand
| | - Worata Klinsawat
- Conservation Ecology Program, King Mongkut's University of Technology Thonburi, Bangkok, 10150, Thailand
| | - Taweerat Vichitsoonthonkul
- School of Bioresources and Technology, King Mongkut's University of Technology Thonburi, Bangkok, 10150, Thailand
| |
Collapse
|
49
|
Haugen H, Linløkken A, Østbye K, Heggenes J. Landscape genetics of northern crested newt Triturus cristatus populations in a contrasting natural and human-impacted boreal forest. CONSERV GENET 2020. [DOI: 10.1007/s10592-020-01266-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
AbstractAmong vertebrates, amphibians currently have the highest proportion of threatened species worldwide, mainly through loss of habitat, leading to increased population isolation. Smaller amphibian populations may lose more genetic diversity, and become more dependent on immigration for survival. Investigations of landscape factors and patterns mediating migration and population genetic differentiation are fundamental for knowledge-based conservation. The pond-breeding northern crested newt (Triturus cristatus) populations are decreasing throughout Europe, and are a conservation concern. Using microsatellites, we studied the genetic structure of the northern crested newt in a boreal forest ecosystem containing two contrasting landscapes, one subject to recent change and habitat loss by clear-cutting and roadbuilding, and one with little anthropogenic disturbance. Newts from 12 breeding ponds were analyzed for 13 microsatellites and 7 landscape and spatial variables. With a Maximum-likelihood population-effects model we investigated important landscape factors potentially explaining genetic patterns. Results indicate that intervening landscape factors between breeding ponds, explain the genetic differentiation in addition to an isolation-by-distance effect. Geographic distance, gravel roads, and south/south-west facing slopes reduced landscape permeability and increased genetic differentiation for these newts. The effect was opposite for streams, presumably being more favorable for newt dispersal. Populations within or bordering on old growth forest had a higher allelic richness than populations in managed forest outside these areas. Old growth forest areas may be important source habitats in the conservation of northern crested newt populations.
Collapse
|
50
|
Kaszta Ż, Cushman SA, Macdonald DW. Prioritizing habitat core areas and corridors for a large carnivore across its range. Anim Conserv 2020. [DOI: 10.1111/acv.12575] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Ż. Kaszta
- Wildlife Conservation Research Unit (WildCRU) Department of Zoology The Recanati‐Kaplan Centre University of Oxford Tubney UK
| | - S. A. Cushman
- Wildlife Conservation Research Unit (WildCRU) Department of Zoology The Recanati‐Kaplan Centre University of Oxford Tubney UK
- USDA Forest Service Rocky Mountain Research Station Flagstaff AZ USA
| | - D. W. Macdonald
- Wildlife Conservation Research Unit (WildCRU) Department of Zoology The Recanati‐Kaplan Centre University of Oxford Tubney UK
| |
Collapse
|