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Guan B, Liu Q, Liu X, Gong X. Environment influences the genetic structure and genetic differentiation of Sassafras tzumu (Lauraceae). BMC Ecol Evol 2024; 24:80. [PMID: 38872114 PMCID: PMC11170782 DOI: 10.1186/s12862-024-02264-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Accepted: 05/24/2024] [Indexed: 06/15/2024] Open
Abstract
BACKGROUND Sassafras tzumu, an elegant deciduous arboreal species, belongs to the esteemed genus Sassafras within the distinguished family Lauraceae. With its immense commercial value, escalating market demands and unforeseen human activities within its natural habitat have emerged as new threats to S. tzumu in recent decades, so it is necessary to study its genetic diversity and influencing factors, to propose correlative conservation strategies. RESULTS By utilizing genotyping-by-sequence (GBS) technology, we acquired a comprehensive database of single nucleotide polymorphisms (SNPs) from a cohort of 106 individuals sourced from 13 diverse Sassafras tzumu natural populations, scattered across various Chinese mountainous regions. Through our meticulous analysis, we aimed to unravel the intricate genetic diversity and structure within these S. tzumu populations, while simultaneously investigating the various factors that potentially shape genetic distance. Our preliminary findings unveiled a moderate level of genetic differentiation (FST = 0.103, p < 0.01), accompanied by a reasonably high genetic diversity among the S. tzumu populations. Encouragingly, our principal component analysis painted a vivid picture of two distinct genetic and geographical regions across China, where gene flow appeared to be somewhat restricted. Furthermore, employing the sophisticated multiple matrix regression with randomization (MMRR) analysis method, we successfully ascertained that environmental distance exerted a more pronounced impact on genetic distance when compared to geographical distance (βE = 0.46, p < 0.01; βD = 0.16, p < 0.01). This intriguing discovery underscores the potential significance of environmental factors in shaping the genetic landscape of S. tzumu populations. CONCLUSIONS The genetic variance among populations of S. tzumu in our investigation exhibited a moderate degree of differentiation, alongside a heightened level of genetic diversity. The environmental distance of S. tzumu had a greater impact on its genetic diversity than geographical distance. It is of utmost significance to formulate and implement meticulous management and conservation strategies to safeguard the invaluable genetic resources of S. tzumu.
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Affiliation(s)
- Bicai Guan
- School of Life Sciences, Nanchang University, Nanchang, 330031, China
| | - Qian Liu
- School of Life Sciences, Nanchang University, Nanchang, 330031, China
| | - Xiang Liu
- School of Life Sciences, Nanchang University, Nanchang, 330031, China
| | - Xi Gong
- School of Life Sciences, Nanchang University, Nanchang, 330031, China.
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2
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Fonseca EM, Pope NS, Peterman WE, Werneck FP, Colli GR, Carstens BC. Genetic structure and landscape effects on gene flow in the Neotropical lizard Norops brasiliensis (Squamata: Dactyloidae). Heredity (Edinb) 2024; 132:284-295. [PMID: 38575800 PMCID: PMC11166928 DOI: 10.1038/s41437-024-00682-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Revised: 03/12/2024] [Accepted: 03/18/2024] [Indexed: 04/06/2024] Open
Abstract
One key research goal of evolutionary biology is to understand the origin and maintenance of genetic variation. In the Cerrado, the South American savanna located primarily in the Central Brazilian Plateau, many hypotheses have been proposed to explain how landscape features (e.g., geographic distance, river barriers, topographic compartmentalization, and historical climatic fluctuations) have promoted genetic structure by mediating gene flow. Here, we asked whether these landscape features have influenced the genetic structure and differentiation in the lizard species Norops brasiliensis (Squamata: Dactyloidae). To achieve our goal, we used a genetic clustering analysis and estimate an effective migration surface to assess genetic structure in the focal species. Optimized isolation-by-resistance models and a simulation-based approach combined with machine learning (convolutional neural network; CNN) were then used to infer current and historical effects on population genetic structure through 12 unique landscape models. We recovered five geographically distributed populations that are separated by regions of lower-than-expected gene flow. The results of the CNN showed that geographic distance is the sole predictor of genetic variation in N. brasiliensis, and that slope, rivers, and historical climate had no discernible influence on gene flow. Our novel CNN approach was accurate (89.5%) in differentiating each landscape model. CNN and other machine learning approaches are still largely unexplored in landscape genetics studies, representing promising avenues for future research with increasingly accessible genomic datasets.
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Affiliation(s)
- Emanuel M Fonseca
- Department of Evolution, Ecology and Organismal Biology, The Ohio State University, Columbus, OH, USA
| | - Nathaniel S Pope
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR, 97403, USA
| | - William E Peterman
- School of Environment and Natural Resources, The Ohio State University, Columbus, OH, USA
| | - Fernanda P Werneck
- Coordenação de Biodiversidade, Programa de Coleções Científicas Biológicas, Instituto Nacional de Pesquisas da Amazônia (INPA), Manaus, Brazil
| | - Guarino R Colli
- Departamento de Zoologia, Universidade de Brasília, Brasília, Brazil
| | - Bryan C Carstens
- Department of Evolution, Ecology and Organismal Biology, The Ohio State University, Columbus, OH, USA.
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3
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Walter WD, Fameli A, Russo‐Petrick K, Edson JE, Rosenberry CS, Schuler KL, Tonkovich MJ. Large-scale assessment of genetic structure to assess risk of populations of a large herbivore to disease. Ecol Evol 2024; 14:e11347. [PMID: 38774134 PMCID: PMC11106048 DOI: 10.1002/ece3.11347] [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: 10/27/2023] [Revised: 03/28/2024] [Accepted: 04/12/2024] [Indexed: 05/24/2024] Open
Abstract
Chronic wasting disease (CWD) can spread among cervids by direct and indirect transmission, the former being more likely in emerging areas. Identifying subpopulations allows the delineation of focal areas to target for intervention. We aimed to assess the population structure of white-tailed deer (Odocoileus virginianus) in the northeastern United States at a regional scale to inform managers regarding gene flow throughout the region. We genotyped 10 microsatellites in 5701 wild deer samples from Maryland, New York, Ohio, Pennsylvania, and Virginia. We evaluated the distribution of genetic variability through spatial principal component analysis and inferred genetic structure using non-spatial and spatial Bayesian clustering algorithms (BCAs). We simulated populations representing each inferred wild cluster, wild deer in each state and each physiographic province, total wild population, and a captive population. We conducted genetic assignment tests using these potential sources, calculating the probability of samples being correctly assigned to their origin. Non-spatial BCA identified two clusters across the region, while spatial BCA suggested a maximum of nine clusters. Assignment tests correctly placed deer into captive or wild origin in most cases (94%), as previously reported, but performance varied when assigning wild deer to more specific origins. Assignments to clusters inferred via non-spatial BCA performed well, but efficiency was greatly reduced when assigning samples to clusters inferred via spatial BCA. Differences between spatial BCA clusters are not strong enough to make assignment tests a reliable method for inferring the geographic origin of deer using 10 microsatellites. However, the genetic distinction between clusters may indicate natural and anthropogenic barriers of interest for management.
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Affiliation(s)
- W. David Walter
- U.S. Geological Survey, Pennsylvania Cooperative Fish and Wildlife Research UnitThe Pennsylvania State UniversityUniversity ParkPennsylvaniaUSA
| | - Alberto Fameli
- Pennsylvania Cooperative Fish and Wildlife Research UnitThe Pennsylvania State UniversityUniversity ParkPennsylvaniaUSA
| | - Kelly Russo‐Petrick
- Pennsylvania Cooperative Fish and Wildlife Research UnitThe Pennsylvania State UniversityUniversity ParkPennsylvaniaUSA
| | - Jessie E. Edson
- Pennsylvania Cooperative Fish and Wildlife Research UnitThe Pennsylvania State UniversityUniversity ParkPennsylvaniaUSA
| | | | - Krysten L. Schuler
- Cornell Wildlife Health Lab, New York State Wildlife Health ProgramIthacaNew YorkUSA
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4
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Rodrigues NT, Saranholi BH, Inforzato AR, Silveira L, Desbiez ALJ, Galetti PM. Reduced gene flow and bottleneck in the threatened giant armadillo (Priodontes maximus): implications for its conservation. Genet Mol Biol 2024; 47:e20230252. [PMID: 38446984 PMCID: PMC10917080 DOI: 10.1590/1678-4685-gmb-2023-0252] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Accepted: 12/30/2023] [Indexed: 03/08/2024] Open
Abstract
The progressive fragmentation and loss of habitats represent the main threats for endangered species, causing genetic consequences that may have potential implications for a population's long-term persistence. Large mammals are the most affected species among vertebrates. The giant armadillo Priodontes maximus is a large South American mammal threatened species, showing nocturnal, solitary and fossorial behavior, occurring at low population densities, and its population dynamics are still poorly known. In this study, we carried out the first assessment of genetic variability and population genetic structure of the species, using a panel of 15 polymorphic microsatellites developed by high-throughput genome sequencing. The spatial Bayesian clustering, Fst and Dest results indicated the presence of two genetic clusters (K = 2) in the study area. These results suggest a reduction in gene flow between individuals inhabiting the Brazilian savanna (Cerrado) and the Pantanal wetlands, with the increased human-driven habitat modifications possibly contributing for this scenario. A bottleneck signal was detected in both populations, and a subpopulation structuring in the Cerrado may also be reflecting consequences of the extensive habitat modifications. Findings from this study provide important and useful information for the future maintenance of genetic diversity and long-term conservation of this flagship species.
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Affiliation(s)
- Nayra T. Rodrigues
- Universidade Federal de São Carlos, Departamento de Genética e Evolução, São Carlos, SP, Brazil
| | - Bruno H. Saranholi
- Universidade Federal de São Carlos, Departamento de Genética e Evolução, São Carlos, SP, Brazil
- Imperial College London, Department of Life Sciences, Ascot, United Kingdom
| | - Alexandre R. Inforzato
- Universidade Federal de São Carlos, Departamento de Genética e Evolução, São Carlos, SP, Brazil
| | | | - Arnaud Leonard Jean Desbiez
- Instituto de Conservação de Animais Silvestres (ICAS), Campo Grande, Mato Grosso do Sul, Brazil
- Royal Zoological Society of Scotland (RZSS), Murrayfield, Edinburgh, United Kingdom
- Instituto de Pesquisas Ecológicas (IPE), Nazaré Paulista, São Paulo, Brazil
| | - Pedro M. Galetti
- Universidade Federal de São Carlos, Departamento de Genética e Evolução, São Carlos, SP, Brazil
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5
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Santos AS, Cazetta E, Faria D, Lima TM, Lopes MTG, Carvalho CDS, Alves‐Pereira A, Morante‐Filho JC, Gaiotto FA. Tropical forest loss and geographic location drive the functional genomic diversity of an endangered palm tree. Evol Appl 2023; 16:1257-1273. [PMID: 37492151 PMCID: PMC10363835 DOI: 10.1111/eva.13525] [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: 01/17/2022] [Revised: 12/10/2022] [Accepted: 12/13/2022] [Indexed: 07/27/2023] Open
Abstract
Human activity has diminished forests in different terrestrial ecosystems. This is well illustrated in the Brazilian Atlantic Forest, which still hosts high levels of species richness and endemism, even with only 28% of its original extent remaining. The consequences of such forest loss in remaining populations can be investigated with several approaches, including the genomic perspective, which allows a broader understanding of how human disturbance influences the genetic variability in natural populations. In this context, our study investigated the genomic responses of Euterpe edulis Martius, an endangered palm tree, in forest remnants located in landscapes presenting different forest cover amount and composed by distinct bird assemblage that disperse its seeds. We sampled 22 areas of the Brazilian Atlantic Forest in four regions using SNP markers inserted into transcribed regions of the genome of E. edulis, distinguishing neutral loci from those putatively under natural selection (outlier). We demonstrate that populations show patterns of structure and genetic variability that differ between regions, as a possible reflection of deforestation and biogeographic histories. Deforested landscapes still maintain high neutral genetic diversity due to gene flow over short distances. Overall, we not only support previous evidence with microsatellite markers, but also show that deforestation can influence the genetic variability outlier, in the scenario of selective pressures imposed by these stressful environments. Based on our findings, we suggest that, to protect genetic diversity in the long term, it is necessary to reforest and enrich deforested areas, using seeds from populations in the same management target region.
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Affiliation(s)
- Alesandro Souza Santos
- Laboratório de Ecologia Aplicada à Conservação, Programa de Pós‐Graduação em Ecologia e Conservação da BiodiversidadeUniversidade Estadual de Santa CruzIlhéusBrazil
- Laboratório de Marcadores Moleculares, Centro de Biotecnologia e GenéticaUniversidade Estadual de Santa CruzIlhéusBrazil
| | - Eliana Cazetta
- Laboratório de Ecologia Aplicada à Conservação, Programa de Pós‐Graduação em Ecologia e Conservação da BiodiversidadeUniversidade Estadual de Santa CruzIlhéusBrazil
| | - Deborah Faria
- Laboratório de Ecologia Aplicada à Conservação, Programa de Pós‐Graduação em Ecologia e Conservação da BiodiversidadeUniversidade Estadual de Santa CruzIlhéusBrazil
| | - Thâmara Moura Lima
- Instituto Federal de Educação, Ciência e Tecnologia da Bahia – Campus SeabraSeabraBrazil
| | | | | | | | - José Carlos Morante‐Filho
- Laboratório de Ecologia Aplicada à Conservação, Programa de Pós‐Graduação em Ecologia e Conservação da BiodiversidadeUniversidade Estadual de Santa CruzIlhéusBrazil
| | - Fernanda Amato Gaiotto
- Laboratório de Ecologia Aplicada à Conservação, Programa de Pós‐Graduação em Ecologia e Conservação da BiodiversidadeUniversidade Estadual de Santa CruzIlhéusBrazil
- Laboratório de Marcadores Moleculares, Centro de Biotecnologia e GenéticaUniversidade Estadual de Santa CruzIlhéusBrazil
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6
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Kim S, Carrel M, Kitchen A. Spatial genetic structure of 2009 H1N1 pandemic influenza established as a result of interaction with human populations in mainland China. PLoS One 2023; 18:e0284716. [PMID: 37196010 PMCID: PMC10191359 DOI: 10.1371/journal.pone.0284716] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Accepted: 04/06/2023] [Indexed: 05/19/2023] Open
Abstract
Identifying the spatial patterns of genetic structure of influenza A viruses is a key factor for understanding their spread and evolutionary dynamics. In this study, we used phylogenetic and Bayesian clustering analyses of genetic sequences of the A/H1N1pdm09 virus with district-level locations in mainland China to investigate the spatial genetic structure of the A/H1N1pdm09 virus across human population landscapes. Positive correlation between geographic and genetic distances indicates high degrees of genetic similarity among viruses within small geographic regions but broad-scale genetic differentiation, implying that local viral circulation was a more important driver in the formation of the spatial genetic structure of the A/H1N1pdm09 virus than even, countrywide viral mixing and gene flow. Geographic heterogeneity in the distribution of genetic subpopulations of A/H1N1pdm09 virus in mainland China indicates both local to local transmission as well as broad-range viral migration. This combination of both local and global structure suggests that both small-scale and large-scale population circulation in China is responsible for viral genetic structure. Our study provides implications for understanding the evolution and spread of A/H1N1pdm09 virus across the population landscape of mainland China, which can inform disease control strategies for future pandemics.
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Affiliation(s)
- Seungwon Kim
- Department of Geographical and Sustainability Sciences, University of Iowa, Iowa City, Iowa, United States of America
| | - Margaret Carrel
- Department of Geographical and Sustainability Sciences, University of Iowa, Iowa City, Iowa, United States of America
- Department of Epidemiology, University of Iowa, Iowa City, Iowa, United States of America
| | - Andrew Kitchen
- Department of Anthropology, University of Iowa, Iowa City, Iowa, United States of America
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7
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Wishingrad V, Thomson RC. Biogeographic inferences across spatial and evolutionary scales. Mol Ecol 2023; 32:2055-2070. [PMID: 36695049 DOI: 10.1111/mec.16861] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Revised: 01/05/2023] [Accepted: 01/19/2023] [Indexed: 01/26/2023]
Abstract
The field of biogeography unites landscape genetics and phylogeography under a common conceptual framework. Landscape genetics traditionally focuses on recent-time, population-based, spatial genetics processes at small geographical scales, while phylogeography typically investigates deep past, lineage- and species-based processes at large geographical scales. Here, we evaluate the link between landscape genetics and phylogeographical methods using the western fence lizard (Sceloporus occidentalis) as a model species. First, we conducted replicated landscape genetics studies across several geographical scales to investigate how population genetics inferences change depending on the spatial extent of the study area. Then, we carried out a phylogeographical study of population structure at two evolutionary scales informed by inferences derived from landscape genetics results to identify concordance and conflict between these sets of methods. We found significant concordance in landscape genetics processes at all but the largest geographical scale. Phylogeographical results indicate major clades are restricted to distinct river drainages or distinct hydrological regions. At a more recent timescale, we find minor clades are restricted to single river canyons in the majority of cases, while the remainder of river canyons include samples from at most two clades. Overall, the broad-scale pattern implicating stream and river valleys as key features linking populations in the landscape genetics results, and high degree of clade specificity within major topographic subdivisions in the phylogeographical results, is consistent. As landscape genetics and phylogeography share many of the same objectives, synthesizing theory, models and methods between these fields will help bring about a better understanding of ecological and evolutionary processes structuring genetic variation across space and time.
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Affiliation(s)
- Van Wishingrad
- School of Life Sciences, University of Hawai'i at Mānoa, Honolulu, Hawaii, USA.,Hawai'i, Institute of Marine Biology, Kāne'ohe, Hawai'i, USA
| | - Robert C Thomson
- School of Life Sciences, University of Hawai'i at Mānoa, Honolulu, Hawaii, USA
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8
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French CM, Berezin CT, Overcast I, Méndez De La Cruz FR, Basu S, Martínez Bernal RL, Murphy RW, Hickerson MJ, Blair C. Forest cover and geographical distance influence fine-scale genetic structure of leaf-toed geckos in the tropical dry forests of western Mexico. Biol J Linn Soc Lond 2022. [DOI: 10.1093/biolinnean/blac118] [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]
Abstract
Abstract
The biodiversity within tropical dry forests (TDFs) is astounding and yet poorly catalogued due to inadequate sampling and the presence of cryptic species. In the Mexican TDF, endemic species are common, and the landscape has been continually altered by geological and anthropogenic changes. To understand how landscape and environmental variables have shaped the population structure of endemic species, we studied the recently described species of leaf-toed gecko, Phyllodactylus benedettii, in coastal western Mexico. Using double-digest restriction site-associated DNA sequencing data, we first explore population structure and estimate the number of ancestral populations. The results indicate a high degree of genetic structure with little admixture, and patterns corresponding to both latitudinal and altitudinal gradients. We find that genetic structure cannot be explained purely by geographical distance, and that ecological corridors may facilitate dispersal and gene flow. We then model the spatial distribution of P. benedettii in the TDF through time and find that the coastline has been climatically suitable for the species since the Last Glacial Maximum. Landscape genetic analyses suggest that the combination of isolation by distance (IBD) and isolation by resistance (IBR; forest cover) has influenced the spatial genetic structure of the species. Overall, our genomic data demonstrate fine-scale population structure in TDF habitat, a complex colonization history, and spatial patterns consistent with both IBD and other ecological factors. These results further highlight the Mexican TDF as a diversity hotspot and suggest that continued anthropogenic changes are likely to affect native fauna.
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Affiliation(s)
- Connor M French
- Biology PhD Program, CUNY Graduate Center , 365 5th Avenue, New York, NY 10016 , USA
| | - Casey-Tyler Berezin
- Department of Biology, City College of New York , 160 Convent Avenue, New York, NY 10031 , USA
| | - Isaac Overcast
- Biology PhD Program, CUNY Graduate Center , 365 5th Avenue, New York, NY 10016 , USA
- Institut de Biologie de l’Ecole Normale Superieure , 46 Rue d’Ulm, 75005 Paris , France
- Division of Vertebrate Zoology, American Museum of Natural History , 200 Central Park West, New York, NY 10024 , USA
| | | | - Saptarsi Basu
- Department of Biological Sciences, New York City College of Technology, The City University of New York , 285 Jay Street, Brooklyn, NY 11201 , USA
| | | | - Robert W Murphy
- Centre for Biodiversity, Royal Ontario Museum , 100 Queen’s Park, Toronto, ON M5S 2C6 , Canada
| | - Michael J Hickerson
- Biology PhD Program, CUNY Graduate Center , 365 5th Avenue, New York, NY 10016 , USA
- Department of Biology, City College of New York , 160 Convent Avenue, New York, NY 10031 , USA
| | - Christopher Blair
- Biology PhD Program, CUNY Graduate Center , 365 5th Avenue, New York, NY 10016 , USA
- Department of Biological Sciences, New York City College of Technology, The City University of New York , 285 Jay Street, Brooklyn, NY 11201 , USA
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9
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Akomo-Okoue EF, Inoue E, Atteke C, Nakashima Y, Hongo S, Inoue-Murayama M, Yamagiwa J. Effect of landscape features on the genetic structure of forest duikers (Cephalophinae) in Moukalaba forest, Gabon. Mamm Biol 2022. [DOI: 10.1007/s42991-022-00301-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
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10
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MacDonald ZG, Snape KL, Roe AD, Sperling FAH. Host association, environment, and geography underlie genomic differentiation in a major forest pest. Evol Appl 2022; 15:1749-1765. [PMID: 36426133 PMCID: PMC9679251 DOI: 10.1111/eva.13466] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Accepted: 07/29/2022] [Indexed: 11/30/2022] Open
Abstract
Diverse geographic, environmental, and ecological factors affect gene flow and adaptive genomic variation within species. With recent advances in landscape ecological modelling and high‐throughput DNA sequencing, it is now possible to effectively quantify and partition their relative contributions. Here, we use landscape genomics to identify determinants of genomic differentiation in the forest tent caterpillar, Malacosoma disstria, a widespread and irruptive pest of numerous deciduous tree species in North America. We collected larvae from multiple populations across Eastern Canada, where the species experiences a diversity of environmental gradients and feeds on a number of different host tree species, including trembling aspen (Populus tremuloides), sugar maple (Acer saccharum), red oak (Quercus rubra), and white birch (Betula papyrifera). Using a combination of reciprocal causal modelling (RCM) and distance‐based redundancy analyses (dbRDA), we show that differentiation of thousands of genome‐wide single nucleotide polymorphisms (SNPs) among individuals is best explained by a combination of isolation by distance, isolation by environment (spatial variation in summer temperatures and length of the growing season), and differences in host association. Configuration of suitable habitat inferred from ecological niche models was not significantly related to genomic differentiation, suggesting that M. disstria dispersal is agnostic with respect to habitat quality. Although population structure was not discretely related to host association, our modelling framework provides the first molecular evidence of host‐associated differentiation in M. disstria, congruent with previous documentation of reduced growth and survival of larvae moved between natal host species. We conclude that ecologically mediated selection is contributing to variation within M. disstria, and that divergent adaptation related to both environmental conditions and host association should be considered in ongoing research and management of this important forest pest.
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Affiliation(s)
- Zachary G. MacDonald
- Department of Biological Sciences University of Alberta Edmonton Alberta Canada
- UCLA La Kretz Center for California Conservation Science University of California Los Angeles Los Angeles CA USA
- Institute of the Environmental and Sustainability University of California Los Angeles Los Angeles CA USA
| | - Kyle L. Snape
- Department of Biological Sciences University of Alberta Edmonton Alberta Canada
| | - Amanda D. Roe
- Great Lakes Forestry Centre, Canadian Forest Service, Natural Resources Canada Sault Ste. Marie ON Canada
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11
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Massatti R, Winkler DE. Spatially explicit management of genetic diversity using ancestry probability surfaces. Methods Ecol Evol 2022. [DOI: 10.1111/2041-210x.13902] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Rob Massatti
- US Geological Survey, Southwest Biological Science Center Flagstaff AZ USA
| | - Daniel E. Winkler
- US Geological Survey, Southwest Biological Science Center Tucson AZ USA
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12
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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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13
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The role of climatic niche divergence in the speciation of the genus Neurergus: An inter-and intraspecific survey. Evol Ecol 2022. [DOI: 10.1007/s10682-022-10172-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
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14
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Milton A, Muhanguzi D, Male A, Kajubi A, Buah S, Kubiriba J, Tumuhimbise R. Analysis of Genetic Diversity of Banana Weevils (Cosmopolites sordidus) (Coleoptera: Curculionidae) Using Transcriptome-Derived Simple Sequence Repeat Markers. JOURNAL OF ECONOMIC ENTOMOLOGY 2022; 115:637-646. [PMID: 35021224 DOI: 10.1093/jee/toab213] [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: 07/30/2021] [Indexed: 06/14/2023]
Abstract
The banana weevil, Cosmopolites sordidus (Germar) (Coleoptera: Curculionidae) is an economically important insect pest of bananas. It causes up to 100% yield losses and substantial lifespan reduction in bananas. Advances in genomics, proteomics, and sequencing technologies have provided powerful pathways to genotyping disastrous pests such as C. sordidus. However, such technologies are often not available to the majority of rural subtropical African banana growers and pest control managers. This study was therefore motivated by the need to create cheap and easily accessible C. sordidus genotyping methods that could be deployed by banana pest control managers to the benefit of C. sordidus control programs in the tropics where such advanced technologies are not readily accessible. We used an in-house C. sordidus transcriptome from the an-ongoing study from which we mined an array of simple sequence repeat (SSR) markers. Of these, six highly polymorphic transcriptome-derived SSR markers were used to successfully genotype within and among banana weevil population genetic diversity of 12 C. sordidus populations collected from four banana-growing agro-ecological zones (AEZs) in Uganda. The developed transcriptome-derived SSR markers can be used by researchers in population genetics for characterization of the C. sordidus and identification of new genes that are linked to traits of particular interest. The significant genetic diversity revealed in C. sordidus provides pertinent information for integrated pest management strategies.
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Affiliation(s)
- Ali Milton
- National Agricultural Research Laboratories-Kawanda, Kampala, Uganda
- College of Veterinary Medicine Animal Resources and Biosecurity, Makerere University, Kampala, Uganda
| | - Dennis Muhanguzi
- College of Veterinary Medicine Animal Resources and Biosecurity, Makerere University, Kampala, Uganda
| | - Allan Male
- International Center for Tropical Agriculture, Kampala, Uganda
| | - Ali Kajubi
- National Agricultural Research Laboratories-Kawanda, Kampala, Uganda
| | - Stephen Buah
- National Agricultural Research Laboratories-Kawanda, Kampala, Uganda
| | - Jerome Kubiriba
- National Agricultural Research Laboratories-Kawanda, Kampala, Uganda
| | - Robooni Tumuhimbise
- Rwebitaba Zonal Agricultural Research and Development Institute, Fort-Portal, Uganda
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15
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Lecis R, Dondina O, Orioli V, Biosa D, Canu A, Fabbri G, Iacolina L, Cossu A, Bani L, Apollonio M, Scandura M. Main roads and land cover shaped the genetic structure of a Mediterranean island wild boar population. Ecol Evol 2022; 12:e8804. [PMID: 35414901 PMCID: PMC8986547 DOI: 10.1002/ece3.8804] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Revised: 03/12/2022] [Accepted: 03/21/2022] [Indexed: 01/12/2023] Open
Abstract
Patterns of genetic differentiation within and among animal populations might vary due to the simple effect of distance or landscape features hindering gene flow. An assessment of how landscape connectivity affects gene flow can help guide management, especially in fragmented landscapes. Our objective was to analyze population genetic structure and landscape genetics of the native wild boar (Sus scrofa meridionalis) population inhabiting the island of Sardinia (Italy), and test for the existence of Isolation-by-Distance (IBD), Isolation-by-Barrier (IBB), and Isolation-by-Resistance (IBR). A total of 393 Sardinian wild boar samples were analyzed using a set of 16 microsatellite loci. Signals of genetic introgression from introduced non-native wild boars or from domestic pigs were revealed by a Bayesian cluster analysis including 250 reference individuals belonging to European wild populations and domestic breeds. After removal of introgressed individuals, genetic structure in the population was investigated by different statistical approaches, supporting a partition into five discrete subpopulations, corresponding to five geographic areas on the island: north-west (NW), central west (CW), south-west (SW), north-central east (NCE), and south-east (SE). To test the IBD, IBB, and IBR hypotheses, we optimized resistance surfaces using genetic algorithms and linear mixed-effects models with a maximum likelihood population effects parameterization. Landscape genetics analyses revealed that genetic discontinuities between subpopulations can be explained by landscape elements, suggesting that main roads, urban settings, and intensively cultivated areas are hampering gene flow (and thus individual movements) within the Sardinian wild boar population. Our results reveal how human-transformed landscapes can affect genetic connectivity even in a large-sized and highly mobile mammal such as the wild boar, and provide crucial information to manage the spread of pathogens, including the African Swine Fever virus, endemic in Sardinia.
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Affiliation(s)
- Roberta Lecis
- Department of Veterinary MedicineUniversity of SassariSassariItaly
| | - Olivia Dondina
- Department of Earth and Environmental SciencesUniversity of Milano BicoccaMilanoItaly
| | - Valerio Orioli
- Department of Earth and Environmental SciencesUniversity of Milano BicoccaMilanoItaly
| | - Daniela Biosa
- Department of Veterinary MedicineUniversity of SassariSassariItaly
| | - Antonio Canu
- Department of Veterinary MedicineUniversity of SassariSassariItaly
| | - Giulia Fabbri
- Department of Veterinary MedicineUniversity of SassariSassariItaly
| | - Laura Iacolina
- Faculty of Mathematics, Natural Sciences and Information TechnologiesUniversity of PrimorskaKoperSlovenia
- Department of Chemistry and BioscienceAalborg UniversityAalborgDenmark
| | - Antonio Cossu
- Department of Veterinary MedicineUniversity of SassariSassariItaly
| | - Luciano Bani
- Department of Earth and Environmental SciencesUniversity of Milano BicoccaMilanoItaly
| | - Marco Apollonio
- Department of Veterinary MedicineUniversity of SassariSassariItaly
| | - Massimo Scandura
- Department of Veterinary MedicineUniversity of SassariSassariItaly
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16
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Łopucki R, Mróz I, Nowak-Życzyńska Z, Perlińska-Teresiak M, Owadowska-Cornil E, Klich D. Genetic Structure of the Root Vole Microtus oeconomus: Resistance of the Habitat Specialist to the Natural Fragmentation of Preferred Moist Habitats. Genes (Basel) 2022; 13:genes13030434. [PMID: 35327989 PMCID: PMC8954809 DOI: 10.3390/genes13030434] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2022] [Revised: 02/11/2022] [Accepted: 02/22/2022] [Indexed: 11/16/2022] Open
Abstract
Climate-related changes have a severe impact on wetland ecosystems and pose a serious challenge for wetland-dependent animals as their preferred habitats decline, lose spatial continuity, and appear as isolated islands in the landscape. In this paper, we studied the effects of long-term habitat changes (drying out and fragmentation of wet non-forest habitats) on the genetic structure of the population of the root vole Microtus oeconomus, a species preferring moist habitats. We intended to check what barriers and what distances affected its genetic isolation on a local scale. The study was conducted in the area of Kampinoski National Park in central Poland (Europe). DNA variability of 218 root vole individuals was assessed by genotyping nine microsatellite loci. Despite its spatial fragmentation, the studied population did not seem to be highly structured, and isolation through distance was the main differentiating factor. Even a distance of several kilometres of unfavourable natural habitats and unfavourable terrain did not exclude the exchange of genes between subpopulations. Our results suggest that the genetic effects of the fragmentation of wetlands have been considerably compensated (delayed) due to the migratory abilities of this species. Our study does not provide clear results on the impact of anthropogenic barriers but suggests that such barriers may have a much stronger effect than natural barriers.
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Affiliation(s)
- Rafał Łopucki
- Centre for Interdisciplinary Research, The John Paul II Catholic University of Lublin, Konstantynów 1J, 20-708 Lublin, Poland;
- Department of Animal Genetics and Conservation, Warsaw University of Life Sciences-SGGW, Ciszewskiego 8, 02-786 Warsaw, Poland; (Z.N.-Ż.); (M.P.-T.)
| | - Iwona Mróz
- The John Paul II Catholic University of Lublin, Racławickie 14, 20-950 Lublin, Poland;
| | - Zuzanna Nowak-Życzyńska
- Department of Animal Genetics and Conservation, Warsaw University of Life Sciences-SGGW, Ciszewskiego 8, 02-786 Warsaw, Poland; (Z.N.-Ż.); (M.P.-T.)
| | - Magdalena Perlińska-Teresiak
- Department of Animal Genetics and Conservation, Warsaw University of Life Sciences-SGGW, Ciszewskiego 8, 02-786 Warsaw, Poland; (Z.N.-Ż.); (M.P.-T.)
| | - Edyta Owadowska-Cornil
- Science and Nature Monitoring Department, Kampinoski National Park, Tetmajera 38, 05-080 Izabelin, Poland;
| | - Daniel Klich
- Department of Animal Genetics and Conservation, Warsaw University of Life Sciences-SGGW, Ciszewskiego 8, 02-786 Warsaw, Poland; (Z.N.-Ż.); (M.P.-T.)
- Correspondence:
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17
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Assessing the influence of the amount of reachable habitat on genetic structure using landscape and genetic graphs. Heredity (Edinb) 2022; 128:120-131. [PMID: 34963701 PMCID: PMC8814055 DOI: 10.1038/s41437-021-00495-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Revised: 12/16/2021] [Accepted: 12/17/2021] [Indexed: 02/03/2023] Open
Abstract
Genetic structure, i.e. intra-population genetic diversity and inter-population genetic differentiation, is influenced by the amount and spatial configuration of habitat. Measuring the amount of reachable habitat (ARH) makes it possible to describe habitat patterns by considering intra-patch and inter-patch connectivity, dispersal capacities and matrix resistance. Complementary ARH metrics computed under various resistance scenarios are expected to reflect both drift and gene flow influence on genetic structure. Using an empirical genetic dataset concerning the large marsh grasshopper (Stethophyma grossum), we tested whether ARH metrics are good predictors of genetic structure. We further investigated (i) how the components of the ARH influence genetic structure and (ii) which resistance scenario best explains these relationships. We computed local genetic diversity and genetic differentiation indices in genetic graphs, and ARH metrics in the unified and flexible framework offered by landscape graphs, and we tested the relationships between these variables. ARH metrics were relevant predictors of the two components of genetic structure, providing an advantage over commonly used habitat metrics. Although allelic richness was significantly explained by three complementary ARH metrics in the best PLS regression model, private allelic richness and MIW indices were essentially related with the ARH measured outside the focal patch. Considering several matrix resistance scenarios was also key for explaining the different genetic responses. We thus call for further use of ARH metrics in landscape genetics to explain the influence of habitat patterns on the different components of genetic structure.
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18
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Blattner L, Lucek K, Beck N, Berner D, Fumetti S. Intra‐Alpine Islands: Population genomic inference reveals high degree of isolation between freshwater spring habitats. DIVERS DISTRIB 2021. [DOI: 10.1111/ddi.13461] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Affiliation(s)
- Lucas Blattner
- Department of Environmental Sciences, Geoecology University of Basel Basel Switzerland
| | - Kay Lucek
- Department of Environmental Sciences, Plant Ecology and Evolution University of Basel Basel Switzerland
| | - Nathanael Beck
- Department of Environmental Sciences, Geoecology University of Basel Basel Switzerland
| | - Daniel Berner
- Department of Environmental Sciences, Animal Diversity and Evolution University of Basel Basel Switzerland
| | - Stefanie Fumetti
- Department of Environmental Sciences, Geoecology University of Basel Basel Switzerland
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19
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DNA barcodes evidence the contact zone of eastern and western caddisfly lineages in the Western Carpathians. Sci Rep 2021; 11:24020. [PMID: 34912013 PMCID: PMC8674257 DOI: 10.1038/s41598-021-03411-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Accepted: 12/02/2021] [Indexed: 11/28/2022] Open
Abstract
The region of the Western Carpathians is, among other aspects, very important for survival and diversity of European freshwater fauna due to the presence of a large number of (sub)mountain springs and streams. However, these ecologically and faunistically diversified habitats are still understudied in the context of genetic diversity and population structure of their inhabitants. This study focuses on genetic diversity and distribution patterns of the caddisfly Rhyacophila tristis, common and widespread representative of mountain freshwater fauna. Analysis of the COI mitochondrial marker revealed presence of the western and eastern lineages, with samples from both lineages being grouped in BOLD (Barcode of Life Data System) into separate BINs (Barcode Index Numbers). Our data indicates that eastern lineage (BIN_E) is more closely related to the Balkan populations than to co-occurring western lineage (BIN_W), and that the contact zone of the lineages passes through the W Carpathians. The study revealed phylogeographic and demographic differences between lineages, supporting hypothesis of their evolutionary independence and specific ecological preferences. The obtained genetic data of the R. tristis population from W Carpathians improved our knowledge about population genetics of this aquatic species and can contribute to understanding the state and evolution of biodiversity of freshwater ecosystems in Europe.
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20
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Atzeni L, Cushman SA, Wang J, Riordan P, Shi K, Bauman D. Evidence of spatial genetic structure in a snow leopard population from Gansu, China. Heredity (Edinb) 2021; 127:522-534. [PMID: 34743188 PMCID: PMC8626472 DOI: 10.1038/s41437-021-00483-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2021] [Revised: 10/22/2021] [Accepted: 10/22/2021] [Indexed: 11/09/2022] Open
Abstract
Understanding the spatial structure of genetic diversity provides insights into a populations' genetic status and enables assessment of its capacity to counteract the effects of genetic drift. Such knowledge is particularly scarce for the snow leopard, a conservation flagship species of Central Asia mountains. Focusing on a snow leopard population in the Qilian mountains of Gansu Province, China, we characterised the spatial genetic patterns by incorporating spatially explicit indices of diversity and multivariate analyses, based on different inertia levels of Principal Component Analysis (PCA). We compared two datasets differing in the number of loci and individuals. We found that genetic patterns were significantly spatially structured and were characterised by a broad geographical division coupled with a fine-scale cline of differentiation. Genetic admixture was detected in two adjoining core areas characterised by higher effective population size and allelic diversity, compared to peripheral localities. The power to detect significant spatial relationships depended primarily on the number of loci, and secondarily on the number of PCA axes. Spatial patterns and indices of diversity highlighted the cryptic structure of snow leopard genetic diversity, likely driven by its ability to disperse over large distances. In combination, the species' low allelic richness and large dispersal ability result in weak genetic differentiation related to major geographical features and isolation by distance. This study illustrates how cryptic genetic patterns can be investigated and analysed at a fine spatial scale, providing insights into the spatially variable isolation effects of both geographic distance and landscape resistance.
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Affiliation(s)
- Luciano Atzeni
- Wildlife Institute, School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, China
| | - Samuel A Cushman
- US Forest Service, Rocky Mountain Research Station, Flagstaff, AZ, USA
| | - Jun Wang
- Wildlife Institute, School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, China
- Department of Natural Sciences, Manchester Metropolitan University, Manchester, UK
| | - Philip Riordan
- Wildlife Institute, School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, China
- Marwell Wildlife, Winchester, UK
- Department of Biological Sciences, University of Southampton, Southampton, UK
| | - Kun Shi
- Wildlife Institute, School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, China.
- Eco-Bridge Continental, Beijing, China.
| | - David Bauman
- Smithsonian Environmental Research Center, Edgewater, MD, USA
- Environmental Change Institute, School of Geography and the Environment, University of Oxford, Oxford, UK
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21
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Trense D, Hoffmann AA, Fischer K. Large- and small-scale geographic structures affecting genetic patterns across populations of an Alpine butterfly. Ecol Evol 2021; 11:14697-14714. [PMID: 34765135 PMCID: PMC8571576 DOI: 10.1002/ece3.8157] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 09/04/2021] [Accepted: 09/08/2021] [Indexed: 11/09/2022] Open
Abstract
Understanding factors influencing patterns of genetic diversity and the population genetic structure of species is of particular importance in the current era of global climate change and habitat loss. These factors include the evolutionary history of a species as well as heterogeneity in the environment it occupies, which in turn can change across time. Most studies investigating spatio-temporal genetic patterns have focused on patterns across wide geographic areas rather than local variation, but the latter can nevertheless be important particularly in topographically complex areas. Here, we consider these issues in the Sooty Copper butterfly (Lycaena tityrus) from the European Alps, using genome-wide SNPs identified through RADseq. We found strong genetic differentiation within the Alps with four genetic clusters, indicating western, central, and eastern refuges, and a strong reduction of genetic diversity from west to east. This reduction in diversity may suggest that the southwestern refuge was the largest one in comparison to other refuges. Also, the high genetic diversity in the west may result from (a) admixture of different western refuges, (b) more recent demographic changes, or (c) introgression of lowland L. tityrus populations. At small spatial scales, populations were structured by several landscape features and especially by high mountain ridges and large river valleys. We detected 36 outlier loci likely under altitudinal selection, including several loci related to membranes and cellular processes. We suggest that efforts to preserve alpine L. tityrus should focus on the genetically diverse populations in the western Alps, and that the dolomite populations should be treated as genetically distinct management units, since they appear to be currently more threatened than others. This study demonstrates the usefulness of SNP-based approaches for understanding patterns of genetic diversity, gene flow, and selection in a region that is expected to be particularly vulnerable to climate change.
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Affiliation(s)
- Daronja Trense
- Institute for Integrated Natural Sciences, ZoologyUniversity Koblenz‐LandauKoblenzGermany
| | - Ary A. Hoffmann
- Pest & Environmental Adaptation Research GroupSchool of BiosciencesBio21 InstituteParkvilleVic.Australia
| | - Klaus Fischer
- Institute for Integrated Natural Sciences, ZoologyUniversity Koblenz‐LandauKoblenzGermany
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22
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Sun Z, Orozco-terWengel P, Chen G, Sun R, Sun L, Wang H, Shi W, Zhang B. Spatial dynamics of Chinese Muntjac related to past and future climate fluctuations. Curr Zool 2021; 67:361-370. [PMID: 34616935 PMCID: PMC8489110 DOI: 10.1093/cz/zoaa080] [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: 07/26/2020] [Accepted: 12/16/2020] [Indexed: 11/23/2022] Open
Abstract
Climate fluctuations in the past and in the future are likely to result in population expansions, shifts, or the contraction of the ecological niche of many species, and potentially leading to the changes in their geographical distributions. Prediction of suitable habitats has been developed as a useful tool for the assessment of habitat suitability and resource conservation to protect wildlife. Here, we model the ancestral demographic history of the extant modern Chinese Muntjac Muntiacus reevesi populations using approximate Bayesian computation (ABC) and used the maximum entropy model to simulate the past and predict the future spatial dynamics of the species under climate oscillations. Our results indicated that the suitable habitats for the M. reevesi shifted to the Southeast and contracted during the Last Glacial Maximum, whereas they covered a broader and more northern position in the Middle Holocene. The ABC analyses revealed that the modern M. reevesi populations diverged in the Middle Holocene coinciding with the significant contraction of the highly suitable habitat areas. Furthermore, our predictions suggest that the potentially suitable environment distribution for the species will expand under all future climate scenarios. These results indicated that the M. reevesi diverged in the recent time after the glacial period and simultaneously as its habitat’s expanded in the Middle Holocene. Furthermore, the past and future climate fluctuation triggered the change of Chinese muntjac spatial distribution, which has great influence on the Chinese muntjac’s population demographic history.
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Affiliation(s)
- Zhonglou Sun
- School of Life Sciences, Anhui University, Hefei, 230601, China
| | | | - Guotao Chen
- School of Life Sciences, Anhui University, Hefei, 230601, China
| | - Ruolei Sun
- School of Life Sciences, Anhui University, Hefei, 230601, China
| | - Lu Sun
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
| | - Hui Wang
- School of Life Sciences, Anhui University, Hefei, 230601, China
| | - Wenbo Shi
- School of Life Sciences, Anhui University, Hefei, 230601, China
| | - Baowei Zhang
- School of Life Sciences, Anhui University, Hefei, 230601, China
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23
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A machine-learning approach to map landscape connectivity in Aedes aegypti with genetic and environmental data. Proc Natl Acad Sci U S A 2021; 118:2003201118. [PMID: 33619083 PMCID: PMC7936321 DOI: 10.1073/pnas.2003201118] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Aedes mosquitoes are projected to continue expanding their ranges, which could expose millions more humans to the diseases they carry. The implementation of vector control methods ranging from traditional (e.g., insecticides) to cutting edge (e.g., genetic modification) could be improved with landscape connectivity maps and increased understanding of the factors that affect mosquito dispersal. Here we present an iterative random forest method for integrating genetic and environmental data to map landscape connectivity. We achieve a correlation of 0.83 between the model’s predicted genetic distance and actual genetic distance. We produce a genetic connectivity map for the southern tier of the United States and discuss important factors to consider in mosquito control, e.g., the release of genetically modified mosquitoes. Mapping landscape connectivity is important for controlling invasive species and disease vectors. Current landscape genetics methods are often constrained by the subjectivity of creating resistance surfaces and the difficulty of working with interacting and correlated environmental variables. To overcome these constraints, we combine the advantages of a machine-learning framework and an iterative optimization process to develop a method for integrating genetic and environmental (e.g., climate, land cover, human infrastructure) data. We validate and demonstrate this method for the Aedes aegypti mosquito, an invasive species and the primary vector of dengue, yellow fever, chikungunya, and Zika. We test two contrasting metrics to approximate genetic distance and find Cavalli-Sforza–Edwards distance (CSE) performs better than linearized FST. The correlation (R) between the model’s predicted genetic distance and actual distance is 0.83. We produce a map of genetic connectivity for Ae. aegypti’s range in North America and discuss which environmental and anthropogenic variables are most important for predicting gene flow, especially in the context of vector control.
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24
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Medina R, Wogan GOU, Bi K, Termignoni-García F, Bernal MH, Jaramillo-Correa JP, Wang IJ, Vázquez-Domínguez E. Phenotypic and genomic diversification with isolation by environment along elevational gradients in a neotropical treefrog. Mol Ecol 2021; 30:4062-4076. [PMID: 34160853 DOI: 10.1111/mec.16035] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2020] [Revised: 06/10/2021] [Accepted: 06/16/2021] [Indexed: 01/03/2023]
Abstract
Understanding how geographic and environmental heterogeneity drive local patterns of genetic variation is a major goal of ecological genomics and a key question in evolutionary biology. The tropical Andes and inter-Andean valleys are shaped by markedly heterogeneous landscapes, where species experience strong selective processes. We examined genome-wide SNP data together with behavioural and ecological traits (mating calls and body size) known to contribute to genetic isolation in anurans in the banana tree-dwelling frog, Boana platanera, distributed across an environmental gradient in Central Colombia (northern South America). Here, we analysed the relationships between environmentally (temperature and precipitation) associated genetic and phenotypic differentiation and the potential drivers of isolation by environment along an elevation gradient. We identified candidate SNPs associated with temperature and body size, which follow a clinal pattern of genome-wide differentiation tightly coupled with phenotypic variation: as elevation increases, B. platanera exhibits larger body size and longer call duration with more pulses but lower pulse rate and frequency. Thus, the environmental landscape has rendered a scenario where isolation by environment and candidate loci show concordance with phenotypic divergence in this tropical frog along an elevation gradient in the Colombian Andes. Our study sets the basis for evaluating the role of temperature in the genetic structure and local adaptation in tropical treefrogs and its putative effect on life cycle (embryos, tadpoles, adults) along elevation gradients.
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Affiliation(s)
- Ricardo Medina
- Departamento de Ecología de la Biodiversidad, Instituto de Ecología, Universidad Nacional Autónoma de México, Coyoacán, Ciudad de México, México.,Posgrado en Ciencias Biológicas, Universidad Nacional Autónoma de México, Coyoacán, Ciudad de México, México.,Grupo de Herpetología, Eco-Fisiología & Etología, Departamento de Biología, Universidad del Tolima, Altos de Santa Helena, Ibagué, Colombia
| | - Guinevere O U Wogan
- Department of Environmental Science, Policy, and Management, College of Natural Resources, University of California, Berkeley, California, USA.,Department of Integrative Biology, Oklahoma State University, Oklahoma, USA
| | - Ke Bi
- Museum of Vertebrate Zoology, University of California, Berkeley, California, USA.,Computational Genomics Resource Laboratory (CGRL, California Institute for Quantitative Biosciences (QB3, University of California, Berkeley, California, USA
| | - Flavia Termignoni-García
- Department of Organismic and Evolutionary Biology (OEB, Harvard University, Cambridge, Massachusetts, USA
| | - Manuel Hernando Bernal
- Grupo de Herpetología, Eco-Fisiología & Etología, Departamento de Biología, Universidad del Tolima, Altos de Santa Helena, Ibagué, Colombia
| | - Juan P Jaramillo-Correa
- Departamento de Ecología de la Biodiversidad, Instituto de Ecología, Universidad Nacional Autónoma de México, Coyoacán, Ciudad de México, México
| | - Ian J Wang
- Department of Environmental Science, Policy, and Management, College of Natural Resources, University of California, Berkeley, California, USA
| | - Ella Vázquez-Domínguez
- Departamento de Ecología de la Biodiversidad, Instituto de Ecología, Universidad Nacional Autónoma de México, Coyoacán, Ciudad de México, México
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25
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Barragán-Ruiz CE, Silva-Santos R, Saranholi BH, Desbiez ALJ, Galetti PM. Moderate Genetic Diversity and Demographic Reduction in the Threatened Giant Anteater, Myrmecophaga tridactyla. Front Genet 2021; 12:669350. [PMID: 34276776 PMCID: PMC8280777 DOI: 10.3389/fgene.2021.669350] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Accepted: 05/24/2021] [Indexed: 11/15/2022] Open
Abstract
In general, large mammal species with highly specialized feeding behavior and solitary habits are expected to suffer genetic consequences from habitat loss and fragmentation. To test this hypothesis, we analyzed the genetic diversity distribution of the threatened giant anteater inhabiting a human-modified landscape. We used 10 microsatellite loci to assess the genetic diversity and population structure of 107 giant anteaters sampled in the Brazilian Central-Western region. No genetic population structuring was observed in this region suggesting no gene flow restriction within the studied area. On the other hand, the moderate level of genetic diversity (Ho = 0.54), recent bottleneck detected and inbreeding (Fis, 0.13; p ≤ 0.001) signatures suggest potential impacts on the genetic variation of this Xenarthra. Additionally, a previous demographic reduction was suggested. Thus, considering the increased human-promoted impacts across the entire area of distribution of the giant anteater, our results can illustrate the potential effects of these disturbances on the genetic variation, allowing us to request the long-term conservation of this emblematic species.
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Affiliation(s)
| | - Rosane Silva-Santos
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, Brazil
| | - Bruno H Saranholi
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, Brazil.,Department of Life Sciences, Imperial College London, Ascot, United Kingdom
| | - Arnaud L J Desbiez
- Instituto de Conservação de Animais Silvestres, Campo Grande, Brazil.,Royal Zoological Society of Scotland, Edinburgh, United Kingdom.,Instituto de Pesquisas Ecológicas, Nazaré Paulista, Brazil
| | - Pedro Manoel Galetti
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, Brazil
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26
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Hecht L. The importance of considering age when quantifying wild animals' welfare. Biol Rev Camb Philos Soc 2021; 96:2602-2616. [PMID: 34155749 DOI: 10.1111/brv.12769] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Revised: 06/15/2021] [Accepted: 06/16/2021] [Indexed: 01/18/2023]
Abstract
Wild animals experience different challenges and opportunities as they mature, and this variety of experiences can lead to different levels of welfare characterizing the day-to-day lives of individuals of different ages. At the same time, most wild animals who are born do not survive to adulthood. Individuals who die as juveniles do not simply experience a homogeneous fraction of the lifetimes of older members of their species; rather, their truncated lives may be characterized by very different levels of welfare. Here, I propose the concept of welfare expectancy as a framework for quantifying wild animal welfare at a population level, given individual-level data on average welfare with respect to age. This concept fits conveniently alongside methods of analysis already used in population ecology, such as demographic sensitivity analysis, and is applicable to evaluating the welfare consequences of human interventions and natural pressures that disproportionately affect individuals of different ages. In order to understand better and improve the state of wild animal welfare, more attention should be directed towards young animals and the particular challenges they face.
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Affiliation(s)
- Luke Hecht
- Wild Animal Initiative, 115 Elm Street, Suite I, PMB 2321, Farmington, MN, 55024, U.S.A.,Department of Biosciences, Durham University, Stockton Road, Durham, DH1 3LE, U.K
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27
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Cancellare IA, Kierepka EM, Janecka J, Weckworth B, Kazmaier RT, Ward R. Multiscale patterns of isolation by ecology and fine-scale population structure in Texas bobcats. PeerJ 2021; 9:e11498. [PMID: 34141475 PMCID: PMC8180196 DOI: 10.7717/peerj.11498] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Accepted: 05/01/2021] [Indexed: 12/03/2022] Open
Abstract
Patterns of spatial genetic variation can be generated by a variety of ecological processes, including individual preferences based on habitat. These ecological processes act at multiple spatial and temporal scales, generating scale-dependent effects on gene flow. In this study, we focused on bobcats (Lynx rufus), a highly mobile, generalist felid that exhibits ecological and behavioral plasticity, high abundance, and broad connectivity across much of their range. However, bobcats also show genetic differentiation along habitat breaks, a pattern typically observed in cases of isolation-by-ecology (IBE). The IBE observed in bobcats is hypothesized to occur due to habitat-biased dispersal, but it is unknown if this occurs at other habitat breaks across their range or at what spatial scale IBE becomes most apparent. Thus, we used a multiscale approach to examine isolation by ecology (IBE) patterns in bobcats (Lynx rufus) at both fine and broad spatial scales in western Texas. We genotyped 102 individuals at nine microsatellite loci and used partial redundancy analysis (pRDA) to test if a suite of landscape variables influenced genetic variation in bobcats. Bobcats exhibited a latitudinal cline in population structure with a spatial signature of male-biased dispersal, and no clear barriers to gene flow. Our pRDA tests revealed high genetic similarity in similar habitats, and results differed by spatial scale. At the fine spatial scale, herbaceous rangeland was an important influence on gene flow whereas mixed rangeland and agriculture were significant at the broad spatial scale. Taken together, our results suggests that complex interactions between spatial-use behavior and landscape heterogeneity can create non-random gene flow in highly mobile species like bobcats. Furthermore, our results add to the growing body of data highlighting the importance of multiscale study designs when assessing spatial genetic structure.
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Affiliation(s)
- Imogene A Cancellare
- Department of Life, Earth, and Environmental Sciences, West Texas A&M University, Canyon, Texas, USA.,Department of Entomology and Wildlife Ecology, University of Delaware, Newark, DE, USA
| | - Elizabeth M Kierepka
- Department of Forestry and Environmental Resources, North Carolina Museum of Natural Sciences, Raleigh, North Carolina, USA
| | - Jan Janecka
- Department of Biological Sciences, Duquesne University, Pittsburgh, Pennsylvania, USA
| | | | - Richard T Kazmaier
- Department of Life, Earth, and Environmental Sciences, West Texas A&M University, Canyon, Texas, USA
| | - Rocky Ward
- Department of Life, Earth, and Environmental Sciences, West Texas A&M University, Canyon, Texas, USA
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28
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Kelemen KA, Urzi F, Buzan E, Horváth GF, Tulis F, Baláž I. Genetic variability and conservation of the endangered Pannonian root vole in fragmented habitats of an agricultural landscape. NATURE CONSERVATION 2021. [DOI: 10.3897/natureconservation.43.58798] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
The distribution of the endangered glacial relict subspecies, the Pannonian root vole Alexandromys oeconomus mehelyi Éhik, 1928, is restricted to scattered localities in south-western Slovakia, which belong to the north-eastern zone of its range. Human-induced changes and fragmentation of the landscape have led to the gradual loss of suitable habitats and threaten its long-term survival. The study area in the Danubian Lowland is characterised by small habitat fragments and temporal fluctuations of the habitat area. Root voles were sampled at nine sites to study the level of genetic variability and structure of local subpopulations by scoring 13 microsatellite loci in 69 individuals. Genetic differentiation varied amongst local populations and we did not find a significant isolation-by-distance pattern. Bayesian clustering analysis suggested that dispersal effectively prevents marked genetic subdivision between studied habitat fragments. Significant pairwise differentiation between some subpopulations, however, may be the result of putatively suppressed gene flow. Low genetic diversity in the recent populations probably reflects the isolated location of the study area in the agricultural landscape, suggesting that long-term survival may not be assured. In order to maintain genetic diversity, it is essential to preserve (or even restore) habitats and ensure the possibility of gene flow; habitat protection is, therefore, recommended. Continuous assessment is necessary for effective conservation management and to predict the long-term survival chances of the Pannonian root vole in the study area.
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29
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Ribeiro SE, de Almeida-Rocha JM, Weber MM, Kajin M, Lorini ML, Cerqueira R. Do anthropogenic matrix and life-history traits structure small mammal populations? A meta-analytical approach. CONSERV GENET 2021. [DOI: 10.1007/s10592-021-01352-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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30
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Westphal D, Mancini AN, Baden AL. Primate landscape genetics: A review and practical guide. Evol Anthropol 2021; 30:171-184. [PMID: 33720482 DOI: 10.1002/evan.21891] [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: 04/15/2019] [Revised: 06/12/2020] [Accepted: 02/17/2021] [Indexed: 11/06/2022]
Abstract
Landscape genetics is an emerging field that integrates population genetics, landscape ecology, and spatial statistics to investigate how geographical and environmental features and evolutionary processes such as gene flow, genetic drift, and selection structure genetic variation at both the population and individual levels, with implications for ecology, evolution, and conservation biology. Despite being particularly well suited for primatologists, this method is currently underutilized. Here, we synthesize the current state of research on landscape genetics in primates. We begin by outlining how landscape genetics has been used to disentangle the drivers of diversity, followed by a review of how landscape genetic methods have been applied to primates. This is followed by a section highlighting special considerations when applying the methods to primates, and a practical guide to facilitate further landscape genetics studies using both existing and de novo datasets. We conclude by exploring future avenues of inquiry that could be facilitated by recent developments as well as underdeveloped applications of landscape genetics to primates.
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Affiliation(s)
- Darice Westphal
- Department of Anthropology, The Graduate Center, City University of New York, New York, New York, USA.,The New York Consortium in Evolutionary Primatology (NYCEP), New York, New York, USA
| | - Amanda N Mancini
- Department of Anthropology, The Graduate Center, City University of New York, New York, New York, USA.,The New York Consortium in Evolutionary Primatology (NYCEP), New York, New York, USA
| | - Andrea L Baden
- Department of Anthropology, The Graduate Center, City University of New York, New York, New York, USA.,The New York Consortium in Evolutionary Primatology (NYCEP), New York, New York, USA.,Department of Anthropology, Hunter College, New York, New York, USA
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31
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Matthews AE, Kellner K, Seal JN. Male-biased dispersal in a fungus-gardening ant symbiosis. Ecol Evol 2021; 11:2307-2320. [PMID: 33717457 PMCID: PMC7920773 DOI: 10.1002/ece3.7198] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2020] [Revised: 12/08/2020] [Accepted: 12/11/2020] [Indexed: 02/06/2023] Open
Abstract
For nearly all organisms, dispersal is a fundamental life-history trait that can shape their ecology and evolution. Variation in dispersal capabilities within a species exists and can influence population genetic structure and ecological interactions. In fungus-gardening (attine) ants, co-dispersal of ants and mutualistic fungi is crucial to the success of this obligate symbiosis. Female-biased dispersal (and gene flow) may be favored in attines because virgin queens carry the responsibility of dispersing the fungi, but a paucity of research has made this conclusion difficult. Here, we investigate dispersal of the fungus-gardening ant Trachymyrmex septentrionalis using a combination of maternally (mitochondrial DNA) and biparentally inherited (microsatellites) markers. We found three distinct, spatially isolated mitochondrial DNA haplotypes; two were found in the Florida panhandle and the other in the Florida peninsula. In contrast, biparental markers illustrated significant gene flow across this region and minimal spatial structure. The differential patterns uncovered from mitochondrial DNA and microsatellite markers suggest that most long-distance ant dispersal is male-biased and that females (and concomitantly the fungus) have more limited dispersal capabilities. Consequently, the limited female dispersal is likely an important bottleneck for the fungal symbiont. This bottleneck could slow fungal genetic diversification, which has significant implications for both ant hosts and fungal symbionts regarding population genetics, species distributions, adaptive responses to environmental change, and coevolutionary patterns.
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Affiliation(s)
- Alix E. Matthews
- Department of BiologyThe University of Texas at TylerTylerTXUSA
- Present address:
College of Sciences and Mathematics and Molecular Biosciences ProgramArkansas State UniversityJonesboroARUSA
| | - Katrin Kellner
- Department of BiologyThe University of Texas at TylerTylerTXUSA
| | - Jon N. Seal
- Department of BiologyThe University of Texas at TylerTylerTXUSA
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32
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River drying influences genetic variation and population structure in an Arctic freshwater fish. CONSERV GENET 2021. [DOI: 10.1007/s10592-021-01339-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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33
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34
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Yannic G, Helfer V, Sermier R, Schmidt BR, Fumagalli L. Fine scale genetic structure in fire salamanders (Salamandra salamandra) along a rural-to-urban gradient. CONSERV GENET 2021. [DOI: 10.1007/s10592-021-01335-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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35
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do Amaral TS, Dos Santos JS, Rosa FF, Pessôa MB, Chaves LJ, Ribeiro MC, Collevatti RG. Agricultural Landscape Heterogeneity Matter: Responses of Neutral Genetic Diversity and Adaptive Traits in a Neotropical Savanna Tree. Front Genet 2021; 11:606222. [PMID: 33613620 PMCID: PMC7890196 DOI: 10.3389/fgene.2020.606222] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Accepted: 12/31/2020] [Indexed: 11/27/2022] Open
Abstract
Plants are one of the most vulnerable groups to fragmentation and habitat loss, that may affect community richness, abundance, functional traits, and genetic diversity. Here, we address the effects of landscape features on adaptive quantitative traits and evolutionary potential, and on neutral genetic diversity in populations of the Neotropical savanna tree Caryocar brasiliense. We sampled adults and juveniles in 10 savanna remnants within five landscapes. To obtain neutral genetic variation, we genotyped all individuals from each site using nine microsatellite loci. For adaptive traits we measured seed size and mass and grown seeds in nursery in completely randomized experimental design. We obtained mean, additive genetic variance (Va) and coefficient of variation (CVa%), which measures evolvability, for 17 traits in seedlings. We found that landscapes with higher compositional heterogeneity (SHDI) had lower evolutionary potential (CVa%) in leaf length (LL) and lower aboveground dry mass (ADM) genetic differentiation (QST). We also found that landscapes with higher SHDI had higher genetic diversity (He) and allelic richness (AR) in adults, and lower genetic differentiation (FST). In juveniles, SHDI was also positively related to AR. These results are most likely due to longer dispersal distance of pollen in landscapes with lower density of flowering individuals. Agricultural landscapes with low quality mosaic may be more stressful for plant species, due to the lower habitat cover (%), higher cover of monocropping (%) and other land covers, and edge effects. However, in landscapes with higher SHDI with high quality mosaic, forest nearby savanna habitat and the other environments may facilitate the movement or provide additional habitat and resources for seed disperses and pollinators, increasing gene flow and genetic diversity. Finally, despite the very recent agriculture expansion in Central Brazil, we found no time lag in response to habitat loss, because both adults and juveniles were affected by landscape changes.
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Affiliation(s)
- Tatiana Souza do Amaral
- Laboratório de Genética & Biodiversidade, ICB, Universidade Federal de Goiás (UFG), Goiânia, Brazil
| | - Juliana Silveira Dos Santos
- Laboratório de Genética & Biodiversidade, ICB, Universidade Federal de Goiás (UFG), Goiânia, Brazil.,Laboratório de Ecologia Espacial e Conservação (LEEC), Departamento de Biodiversidade, Universidade Estadual Paulista (UNESP), Rio Claro, Brazil
| | - Fernanda Fraga Rosa
- Laboratório de Genética & Biodiversidade, ICB, Universidade Federal de Goiás (UFG), Goiânia, Brazil
| | - Marcelo Bruno Pessôa
- Laboratório de Metacomunidades e Paisagem, ICB, Universidade Federal de Goiás (UFG), Goiânia, Brazil
| | - Lázaro José Chaves
- Escola de Agronomia, Universidade Federal de Goiás (UFG), Goiânia, Brazil
| | - Milton Cezar Ribeiro
- Laboratório de Ecologia Espacial e Conservação (LEEC), Departamento de Biodiversidade, Universidade Estadual Paulista (UNESP), Rio Claro, Brazil
| | - Rosane Garcia Collevatti
- Laboratório de Genética & Biodiversidade, ICB, Universidade Federal de Goiás (UFG), Goiânia, Brazil
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36
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Savary P, Foltête JC, Moal H, Vuidel G, Garnier S. Analysing landscape effects on dispersal networks and gene flow with genetic graphs. Mol Ecol Resour 2021; 21:1167-1185. [PMID: 33460526 DOI: 10.1111/1755-0998.13333] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Revised: 01/08/2021] [Accepted: 01/12/2021] [Indexed: 12/16/2022]
Abstract
Graph-theoretic approaches have relevant applications in landscape genetic analyses. When species form populations in discrete habitat patches, genetic graphs can be used (a) to identify direct dispersal paths followed by propagules or (b) to quantify landscape effects on multi-generational gene flow. However, the influence of their construction parameters remains to be explored. Using a simulation approach, we constructed genetic graphs using several pruning methods (geographical distance thresholds, topological constraints, statistical inference) and genetic distances to weight graph links (FST , DPS , Euclidean genetic distances). We then compared the capacity of these different graphs to (a) identify the precise topology of the dispersal network and (b) to infer landscape resistance to gene flow from the relationship between cost-distances and genetic distances. Although not always clear-cut, our results showed that methods based on geographical distance thresholds seem to better identify dispersal networks in most cases. More interestingly, our study demonstrates that a sub-selection of pairwise distances through graph pruning (thereby reducing the number of data points) can counter-intuitively lead to improved inferences of landscape effects on dispersal. Finally, we showed that genetic distances such as the DPS or Euclidean genetic distances should be preferred over the FST for landscape effect inference as they respond faster to landscape changes.
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Affiliation(s)
- Paul Savary
- ARP-Astrance, 9 Avenue Percier, Paris, 75008, France.,ThéMA, UMR 6049 CNRS, Université Bourgogne-Franche-Comté, 32 Rue Mégevand, Besançon Cedex, 25030, France.,Biogéosciences, UMR 6282 CNRS, Université Bourgogne-Franche-Comté, 6 Boulevard Gabriel, Dijon, 21000, France
| | - Jean-Christophe Foltête
- ThéMA, UMR 6049 CNRS, Université Bourgogne-Franche-Comté, 32 Rue Mégevand, Besançon Cedex, 25030, France
| | - Hervé Moal
- ARP-Astrance, 9 Avenue Percier, Paris, 75008, France
| | - Gilles Vuidel
- ThéMA, UMR 6049 CNRS, Université Bourgogne-Franche-Comté, 32 Rue Mégevand, Besançon Cedex, 25030, France
| | - Stéphane Garnier
- Biogéosciences, UMR 6282 CNRS, Université Bourgogne-Franche-Comté, 6 Boulevard Gabriel, Dijon, 21000, France
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37
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Moir M, Richards LR, Rambau RV, Wannenburgh A, Cherry MI. Fragmentation does not affect gene flow in forest populations of the dusky pipistrelle bat on the eastern seaboard of South Africa. J Mammal 2021. [DOI: 10.1093/jmammal/gyaa125] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Abstract
The Eastern Cape Province harbors almost half of the indigenous forest in South Africa, but these forests are threatened by large-scale agricultural and urban development planned for the coming decade. Additional anthropogenic development is likely to cause further fragmentation and degradation of forests inhabited by the dusky pipistrelle bat (Pipistrellus hesperidus). We used eight microsatellite markers to study the genetic diversity, population structure, and migration, of P. hesperidus (n = 120) across 14 sites in the Eastern Cape and KwaZulu-Natal provinces of South Africa. We examined the effect of contemporary land cover types on genetic differentiation to assess whether current levels of urbanization and agricultural development affect gene flow. High gene flow and low population structure were evident across sampled sites, apart from genetic discontinuities at the northern (Oribi Gorge Nature Reserve) and southern (Alexandria Forest) ends of the seaboard. Genetic discontinuity at Oribi Gorge may relate to anthropogenic modification of two rivers surrounding the forest, while the Alexandria-linked barrier is a climatic break known as the Bedford gap. Migration rates generally were low between sites except for one Scarp forest, Manubi State Forest, from which individuals dispersed to other sites. The Amatole Mistbelt forests supported high genetic diversity, and likely served as a refugium for P. hesperidus during the Last Glacial Maximum. The composition of land cover classes between sites was a poor predictor of genetic differentiation, although it seems likely that P. hesperidus uses riparian habitats and wetlands for dispersal. Lastly, urban and agricultural development did not have a significant effect on genetic differentiation, which may reflect the wide niche breadth and intermediate distribution range of the species. This study provides insights into genetic diversity and gene flow of P. hesperidus across the study region prior to agricultural intensification and large-scale urbanization.
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Affiliation(s)
- Monika Moir
- Department of Botany and Zoology, Faculty of Natural Sciences, Stellenbosch University, Stellenbosch, South Africa
| | | | - Ramugondo V Rambau
- Department of Botany and Zoology, Faculty of Natural Sciences, Stellenbosch University, Stellenbosch, South Africa
| | - Andrew Wannenburgh
- Natural Resource Management, Department of Environmental Affairs, Cape Town, South Africa
| | - Michael I Cherry
- Department of Botany and Zoology, Faculty of Natural Sciences, Stellenbosch University, Stellenbosch, South Africa
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38
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Da Silva MF, Cruz MV, Vidal Júnior JDD, Zucchi MI, Mori GM, De Souza AP. Geographical and environmental contributions to genomic divergence in mangrove forests. Biol J Linn Soc Lond 2021. [DOI: 10.1093/biolinnean/blaa199] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
Abstract
Assessing the relative importance of geographical and environmental factors to the spatial distribution of genetic variation can provide information about the processes that maintain genetic variation in natural populations. With a globally wide but very restricted habitat distribution, mangrove trees are a useful model for studies aiming to understand the contributions of these factors. Mangroves occur along the continent–ocean interface of tropical and subtropical latitudes, regions considered inhospitable to many other types of plants. Here, we used landscape genomics approaches to investigate the relative contributions of geographical and environmental variables to the genetic variation of two black mangrove species, Avicennia schaueriana and Avicennia germinans, along the South American coast. Using single nucleotide polymorphisms, our results revealed an important role of ocean currents and geographical distance in the gene flow of A. schaueriana and an isolation-by-environment pattern in the organization of the genetic diversity of A. germinans. Additionally, for A. germinans, we observed significant correlations between genetic variation with evidence of selection and the influence of precipitation regimens, solar radiation and temperature patterns. These discoveries expand our knowledge about the evolution of mangrove trees and provide important information to predict future responses of coastal species to the expected global changes during this century.
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Affiliation(s)
- Michele Fernandes Da Silva
- Department of Plant Biology, Institute of Biology, University of Campinas (UNICAMP), Campinas, SP, Brazil
- Center for Molecular Biology and Genetic Engineering, University of Campinas (UNICAMP), Campinas, SP, Brazil
| | - Mariana Vargas Cruz
- Department of Plant Biology, Institute of Biology, University of Campinas (UNICAMP), Campinas, SP, Brazil
- Center for Molecular Biology and Genetic Engineering, University of Campinas (UNICAMP), Campinas, SP, Brazil
| | - João De Deus Vidal Júnior
- Department of Plant Biology, Institute of Biology, University of Campinas (UNICAMP), Campinas, SP, Brazil
- Center for Molecular Biology and Genetic Engineering, University of Campinas (UNICAMP), Campinas, SP, Brazil
| | | | - Gustavo Maruyama Mori
- Institute of Biosciences, São Paulo State University (UNESP), São Vicente, SP, Brazil
| | - Anete Pereira De Souza
- Department of Plant Biology, Institute of Biology, University of Campinas (UNICAMP), Campinas, SP, Brazil
- Center for Molecular Biology and Genetic Engineering, University of Campinas (UNICAMP), Campinas, SP, Brazil
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39
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Emel SL, Wang S, Metz RP, Spigler RB. Type and intensity of surrounding human land use, not local environment, shape genetic structure of a native grassland plant. Mol Ecol 2021; 30:639-655. [PMID: 33245827 DOI: 10.1111/mec.15753] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2019] [Revised: 11/01/2020] [Accepted: 11/13/2020] [Indexed: 12/28/2022]
Abstract
Landscape heterogeneity can shape genetic structure and functional connectivity of populations. When this heterogeneity imposes variable costs of moving across the landscape, populations can be structured according to a pattern of "isolation by resistance" (IBR). At the same time, divergent local environmental filters can limit gene flow, creating an alternative pattern of "isolation by environment" (IBE). Here, we evaluate IBR and IBE in the insect-pollinated, biennial plant Sabatia angularis (L.) Pursh (Gentianaceae) across serpentine grasslands in the fragmented landscape of SE Pennsylvania, USA using ~4500 neutral SNP loci. Specifically, we test the extent to which radical alteration of the landscape matrix by humans has fundamentally altered the cost of movement, imprinting a pattern of IBR dictated by land use type and intensity, and the potential for IBE in relation to a gradient of heavy metal concentrations found in serpentine soil. We reveal a strong signal of IBR and a weak signal of IBE across sites, indicating the greater importance of the landscape matrix in shaping genetic structure of S. angularis populations in the study region. Based on Circuitscape and least cost path approaches, we find that both low- and high-intensity urbanization resist gene flow by orders of magnitude greater than "natural" habitats, although resistance to low-intensity urbanization weakens at larger spatial scales. While cropland presents a substantially lower barrier than urban development, cumulative human land use surrounding populations predicts within-population genetic diversity and inbreeding in S. angularis. Our results emphasize the role of forest buffers and corridors in facilitating gene flow between serpentine grassland patches and averting local extinction of plant populations.
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Affiliation(s)
- Sarah L Emel
- Department of Biology, Temple University, Philadelphia, PA, USA.,Department of Biology, Indiana University of Pennsylvania, Indiana, PA, USA
| | - Shichen Wang
- Genomics and Bioinformatics Service, Texas A&M AgriLife Research, TX, USA
| | - Richard P Metz
- Genomics and Bioinformatics Service, Texas A&M AgriLife Research, TX, USA
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40
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Ballare KM, Jha S. Genetic structure across urban and agricultural landscapes reveals evidence of resource specialization and philopatry in the Eastern carpenter bee, Xylocopa virginica L. Evol Appl 2021; 14:136-149. [PMID: 33519961 PMCID: PMC7819568 DOI: 10.1111/eva.13078] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Revised: 05/27/2020] [Accepted: 07/06/2020] [Indexed: 01/03/2023] Open
Abstract
Human activity continues to impact global ecosystems, often by altering the habitat suitability, persistence, and movement of native species. It is thus critical to examine the population genetic structure of key ecosystemservice providers across human-altered landscapes to provide insight into the forces that limit wildlife persistence and movement across multiple spatial scales. While some studies have documented declines of bee pollinators as a result of human-mediated habitat alteration, others suggest that some bee species may benefit from altered land use due to increased food or nesting resource availability; however, detailed population and dispersal studies have been lacking. We investigated the population genetic structure of the Eastern carpenter bee, Xylocopa virginica, across 14 sites spanning more than 450 km, including dense urban areas and intensive agricultural habitat. X. virginica is a large bee which constructs nests in natural and human-associated wooden substrates, and is hypothesized to disperse broadly across urbanizing areas. Using 10 microsatellite loci, we detected significant genetic isolation by geographic distance and significant isolation by land use, where urban and cultivated landscapes were most conducive to gene flow. This is one of the first population genetic analyses to provide evidence of enhanced insect dispersal in human-altered areas as compared to semi-natural landscapes. We found moderate levels of regional-scale population structure across the study system (G'ST = 0.146) and substantial co-ancestry between the sampling regions, where co-ancestry patterns align with major human transportation corridors, suggesting that human-mediated movement may be influencing regional dispersal processes. Additionally, we found a signature of strong site-level philopatry where our analyses revealed significant levels of high genetic relatedness at very fine scales (<1 km), surprising given X. virginica's large body size. These results provide unique genetic evidence that insects can simultaneously exhibit substantial regional dispersal as well as high local nesting fidelity in landscapes dominated by human activity.
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Affiliation(s)
- Kimberly M. Ballare
- Department of Integrative BiologyBiological LaboratoriesThe University of Texas at AustinAustinTXUSA
- Department of Ecology and Evolutionary BiologyUniversity of California Santa CruzSanta CruzCAUSA
| | - Shalene Jha
- Department of Integrative BiologyBiological LaboratoriesThe University of Texas at AustinAustinTXUSA
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41
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Savary P, Foltête J, Moal H, Vuidel G, Garnier S. graph4lg: A package for constructing and analysing graphs for landscape genetics in R. Methods Ecol Evol 2020. [DOI: 10.1111/2041-210x.13530] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Affiliation(s)
- Paul Savary
- ARP‐Astrance Paris France
- ThéMA UMR 6049 CNRSUniversité Bourgogne‐Franche‐Comté Besançon Cedex France
- Biogéosciences UMR 6282 CNRSUniversité Bourgogne‐Franche‐Comté Dijon France
| | | | | | - Gilles Vuidel
- ThéMA UMR 6049 CNRSUniversité Bourgogne‐Franche‐Comté Besançon Cedex France
| | - Stéphane Garnier
- Biogéosciences UMR 6282 CNRSUniversité Bourgogne‐Franche‐Comté Dijon France
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Peterman WE, Pope NS. The use and misuse of regression models in landscape genetic analyses. Mol Ecol 2020; 30:37-47. [PMID: 33128830 DOI: 10.1111/mec.15716] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Revised: 08/21/2020] [Accepted: 10/22/2020] [Indexed: 12/27/2022]
Abstract
The field of landscape genetics has been rapidly evolving, adopting and adapting analytical frameworks to address research questions. Current studies are increasingly using regression-based frameworks to infer the individual contributions of landscape and habitat variables on genetic differentiation. This paper outlines appropriate and inappropriate uses of multiple regression for these purposes, and demonstrates through simulation the limitations of different analytical frameworks for making correct inference. Of particular concern are recent studies seeking to explain genetic differences by fitting regression models with effective distance variables calculated independently on separate landscape resistance surfaces. When moving across the landscape, organisms cannot respond independently and uniquely to habitat and landscape features. Analyses seeking to understand how landscape features affect gene flow should model a single conductance or resistance surface as a parameterized function of relevant spatial covariates, and estimate the values of these parameters by linking a single set of resistance distances to observed genetic dissimilarity via a loss function. While this loss function may involve a regression-like step, the associated nuisance parameters are not interpretable in terms of organismal movement and should not be conflated with what is actually of interest: the mapping between spatial covariates and conductance/resistance. The growth and evolution of landscape genetics as a field has been rapid and exciting. It is the goal of this paper to highlight past missteps and demonstrate limitations of current approaches to ensure that future use of regression models will appropriately consider the process being modeled, which will provide clarity to model interpretation.
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Affiliation(s)
- William E Peterman
- School of Environment and Natural Resources, The Ohio State University, Columbus, OH, USA
| | - Nathaniel S Pope
- Department of Entomology, The Pennsylvania State University, University Park, PA, USA
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43
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Prunier JG, Poesy C, Dubut V, Veyssière C, Loot G, Poulet N, Blanchet S. Quantifying the individual impact of artificial barriers in freshwaters: A standardized and absolute genetic index of fragmentation. Evol Appl 2020; 13:2566-2581. [PMID: 33294009 PMCID: PMC7691472 DOI: 10.1111/eva.13044] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Revised: 06/02/2020] [Accepted: 06/09/2020] [Indexed: 12/27/2022] Open
Abstract
Fragmentation by artificial barriers is an important threat to freshwater biodiversity. Mitigating the negative aftermaths of fragmentation is of crucial importance, and it is now essential for environmental managers to benefit from a precise estimate of the individual impact of weirs and dams on river connectivity. Although the indirect monitoring of fragmentation using molecular data constitutes a promising approach, it is plagued with several constraints preventing a standardized quantification of barrier effects. Indeed, observed levels of genetic differentiation GD depend on both the age of the obstacle and the effective size of the populations it separates, making comparisons of the actual barrier effect of different obstacles difficult. Here, we developed a standardized genetic index of fragmentation (F INDEX), allowing an absolute and independent assessment of the individual effects of obstacles on connectivity. The F INDEX is the standardized ratio between the observed GD between pairs of populations located on either side of an obstacle and the GD expected if this obstacle completely prevented gene flow. The expected GD is calculated from simulations taking into account two parameters: the number of generations since barrier creation and the expected heterozygosity of the populations, a proxy for effective population size. Using both simulated and empirical datasets, we explored the validity and the limits of the F INDEX. We demonstrated that it allows quantifying effects of fragmentation only from a few generations after barrier creation and provides valid comparisons among obstacles of different ages and populations (or species) of different effective sizes. The F INDEX requires a minimum amount of fieldwork and genotypic data and solves some of the difficulties inherent to the study of artificial fragmentation in rivers and potentially in other ecosystems. This makes the F INDEX promising to support the management of freshwater species affected by barriers, notably for planning and evaluating restoration programs.
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Affiliation(s)
- Jérôme G. Prunier
- Centre National de la Recherche Scientifique (CNRS)Université Paul Sabatier (UPS)UMR 5321Station d’Ecologie Théorique et ExpérimentaleMoulisFrance
| | - Camille Poesy
- Centre National de la Recherche Scientifique (CNRS)Université Paul Sabatier (UPS)UMR 5321Station d’Ecologie Théorique et ExpérimentaleMoulisFrance
| | - Vincent Dubut
- CNRSIRDAvignon UniversitéIMBEAix Marseille UnivMarseille UniversitéFrance
| | - Charlotte Veyssière
- CNRSUPSUMR 5174 EDB (Laboratoire Évolution & Diversité Biologique)École Nationale de Formation Agronomique (ENFA)Toulouse Cedex 4France
| | - Géraldine Loot
- CNRSUPSUMR 5174 EDB (Laboratoire Évolution & Diversité Biologique)École Nationale de Formation Agronomique (ENFA)Toulouse Cedex 4France
| | - Nicolas Poulet
- DRAS, Pôle R&D écohydraulique OFBIMFT‐PPRIMEOffice Français de la BiodiversitéToulouseFrance
| | - Simon Blanchet
- Centre National de la Recherche Scientifique (CNRS)Université Paul Sabatier (UPS)UMR 5321Station d’Ecologie Théorique et ExpérimentaleMoulisFrance
- CNRSUPSUMR 5174 EDB (Laboratoire Évolution & Diversité Biologique)École Nationale de Formation Agronomique (ENFA)Toulouse Cedex 4France
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44
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Hemming-Schroeder E, Zhong D, Machani M, Nguyen H, Thong S, Kahindi S, Mbogo C, Atieli H, Githeko A, Lehmann T, Kazura JW, Yan G. Ecological drivers of genetic connectivity for African malaria vectors Anopheles gambiae and An. arabiensis. Sci Rep 2020; 10:19946. [PMID: 33203917 PMCID: PMC7673128 DOI: 10.1038/s41598-020-76248-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Accepted: 10/15/2020] [Indexed: 12/30/2022] Open
Abstract
Anopheles gambiae and An. arabiensis are major malaria vectors in sub-Saharan Africa. Knowledge of how geographical factors drive the dispersal and gene flow of malaria vectors can help in combatting insecticide resistance spread and planning new vector control interventions. Here, we used a landscape genetics approach to investigate population relatedness and genetic connectivity of An. gambiae and An. arabiensis across Kenya and determined the changes in mosquito population genetic diversity after 20 years of intensive malaria control efforts. We found a significant reduction in genetic diversity in An. gambiae, but not in An. arabiensis as compared to prior to the 20-year period in western Kenya. Significant population structure among populations was found for both species. The most important ecological driver for dispersal and gene flow of An. gambiae and An. arabiensis was tree cover and cropland, respectively. These findings highlight that human induced environmental modifications may enhance genetic connectivity of malaria vectors.
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Affiliation(s)
- Elizabeth Hemming-Schroeder
- Department of Ecology and Evolutionary Biology and Program in Public Health, University of California, Irvine, CA, 92617, USA.,Center for Global Health and Diseases, Case Western Reserve University, Cleveland, OH, 44106, USA
| | - Daibin Zhong
- Department of Ecology and Evolutionary Biology and Program in Public Health, University of California, Irvine, CA, 92617, USA
| | - Maxwell Machani
- Center for Global Health Research, Kenya Medical Research Institute, Kisumu, Kenya
| | - Hoan Nguyen
- Department of Ecology and Evolutionary Biology and Program in Public Health, University of California, Irvine, CA, 92617, USA
| | - Sarah Thong
- Department of Ecology and Evolutionary Biology and Program in Public Health, University of California, Irvine, CA, 92617, USA
| | - Samuel Kahindi
- School of Pure and Applied Sciences, Pwani University, Kilifi, Kenya
| | - Charles Mbogo
- Center for Global Health Research, Kenya Medical Research Institute, Kisumu, Kenya
| | - Harrysone Atieli
- Center for Global Health Research, Kenya Medical Research Institute, Kisumu, Kenya.,School of Public Health and Community Development, Maseno University, Kisumu, Kenya
| | - Andrew Githeko
- Center for Global Health Research, Kenya Medical Research Institute, Kisumu, Kenya
| | - Tovi Lehmann
- Laboratory of Malaria and Vector Research, National Institutes of Health, Bethesda, MD, 20892, USA
| | - James W Kazura
- Center for Global Health and Diseases, Case Western Reserve University, Cleveland, OH, 44106, USA
| | - Guiyun Yan
- Department of Ecology and Evolutionary Biology and Program in Public Health, University of California, Irvine, CA, 92617, USA.
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45
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Cruzan MB, Hendrickson EC. Landscape Genetics of Plants: Challenges and Opportunities. PLANT COMMUNICATIONS 2020; 1:100100. [PMID: 33367263 PMCID: PMC7748010 DOI: 10.1016/j.xplc.2020.100100] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2020] [Revised: 06/03/2020] [Accepted: 07/17/2020] [Indexed: 05/06/2023]
Abstract
Dispersal is one of the most important but least understood processes in plant ecology and evolutionary biology. Dispersal of seeds maintains and establishes populations, and pollen and seed dispersal are responsible for gene flow within and among populations. Traditional views of dispersal and gene flow assume models that are governed solely by geographic distance and do not account for variation in dispersal vector behavior in response to heterogenous landscapes. Landscape genetics integrates population genetics with Geographic Information Systems (GIS) to evaluate the effects of landscape features on gene flow patterns (effective dispersal). Surprisingly, relatively few landscape genetic studies have been conducted on plants. Plants present advantages because their populations are stationary, allowing more reliable estimates of the effects of landscape features on effective dispersal rates. On the other hand, plant dispersal is intrinsically complex because it depends on the habitat preferences of the plant and its pollen and seed dispersal vectors. We discuss strategies to assess the separate contributions of pollen and seed movement to effective dispersal and to delineate the effects of plant habitat quality from those of landscape features that affect vector behavior. Preliminary analyses of seed dispersal for three species indicate that isolation by landscape resistance is a better predictor of the rates and patterns of dispersal than geographic distance. Rates of effective dispersal are lower in areas of high plant habitat quality, which may be due to the effects of the shape of the dispersal kernel or to movement behaviors of biotic vectors. Landscape genetic studies in plants have the potential to provide novel insights into the process of gene flow among populations and to improve our understanding of the behavior of biotic and abiotic dispersal vectors in response to heterogeneous landscapes.
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46
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White SL, Hanks EM, Wagner T. A novel quantitative framework for riverscape genetics. ECOLOGICAL APPLICATIONS : A PUBLICATION OF THE ECOLOGICAL SOCIETY OF AMERICA 2020; 30:e02147. [PMID: 32338800 DOI: 10.1002/eap.2147] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Revised: 03/08/2020] [Accepted: 03/30/2020] [Indexed: 06/11/2023]
Abstract
Riverscape genetics, which applies concepts in landscape genetics to riverine ecosystems, lack appropriate quantitative methods that address the spatial autocorrelation structure of linear stream networks and account for bidirectional geneflow. To address these challenges, we present a general framework for the design and analysis of riverscape genetic studies. Our framework starts with the estimation of pairwise genetic distance at sample sites and the development of a spatially structured ecological network (SSEN) on which riverscape covariates are measured. We then introduce the novel bidirectional geneflow in riverscapes (BGR) model that uses principles of isolation-by-resistance to quantify the effects of environmental covariates on genetic connectivity, with spatial covariance defined using simultaneous autoregressive models on the SSEN and the generalized Wishart distribution to model pairwise distance matrices arising through a random walk model of geneflow. We highlight the utility of this framework in an analysis of riverscape genetics for brook trout (Salvelinus fontinalis) in north central Pennsylvania, USA. Using the fixation index (FST ) as the measure of genetic distance, we estimated the effects of 12 riverscape covariates on geneflow by evaluating the relative support of eight competing BGR models. We then compared the performance of the top-ranked BGR model to results obtained from comparable analyses using multiple regression on distance matrices (MRM) and the program STRUCTURE. We found that the BGR model had more power to detect covariate effects, particularly for variables that were only partial barriers to geneflow and/or uncommon in the riverscape, making it more informative for assessing patterns of population connectivity and identifying threats to species conservation. This case study highlights the utility of our modeling framework over other quantitative methods in riverscape genetics, particularly the ability to rigorously test hypotheses about factors that influence geneflow and probabilistically estimate the effect of riverscape covariates, including stream flow direction. This framework is flexible across taxa and riverine networks, is easily executable, and provides intuitive results that can be used to investigate the likely outcomes of current and future management scenarios.
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Affiliation(s)
- Shannon L White
- Pennsylvania Cooperative Fish and Wildlife Research Unit, Pennsylvania State University, University Park, Pennsylvania, 16802, USA
- Department of Ecosystem Science and Management, Pennsylvania State University, University Park, Pennsylvania, 16802, USA
| | - Ephraim M Hanks
- Department of Statistics, Pennsylvania State University, University Park, Pennsylvania, 16802, USA
| | - Tyler Wagner
- U.S. Geological Survey, Pennsylvania Cooperative Fish and Wildlife Research Unit, Pennsylvania State University, University Park, Pennsylvania, 16802, USA
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47
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Ferreira AS, Lima AP, Jehle R, Ferrão M, Stow A. The Influence of Environmental Variation on the Genetic Structure of a Poison Frog Distributed Across Continuous Amazonian Rainforest. J Hered 2020; 111:457-470. [PMID: 32827440 DOI: 10.1093/jhered/esaa034] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Accepted: 08/20/2020] [Indexed: 11/13/2022] Open
Abstract
Biogeographic barriers such as rivers have been shown to shape spatial patterns of biodiversity in the Amazon basin, yet relatively little is known about the distribution of genetic variation across continuous rainforest. Here, we characterize the genetic structure of the brilliant-thighed poison frog (Allobates femoralis) across an 880-km-long transect along the Purus-Madeira interfluve south of the Amazon river, based on 64 individuals genotyped at 7609 single-nucleotide polymorphism (SNP) loci. A population tree and clustering analyses revealed 4 distinct genetic groups, one of which was strongly divergent. These genetic groups were concomitant with femoral spot coloration differences, which was intermediate within a zone of admixture between two of the groups. The location of these genetic groups did not consistently correspond to current ecological transitions between major forest types. A multimodel approach to quantify the relative influence of isolation-by-geographic distance (IBD) and isolation-by-environmental resistance (IBR) nevertheless revealed that, in addition to a strong signal of IBD, spatial genetic differentiation was explained by IBR primarily linked to dry season intensity (r2 = 8.4%) and canopy cover (r2 = 6.4%). We show significant phylogenetic divergence in the absence of obvious biogeographical barriers and that finer-scaled measures of genetic structure are associated with environmental variables also known to predict the density of A. femoralis.
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Affiliation(s)
- Anthony S Ferreira
- Programa de Capacitação Institucional, Instituto Nacional de Pesquisas da Amazônia, Manaus, Amazonas, Brazil
| | - Albertina P Lima
- Coordenacão de Biodiversidade, Instituto Nacional de Pesquisas da Amazônia, Manaus, Amazonas, Brazil
| | - Robert Jehle
- School of Science, Engineering and Environment, University of Salford, Salford, UK
| | - Miquéias Ferrão
- Museum of Comparative Zoology, Harvard University, Cambridge, MA, USA
| | - Adam Stow
- Department of Biological Sciences, Macquarie University, Sydney, NSW, Australia
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Abstract
AbstractMany species on endangered species lists such as the IUCN Red List (RL) are categorized using demographic factors such as numbers of mature individuals. Genetic factors are not currently used in the RL even though their explicit consideration, including effective population size (Ne) and expected heterozygosity-loss (H-loss), could improve the assessment of extinction risk. Here, we consider the estimation of Ne and H-loss in the context of RL species. First, we investigate the reporting of number of mature individuals for RL Endangered species, which is needed to estimate Ne and H-loss. We found 77% of species assessments studied here did not report methods used to estimate the number of mature adults, and that these assessments rarely report other important determinants of Ne (e.g., sex ratio, variance in family size). We therefore applied common rules of thumb to estimate Ne, and found that Ne was likely < 50 for at least 25% of the 170 RL Endangered species studied here. We also estimated mean expected H-loss for these species over the next 100 years, and found it to be 9–29%. These estimates of high H-loss and low Ne suggest that some species listed as Endangered likely warrant listing as Critically Endangered if genetic considerations were included. We recommend that RL and other assessment frameworks (i) report methods used for estimating the number of mature adults, (ii) include standardized information on species traits that influence Ne to facilitate Ne estimation, and (iii) consider using concepts like Ne and heterozygosity-loss in risk assessments.
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49
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Pimentel JDSM, Ludwig S, Resende LC, Brandão-Dias PFP, Pereira AH, de Abreu NL, Rosse IC, Martins APV, Facchin S, Lopes JDM, Santos GB, Alves CBM, Kalapothakis E. Genetic evaluation of migratory fish: Implications for conservation and stocking programs. Ecol Evol 2020; 10:10314-10324. [PMID: 33072261 PMCID: PMC7548202 DOI: 10.1002/ece3.6231] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2019] [Revised: 12/09/2019] [Accepted: 02/19/2020] [Indexed: 02/04/2023] Open
Abstract
Fish stocking programs have been implemented to mitigate the blockage of original riverbeds by the construction of hydropower dams, which affects the natural migration of fish populations. However, this method raises concerns regarding the genetic rescue of the original populations of migratory fish species. We investigated the spatial distribution of genetic properties, such as genetic diversity, population structure, and gene flow (migration), of the Neotropical migratory fish Prochilodus costatus in the Três Marias dam in the São Francisco River basin, Brazil, and examined the possible effects of fish stocking programs on P. costatus populations in this region. In total, 1,017 specimens were sampled from 12 natural sites and a fish stocking program, and genotyped for high‐throughput sequencing at 8 microsatellite loci. The populations presented low genetic variability, with evidence of inbreeding and the presence of only four genetic pools; three pools were observed throughout the study region, and the fourth was exclusive to one area in the Paraopeba River. Additionally, we identified high unidirectional gene flow between regions, and a preferred migratory route between the Pará River and the upper portion of the São Francisco River. The fish stocking program succeeded in transposing the genetic pools from downstream to upstream of the Três Marias dam, but, regrettably, promoted genetic homogenization in the upper São Francisco River basin. Moreover, the data show the fragility of this species at the genetic level. This monitoring strategy could be a model for the development of conservation and management measures for migratory fish populations that are consumed by humans.
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Affiliation(s)
- Juliana da Silva Martins Pimentel
- Department of Genetic, Ecology and Evolution Institute of Biological Sciences Federal University of Minas Gerais Belo Horizonte Brazil.,Pitágoras College Belo Horizonte Brazil
| | - Sandra Ludwig
- Department of Genetic, Ecology and Evolution Institute of Biological Sciences Federal University of Minas Gerais Belo Horizonte Brazil.,Department of Zoology Institute of Biological Sciences Federal University of Minas Gerais Belo Horizonte Brazil
| | - Leonardo Cardoso Resende
- Department of Genetic, Ecology and Evolution Institute of Biological Sciences Federal University of Minas Gerais Belo Horizonte Brazil
| | - Pedro Ferreira Pinto Brandão-Dias
- Department of Genetic, Ecology and Evolution Institute of Biological Sciences Federal University of Minas Gerais Belo Horizonte Brazil
| | - Adriana Heloísa Pereira
- Department of Genetic, Ecology and Evolution Institute of Biological Sciences Federal University of Minas Gerais Belo Horizonte Brazil
| | - Nazaré Lúcio de Abreu
- Department of Genetic, Ecology and Evolution Institute of Biological Sciences Federal University of Minas Gerais Belo Horizonte Brazil
| | - Izinara Cruz Rosse
- Department of Genetic, Ecology and Evolution Institute of Biological Sciences Federal University of Minas Gerais Belo Horizonte Brazil.,Department of Pharmacy Federal University of Ouro Preto Ouro Preto Brazil
| | - Ana Paula Vimieiro Martins
- Department of Genetic, Ecology and Evolution Institute of Biological Sciences Federal University of Minas Gerais Belo Horizonte Brazil
| | - Susanne Facchin
- Department of Genetic, Ecology and Evolution Institute of Biological Sciences Federal University of Minas Gerais Belo Horizonte Brazil
| | | | | | | | - Evanguedes Kalapothakis
- Department of Genetic, Ecology and Evolution Institute of Biological Sciences Federal University of Minas Gerais Belo Horizonte Brazil
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50
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MacDonald ZG, Dupuis JR, Davis CS, Acorn JH, Nielsen SE, Sperling FAH. Gene flow and climate-associated genetic variation in a vagile habitat specialist. Mol Ecol 2020; 29:3889-3906. [PMID: 32810893 DOI: 10.1111/mec.15604] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2020] [Revised: 07/08/2020] [Accepted: 07/16/2020] [Indexed: 12/31/2022]
Abstract
Previous work in landscape genetics suggests that geographic isolation is of greater importance to genetic divergence than variation in environmental conditions. This is intuitive when configurations of suitable habitat are a dominant factor limiting dispersal and gene flow, but has not been thoroughly examined for habitat specialists with strong dispersal capability. Here, we evaluate the effects of geographic and environmental isolation on genetic divergence for a vagile invertebrate with high habitat specificity and a discrete dispersal life stage: Dod's Old World swallowtail butterfly, Papilio machaon dodi. In Canada, P. m. dodi are generally restricted to eroding habitat along major river valleys where their larval host plant occurs. A series of causal and linear mixed effects models indicate that divergence of genome-wide single nucleotide polymorphisms is best explained by a combination of environmental isolation (variation in summer temperatures) and geographic isolation (Euclidean distance). Interestingly, least-cost path and circuit distances through a resistance surface parameterized as the inverse of habitat suitability were not supported. This suggests that, although habitat associations of many butterflies are specific due to reproductive requirements, habitat suitability and landscape permeability are not equivalent concepts due to considerable adult vagility. We infer that divergent selection related to variation in summer temperatures has produced two genetic clusters within P. m. dodi, differing in voltinism and diapause propensity. Within the next century, temperatures are predicted to rise by amounts greater than the present-day difference between regions of the genetic clusters, potentially affecting the persistence of the northern cluster under continued climate change.
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Affiliation(s)
- Zachary G MacDonald
- Department of Renewable Resources, University of Alberta, Edmonton, Alberta, Canada
| | - Julian R Dupuis
- Department of Entomology, University of Kentucky, Lexington, Kentucky, USA
| | - Corey S Davis
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
| | - John H Acorn
- Department of Renewable Resources, University of Alberta, Edmonton, Alberta, Canada
| | - Scott E Nielsen
- Department of Renewable Resources, University of Alberta, Edmonton, Alberta, Canada
| | - Felix A H Sperling
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
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