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Fonseca EM, Carstens BC. Artificial intelligence enables unified analysis of historical and landscape influences on genetic diversity. Mol Phylogenet Evol 2024; 198:108116. [PMID: 38871263 DOI: 10.1016/j.ympev.2024.108116] [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: 07/05/2023] [Revised: 04/04/2024] [Accepted: 06/04/2024] [Indexed: 06/15/2024]
Abstract
While genetic variation in any species is potentially shaped by a range of processes, phylogeography and landscape genetics are largely concerned with inferring how environmental conditions and landscape features impact neutral intraspecific diversity. However, even as both disciplines have come to utilize SNP data over the last decades, analytical approaches have remained for the most part focused on either broad-scale inferences of historical processes (phylogeography) or on more localized inferences about environmental and/or landscape features (landscape genetics). Here we demonstrate that an artificial intelligence model-based analytical framework can consider both deeper historical factors and landscape-level processes in an integrated analysis. We implement this framework using data collected from two Brazilian anurans, the Brazilian sibilator frog (Leptodactylus troglodytes) and granular toad (Rhinella granulosa). Our results indicate that historical demographic processes shape most the genetic variation in the sibulator frog, while landscape processes primarily influence variation in the granular toad. The machine learning framework used here allows both historical and landscape processes to be considered equally, rather than requiring researchers to make an a priori decision about which factors are important.
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Affiliation(s)
- Emanuel M Fonseca
- Museum of Biological Diversity & Department of Evolution, Ecology and Organismal Biology, The Ohio State University, 1315 Kinnear Rd., Columbus OH 43212, USA
| | - Bryan C Carstens
- Museum of Biological Diversity & Department of Evolution, Ecology and Organismal Biology, The Ohio State University, 1315 Kinnear Rd., Columbus OH 43212, USA.
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2
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Tyagi A, Yadav N, Pandit A, Ramakrishnan U. On the road to losing connectivity: Faecal samples provide genome-wide insights into anthropogenic impacts on two large herbivore species in central India. Mol Ecol 2024:e17461. [PMID: 38958291 DOI: 10.1111/mec.17461] [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: 11/02/2023] [Revised: 06/12/2024] [Accepted: 06/24/2024] [Indexed: 07/04/2024]
Abstract
Humans have impacted most of the planet, and the ensuing fragmentation results in small, isolated habitat patches posing a risk of genetic diversity loss, inbreeding, and genetic load. Understanding how natural and anthropogenic landscape features affect gene flow among habitat patches is critical for maintaining connectivity. Genome-wide data are required to comprehend the impacts of recent fragmentation, which can be challenging when only non-invasive samples are available. Here, we build upon advancements in conservation genomics to address connectivity of two large herbivores, gaur (Bos gaurus) and sambar (Rusa unicolor) in central India. Given their habitat associations, we expected these species to respond similarly to habitat fragmentation. We used faecal-DNA and methylation-based host-DNA enrichment with modified ddRAD protocol to generate genome-wide single-nucleotide polymorphism (SNP) data for 124 gaur and 99 sambar individuals. Our findings reveal that gaur populations in central India are fragmented, displaying high genetic differentiation, with drift significantly affecting small populations like Umred Karhandla Wildlife Sanctuary. Although sambar shows low genetic structure, another small population, Bor Tiger Reserve is genetically differentiated. Our results suggest that although land cover change and roads restrict animal movement, the extent of this impact varies across the two species. We show that different species respond differently to landscape features, even with similar habitat associations. We highlight small and isolated populations requiring urgent conservation intervention. Such multi-species approaches enhance our understanding of cross-species connectivity patterns. We suggest shifting from single-species to multi-species holistic conservation approach in rapidly developing landscapes to better manage co-occurring endangered species.
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Affiliation(s)
- Abhinav Tyagi
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore, India
- SASTRA Deemed to be University, Thanjavur, India
| | - Nidhi Yadav
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore, India
| | - Awadhesh Pandit
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore, India
| | - Uma Ramakrishnan
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore, India
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3
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Babik W, Marszałek M, Dudek K, Antunes B, Palomar G, Zając B, Taugbøl A, Pabijan M. Limited evidence for genetic differentiation or adaptation in two amphibian species across replicated rural-urban gradients. Evol Appl 2024; 17:e13700. [PMID: 38832082 PMCID: PMC11146147 DOI: 10.1111/eva.13700] [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: 12/05/2023] [Revised: 03/05/2024] [Accepted: 04/24/2024] [Indexed: 06/05/2024] Open
Abstract
Urbanization leads to complex environmental changes and poses multiple challenges to organisms. Amphibians are highly susceptible to the effects of urbanization, with land use conversion, habitat destruction, and degradation ranked as the most significant threats. Consequently, amphibians are declining in urban areas, in both population numbers and abundance, however, the effect of urbanization on population genetic parameters remains unclear. Here, we studied the genomic response to urbanization in two widespread European species, the common toad Bufo bufo (26 localities, 480 individuals), and the smooth newt Lissotriton vulgaris (30 localities, 516 individuals) in three geographic regions: southern and northern Poland and southern Norway. We assessed genome-wide SNP variation using RADseq (ca. 42 and 552 thousand SNPs in toads and newts, respectively) and adaptively relevant major histocompatibility complex (MHC) class I and II genes. The results linked most of the genetic differentiation in both marker types to regional (latitudinal) effects, which also correspond to historical biogeography. Further, we did not find any association between genetic differentiation and level of urbanization at local scales for either species. However, urban smooth newts, but not toads, have lower levels of within-population genome-wide diversity, suggesting higher susceptibility to the negative effects of urbanization. A decreasing level of genetic diversity linked to increasing urbanization was also found for MHC II in smooth newts, while the relationship between MHC class I diversity and urbanization differed between geographic regions. We did not find any effects of urbanization on MHC diversity in the toad populations. Although two genetic environment association analyses of genome-wide data, LFMM and BayPass, revealed numerous (219 in B. bufo and 7040 in L. vulgaris) SNPs statistically associated with urbanization, we found a marked lack of repeatability between geographic regions, suggesting a complex and multifaceted response to natural selection elicited by life in the city.
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Affiliation(s)
- W. Babik
- Faculty of Biology, Institute of Environmental SciencesJagiellonian UniversityKrakówPoland
| | - M. Marszałek
- Faculty of Biology, Institute of Environmental SciencesJagiellonian UniversityKrakówPoland
| | - K. Dudek
- Faculty of Biology, Institute of Environmental SciencesJagiellonian UniversityKrakówPoland
| | - B. Antunes
- Faculty of Biology, Institute of Environmental SciencesJagiellonian UniversityKrakówPoland
| | - G. Palomar
- Faculty of Biology, Institute of Environmental SciencesJagiellonian UniversityKrakówPoland
- Department of Genetics, Physiology and Microbiology, Faculty of Biological SciencesComplutense University of MadridMadridSpain
| | - B. Zając
- Faculty of Biology, Institute of Zoology and Biomedical ResearchJagiellonian UniversityKrakówPoland
| | - A. Taugbøl
- Norwegian Institute for Nature ResearchLillehammerNorway
| | - M. Pabijan
- Faculty of Biology, Institute of Zoology and Biomedical ResearchJagiellonian UniversityKrakówPoland
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4
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Bustillo‐de la Rosa D, Barrero A, Traba J, García JT, Morales MB, Vázquez‐Domínguez E. Landscape features influencing gene flow and connectivity of an endangered passerine. Ecol Evol 2024; 14:e11078. [PMID: 38756688 PMCID: PMC11097005 DOI: 10.1002/ece3.11078] [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: 04/18/2023] [Revised: 01/10/2024] [Accepted: 02/12/2024] [Indexed: 05/18/2024] Open
Abstract
Dispersal of individuals and gene flow are crucial aspects to maintain genetic diversity and viability of populations, especially in the case of threatened species. Landscape composition and structure may facilitate or limit individual movement within and among populations. We used a landscape genetics approach to assess the connectivity patterns of the threatened Dupont's lark (Chersophilus duponti subsp. duponti), considering their genetic patterns and the landscape features associated with its gene flow in Spain. We analysed the genetic relatedness based on 11 species-specific polymorphic microsatellites on 416 Dupont's lark individuals sampled across peninsular Spain between 2017 and 2019, covering most of the European distribution of the species. To assess the relationship between the landscape composition and the species gene flow, we estimated genetic distance at the individual level (Dps). Next, we built a set of environmental surfaces from two time periods (years 1990 and 2018), based on factors such as land use and topography, influencing individuals' movement. We then obtained resistance surfaces from an optimization process on landscape variables. Landscape genetics analyses were done for single and composite surface models for each year separately. Our findings from both time points show that scatter or mosaic-structured vegetation composed by low agricultural and tree cover and high presence of sclerophyllous shrubs favoured Dupont's lark dispersal, while dense and continuous tree cover, as well as areas of intensive agriculture, were limiting factors. Our results suggest the importance of steppe habitat patches for the species' establishment and dispersal. In addition, our results provide key information to develop conservation measures, including conserving and restoring steppe habitats as scattered and/or mosaic-structured vegetation that could warrant the connectivity and persistence of Dupont's lark populations.
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Affiliation(s)
- Daniel Bustillo‐de la Rosa
- Terrestrial Ecology Group (TEG‐UAM). Department of EcologyUniversidad Autónoma de MadridMadridSpain
- Centro de Investigación en Biodiversidad y Cambio Global (CIBC‐UAM)Universidad Autónoma de MadridMadridSpain
| | - Adrián Barrero
- Terrestrial Ecology Group (TEG‐UAM). Department of EcologyUniversidad Autónoma de MadridMadridSpain
- Centro de Investigación en Biodiversidad y Cambio Global (CIBC‐UAM)Universidad Autónoma de MadridMadridSpain
| | - Juan Traba
- Terrestrial Ecology Group (TEG‐UAM). Department of EcologyUniversidad Autónoma de MadridMadridSpain
- Centro de Investigación en Biodiversidad y Cambio Global (CIBC‐UAM)Universidad Autónoma de MadridMadridSpain
| | - Jesús T. García
- Instituto de Investigación en Recursos Cinegéticos (IREC, CSIC‐UCLM)Ciudad RealSpain
| | - Manuel B. Morales
- Terrestrial Ecology Group (TEG‐UAM). Department of EcologyUniversidad Autónoma de MadridMadridSpain
- Centro de Investigación en Biodiversidad y Cambio Global (CIBC‐UAM)Universidad Autónoma de MadridMadridSpain
| | - Ella Vázquez‐Domínguez
- Departamento de Ecología de la Biodiversidad, Instituto de EcologíaUniversidad Nacional Autónoma de MéxicoCiudad de MéxicoMexico
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García-Castro KL, Márquez EJ. Temporal analysis of genetic diversity and gene flow in the threatened catfish Pseudoplatystoma magdaleniatum from a dammed neotropical river. PLoS One 2024; 19:e0301577. [PMID: 38635781 PMCID: PMC11025948 DOI: 10.1371/journal.pone.0301577] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Accepted: 03/19/2024] [Indexed: 04/20/2024] Open
Abstract
The striped catfish Pseudoplatystoma magdaleniatum is a large-sized migratory species from the north Andes region, endemic to Magdalena basin and one of the major fishery resources. Despite the estimated reduction of over 80% of the fisheries production of this species throughout the basin in recent decades, its population in the lower Magdalena-Cauca basin showed healthy genetics after molecular analyses. However, the current conservation status of this species and several habitat disturbances demand the re-evaluation of its population genetics to infer evolutionary risks and assess potential changes. This work analyzed a total of 164 samples from the Cauca River collected downstream the Ituango Dam between 2019-2021 using species-specific microsatellite markers to compare the genetic diversity and structure in samples collected between 2010-2014 from the lower Magdalena-Cauca basin, previously analyzed. Our results showed a relatively stable panmictic population over time (4 to 10 years), with high genetic diversity and evidence of recent bottleneck. Promoting habitat connectivity to conserve gene flow, characterizing diversity and genetic structure over the entire basin, and integrating the results with future monitoring are important aspects for the management planning for P. magdaleniatum in the Magdalena-Cauca basin.
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Affiliation(s)
- Kevin León García-Castro
- Facultad de Ciencias Universidad Nacional de Colombia–Sede Medellín, Laboratorio de Biología Molecular y Celular, Escuela de Biociencias, Medellín, Antioquia, Colombia
| | - Edna Judith Márquez
- Facultad de Ciencias Universidad Nacional de Colombia–Sede Medellín, Laboratorio de Biología Molecular y Celular, Escuela de Biociencias, Medellín, Antioquia, Colombia
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Wilson RE, Boyd WS, Sonsthagen SA, Ward DH, Clausen P, Dickson KM, Ebbinge BS, Gudmundsson GA, Sage GK, Rearick JR, Derksen DV, Talbot SL. Where east meets west: Phylogeography of the high Arctic North American brant goose. Ecol Evol 2024; 14:e11245. [PMID: 38601857 PMCID: PMC11004662 DOI: 10.1002/ece3.11245] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Revised: 03/07/2024] [Accepted: 03/22/2024] [Indexed: 04/12/2024] Open
Abstract
Genetic variation in Arctic species is often influenced by vicariance during the Pleistocene, as ice sheets fragmented the landscape and displaced populations to low- and high-latitude refugia. The formation of secondary contact or suture zones during periods of ice sheet retraction has important consequences on genetic diversity by facilitating genetic connectivity between formerly isolated populations. Brant geese (Branta bernicla) are a maritime migratory waterfowl (Anseriformes) species that almost exclusively uses coastal habitats. Within North America, brant geese are characterized by two phenotypically distinct subspecies that utilize disjunct breeding and wintering areas in the northern Pacific and Atlantic. In the Western High Arctic of Canada, brant geese consist of individuals with an intermediate phenotype that are rarely observed nesting outside this region. We examined the genetic structure of brant geese populations from each subspecies and areas consisting of intermediate phenotypes using mitochondrial DNA (mtDNA) control region sequence data and microsatellite loci. We found a strong east-west partition in both marker types consistent with refugial populations. Within subspecies, structure was also observed at mtDNA while microsatellite data suggested the presence of only two distinct genetic clusters. The Western High Arctic (WHA) appears to be a secondary contact zone for both Atlantic and Pacific lineages as mtDNA and nuclear genotypes were assigned to both subspecies, and admixed individuals were observed in this region. The mtDNA sequence data outside WHA suggests no or very restricted intermixing between Atlantic and Pacific wintering populations which is consistent with published banding and telemetry data. Our study indicates that, although brant geese in the WHA are not a genetically distinct lineage, this region may act as a reservoir of genetic diversity and may be an area of high conservation value given the potential of low reproductive output in this species.
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Affiliation(s)
- Robert E. Wilson
- School of Natural ResourcesUniversity of Nebraska‐LincolnLincolnNebraskaUSA
- Nebraska State MuseumUniversity of Nebraska‐LincolnLincolnNebraskaUSA
| | - W. Sean Boyd
- Environment and Climate Change CanadaScience and Technology BranchDeltaBritish ColumbiaCanada
| | - Sarah A. Sonsthagen
- U.S. Geological Survey, Nebraska Cooperative Fish and Wildlife Research Unit, School of Natural ResourcesUniversity of Nebraska‐LincolnLincolnNebraskaUSA
| | - David H. Ward
- U.S. Geological SurveyAlaska Science CenterAnchorageAlaskaUSA
| | | | - Kathryn M. Dickson
- Canadian Wildlife ServiceEnvironment and Climate Change CanadaOttawaOntarioCanada
| | | | | | - George K. Sage
- Far Northwestern Institute of Art and ScienceAnchorageAlaskaUSA
| | | | - Dirk V. Derksen
- U.S. Geological SurveyAlaska Science CenterAnchorageAlaskaUSA
| | - Sandra L. Talbot
- Far Northwestern Institute of Art and ScienceAnchorageAlaskaUSA
- Alaska Center for Conservation ScienceUniversity of AlaskaAnchorageAlaskaUSA
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Song Y, Xu GB, Long KX, Wang CC, Chen R, Li H, Jiang XL, Deng M. Ensemble species distribution modeling and multilocus phylogeography provide insight into the spatial genetic patterns and distribution dynamics of a keystone forest species, Quercus glauca. BMC PLANT BIOLOGY 2024; 24:168. [PMID: 38438905 PMCID: PMC10910841 DOI: 10.1186/s12870-024-04830-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Accepted: 02/16/2024] [Indexed: 03/06/2024]
Abstract
BACKGROUND Forests are essential for maintaining species diversity, stabilizing local and global climate, and providing ecosystem services. Exploring the impact of paleogeographic events and climate change on the genetic structure and distribution dynamics of forest keystone species could help predict responses to future climate change. In this study, we combined an ensemble species distribution model (eSDM) and multilocus phylogeography to investigate the spatial genetic patterns and distribution change of Quercus glauca Thunb, a keystone of East Asian subtropical evergreen broad-leaved forest. RESULTS A total of 781 samples were collected from 77 populations, largely covering the natural distribution of Q. glauca. The eSDM showed that the suitable habitat experienced a significant expansion after the last glacial maximum (LGM) but will recede in the future under a general climate warming scenario. The distribution centroid will migrate toward the northeast as the climate warms. Using nuclear SSR data, two distinct lineages split between east and west were detected. Within-group genetic differentiation was higher in the West than in the East. Based on the identified 58 haplotypes, no clear phylogeographic structure was found. Populations in the Nanling Mountains, Wuyi Mountains, and the southwest region were found to have high genetic diversity. CONCLUSIONS A significant negative correlation between habitat stability and heterozygosity might be explained by the mixing of different lineages in the expansion region after LGM and/or hybridization between Q. glauca and closely related species. The Nanling Mountains may be important for organisms as a dispersal corridor in the west-east direction and as a refugium during the glacial period. This study provided new insights into spatial genetic patterns and distribution dynamics of Q. glauca.
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Affiliation(s)
- Ying Song
- College of Forestry, The Laboratory of Forestry Genetics, Central South University of Forestry and Technology, Changsha, 410004, Hunan, China
| | - Gang-Biao Xu
- College of Forestry, The Laboratory of Forestry Genetics, Central South University of Forestry and Technology, Changsha, 410004, Hunan, China
| | - Ke-Xin Long
- College of Forestry, The Laboratory of Forestry Genetics, Central South University of Forestry and Technology, Changsha, 410004, Hunan, China
| | - Chun-Cheng Wang
- College of Landscape Architecture, Central South University of Forestry and Technology, Changsha, 410004, Hunan, China
| | - Ran Chen
- College of Forestry, The Laboratory of Forestry Genetics, Central South University of Forestry and Technology, Changsha, 410004, Hunan, China
| | - He Li
- College of Forestry, The Laboratory of Forestry Genetics, Central South University of Forestry and Technology, Changsha, 410004, Hunan, China
| | - Xiao-Long Jiang
- College of Forestry, The Laboratory of Forestry Genetics, Central South University of Forestry and Technology, Changsha, 410004, Hunan, China.
| | - Min Deng
- School of Ecology and Environmental Sciences, Yunnan University, Kunming, Yunnan, 650500, China.
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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.
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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
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Beer MA, Proft KM, Veillet A, Kozakiewicz CP, Hamilton DG, Hamede R, McCallum H, Hohenlohe PA, Burridge CP, Margres MJ, Jones ME, Storfer A. Disease-driven top predator decline affects mesopredator population genomic structure. Nat Ecol Evol 2024; 8:293-303. [PMID: 38191839 DOI: 10.1038/s41559-023-02265-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Accepted: 11/02/2023] [Indexed: 01/10/2024]
Abstract
Top predator declines are pervasive and often have dramatic effects on ecological communities via changes in food web dynamics, but their evolutionary consequences are virtually unknown. Tasmania's top terrestrial predator, the Tasmanian devil, is declining due to a lethal transmissible cancer. Spotted-tailed quolls benefit via mesopredator release, and they alter their behaviour and resource use concomitant with devil declines and increased disease duration. Here, using a landscape community genomics framework to identify environmental drivers of population genomic structure and signatures of selection, we show that these biotic factors are consistently among the top variables explaining genomic structure of the quoll. Landscape resistance negatively correlates with devil density, suggesting that devil declines will increase quoll genetic subdivision over time, despite no change in quoll densities detected by camera trap studies. Devil density also contributes to signatures of selection in the quoll genome, including genes associated with muscle development and locomotion. Our results provide some of the first evidence of the evolutionary impacts of competition between a top predator and a mesopredator species in the context of a trophic cascade. As top predator declines are increasing globally, our framework can serve as a model for future studies of evolutionary impacts of altered ecological interactions.
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Affiliation(s)
- Marc A Beer
- School of Biological Sciences, Washington State University, Pullman, WA, USA
| | - Kirstin M Proft
- School of Natural Sciences, University of Tasmania, Hobart, Tasmania, Australia
| | - Anne Veillet
- Hilo Core Genomics Facility, University of Hawaii at Hilo, Hilo, HI, USA
| | - Christopher P Kozakiewicz
- Department of Integrative Biology, Michigan State University, W.K. Kellogg Biological Station, Hickory Corners, MI, USA
| | - 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
- CANECEV, Centre de Recherches Ecologiques et Evolutives sur le Cancer, Montpellier, France
| | - Hamish McCallum
- Environmental Futures Research Institute, Griffith University, Nathan, Queensland, Australia
| | - Paul A Hohenlohe
- Institute for Bioinformatics and Evolutionary Studies, University of Idaho, Moscow, ID, USA
| | | | - Mark J Margres
- Department of Integrative Biology, University of South Florida, Tampa, FL, USA
| | - Menna E Jones
- School of Natural Sciences, University of Tasmania, Hobart, Tasmania, Australia
| | - Andrew Storfer
- School of Biological Sciences, Washington State University, Pullman, WA, USA.
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10
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Haugen H, Dervo BK, Østbye K, Heggenes J, Devineau O, Linløkken A. Genetic diversity, gene flow, and landscape resistance in a pond-breeding amphibian in agricultural and natural forested landscapes in Norway. Evol Appl 2024; 17:e13633. [PMID: 38283603 PMCID: PMC10810167 DOI: 10.1111/eva.13633] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Revised: 11/23/2023] [Accepted: 12/07/2023] [Indexed: 01/30/2024] Open
Abstract
Genetic diversity is a key part of biodiversity, threatened by human activities that lead to loss of gene flow and reduction of effective population sizes. Gene flow is a result of both landscape connectivity and demographic processes determining the number of dispersing individuals in space and time. Thus, the effect of human impact on processes determining the level of genetic diversity must be interpreted in the context of basic ecological conditions affecting survival and recruitment. When the intensity of human impact and habitat suitability correlate, the effect on genetic diversity and gene flow may be challenging to predict. We compared genetic diversity, gene flow and landscape resistance in two contrasting landscapes in Norway for the pond-breeding amphibian Triturus cristatus: a highly human-impacted, agricultural landscape with ecologically productive habitats, and a forested landscape with less productive habitats and lower levels of human impact. Our results show that genetic diversity was higher and gene flow lower within the forested landscape. Microclimatic moisture conditions and vegetation cover were important determinants of landscape resistance to gene flow within both landscapes. There were indications that landscape resistance was increased by minor roads in the forested landscape, which was not the case for the agricultural landscape, suggesting a higher vulnerability to human interference within the landscape matrix for the populations in less productive habitats. Our findings suggest that the effect of human impact on genetic diversity may not be straightforward but modulated by the ecological conditions underlying local demographic processes. Populations within both landscapes seem to be vulnerable to loss of genetic diversity, but due to different mechanisms. This has implications for the choice of relevant management actions, that is, increasing population stability may be more relevant within an agricultural landscape still permeable for dispersal, while conserving dispersal corridors may be more appropriate in the forested landscape, to avoid isolation and increased genetic drift.
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Affiliation(s)
- Hanne Haugen
- Department of Forestry and Wildlife ManagementInland Norway University of Applied SciencesHamarNorway
| | - Børre K. Dervo
- Norwegian Institute for Nature Research (NINA)OsloNorway
| | - Kjartan Østbye
- Department of Forestry and Wildlife ManagementInland Norway University of Applied SciencesHamarNorway
- Department of BiosciencesCenter for Ecological and Evolutionary Synthesis (CEES)University of OsloOsloNorway
| | - Jan Heggenes
- Department of Natural Sciences and Environmental HealthUniversity of South‐Eastern NorwayUniversity of South‐Eastern NorwayNotoddenNorway
| | - Olivier Devineau
- Department of Forestry and Wildlife ManagementInland Norway University of Applied SciencesHamarNorway
| | - Arne Linløkken
- Department of Forestry and Wildlife ManagementInland Norway University of Applied SciencesHamarNorway
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11
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Chen X, Wang Q, Cui B, Chen G, Xie T, Yang W. Ecological time lags in biodiversity response to habitat changes. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2023; 346:118965. [PMID: 37741191 DOI: 10.1016/j.jenvman.2023.118965] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Revised: 09/08/2023] [Accepted: 09/08/2023] [Indexed: 09/25/2023]
Abstract
The decline of biodiversity can occur with a substantial delay following habitat loss, degradation, and other environmental changes, such as global warming. Considerable time lags may be involved in these responses. However, such time lags typically pose a significant but often unrecognized challenge for biodiversity conservation across a wide range of taxa and ecosystems. Here, we synthesize the current knowledge, categories, manifestations under different scenarios and impacts of ecological time lags. Our work reveals that studies on ecosystem structure lags are far more than ecosystem process and function lags. Due to the presence of these time-lag effects, the 'window phase' typically exists, which is widely recognized as 'relaxation time', providing a particular opportunity for biodiversity conservation. The manifestations of time lags vary under different scenarios. In addition, the different mechanisms that can result in ecological time lags are hierarchically nested, in which mechanisms at the population and metapopulation level have routinely been suggested as explanations for ecological time lags. It generally takes longer time to reach equilibrium at the metapopulation level than it takes for effects to be fully expressed at the level of individuals. Finally, we propose corresponding implications for biodiversity conservation and management. Our research will provide priorities for science and management on how to address the impact of ecological time lags to mitigate future attrition of biodiversity.
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Affiliation(s)
- Xuejuan Chen
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, School of Environment, Beijing Normal University, Beijing, China
| | - Qing Wang
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, School of Environment, Beijing Normal University, Beijing, China; Research and Development Center for Watershed Environmental Eco-Engineering, Advanced Institute of Natural Sciences, Beijing Normal University, Zhuhai, China; Yellow River Estuary Wetland Ecosystem Observation and Research Station, Ministry of Education, Shandong, China
| | - Baoshan Cui
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, School of Environment, Beijing Normal University, Beijing, China; Research and Development Center for Watershed Environmental Eco-Engineering, Advanced Institute of Natural Sciences, Beijing Normal University, Zhuhai, China; Yellow River Estuary Wetland Ecosystem Observation and Research Station, Ministry of Education, Shandong, China.
| | - Guogui Chen
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, School of Environment, Beijing Normal University, Beijing, China; Research and Development Center for Watershed Environmental Eco-Engineering, Advanced Institute of Natural Sciences, Beijing Normal University, Zhuhai, China
| | - Tian Xie
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, School of Environment, Beijing Normal University, Beijing, China; Yellow River Estuary Wetland Ecosystem Observation and Research Station, Ministry of Education, Shandong, China
| | - Wenxin Yang
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, School of Environment, Beijing Normal University, Beijing, China
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12
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Reem E, Douek J, Rinkevich B. Historical navigation routes in European waters leave their footprint on the contemporary seascape genetics of a colonial urochordate. Sci Rep 2023; 13:19076. [PMID: 37925572 PMCID: PMC10625628 DOI: 10.1038/s41598-023-46174-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2023] [Accepted: 10/28/2023] [Indexed: 11/06/2023] Open
Abstract
Humans have intensively sailed the Mediterranean and European Atlantic waters throughout history, from the upper Paleolithic until today and centuries of human seafaring have established complex coastal and cross-seas navigation networks. Historical literature revealed three major long-lasting maritime routes (eastern, western, northern) with four commencing locations (Alexandria, Venice, Genoa, Gibraltar) and a fourth route (circum-Italian) that connected between them. Due to oceangoing and technological constraints, most voyages were coastal, lasted weeks to months, with extended resting periods, allowing the development of fouling organisms on ship hulls. One of the abiding travellers in maritime routes is the colonial ascidian Botryllus schlosseri already known since the eighteenth century in European and Mediterranean ports. This species, was almost certainly one of the common hull fouling travellers in all trade routes for centuries. Employing COI haplotypes (1008 samples) and microsatellite alleles (995 samples) on colonies sampled from 64 pan-European sites, present-day Botryllus populations in the Mediterranean Sea/European Atlantic revealed significant segregation between all four maritime routes with a conspicuous partition of the northern route. These results reveal that past anthropogenic transports of sedentary marine species throughout millennia long seafaring have left their footprint on contemporary seascape genetics of marine organisms.
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Affiliation(s)
- Eitan Reem
- Israel Oceanography and Limnological Research, National Institute of Oceanography, Tel Shikmona, P.O. Box 9753, 3109701, Haifa, Israel.
| | - Jacob Douek
- Israel Oceanography and Limnological Research, National Institute of Oceanography, Tel Shikmona, P.O. Box 9753, 3109701, Haifa, Israel
| | - Baruch Rinkevich
- Israel Oceanography and Limnological Research, National Institute of Oceanography, Tel Shikmona, P.O. Box 9753, 3109701, Haifa, Israel
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13
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Sherpa S, Paris JR, Silva‐Rocha I, Di Canio V, Carretero MA, Ficetola GF, Salvi D. Genetic depletion does not prevent rapid evolution in island-introduced lizards. Ecol Evol 2023; 13:e10721. [PMID: 38034325 PMCID: PMC10682264 DOI: 10.1002/ece3.10721] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Revised: 10/02/2023] [Accepted: 10/23/2023] [Indexed: 12/02/2023] Open
Abstract
Experimental introductions of species have provided some of the most tractable examples of rapid phenotypic changes, which may reflect plasticity, the impact of stochastic processes, or the action of natural selection. Yet to date, very few studies have investigated the neutral and potentially adaptive genetic impacts of experimental introductions. We dissect the role of these processes in shaping the population differentiation of wall lizards in three Croatian islands (Sušac, Pod Kopište, and Pod Mrčaru), including the islet of Pod Mrčaru, where experimentally introduced lizards underwent rapid (~30 generations) phenotypic changes associated with a shift from an insectivorous to a plant-based diet. Using a genomic approach (~82,000 ddRAD loci), we confirmed a founder effect during introduction and very low neutral genetic differentiation between the introduced population and its source. However, genetic depletion did not prevent rapid population growth, as the introduced lizards exhibited population genetic signals of expansion and are known to have reached a high density. Our genome-scan analysis identified just a handful of loci showing large allelic shifts between ecologically divergent populations. This low overall signal of selection suggests that the extreme phenotypic differences observed among populations are determined by a small number of large-effect loci and/or that phenotypic plasticity plays a major role in phenotypic changes. Nonetheless, functional annotation of the outlier loci revealed some candidate genes relevant to diet-induced adaptation, in agreement with the hypothesis of directional selection. Our study provides important insights on the evolutionary potential of bottlenecked populations in response to new selective pressures on short ecological timescales.
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Affiliation(s)
- Stéphanie Sherpa
- Dipartimento di Scienze e Politiche AmbientaliUniversità degli Studi di MilanoMilanoItaly
| | - Josephine R. Paris
- Dipartimento di Medicina Clinica, Sanità Pubblica, Scienze della Vita e dell'AmbienteUniversità degli Studi dell'AquilaL'Aquila‐CoppitoItaly
| | - Iolanda Silva‐Rocha
- Centro de Investigação em Biodiversidade e Recursos Genéticos (CIBIO), InBIO Laboratório AssociadoUniversidade do PortoVairãoPortugal
- BIOPOLIS Program in Genomics, Biodiversity and Land PlanningCIBIOVairãoPortugal
| | - Viola Di Canio
- Dipartimento di Scienze e Politiche AmbientaliUniversità degli Studi di MilanoMilanoItaly
| | - Miguel Angel Carretero
- Centro de Investigação em Biodiversidade e Recursos Genéticos (CIBIO), InBIO Laboratório AssociadoUniversidade do PortoVairãoPortugal
- BIOPOLIS Program in Genomics, Biodiversity and Land PlanningCIBIOVairãoPortugal
- Departamento de Biologia, Faculdade de CiênciasUniversidade do PortoPortoPortugal
| | | | - Daniele Salvi
- Dipartimento di Medicina Clinica, Sanità Pubblica, Scienze della Vita e dell'AmbienteUniversità degli Studi dell'AquilaL'Aquila‐CoppitoItaly
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14
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Palm EC, Landguth EL, Holden ZA, Day CC, Lamb CT, Frame PF, Morehouse AT, Mowat G, Proctor MF, Sawaya MA, Stenhouse G, Whittington J, Zeller KA. Corridor-based approach with spatial cross-validation reveals scale-dependent effects of geographic distance, human footprint and canopy cover on grizzly bear genetic connectivity. Mol Ecol 2023; 32:5211-5227. [PMID: 37602946 DOI: 10.1111/mec.17098] [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: 03/11/2023] [Revised: 06/17/2023] [Accepted: 07/25/2023] [Indexed: 08/22/2023]
Abstract
Understanding how human infrastructure and other landscape attributes affect genetic differentiation in animals is an important step for identifying and maintaining dispersal corridors for these species. We built upon recent advances in the field of landscape genetics by using an individual-based and multiscale approach to predict landscape-level genetic connectivity for grizzly bears (Ursus arctos) across ~100,000 km2 in Canada's southern Rocky Mountains. We used a genetic dataset with 1156 unique individuals genotyped at nine microsatellite loci to identify landscape characteristics that influence grizzly bear gene flow at multiple spatial scales and map predicted genetic connectivity through a matrix of rugged terrain, large protected areas, highways and a growing human footprint. Our corridor-based modelling approach used a machine learning algorithm that objectively parameterized landscape resistance, incorporated spatial cross validation and variable selection and explicitly accounted for isolation by distance. This approach avoided overfitting, discarded variables that did not improve model performance across withheld test datasets and spatial predictive capacity compared to random cross-validation. We found that across all spatial scales, geographic distance explained more variation in genetic differentiation in grizzly bears than landscape variables. Human footprint inhibited connectivity across all spatial scales, while open canopies inhibited connectivity at the broadest spatial scale. Our results highlight the negative effect of human footprint on genetic connectivity, provide strong evidence for using spatial cross-validation in landscape genetics analyses and show that multiscale analyses provide additional information on how landscape variables affect genetic differentiation.
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Affiliation(s)
- Eric C Palm
- Computational Ecology Lab, School of Public and Community Health Sciences, University of Montana, Missoula, Montana, USA
- Rocky Mountain Research Station, Aldo Leopold Wilderness Research Institute, US Forest Service, Missoula, Montana, USA
| | - Erin L Landguth
- Computational Ecology Lab, School of Public and Community Health Sciences, University of Montana, Missoula, Montana, USA
- Center for Population Health Research, School of Public and Community Health Sciences, University of Montana, Missoula, Montana, USA
| | | | - Casey C Day
- Computational Ecology Lab, School of Public and Community Health Sciences, University of Montana, Missoula, Montana, USA
| | - Clayton T Lamb
- Department of Biology, University of British Columbia, Kelowna, British Columbia, Canada
| | - Paul F Frame
- Fish and Wildlife Stewardship Branch, Government of Alberta, Whitecourt, Alberta, Canada
| | | | - Garth Mowat
- Wildlife & Habitat Branch, British Columbia Ministry of Forests, Lands, Natural Resource Operations & Rural Development, Nelson, British Columbia, Canada
- Department of Earth, Environmental and Geographic Sciences, UBC Okanagan, Kelowna, British Columbia, Canada
| | | | | | | | - Jesse Whittington
- Parks Canada, Banff National Park Resource Conservation, Banff, Alberta, Canada
| | - Katherine A Zeller
- Rocky Mountain Research Station, Aldo Leopold Wilderness Research Institute, US Forest Service, Missoula, Montana, USA
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15
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Mollashahi H, Urbaniak J, Szymura TH, Szymura M. Genetic structure of Trifolium pratense populations in a cityscape. PeerJ 2023; 11:e15927. [PMID: 37692122 PMCID: PMC10487591 DOI: 10.7717/peerj.15927] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Accepted: 07/30/2023] [Indexed: 09/12/2023] Open
Abstract
Urban grasslands provide numerous ecosystem services, and their maintenance should be based on naturally regenerating plant populations. However, the urban environment is challenging for preserving viable populations, mostly because of their high fragmentation and small size, which can lead to genetic drift. We examined red clover (Trifolium pratense) in a medium-size city in Central Europe to test the cityscape effect on within- and among-population genetic diversity. We used eight inter-simple sequence repeat markers to examine the genetic structure of 16 populations, each represented by eight individuals. The isolation by resistance was analysed using a least cost patch approach, focusing on gene flow via pollinators. We found great variation among T. pratense populations, with no discernible geographic pattern in genetic diversity. We linked the diversity to the long history of the city and high stochasticity of land use changes that occurred with city development. In particular, we did not find that the Odra River (ca. 100 m wide) was a strong barrier to gene transfer. However, notable isolation was present due to resistance and distance, indicating that the populations are threatened by genetic drift. Therefore, gene movement between populations should be increased by appropriate management of urban green areas. We also found that small urban grassland (UG) patches with small populations can still hold rare alleles which significantly contribute to the overall genetic variation of T. pratense in the city.
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Affiliation(s)
- Hassanali Mollashahi
- Institute of Agroecology and Plant Production, Wrocław University of Environmental and Life Sciences, Wrocław, Poland
| | - Jacek Urbaniak
- Department of Botany and Plant Ecology, Wrocław University of Environmental and Life Sciences, Wrocław, Poland
| | | | - Magdalena Szymura
- Institute of Agroecology and Plant Production, Wrocław University of Environmental and Life Sciences, Wrocław, Poland
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16
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Antunes B, Figueiredo-Vázquez C, Dudek K, Liana M, Pabijan M, Zieliński P, Babik W. Landscape genetics reveals contrasting patterns of connectivity in two newt species (Lissotriton montandoni and L. vulgaris). Mol Ecol 2023; 32:4515-4530. [PMID: 35593303 DOI: 10.1111/mec.16543] [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: 08/05/2021] [Revised: 03/28/2022] [Accepted: 04/04/2022] [Indexed: 11/30/2022]
Abstract
Ecologically distinct species may respond to landscape changes in different ways. In addition to basic ecological data, the extent of the geographic range has been successfully used as an indicator of species sensitivity to anthropogenic landscapes, with widespread species usually found to be less sensitive compared to range-restricted species. In this study, we investigate connectivity patterns of two closely related but ecologically distinct newt species - the range-restricted, Lissotriton montandoni and the widespread, L. vulgaris - using genomic data, a highly replicated setting (six geographic regions per species), and tools from landscape genetics. Our results show the importance of forest for connectivity in both species, but at the same time suggest differential use of forested habitat, with L. montandoni and L. vulgaris showing the highest connectivity at forest-core and forest-edges, respectively. Anthropogenic landscapes (i.e., higher crop- or urban-cover) increased resistance in both species, but the effect was one to three orders of magnitude stronger in L. montandoni than in L. vulgaris. This result is consistent with a view of L. vulgaris as an ecological generalist. Even so, currently, the negative impact of anthropogenic landscapes is mainly seen in connectivity among L. vulgaris populations, which show significantly stronger isolation and lower effective sizes relative to L. montandoni. Overall, this study emphasizes how habitat destruction is compromising genetic connectivity not only in endemic, range-restricted species of conservation concern but also in widespread generalist species, despite their comparatively lower sensitivity to anthropogenic landscape changes.
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Affiliation(s)
- Bernardo Antunes
- Institute of Environmental Sciences, Faculty of Biology, Jagiellonian University, Kraków, Poland
| | - Clara Figueiredo-Vázquez
- Institute of Environmental Sciences, Faculty of Biology, Jagiellonian University, Kraków, Poland
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Porto, Portugal
| | - Katarzyna Dudek
- Institute of Environmental Sciences, Faculty of Biology, Jagiellonian University, Kraków, Poland
| | | | - Maciej Pabijan
- Institute of Zoology and Biomedical Research, Faculty of Biology, Jagiellonian University, Kraków, Poland
| | - Piotr Zieliński
- Institute of Environmental Sciences, Faculty of Biology, Jagiellonian University, Kraków, Poland
| | - Wiesław Babik
- Institute of Environmental Sciences, Faculty of Biology, Jagiellonian University, Kraków, Poland
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17
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Wu Y, Zhang Z, Hipsey MR, Zhang M. Tidal action enhances coastal wetland plant connectivity. CHEMOSPHERE 2023; 331:138784. [PMID: 37119931 DOI: 10.1016/j.chemosphere.2023.138784] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Revised: 04/18/2023] [Accepted: 04/24/2023] [Indexed: 05/19/2023]
Abstract
Coastal wetlands are being greatly affected by global climate change, and understanding how tides influence plant connectivity can provide a basis for plant conservation and wetland restoration decisions in degraded and at-risk areas. In our study, we quantified the structural and functional connectivity of Suaeda salsa in the Yellow River Delta and explored the impact of tidal action on connectivity. The results showed that plant structural connectivity increased with distance inland from the sea. Similarly, seed connectivity was enhanced but gene connectivity was diminished when moving inland. An increase in the tidal channel branching rate was associated with a significant reduction in plant structural connectivity, and tidal inundation frequency significantly promoted gene connectivity. Tidal action was found to reduce seed circulation and germination, but this effect was not significant. Overall, it was established that plant structural connectivity is not equivalent to functional connectivity and that the effects of tides on structural and functional connectivity are inconsistent. In terms of achieving effective plant connectivity, tides can promote connectivity. In addition, when studying plant connectivity, temporal and spatial scales should be considered. This study provides a more comprehensive and insightful understanding tidal drivers of plant connectivity.
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Affiliation(s)
- Yanan Wu
- College of Ecology and Nature Conservation, Beijing Forestry University, Beijing, 100083, China; The Key Laboratory of Ecological Protection in the Yellow River Basin of National Forestry and Grassland Administration, Beijing, 100083, China
| | - Zhenming Zhang
- College of Ecology and Nature Conservation, Beijing Forestry University, Beijing, 100083, China; The Key Laboratory of Ecological Protection in the Yellow River Basin of National Forestry and Grassland Administration, Beijing, 100083, China.
| | - Matthew R Hipsey
- Centre for Water and Spatial Science, The University of Western Australia, Perth, WA, 6009, Australia
| | - Mingxiang Zhang
- College of Ecology and Nature Conservation, Beijing Forestry University, Beijing, 100083, China; The Key Laboratory of Ecological Protection in the Yellow River Basin of National Forestry and Grassland Administration, Beijing, 100083, China.
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18
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Asadi Aghbolaghi M, Keyghobadi N, Azarakhsh Z, Dadizadeh M, Asadi Aghbolaghi S, Zamani N. An evaluation of isolation by distance and isolation by resistance on genetic structure of the Persian squirrel ( Sciurus anomalus) in the Zagros forests of Iran. Ecol Evol 2023; 13:e10225. [PMID: 37408621 PMCID: PMC10318582 DOI: 10.1002/ece3.10225] [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: 12/08/2022] [Revised: 05/27/2023] [Accepted: 06/11/2023] [Indexed: 07/07/2023] Open
Abstract
For the conservation of wild species, it is important to understand how landscape change and land management can affect gene flow and movement. Landscape genetic analyses provide a powerful approach to infer effects of various landscape factors on gene flow, thereby informing conservation actions. The Persian squirrel is a keystone species in the woodlands and oak forests of Western Asia, where it has experienced recent habitat loss and fragmentation. We conducted landscape genetic analyses of individuals sampled in the northern Zagros Mountains of Iran (provinces of Kurdistan, Kermanshah, and Ilam), focusing on the evaluation of isolation by distance (IBD) and isolation by resistance (IBR), using 16 microsatellite markers. The roles of geographical distance and landscape features including roads, rivers, developed areas, farming and agriculture, forests, lakes, plantation forests, rangelands, shrublands, and rocky areas of varying canopy cover, and swamp margins on genetic structure were quantified using individual-based approaches and resistance surface modeling. We found a significant pattern of IBD but only weak support for an effect of forest cover on genetic structure and gene flow. It seems that geographical distance is an important factor limiting the dispersal of the Persian squirrel in this region. The results of the current study inform ongoing conservation programs for the Persian squirrel in the Zagros oak forest.
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Affiliation(s)
- Marzieh Asadi Aghbolaghi
- Department of Biodiversity and Ecosystem Management, Environmental Sciences Research InstituteShahid Beheshti UniversityTehranIran
| | - Nusha Keyghobadi
- Department of BiologyThe University of Western OntarioLondonCanada
| | - Zeinab Azarakhsh
- Center of Remote Sensing and GIS Research, Faculty of Earth SciencesShahid Beheshti UniversityTehranIran
| | - Marzieh Dadizadeh
- Center of Remote Sensing and GIS Research, Faculty of Earth SciencesShahid Beheshti UniversityTehranIran
| | - Shahab Asadi Aghbolaghi
- Department of Education of Chaharmahal and Bakhtiari Province (Ministry of Education)ShahrekordIran
| | - Navid Zamani
- Department of Environmental Science, Faculty of Natural ResourceUniversity of KurdistanSanandajIran
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19
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Mancini AN, Chandrashekar A, Lahitsara JP, Ogbeta DG, Rajaonarivelo JA, Ranaivorazo NR, Rasoazanakolona J, Safwat M, Solo J, Razafindraibe JG, Razafindrakoto G, Baden AL. Terrain Ruggedness and Canopy Height Predict Short-Range Dispersal in the Critically Endangered Black-and-White Ruffed Lemur. Genes (Basel) 2023; 14:746. [PMID: 36981017 PMCID: PMC10048730 DOI: 10.3390/genes14030746] [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: 01/01/2023] [Revised: 03/06/2023] [Accepted: 03/09/2023] [Indexed: 03/30/2023] Open
Abstract
Dispersal is a fundamental aspect of primates' lives and influences both population and community structuring, as well as species evolution. Primates disperse within an environmental context, where both local and intervening environmental factors affect all phases of dispersal. To date, research has primarily focused on how the intervening landscape influences primate dispersal, with few assessing the effects of local habitat characteristics. Here, we use a landscape genetics approach to examine between- and within-site environmental drivers of short-range black-and-white ruffed lemur (Varecia variegata) dispersal in the Ranomafana region of southeastern Madagascar. We identified the most influential drivers of short-range ruffed lemur dispersal as being between-site terrain ruggedness and canopy height, more so than any within-site habitat characteristic evaluated. Our results suggest that ruffed lemurs disperse through the least rugged terrain that enables them to remain within their preferred tall-canopied forest habitat. Furthermore, we noted a scale-dependent environmental effect when comparing our results to earlier landscape characteristics identified as driving long-range ruffed lemur dispersal. We found that forest structure drives short-range dispersal events, whereas forest presence facilitates long-range dispersal and multigenerational gene flow. Together, our findings highlight the importance of retaining high-quality forests and forest continuity to facilitate dispersal and maintain functional connectivity in ruffed lemurs.
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Affiliation(s)
- Amanda N. Mancini
- Department of Anthropology, The Graduate Center, City University of New York, New York, NY 10016, USA
- The New York Consortium in Evolutionary Primatology (NYCEP), New York, NY 10065, USA
| | - Aparna Chandrashekar
- Department of Anthropology, The Graduate Center, City University of New York, New York, NY 10016, USA
- The New York Consortium in Evolutionary Primatology (NYCEP), New York, NY 10065, USA
| | | | - Daisy Gold Ogbeta
- Department of Nursing, Helene Fuld College of Nursing, New York, NY 10035, USA
- Department of Chemistry, Hunter College, New York, NY 10065, USA
| | - Jeanne Arline Rajaonarivelo
- UMI 233 TransVIHMI, Institut de Recherche pour le Développement (IRD), University of Montpellier, Inserm U 1175, 34000 Montpellier, France
| | | | - Joseane Rasoazanakolona
- Department of Zoology and Animal Biodiversity, Faculty of Science, University of Antananarivo, Antananarivo 101, Madagascar
| | - Mayar Safwat
- Department of Chemistry, Hunter College, New York, NY 10065, USA
| | - Justin Solo
- Centre ValBio Research Center, Ranomafana, Ifanadiana 312, Madagascar (J.G.R.)
| | | | | | - Andrea L. Baden
- Department of Anthropology, The Graduate Center, City University of New York, New York, NY 10016, USA
- The New York Consortium in Evolutionary Primatology (NYCEP), New York, NY 10065, USA
- Department of Anthropology, Hunter College, New York, NY 10065, USA
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20
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Effective dispersal and genetic structure of a small mammal in an intensively managed agricultural landscape: is there any barrier to movement? Evol Ecol 2023. [DOI: 10.1007/s10682-023-10233-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/07/2023]
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21
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Gargiulo R, Waples RS, Grow AK, Shefferson RP, Viruel J, Fay MF, Kull T. Effective population size in a partially clonal plant is not predicted by the number of genetic individuals. Evol Appl 2023; 16:750-766. [PMID: 36969138 PMCID: PMC10033856 DOI: 10.1111/eva.13535] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Revised: 11/22/2022] [Accepted: 02/02/2023] [Indexed: 02/23/2023] Open
Abstract
Estimating effective population size (N e) is important for theoretical and practical applications in evolutionary biology and conservation. Nevertheless, estimates of N e in organisms with complex life-history traits remain scarce because of the challenges associated with estimation methods. Partially clonal plants capable of both vegetative (clonal) growth and sexual reproduction are a common group of organisms for which the discrepancy between the apparent number of individuals (ramets) and the number of genetic individuals (genets) can be striking, and it is unclear how this discrepancy relates to N e. In this study, we analysed two populations of the orchid Cypripedium calceolus to understand how the rate of clonal versus sexual reproduction affected N e. We genotyped >1000 ramets at microsatellite and SNP loci, and estimated contemporary N e with the linkage disequilibrium method, starting from the theoretical expectation that variance in reproductive success among individuals caused by clonal reproduction and by constraints on sexual reproduction would lower N e. We considered factors potentially affecting our estimates, including different marker types and sampling strategies, and the influence of pseudoreplication in genomic data sets on N e confidence intervals. The magnitude of N e/N ramets and N e/N genets ratios we provide may be used as reference points for other species with similar life-history traits. Our findings demonstrate that N e in partially clonal plants cannot be predicted based on the number of genets generated by sexual reproduction, because demographic changes over time can strongly influence N e. This is especially relevant in species of conservation concern in which population declines may not be detected by only ascertaining the number of genets.
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Affiliation(s)
| | - Robin S. Waples
- NOAA Fisheries, Northwest Fisheries Science Center Seattle Washington USA
- University of Washington Seattle Washington USA
| | - Adri K. Grow
- Department of Biological Sciences Smith College Northampton Massachusetts USA
| | | | | | - Michael F. Fay
- Royal Botanic Gardens, Kew Richmond UK
- School of Biological Sciences University of Western Australia Crawley Western Australia Australia
| | - Tiiu Kull
- Estonian University of Life Sciences Tartu Estonia
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22
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Daniel A, Savary P, Foltête JC, Khimoun A, Faivre B, Ollivier A, Éraud C, Moal H, Vuidel G, Garnier S. Validating graph-based connectivity models with independent presence-absence and genetic data sets. CONSERVATION BIOLOGY : THE JOURNAL OF THE SOCIETY FOR CONSERVATION BIOLOGY 2023; 37:e14047. [PMID: 36661070 DOI: 10.1111/cobi.14047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Revised: 11/11/2022] [Accepted: 11/22/2022] [Indexed: 05/11/2023]
Abstract
Habitat connectivity is a key objective of current conservation policies and is commonly modeled by landscape graphs (i.e., sets of habitat patches [nodes] connected by potential dispersal paths [links]). These graphs are often built based on expert opinion or species distribution models (SDMs) and therefore lack empirical validation from data more closely reflecting functional connectivity. Accordingly, we tested whether landscape graphs reflect how habitat connectivity influences gene flow, which is one of the main ecoevolutionary processes. To that purpose, we modeled the habitat network of a forest bird (plumbeous warbler [Setophaga plumbea]) on Guadeloupe with graphs based on expert opinion, Jacobs' specialization indices, and an SDM. We used genetic data (712 birds from 27 populations) to compute local genetic indices and pairwise genetic distances. Finally, we assessed the relationships between genetic distances or indices and cost distances or connectivity metrics with maximum-likelihood population-effects distance models and Spearman correlations between metrics. Overall, the landscape graphs reliably reflected the influence of connectivity on population genetic structure; validation R2 was up to 0.30 and correlation coefficients were up to 0.71. Yet, the relationship among graph ecological relevance, data requirements, and construction and analysis methods was not straightforward because the graph based on the most complex construction method (species distribution modeling) sometimes had less ecological relevance than the others. Cross-validation methods and sensitivity analyzes allowed us to make the advantages and limitations of each construction method spatially explicit. We confirmed the relevance of landscape graphs for conservation modeling but recommend a case-specific consideration of the cost-effectiveness of their construction methods. We hope the replication of independent validation approaches across species and landscapes will strengthen the ecological relevance of connectivity models.
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Affiliation(s)
- Alexandrine Daniel
- Biogéosciences, UMR 6282 CNRS, Université Bourgogne-Franche-Comté, Dijon, France
| | - Paul Savary
- Biogéosciences, UMR 6282 CNRS, Université Bourgogne-Franche-Comté, Dijon, France
- ThéMA, UMR 6049 CNRS, Université de Franche-Comté, Besançon, France
- ARP-Astrance, Paris, France
| | | | - Aurélie Khimoun
- Biogéosciences, UMR 6282 CNRS, Université Bourgogne-Franche-Comté, Dijon, France
| | - Bruno Faivre
- Biogéosciences, UMR 6282 CNRS, Université Bourgogne-Franche-Comté, Dijon, France
| | - Anthony Ollivier
- Biogéosciences, UMR 6282 CNRS, Université Bourgogne-Franche-Comté, Dijon, France
| | - Cyril Éraud
- Office Français de la Biodiversité, Chizé, France
| | | | - Gilles Vuidel
- ThéMA, UMR 6049 CNRS, Université de Franche-Comté, Besançon, France
| | - Stéphane Garnier
- Biogéosciences, UMR 6282 CNRS, Université Bourgogne-Franche-Comté, Dijon, France
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Hubbell JP, Schaefer JF, Kreiser BR. The influence of habitat characteristics on the occupancy and dispersal of two headwater fishes in a dendritic network. Ecosphere 2023. [DOI: 10.1002/ecs2.4388] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Affiliation(s)
- Joshua P. Hubbell
- Department of Biological Sciences Hattiesburg University of Southern Mississippi Hattiesburg Mississippi USA
| | - Jacob F. Schaefer
- Department of Biological Sciences Hattiesburg University of Southern Mississippi Hattiesburg Mississippi USA
| | - Brian R. Kreiser
- Department of Biological Sciences Hattiesburg University of Southern Mississippi Hattiesburg Mississippi USA
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Guo XZ, Wei KJ, Yan RJ, Gardner JPA. Pronounced Mitochondrial DNA Population Genetic Structure in a Brooding Coastal Marine Invertebrate. MALACOLOGIA 2022. [DOI: 10.4002/040.065.0108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Xiang-Zhao Guo
- Key Laboratory of Freshwater Animal Breeding, Ministry of Agriculture and Rural Affairs, College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China
| | - Kai-Jian Wei
- Key Laboratory of Freshwater Animal Breeding, Ministry of Agriculture and Rural Affairs, College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China
| | - Ruo-Jin Yan
- School of Biological Sciences, Victoria University of Wellington, P. O. Box 600, Wellington 6140, New Zealand
| | - Jonathan P. A. Gardner
- School of Biological Sciences, Victoria University of Wellington, P. O. Box 600, Wellington 6140, New Zealand
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25
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As the Goose Flies: Migration Routes and Timing Influence Patterns of Genetic Diversity in a Circumpolar Migratory Herbivore. DIVERSITY 2022. [DOI: 10.3390/d14121067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/07/2022]
Abstract
Migration schedules and the timing of other annual events (e.g., pair formation and molt) can affect the distribution of genetic diversity as much as where these events occur. The greater white-fronted goose (Anser albifrons) is a circumpolar goose species, exhibiting temporal and spatial variation of events among populations during the annual cycle. Previous range-wide genetic assessments of the nuclear genome based on eight microsatellite loci suggest a single, largely panmictic population despite up to five subspecies currently recognized based on phenotypic differences. We used double digest restriction-site associated DNA (ddRAD-seq) and mitochondrial DNA (mtDNA) sequence data to re-evaluate estimates of spatial genomic structure and to characterize how past and present processes have shaped the patterns of genetic diversity and connectivity across the Arctic and subarctic. We uncovered previously undetected inter-population differentiation with genetic clusters corresponding to sampling locales associated with current management groups. We further observed subtle genetic clustering within each management unit that can be at least partially explained by the timing and directionality of migration events along with other behaviors during the annual cycle. The Tule Goose (A. a. elgasi) and Greenland subspecies (A. a. flavirostris) showed the highest level of divergence among all sampling locales investigated. The recovery of previously undetected broad and fine-scale spatial structure suggests that the strong cultural transmission of migratory behavior restricts gene flow across portions of the species’ range. Our data further highlight the importance of re-evaluating previous assessments conducted based on a small number of highly variable genetic markers in phenotypically diverse species.
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26
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Fukano Y, Uchida K, Tachiki Y. Urban-rural gradients: how landscape changes drive adaptive evolution of plant competitive traits. Evol Ecol 2022. [DOI: 10.1007/s10682-022-10215-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
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27
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Arntzen JW. A two-species distribution model for parapatric newts, with inferences on their history of spatial replacement. Biol J Linn Soc Lond 2022. [DOI: 10.1093/biolinnean/blac134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Abstract
Related species often engage in abutting or overlapping contact zones with various strengths of interspecific competition. Biotic interactions such as these preclude the registration of the full profile of environmental variables that would describe the otherwise larger species ranges. Here, I advocate to forego full range species distribution modelling and instead focus on the ecography of the contact zone, for example with ‘two-species distribution models’ (TSDMs), in which presence data are contrasted against the background of environmental data. The newts Triturus cristatus and Triturus marmoratus meet in the west of France. A countrywide TSDM suggests that the contact zone of the species is located at a climatic gradient, in line with their north-eastern vs. south-western ranges. The species are also ecologically segregated by elevation and forestation, which is in line with a documented movement of the contact zone caused by hedgerow removal in lowland areas. Hindcasts for the Holocene suggest that the species contact zone was positioned at either the same place as at present or more to the south, depending on the amount of forestation. A forecast under climate warming predicts a fast movement to the north, but this scenario is deemed unrealistic. One reason is that recent habitat loss compromises dispersal and range expansion. Other species pairs to which TSDMs have been applied are listed for comparison.
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Affiliation(s)
- Jan W Arntzen
- Institute of Biology, Leiden University, Sylvius Laboratory , Sylviusweg 72, 2333 BE Leiden , The Netherlands
- Naturalis Biodiversity Center , Darwinweg 2, 2333 CR Leiden , The Netherlands
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28
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Lee SR, Son DC. Genetic diversity pattern reveals the primary determinant of burcucumber ( Sicyos angulatus L.) invasion in Korea. FRONTIERS IN PLANT SCIENCE 2022; 13:997521. [PMID: 36457533 PMCID: PMC9706109 DOI: 10.3389/fpls.2022.997521] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Accepted: 10/24/2022] [Indexed: 06/17/2023]
Abstract
Biological invasion is a complex process associated with propagule pressure, dispersal ability, environmental constraints, and human interventions, which leave genetic signatures. The population genetics of an invasive species thus provides invaluable insights into the patterns of invasion. Burcucumber, one of the most detrimental weeds for soybean production in US, has recently colonized Korea and rapidly spread posing a great threat to the natural ecosystem. We aim to infer the determinants of the rapid burcucumber invasion by examining the genetic diversity, demography, and spread pattern with advanced genomic tools. We employed 2,696 genome-wide single-nucleotide polymorphisms to assess the level of diversity and the spatial pattern associated with the landscape factors and to infer the demographic changes of 24 populations (364 genotypes) across four major river basins with the east coastal streams in South Korea. Through the approximate Bayesian computation, we inferred the likely invasion scenario of burcucumber in Korea. The landscape genetics approach adopting the circuit theory and MaxEnt model was applied to determine the landscape contributors. Our data suggested that most populations have experienced population bottlenecks, which led to lowered within-population genetic diversity and inflated population divergences. Burcucumber colonization in Korea has strongly been affected by demographic bottlenecks and multiple introductions, whereas environmental factors were not the primary determinant of the invasion. Our work highlighted the significance of preventing secondary introductions, particularly for aggressive weedy plants such as the burcucumber.
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Affiliation(s)
- Soo-Rang Lee
- Department of Biology Education, College of Education, Chosun University, Gwangju, South Korea
| | - Dong Chan Son
- Division of Forest Biodiversity and Herbarium, Korea National Arboretum, Pocheon, South Korea
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29
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Painter LE, Weldy MJ, Crowhurst RS, Carraway LN, Epps CW. Landscape Genetics of the Camas Pocket Gopher (Thomomys bulbivorus), an Endemic Mammal of Oregon's Willamette Valley. WEST N AM NATURALIST 2022. [DOI: 10.3398/064.082.0305] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Luke E. Painter
- Department of Fisheries, Wildlife, and Conservation Sciences, Oregon State University, 104 Nash Hall, 2820 SW Campus Way, Corvallis, OR 97331
| | - Matthew J. Weldy
- Department of Fisheries, Wildlife, and Conservation Sciences, Oregon State University, 104 Nash Hall, 2820 SW Campus Way, Corvallis, OR 97331
| | - Rachel S. Crowhurst
- Department of Fisheries, Wildlife, and Conservation Sciences, Oregon State University, 104 Nash Hall, 2820 SW Campus Way, Corvallis, OR 97331
| | - Leslie N. Carraway
- Department of Fisheries, Wildlife, and Conservation Sciences, Oregon State University, 104 Nash Hall, 2820 SW Campus Way, Corvallis, OR 97331
| | - Clinton W. Epps
- Department of Fisheries, Wildlife, and Conservation Sciences, Oregon State University, 104 Nash Hall, 2820 SW Campus Way, Corvallis, OR 97331
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30
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Phylogeography and population genetics of a headwater-stream adapted crayfish, Cambarus pristinus (Decapoda: Cambaridae), from the Cumberland Plateau in Tennessee. CONSERV GENET 2022. [DOI: 10.1007/s10592-022-01477-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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31
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González‐Bernardo E, Delgado MDM, Matos DGG, Zarzo‐Arias A, Morales‐González A, Ruiz‐Villar H, Skuban M, Maiorano L, Ciucci P, Balbontín J, Penteriani V. The influence of road networks on brown bear spatial distribution and habitat suitability in a human‐modified landscape. J Zool (1987) 2022. [DOI: 10.1111/jzo.13023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- E. González‐Bernardo
- Biodiversity Research Institute (IMIB, Spanish National Research Council CSIC‐ University of Oviedo‐Principality of Asturias) Mieres Spain
| | - M. d. M. Delgado
- Biodiversity Research Institute (IMIB, Spanish National Research Council CSIC‐ University of Oviedo‐Principality of Asturias) Mieres Spain
| | - D. G. G. Matos
- Biodiversity Research Institute (IMIB, Spanish National Research Council CSIC‐ University of Oviedo‐Principality of Asturias) Mieres Spain
| | - A. Zarzo‐Arias
- Department of Applied Geoinformatics and Spatial Planning Faculty of Environmental Sciences Czech University of Life Sciences Prague Suchdol Praha Czech Republic
- Universidad de Oviedo Oviedo Asturias Spain
- Department of Biogeography and Global Change Museo Nacional de Ciencias Naturales (MNCN‐CSIC) 28006 Madrid Spain
| | - A. Morales‐González
- Department of Conservation Biology Estación Biológica de Doñana (EBD‐CSIC) Sevilla Spain
| | - H. Ruiz‐Villar
- Biodiversity Research Institute (IMIB, Spanish National Research Council CSIC‐ University of Oviedo‐Principality of Asturias) Mieres Spain
| | - M. Skuban
- Carpathian Wildlife Society Zvolen Slovakia
- Slovak State Nature Conservancy Banská Bystrica Slovakia
| | - L. Maiorano
- Department of Biology and Biotechnologies “Charles Darwin” University of Rome “La Sapienza” Rome Italy
| | - P. Ciucci
- Department of Biology and Biotechnologies “Charles Darwin” University of Rome “La Sapienza” Rome Italy
| | - J. Balbontín
- Departament of Zoology Faculty of Biology University of Seville Sevilla Spain
| | - V. Penteriani
- Biodiversity Research Institute (IMIB, Spanish National Research Council CSIC‐ University of Oviedo‐Principality of Asturias) Mieres Spain
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32
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Wenner SM, Murphy MA, Delaney KS, Pauly GB, Richmond JQ, Fisher RN, Robertson JM. Natural and anthropogenic landscape factors shape functional connectivity of an ecological specialist in urban Southern California. Mol Ecol 2022; 31:5214-5230. [PMID: 35962747 PMCID: PMC9826396 DOI: 10.1111/mec.16656] [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: 04/27/2022] [Revised: 07/28/2022] [Accepted: 08/11/2022] [Indexed: 01/11/2023]
Abstract
Identifying how natural (i.e., unaltered by human activity) and anthropogenic landscape variables influence contemporary functional connectivity in terrestrial organisms can elucidate the genetic consequences of environmental change. We examine population genetic structure and functional connectivity among populations of a declining species, the Blainville's horned lizard (Phrynosoma blainvillii), in the urbanized landscape of the Greater Los Angeles Area in Southern California, USA. Using single nucleotide polymorphism data, we assessed genetic structure among populations occurring at the interface of two abutting evolutionary lineages, and at a fine scale among habitat fragments within the heavily urbanized area. Based on the ecology of P. blainvillii, we predicted which environmental variables influence population structure and gene flow and used gravity models to distinguish among hypotheses to best explain population connectivity. Our results show evidence of admixture between two evolutionary lineages and strong population genetic structure across small habitat fragments. We also show that topography, microclimate, and soil and vegetation types are important predictors of functional connectivity, and that anthropogenic disturbance, including recent fire history and urban development, are key factors impacting contemporary population dynamics. Examining how natural and anthropogenic sources of landscape variation affect contemporary population genetics is critical to understanding how to best manage sensitive species in a rapidly changing landscape.
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Affiliation(s)
- Sarah M. Wenner
- Department of BiologyCalifornia State UniversityNorthridgeCaliforniaUSA
| | - Melanie A. Murphy
- Department of Ecosystem Science and Management, Program in EcologyUniversity of WyomingLaramieWyomingUSA
| | | | - Gregory B. Pauly
- Department of BiologyCalifornia State UniversityNorthridgeCaliforniaUSA,Natural History Museum of Los Angeles CountyLos AngelesCaliforniaUSA
| | | | - Robert N. Fisher
- US Geological SurveyWestern Ecological Research CenterSan DiegoCaliforniaUSA
| | - Jeanne M. Robertson
- Department of BiologyCalifornia State UniversityNorthridgeCaliforniaUSA,Natural History Museum of Los Angeles CountyLos AngelesCaliforniaUSA
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33
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Feigs JT, Holzhauer SIJ, Huang S, Brunet J, Diekmann M, Hedwall PO, Kramp K, Naaf T. Pollinator movement activity influences genetic diversity and differentiation of spatially isolated populations of clonal forest herbs. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.908258] [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
In agricultural landscapes, forest herbs live in small, spatially isolated forest patches. For their long-term survival, their populations depend on animals as genetic linkers that provide pollen- or seed-mediated gene flow among different forest patches. However, whether insect pollinators serve as genetic linkers among spatially isolated forest herb populations in agricultural landscapes remains to be shown. Here, we used population genetic methods to analyze: (A) the genetic diversity and genetic differentiation of populations of two common, slow-colonizing temperate forest herb species [Polygonatum multiflorum (L.) All. and Anemone nemorosa L.] in spatially isolated populations within three agricultural landscapes in Germany and Sweden and (B) the movement activity of their most relevant associated pollinator species, i.e., the bumblebee Bombus pascuorum (Scopoli, 1,763) and the hoverfly Melanostoma scalare (Fabricus, 1,794), respectively, which differ in their mobility. We tested whether the indicated pollinator movement activity affected the genetic diversity and genetic differentiation of the forest herb populations. Bumblebee movement indicators that solely indicated movement activity between the forest patches affected both genetic diversity and genetic differentiation of the associated forest herb P. multiflorum in a way that can be explained by pollen-mediated gene flow among the forest herb populations. In contrast, movement indicators reflecting the total movement activity at a forest patch (including within-forest patch movement activity) showed unexpected effects for both plant-pollinator pairs that might be explained by accelerated genetic drift due to enhanced sexual reproduction. Our integrated approach revealed that bumblebees serve as genetic linkers of associated forest herb populations, even if they are more than 2 km apart from each other. No such evidence was found for the forest associated hoverfly species which showed significant genetic differentiation among forest patches itself. Our approach also indicated that a higher within-forest patch movement activity of both pollinator species might enhance sexual recruitment and thus diminishes the temporal buffer that clonal growth provides against habitat fragmentation effects.
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34
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A decade of genetic monitoring reveals increased inbreeding for the Endangered western leopard toad, Sclerophrys pantherina. CONSERV GENET 2022. [DOI: 10.1007/s10592-022-01463-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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35
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Hohwieler KR, Villiers DL, Cristescu RH, Frere CH. Genetic erosion detected in a specialist mammal living in a fast‐developing environment. CONSERVATION SCIENCE AND PRACTICE 2022. [DOI: 10.1111/csp2.12738] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Affiliation(s)
- Katrin R. Hohwieler
- Global Change Ecology Research Group University of the Sunshine Coast, School of Science, Technology and Engineering Sippy Down Queensland Australia
| | | | - Romane H. Cristescu
- Global Change Ecology Research Group University of the Sunshine Coast, School of Science, Technology and Engineering Sippy Down Queensland Australia
| | - Celine H. Frere
- School of Biological Sciences University of Queensland St Lucia QLD Australia
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36
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Zimmerman SJ, Aldridge CL, Hooten MB, Oyler-McCance SJ. Scale-dependent influence of the sagebrush community on genetic connectivity of the sagebrush obligate Gunnison sage-grouse. Mol Ecol 2022; 31:3267-3285. [PMID: 35501946 PMCID: PMC9325045 DOI: 10.1111/mec.16470] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Revised: 03/23/2022] [Accepted: 04/01/2022] [Indexed: 11/30/2022]
Abstract
Habitat fragmentation and degradation impacts an organism's ability to navigate the landscape, ultimately resulting in decreased gene flow and increased extinction risk. Understanding how landscape composition impacts gene flow (i.e., connectivity) and interacts with scale is essential to conservation decision‐making. We used a landscape genetics approach implementing a recently developed statistical model based on the generalized Wishart probability distribution to identify the primary landscape features affecting gene flow and estimate the degree to which each component influences connectivity for Gunnison sage‐grouse (Centrocercus minimus). We were interested in two spatial scales: among distinct populations rangewide and among leks (i.e., breeding grounds) within the largest population, Gunnison Basin. Populations and leks are nested within a landscape fragmented by rough terrain and anthropogenic features, although requisite sagebrush habitat is more contiguous within populations. Our best fit models for each scale confirm the importance of sagebrush habitat in connectivity, although the important sagebrush characteristics differ. For Gunnison Basin, taller shrubs and higher quality nesting habitat were the primary drivers of connectivity, while more sagebrush cover and less conifer cover facilitated connectivity rangewide. Our findings support previous assumptions that Gunnison sage‐grouse range contraction is largely the result of habitat loss and degradation. Importantly, we report direct estimates of resistance for landscape components that can be used to create resistance surfaces for prioritization of specific locations for conservation or management (i.e., habitat preservation, restoration, or development) or as we demonstrated, can be combined with simulation techniques to predict impacts to connectivity from potential management actions.
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Affiliation(s)
- Shawna J Zimmerman
- U.S. Geological Survey, Fort Collins Science Center, Fort Collins, Colorado, USA
| | - Cameron L Aldridge
- U.S. Geological Survey, Fort Collins Science Center, Fort Collins, Colorado, USA
| | - Mevin B Hooten
- Department of Statistics and Data Sciences, The University of Texas at Austin, Austin, Texas, USA
| | - Sara J Oyler-McCance
- U.S. Geological Survey, Fort Collins Science Center, Fort Collins, Colorado, USA
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37
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Dalongeville A, Nielsen ES, Teske PR, Heyden S. Comparative phylogeography in a marine biodiversity hotspot provides novel insights into evolutionary processes across the Atlantic‐Indian Ocean transition. DIVERS DISTRIB 2022. [DOI: 10.1111/ddi.13534] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Affiliation(s)
| | - Erica S. Nielsen
- Department of Evolution and Ecology University of California, Davis Davis California USA
| | - Peter R. Teske
- Department of Zoology Centre for Ecological Genomics and Wildlife Conservation University of Johannesburg Auckland Park South Africa
| | - Sophie Heyden
- Department of Botany and Zoology Evolutionary Genomics Group Stellenbosch University Stellenbosch South Africa
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38
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Zhou T, Wang N, Wang Y, Zhang XL, Li BG, Li W, Su JJ, Wang CX, Zhang A, Ma XF, Li ZH. Nucleotide Evolution, Domestication Selection, and Genetic Relationships of Chloroplast Genomes in the Economically Important Crop Genus Gossypium. FRONTIERS IN PLANT SCIENCE 2022; 13:873788. [PMID: 35498673 PMCID: PMC9051515 DOI: 10.3389/fpls.2022.873788] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Accepted: 03/24/2022] [Indexed: 06/14/2023]
Abstract
Gossypium hirsutum (upland cotton) is one of the most economically important crops worldwide, which has experienced the long terms of evolution and domestication process from wild species to cultivated accessions. However, nucleotide evolution, domestication selection, and the genetic relationship of cotton species remain largely to be studied. In this study, we used chloroplast genome sequences to determine the evolutionary rate, domestication selection, and genetic relationships of 72 cotton genotypes (36 cultivated cotton accessions, seven semi-wild races of G. hirsutum, and 29 wild species). Evolutionary analysis showed that the cultivated tetraploid cotton genotypes clustered into a single clade, which also formed a larger lineage with the semi-wild races. Substitution rate analysis demonstrated that the rates of nucleotide substitution and indel variation were higher for the wild species than the semi-wild and cultivated tetraploid lineages. Selection pressure analysis showed that the wild species might have experienced greater selection pressure, whereas the cultivated cotton genotypes underwent artificial and domestication selection. Population clustering analysis indicated that the cultivated cotton accessions and semi-wild races have existed the obviously genetic differentiation. The nucleotide diversity was higher in the semi-wild races compared with the cultivated genotypes. In addition, genetic introgression and gene flow occurred between the cultivated tetraploid cotton and semi-wild genotypes, but mainly via historical rather than contemporary gene flow. These results provide novel molecular mechanisms insights into the evolution and domestication of economically important crop cotton species.
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Affiliation(s)
- Tong Zhou
- Shaanxi Key Laboratory for Animal Conservation, Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), College of Life Sciences, Northwest University, Xi’an, China
| | - Ning Wang
- Shaanxi Key Laboratory for Animal Conservation, Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), College of Life Sciences, Northwest University, Xi’an, China
| | - Yuan Wang
- Shaanxi Key Laboratory for Animal Conservation, Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), College of Life Sciences, Northwest University, Xi’an, China
| | - Xian-Liang Zhang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Bao-Guo Li
- Shaanxi Key Laboratory for Animal Conservation, Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), College of Life Sciences, Northwest University, Xi’an, China
| | - Wei Li
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Jun-Ji Su
- Gansu Provincial Key Laboratory of Aridland Crop Science, College of Life Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Cai-Xiang Wang
- Gansu Provincial Key Laboratory of Aridland Crop Science, College of Life Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Ai Zhang
- Gansu Provincial Key Laboratory of Aridland Crop Science, College of Life Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Xiong-Feng Ma
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Zhong-Hu Li
- Shaanxi Key Laboratory for Animal Conservation, Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), College of Life Sciences, Northwest University, Xi’an, China
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Couch CE, Epps CW. Host, microbiome, and complex space: applying population and landscape genetic approaches to gut microbiome research in wild populations. J Hered 2022; 113:221-234. [PMID: 34983061 DOI: 10.1093/jhered/esab078] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Accepted: 01/03/2022] [Indexed: 11/14/2022] Open
Abstract
In recent years, emerging sequencing technologies and computational tools have driven a tidal wave of research on host-associated microbiomes, particularly the gut microbiome. These studies demonstrate numerous connections between the gut microbiome and vital host functions, primarily in humans, model organisms, and domestic animals. As the adaptive importance of the gut microbiome becomes clearer, interest in studying the gut microbiomes of wild populations has increased, in part due to the potential for discovering conservation applications. The study of wildlife gut microbiomes holds many new challenges and opportunities due to the complex genetic, spatial, and environmental structure of wild host populations, and the potential for these factors to interact with the microbiome. The emerging picture of adaptive coevolution in host-microbiome relationships highlights the importance of understanding microbiome variation in the context of host population genetics and landscape heterogeneity across a wide range of host populations. We propose a conceptual framework for understanding wildlife gut microbiomes in relation to landscape variables and host population genetics, including the potential of approaches derived from landscape genetics. We use this framework to review current research, synthesize important trends, highlight implications for conservation, and recommend future directions for research. Specifically, we focus on how spatial structure and environmental variation interact with host population genetics and microbiome variation in natural populations, and what we can learn from how these patterns of covariation differ depending on host ecological and evolutionary traits.
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Affiliation(s)
- Claire E Couch
- Department of Fisheries, Wildlife, and Conservation Sciences, Oregon State University, Corvallis, Oregon, USA
| | - Clinton W Epps
- Department of Fisheries, Wildlife, and Conservation Sciences, Oregon State University, Corvallis, Oregon, USA
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Butler RG, Lage C, Dobrin SE, Staples JK, Venturini E, Frank J, Drummond FA. Maine's Bumble Bees (Hymenoptera: Apidae)-Part 2: Comparisons of a Common (Bombus ternarius) and a Rare (Bombus terricola) Species. ENVIRONMENTAL ENTOMOLOGY 2021; 50:1358-1369. [PMID: 34532731 DOI: 10.1093/ee/nvab100] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Indexed: 06/13/2023]
Abstract
As part of a quantitative survey of Maine's bumble bee fauna (Butler et al. 2021), we compared and contrasted genetic diversity, parasite and pathogen burdens, and pesticide exposure of the relatively common Bombus ternarius Say, 1937 and the spatially rare Bombus terricola Kirby, 1837. We recorded 11 Bombus species at 40 survey sites across three Maine ecoregions, and B. ternarius was the most common species, while B. terricola was spatially rare. Nonmetric multidimensional scaling indicated that B. terricola was associated with higher elevation sites in Maine, while B. ternarius was more broadly distributed in the state. Pollinator networks constructed for each bee indicated B. ternarius foraged on more plant species than B. terricola, but that there was considerable overlap (73%) in plant species visited. Genetic diversity was greater in the spatially restricted B. terricola, whereas the widely distributed B. ternarius was characterized by greater genetic differentiation among regions. Bombus terricola had higher molecular marker levels of the microsporidian fungi Nosema spp. and the trypanosome Crithidia spp., and both species had high levels of Trypanosoma spp. exposure. No Western Honey Bee (Apis mellifera, Linnaeus, 1758) viruses were detected in either species. Pesticides were not detected in pollen samples collected from workers of either species, and B. ternarius worker tissue samples exhibited only trace levels of diflubenzuron.
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Affiliation(s)
- Ronald G Butler
- Department of Biology, University of Maine, Farmington, ME, USA
| | - Christopher Lage
- College of Arts and Sciences, University of Maine Augusta, Augusta, ME, USA
| | - Scott E Dobrin
- Collegium of Natural Sciences, Eckerd College, St. Petersburg, FL, USA
| | - Joseph K Staples
- Department of Environmental Science and Policy, University of Southern Maine, Gorham, ME, USA
| | - Eric Venturini
- Maine Wild Blueberry Commission, University of Maine, Orono, ME, USA
| | - Jereme Frank
- Maine Forest Service, Department of Agriculture Conservation and Forestry, Old Town, ME, USA
| | - Francis A Drummond
- Professor Emeritus, School of Biology and Ecology, University of Maine, Orono, ME, USA
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Allen JL, McMullin RT, Wiersma YF, Scheidegger C. Population genetics and biogeography of the lungwort lichen in North America support distinct Eastern and Western gene pools. AMERICAN JOURNAL OF BOTANY 2021; 108:2416-2424. [PMID: 34634140 DOI: 10.1002/ajb2.1774] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Revised: 09/20/2021] [Accepted: 09/21/2021] [Indexed: 06/13/2023]
Abstract
PREMISE Populations of species with large spatial distributions are shaped by complex forces that differ throughout their ranges. To maintain the genetic diversity of species, genepool-based subsets of widespread species must be considered in conservation assessments. METHODS The population genetics of the lichenized fungus Lobaria pulmonaria and its algal partner, Symbiochloris reticulata, were investigated using microsatellite markers to determine population structure, genetic diversity, and degree of congruency in eastern and western North America. Data loggers measuring temperature and humidity were deployed at selected populations in eastern North America to test for climatic adaptation. To better understand the role Pleistocene glaciations played in shaping population patterns, a North American, range-wide species distribution model was constructed and hindcast to 22,000 years before present and at 500-year time slices from then to the present. RESULTS The presence of two gene pools with minimal admixture was supported, one in the U.S. Pacific Northwest and one in eastern North America. Western populations were significantly more genetically diverse than eastern populations. There was no evidence for climatic adaptation among eastern populations, though there was evidence for range-wide adaptation to evapotranspiration rates. Hindcast distribution models suggest that observed genetic diversity may be due to a drastic Pleistocene range restriction in eastern North America, whereas a substantial coastal refugial area is inferred in the west. CONCLUSIONS Taken together the results show different, complex population histories of L. pulmonaria in eastern and western North America, and suggest that conservation planning for each gene pool should be considered separately.
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Affiliation(s)
- Jessica L Allen
- Eastern Washington University, Biology Department, Cheney, Washington, 99004, USA
- Swiss Federal Institute for Forest, Snow, and Landscape Research WSL, Department of Biodiversity and Conservation Biology, Birmensdorf, 8903, Switzerland
| | - R Troy McMullin
- Canadian Museum of Nature, Research and Collections, Ottawa, Ontario, K1P 6P4, Canada
| | - Yolanda F Wiersma
- Memorial University of Newfoundland and Labrador, Department of Biology, St. John's, Newfoundland and Labrador, A1C 5S7, Canada
| | - Christoph Scheidegger
- Swiss Federal Institute for Forest, Snow, and Landscape Research WSL, Department of Biodiversity and Conservation Biology, Birmensdorf, 8903, Switzerland
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Luiken JM, Gamble T, Berendzen PB. Comparative riverscape genomics of the rainbow darter ( Etheostoma caeruleum) in glaciated and unglaciated environments. Ecol Evol 2021; 11:18305-18318. [PMID: 35003674 PMCID: PMC8717317 DOI: 10.1002/ece3.8422] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Revised: 11/10/2021] [Accepted: 11/11/2021] [Indexed: 11/11/2022] Open
Abstract
Periodic glaciation during the Quaternary period shaped the contemporary riverscape and distribution of freshwater fishes in the Mississippi River drainage of central North America. The rainbow darter (Etheostoma caeruleum) is a member of this ichthyofauna and has a disjunct distribution in glaciated and unglaciated environments west of the Mississippi River. Based on glacial history of the region, there are different expectations on the observed spatial genetic structure of populations in these environments. The aim of this study was to utilize genome-wide SNP data to compare the population genomic structure of the rainbow darter in river networks with disparate glacial histories; the Volga River in the glaciated upper Mississippi River basin and the Meramec River in the unglaciated Ozark Plateau. Individuals were sampled from localities within each river system at distances dictated by the organismal life history and habitat preferences. Riverscape analyses were performed on three datasets: total combined localities of both rivers and one for each river independently. The results revealed a lasting influence of historic glaciation on the population genomic structure of rainbow darter populations. There was evidence of population expansion into the glaciated northern region following glacial retreat. The population genetic signature within the Volga River did not fit expectations of the stream hierarchy model, but revealed a pattern of repeated colonization and extirpation due to cyclic glaciation. The population within the unglaciated Meramec River adhered to the stream hierarchy model, with a directional order of genetic diversity based on the life history and habitat preferences of the species. These results demonstrate the importance of considering the geologic and climatic history of a region as well as the life history of an organism when interpreting spatial genetic patterns.
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Affiliation(s)
- Jon M. Luiken
- Department of BiologyUniversity of Northern IowaCedar FallsIowaUSA
| | - Tony Gamble
- Department of Biological SciencesMarquette UniversityMilwaukeeWisconsinUSA
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Sousa R, Vasconcelos J, Vera-Escalona I, Pinto AR, Hawkins SJ, Freitas M, Delgado J, González JA, Riera R. Pleistocene expansion, anthropogenic pressure and ocean currents: Disentangling the past and ongoing evolutionary history of Patella aspera Röding, 1798 in the archipelago of Madeira. MARINE ENVIRONMENTAL RESEARCH 2021; 172:105485. [PMID: 34715642 DOI: 10.1016/j.marenvres.2021.105485] [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: 07/10/2021] [Revised: 09/12/2021] [Accepted: 09/18/2021] [Indexed: 06/13/2023]
Abstract
AIMS Rising sea-level following the Last Glacial Maximum lead to fragmentation of coastal limpet populations between islands of the Archipelago of Madeira. This fragmentation is reinforced by recent heavy exploitation reducing effective population size on Madeira Island. We use the limpet P. aspera to understand how the role of processes at different time scales (i.e. changes in the sea level and overexploitation) can influence the genetic composition of an extant species, relating these processes to reproductive phenology and seasonal shifts in ocean currents. LOCATION Madeira Island, Porto Santo and Desertas (Archipelago of Madeira, NE Atlantic Ocean). TAXON The limpet Patella aspera. METHODS Twelve microsatellite genetic markers were used. A power analysis was used to evaluate the power of the microsatellite markers to detect a signal of population differentiation. Long-term past migrations were assessed using a Bayesian Markov Montecarlo approach in the software MIGRATE-n to estimate mutation-scaled migration rates (M = m/μ; m, probability of a lineage immigrating per generation; μ, mutation rate). Two scenarios were evaluated using an Approximate Bayesian Computation (ABC) in the software DIYABC 2.1 (i) Scenario 1: considered a population scenario from a reduced Ne at time t3 to a higher Ne at time t2; and (ii) Scenario 2 considering a reduction of Ne from a time t3 to a time t2. RESULTS Colonization of the archipelago by Portuguese settlers six centuries ago probably led to an important decrease in the genetic diversity of the species (Ne). Contemporary gene flow strongly support a pattern of high asymmetric connectivity explained by the reproductive phenology of the species and spatio-temporal seasonal changes in the ocean currents. Spatio-temporal reconstructions using Bayesian methods, including coalescent and Approximate Bayesian Computation (ABC) approaches, suggest changes in the migration patterns from highly symmetric to highly asymmetric connectivity with subtle population differentiation as consequence of post-glacial maximum sea level rise during the Holocene. MAIN CONCLUSIONS Our results suggest that anthropogenic activity could have had serious effects on the genetic diversity of heavily exploited littoral species since the end of the Pleistocene, probably accelerating in recent years.
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Affiliation(s)
- Ricardo Sousa
- Observatório Oceânico da Madeira, Agência Regional para o Desenvolvimento da Investigação Tecnologia e Inovação (OOM/ARDITI) - Edifício Madeira Tecnopolo, Funchal, Madeira, Portugal; Direção Regional do Mar (DRM)/ Direção de Serviços de Monitorização, Estudos e Investigação do Mar (DSEIMar), 9004-562, Funchal, Madeira, Portugal; MARE - Marine and Environmental Sciences Centre, Agência Regional para o Desenvolvimento da Investigação Tecnologia e Inovação (ARDITI), Edifício Madeira Tecnopolo Piso 0, Caminho da Penteada, 9020-105, Funchal, Madeira, Portugal
| | - Joana Vasconcelos
- MARE - Marine and Environmental Sciences Centre, Agência Regional para o Desenvolvimento da Investigação Tecnologia e Inovação (ARDITI), Edifício Madeira Tecnopolo Piso 0, Caminho da Penteada, 9020-105, Funchal, Madeira, Portugal; Faculdade de Ciências de Vida, Universidade da Madeira, Campus Universitário da Madeira, Caminho da Penteada, 9020-020, Funchal, Madeira, Portugal; Departamento de Ecología, Facultad de Ciencias, Universidad Católica de la Santísima Concepción, Casilla 297, Concepción, Chile
| | - Iván Vera-Escalona
- CIBAS, Facultad de Ciencias, Universidad Católica de la Santísima Concepción, Casilla 297, Concepción, Chile; IU-ECOAQUA, Group of Biodiversity and Conservation (BIOCON), Universidad de Las Palmas de Gran Canaria, Las Palmas de Gran Canaria, Spain
| | - Ana Rita Pinto
- Direção Regional do Mar (DRM)/ Direção de Serviços de Monitorização, Estudos e Investigação do Mar (DSEIMar), 9004-562, Funchal, Madeira, Portugal
| | - S J Hawkins
- Marine Biological Association of the UK, Plymouth, PL1 2PB, UK; School of Ocean and Earth Science, University of Southampton, National Oceanography Centre, Southampton, SO14 3ZH, UK
| | - Mafalda Freitas
- Observatório Oceânico da Madeira, Agência Regional para o Desenvolvimento da Investigação Tecnologia e Inovação (OOM/ARDITI) - Edifício Madeira Tecnopolo, Funchal, Madeira, Portugal; Direção Regional do Mar (DRM)/ Direção de Serviços de Monitorização, Estudos e Investigação do Mar (DSEIMar), 9004-562, Funchal, Madeira, Portugal; MARE - Marine and Environmental Sciences Centre, Agência Regional para o Desenvolvimento da Investigação Tecnologia e Inovação (ARDITI), Edifício Madeira Tecnopolo Piso 0, Caminho da Penteada, 9020-105, Funchal, Madeira, Portugal
| | - João Delgado
- Direção Regional do Mar (DRM)/ Direção de Serviços de Monitorização, Estudos e Investigação do Mar (DSEIMar), 9004-562, Funchal, Madeira, Portugal; Centro Interdisciplinar de Investigação Marinha e Ambiental (CIIMAR/CIMAR), Porto, Portugal
| | - José A González
- Ecología Marina Aplicada y Pesquerías (i-UNAT), Universidad de Las Palmas de Gran Canaria, Las Palmas de Gran Canaria, Spain
| | - Rodrigo Riera
- Departamento de Ecología, Facultad de Ciencias, Universidad Católica de la Santísima Concepción, Casilla 297, Concepción, Chile; IU-ECOAQUA, Group of Biodiversity and Conservation (BIOCON), Universidad de Las Palmas de Gran Canaria, Las Palmas de Gran Canaria, Spain.
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Mulvaney JM, Matthee CA, Cherry MI. Species-landscape interactions drive divergent population trajectories in four forest-dependent Afromontane forest songbird species within a biodiversity hotspot in South Africa. Evol Appl 2021; 14:2680-2697. [PMID: 34815747 PMCID: PMC8591328 DOI: 10.1111/eva.13306] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Revised: 07/19/2021] [Accepted: 09/26/2021] [Indexed: 11/27/2022] Open
Abstract
Species confined to naturally fragmented habitats may exhibit intrinsic population complexity which may challenge interpretations of species response to anthropogenic landscape transformation. In South Africa, where native forests are naturally fragmented, forest-dependent birds have undergone range declines since 1992, most notably among insectivores. These insectivores appear sensitive to the quality of natural matrix habitats, and it is unknown whether transformation of the landscape matrix has disrupted gene flow in these species. We undertook a landscape genetics study of four forest-dependent insectivorous songbirds across southeast South Africa. Microsatellite data were used to conduct a priori optimization of landscape resistance surfaces (land cover, rivers and dams, and elevation) using cost-distances along least-cost pathway (LCP), and resistance distances (IBR). We detected pronounced declines in effective population sizes over the past two centuries for the endemic forest specialist Cossypha dichroa and Batis capensis, alongside recent gene flow disruption in B. capensis, C. dichroa and Pogonocichla stellata. Landscape resistance modelling showed both native forest and dense thicket configuration facilitates gene flow in P. stellata, B. capensis and C. dichroa. Facultative dispersal of P. stellata through dense thicket likely aided resilience against historic landscape transformation, whereas combined forest-thicket degradation adversely affected the forest generalist B. capensis. By contrast, Phylloscopus ruficapilla appears least reliant upon landscape features to maintain gene flow and was least impacted by anthropogenic landscape transformation. Collectively, gene flow in all four species is improved at lower elevations, along river valleys, and riparian corridors- where native forest and dense thicket better persist. Consistent outperformance of LCP over IBR land-cover models for P. stellata, B. capensis and C. dichroa demonstrates the benefits of wildlife corridors for South African forest-dependent bird conservation, to ameliorate the extinction debts from past and present anthropogenic forest exploitation.
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Affiliation(s)
- Jake M. Mulvaney
- Department of Botany and ZoologyStellenbosch UniversityMatielandSouth Africa
| | - Conrad A. Matthee
- Department of Botany and ZoologyStellenbosch UniversityMatielandSouth Africa
| | - Michael I. Cherry
- Department of Botany and ZoologyStellenbosch UniversityMatielandSouth Africa
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Chaves CJN, Leal BSS, Rossatto DR, Berger U, Palma-Silva C. Deforestation is the turning point for the spreading of a weedy epiphyte: an IBM approach. Sci Rep 2021; 11:20397. [PMID: 34650134 PMCID: PMC8516858 DOI: 10.1038/s41598-021-99798-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Accepted: 09/27/2021] [Indexed: 11/08/2022] Open
Abstract
The rapid spread of many weeds into intensely disturbed landscapes is boosted by clonal growth and self-fertilization strategies, which conversely increases the genetic structure of populations. Here, we use empirical and modeling approaches to evaluate the spreading dynamics of Tillandsia recurvata (L.) L. populations, a common epiphytic weed with self-reproduction and clonal growth widespread in dry forests and deforested landscapes in the American continent. We introduce the TRec model, an individual-based approach to simulate the spreading of T. recurvata over time and across landscapes subjected to abrupt changes in tree density with the parameters adjusted according to the empirical genetic data based on microsatellites genotypes. Simulations with this model showed that the strong spatial genetic structure observed from empirical data in T. recurvata can be explained by a rapid increase in abundance and gene flow followed by stabilization after ca. 25 years. TRec model's results also indicate that deforestation is a turning point for the rapid increase in both individual abundance and gene flow among T. recurvata subpopulations occurring in formerly dense forests. Active reforestation can, in turn, reverse such a scenario, although with a milder intensity. The genetic-based study suggests that anthropogenic changes in landscapes may strongly affect the population dynamics of species with 'weedy' traits.
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Affiliation(s)
- Cleber Juliano Neves Chaves
- Programa de Pós-Graduação em Ecologia e Biodiversidade, Instituto de Biociências, Universidade Estadual Paulista, Rio Claro, 13506-900, Brazil.
- Departamento de Biologia Vegetal, Instituto de Biologia, Universidade Estadual de Campinas, Campinas, 13083-862, Brazil.
| | - Bárbara Simões Santos Leal
- Programa de Pós-Graduação em Ecologia e Biodiversidade, Instituto de Biociências, Universidade Estadual Paulista, Rio Claro, 13506-900, Brazil
- Departamento de Biologia Vegetal, Instituto de Biologia, Universidade Estadual de Campinas, Campinas, 13083-862, Brazil
| | - Davi Rodrigo Rossatto
- Departamento de Biologia, Universidade Estadual Paulista, Jaboticabal, 14884-900, Brazil
| | - Uta Berger
- Institute of Forest Growth and Computer Sciences, Technische Universität Dresden, 01737, Tharandt, Germany
| | - Clarisse Palma-Silva
- Departamento de Biologia Vegetal, Instituto de Biologia, Universidade Estadual de Campinas, Campinas, 13083-862, Brazil
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Garrick RC, Arantes ÍC, Stubbs MB, Havill NP. Weak spatial-genetic structure in a native invasive, the southern pine beetle ( Dendroctonus frontalis), across the eastern United States. PeerJ 2021; 9:e11947. [PMID: 34557344 PMCID: PMC8418799 DOI: 10.7717/peerj.11947] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Accepted: 07/20/2021] [Indexed: 11/20/2022] Open
Abstract
The southern pine beetle, Dendroctonus frontalis, is a native pest of pine trees that has recently expanded its range into the northeastern United States. Understanding its colonization, dispersal, and connectivity will be critical for mitigating negative economic and ecological impacts in the newly invaded areas. Characterization of spatial-genetic structure can contribute to this; however, previous studies have reached different conclusions about regional population genetic structure, with one study reporting a weak east-west pattern, and the most recent reporting an absence of structure. Here we systematically assessed several explanations for the absence of spatial-genetic structure. To do this, we developed nine new microsatellite markers and combined them with an existing 24-locus data matrix for the same individuals. We then reanalyzed this full dataset alongside datasets in which certain loci were omitted with the goal of creating more favorable signal to noise ratios. We also partitioned the data based on the sex of D. frontalis individuals, and then employed a broad suite of genotypic clustering and isolation-by-distance (IBD) analyses. We found that neither inadequate information content in the molecular marker set, nor unfavorable signal-to-noise ratio, nor insensitivity of the analytical approaches could explain the absence of structure. Regardless of dataset composition, there was little evidence for clusters (i.e., distinct geo-genetic groups) or clines (i.e., gradients of increasing allele frequency differences over larger geographic distances), with one exception: significant IBD was repeatedly detected using an individual-based measure of relatedness whenever datasets included males (but not for female-only datasets). This is strongly indicative of broad-scale female-biased dispersal, which has not previously been reported for D. frontalis, in part owing to logistical limitations of direct approaches (e.g., capture-mark-recapture). Weak spatial-genetic structure suggests long-distance connectivity and that gene flow is high, but additional research is needed to understand range expansion and outbreak dynamics in this species using alternate approaches.
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Affiliation(s)
- Ryan C Garrick
- Department of Biology, University of Mississippi, Oxford, MS, United States of America
| | - Ísis C Arantes
- Department of Biology, University of Mississippi, Oxford, MS, United States of America
| | - Megan B Stubbs
- Department of Biology, University of Mississippi, Oxford, MS, United States of America
| | - Nathan P Havill
- Northern Research Station, USDA Forest Service, Hamden, CT, United States of America
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Demographic modeling informs functional connectivity and management interventions in Graham’s beardtongue. CONSERV GENET 2021. [DOI: 10.1007/s10592-021-01392-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
AbstractFunctional connectivity (i.e., the movement of individuals across a landscape) is essential for the maintenance of genetic variation and persistence of rare species. However, illuminating the processes influencing functional connectivity and ultimately translating this knowledge into management practice remains a fundamental challenge. Here, we combine various population structure analyses with pairwise, population-specific demographic modeling to investigate historical functional connectivity in Graham’s beardtongue (Penstemon grahamii), a rare plant narrowly distributed across a dryland region of the western US. While principal component and population structure analyses indicated an isolation-by-distance pattern of differentiation across the species’ range, spatial inferences of effective migration exposed an abrupt shift in population ancestry near the range center. To understand these seemingly conflicting patterns, we tested various models of historical gene flow and found evidence for recent admixture (~ 3400 generations ago) between populations near the range center. This historical perspective reconciles population structure patterns and suggests management efforts should focus on maintaining connectivity between these previously isolated lineages to promote the ongoing transfer of genetic variation. Beyond providing species-specific knowledge to inform management options, our study highlights how understanding demographic history may be critical to guide conservation efforts when interpreting population genetic patterns and inferring functional connectivity.
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Reinula I, Träger S, Hernández‐Agramonte IM, Helm A, Aavik T. Landscape genetic analysis suggests stronger effects of past than current landscape structure on genetic patterns of
Primula veris. DIVERS DISTRIB 2021. [DOI: 10.1111/ddi.13357] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Affiliation(s)
- Iris Reinula
- Department of Botany Institute of Ecology and Earth Sciences University of Tartu Tartu Estonia
| | - Sabrina Träger
- Department of Botany Institute of Ecology and Earth Sciences University of Tartu Tartu Estonia
- Institute of Biology/Geobotany and Botanical Garden Martin‐Luther‐University Halle‐Wittenberg Halle (Saale) Germany
| | | | - Aveliina Helm
- Department of Botany Institute of Ecology and Earth Sciences University of Tartu Tartu Estonia
| | - Tsipe Aavik
- Department of Botany Institute of Ecology and Earth Sciences University of Tartu Tartu Estonia
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Epps CW, Petro VM, Creech TG, Crowhurst RS, Weldy MJ, Taylor JD. Landscape Genetics of American Beaver in Coastal Oregon. J Wildl Manage 2021. [DOI: 10.1002/jwmg.22102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Clinton W. Epps
- Department of Fisheries and Wildlife Oregon State University Corvallis OR 97331 USA
| | - Vanessa M. Petro
- Department of Forest Ecosystems and Society Oregon State University 321 Richardson Hall Corvallis OR 97331 USA
| | - Tyler G. Creech
- Department of Fisheries and Wildlife Oregon State University Corvallis OR 97331 USA
| | - Rachel S. Crowhurst
- Department of Fisheries and Wildlife Oregon State University Corvallis OR 97331 USA
| | - Matthew J. Weldy
- Department of Fisheries and Wildlife Oregon State University Corvallis OR 97331 USA
| | - Jimmy D. Taylor
- USDA, APHIS, National Wildlife Research Center Oregon Field Station 321 Richardson Hall Corvallis OR 97331 USA
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Population genetics informs the management of a controversial Australian waterbird. CONSERV GENET 2021. [DOI: 10.1007/s10592-021-01393-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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