1
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Izaguirre-Toriz V, Aguirre-Liguori JA, Latorre-Cárdenas MC, Arima EY, González-Rodríguez A. Local adaptation of Pinus leiophylla under climate and land use change models in the Avocado Belt of Michoacán. Mol Ecol 2024; 33:e17424. [PMID: 38813851 DOI: 10.1111/mec.17424] [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: 02/27/2024] [Revised: 05/01/2024] [Accepted: 05/17/2024] [Indexed: 05/31/2024]
Abstract
Climate change and land use change are two main drivers of global biodiversity decline, decreasing the genetic diversity that populations harbour and altering patterns of local adaptation. Landscape genomics allows measuring the effect of these anthropogenic disturbances on the adaptation of populations. However, both factors have rarely been considered simultaneously. Based on a set of 3660 SNPs from which 130 were identified as outliers by a genome-environment association analysis (LFMM), we modelled the spatial turnover of allele frequencies in 19 localities of Pinus leiophylla across the Avocado Belt in Michoacán state, Mexico. Then, we evaluated the effect of climate change and land use change scenarios, in addition to evaluating assisted gene flow strategies and connectivity metrics across the landscape to identify priority conservation areas for the species. We found that localities in the centre-east of the Avocado Belt would be more vulnerable to climate change, while localities in the western area are more threatened by land conversion to avocado orchards. Assisted gene flow actions could aid in mitigating both threats. Connectivity patterns among forest patches will also be modified by future habitat loss, with central and eastern parts of the Avocado Belt maintaining the highest connectivity. These results suggest that areas with the highest priority for conservation are in the eastern part of the Avocado Belt, including the Monarch Butterfly Biosphere Reserve. This work is useful as a framework that incorporates distinct layers of information to provide a more robust representation of the response of tree populations to anthropogenic disturbances.
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Affiliation(s)
- Vanessa Izaguirre-Toriz
- Instituto de Investigaciones en Ecosistemas y Sustentabilidad, Universidad Nacional Autónoma de México, Morelia, Mexico
- Posgrado en Ciencias Biológicas, Universidad Nacional Autónoma de México (Posgrado en Ciencias Biológicas, Unidad de Posgrado, Edificio D, 1° Piso, Circuito de Posgrados, Ciudad Universitaria), Coyoacán, Mexico
| | - Jonás A Aguirre-Liguori
- Departamento de Ecología Tropical, Campus de Ciencias Biológicas y Agropecuarias, Universidad Autónoma de Yucatán, Mérida, Mexico
| | - María Camila Latorre-Cárdenas
- Instituto de Investigaciones en Ecosistemas y Sustentabilidad, Universidad Nacional Autónoma de México, Morelia, Mexico
| | - Eugenio Y Arima
- Department of Geography and the Environment, University of Texas at Austin, Austin, Texas, USA
| | - Antonio González-Rodríguez
- Laboratorio Nacional de Innovación Ecotecnológica Para la Sustentabilidad (LANIES), Instituto de Investigaciones en Ecosistemas y Sustentabilidad, UNAM Campus Morelia, Morelia, Mexico
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2
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Dalapicolla J, Weir JT, Vilaça ST, Quaresma TF, Schneider MPC, Vasconcelos ATR, Aleixo A. Whole genomes show contrasting trends of population size changes and genomic diversity for an Amazonian endemic passerine over the late quaternary. Ecol Evol 2024; 14:e11250. [PMID: 38660467 PMCID: PMC11040105 DOI: 10.1002/ece3.11250] [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: 09/26/2023] [Revised: 03/16/2024] [Accepted: 03/25/2024] [Indexed: 04/26/2024] Open
Abstract
The "Amazon tipping point" is a global change scenario resulting in replacement of upland terra-firme forests by large-scale "savannization" of mostly southern and eastern Amazon. Reduced rainfall accompanying the Last Glacial Maximum (LGM) has been proposed to have acted as such a tipping point in the past, with the prediction that terra-firme inhabiting species should have experienced reductions in population size as drier habitats expanded. Here, we use whole-genomes of an Amazonian endemic organism (Scale-backed antbirds - Willisornis spp.) sampled from nine populations across the region to test this historical demography scenario. Populations from southeastern Amazonia and close to the Amazon-Cerrado ecotone exhibited a wide range of demographic patterns, while most of those from northern and western Amazonia experienced uniform expansions between 400 kya and 80-60 kya, with gradual declines toward 20 kya. Southeastern populations of Willisornis were the last to diversify and showed smaller heterozygosity and higher runs of homozygosity values than western and northern populations. These patterns support historical population declines throughout the Amazon that affected more strongly lineages in the southern and eastern areas, where historical "tipping point" conditions existed due to the widespread replacement of humid forest by drier and open vegetation during the LGM.
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Affiliation(s)
- Jeronymo Dalapicolla
- Instituto Tecnológico ValeBelémParáBrazil
- Departamento de Sistemática e EcologiaUniversidade Federal da Paraíba, João PessoaParaíbaBrazil
| | - Jason T. Weir
- Department of Biological SciencesUniversity of Toronto ScarboroughTorontoOntarioCanada
- Department of Ecology and Evolutionary BiologyUniversity of TorontoTorontoOntarioCanada
- Department of Natural History, Royal Ontario MuseumTorontoOntarioCanada
| | | | | | - Maria P. C. Schneider
- Laboratório de Genômica e BiotecnologiaInstituto de Ciências Biológicas, UFPABelémBrazil
| | - Ana Tereza R. Vasconcelos
- Laboratório de BioinformáticaLaboratório Nacional de Computação Científica, PetrópolisRio de JaneiroBrazil
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3
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Ming Y, Ni G. A dataset of genetic diversity studies in the China Seas. Sci Data 2024; 11:235. [PMID: 38395909 PMCID: PMC10891114 DOI: 10.1038/s41597-024-03082-w] [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: 11/10/2023] [Accepted: 02/16/2024] [Indexed: 02/25/2024] Open
Abstract
Genetic diversity, a fundamental aspect of biodiversity, greatly influences the ecological and evolutionary characteristics of populations and species. Compiling genetic data is crucial as the initial step in comprehending and applying genetic resources; however, regional collating work is still insufficient, especially in marine ecosystems. Here, by conducting a thorough literature search and quality-control procedures, we provide a dataset of genetic diversity studies on marine species in the China Seas. The final dataset comprised a total of 746 studies (encompassing 840 data sets and 3658 populations) across 343 species from 1998 to 2022. For each data set, information including publication year, publication language, studied species, belonged taxonomic group, applied molecular markers, and sampling strategies (number of populations, total number of individuals, etc.) was collated to analyse the scope, strengths, and omissions of these works. This dataset offers a comprehensive overview of genetic diversity studies in the China Seas, which may help to adjust future research focuses, promote conservation and macrogenetics studies in this region, and also facilitate regional cooperation.
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Affiliation(s)
- Yaqian Ming
- Ministry of Education Key Laboratory of Mariculture, Ocean University of China, Qingdao, 266003, China
| | - Gang Ni
- Ministry of Education Key Laboratory of Mariculture, Ocean University of China, Qingdao, 266003, China.
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4
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Madeira AG, Tsuda Y, Nagano Y, Iwasaki T, Zucchi MI, Kajita T, Mori GM. The role of oceanic currents in the dispersal and connectivity of the mangrove Rhizophora mangle on the Southwest Atlantic region. Mol Ecol Resour 2023. [PMID: 37173824 DOI: 10.1111/1755-0998.13807] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2022] [Revised: 04/07/2023] [Accepted: 04/17/2023] [Indexed: 05/15/2023]
Abstract
Dispersal is a crucial mechanism to living beings, allowing them to reach new resources such that populations and species can occupy new environments. However, directly observing the dispersal mechanisms of widespread species can be costly or even impractical, which is the case for mangrove trees. The influence of ocean currents on mangrove dispersal is increasingly evident; however, few studies mechanistically relate the patterns of population distribution with the dispersal by oceanic currents under an integrated framework. Here, we evaluate the role of oceanic currents on connectivity of Rhizophora mangle along the Southwest Atlantic. We inferred population genetic structure and migration rates, simulated the displacement of propagules and tested our hypotheses with Mantel tests and redundancy analysis. We observed populations structured in two major groups, north and south, which is corroborated by other studies with Rhizophora and other coastal plants. Inferred recent migration rates do not indicate ongoing gene flow between sites. Conversely, long-term migration rates were low across groups and contrasting dispersal patterns within each one, which is consistent with long-distance dispersal events. Our hypothesis tests suggest that both isolation by distance and isolation by oceanography (derived from the oceanic currents) can explain the neutral genetic variation of R. mangle in the region. Our findings expand current knowledge of mangrove connectivity and highlight how the association of molecular methods with oceanographic simulations improve the interpretation of the dispersal process. This integrative approach is a cost- and time-efficient strategy to include dispersal and connectivity data into marine protected areas planning and management.
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Affiliation(s)
| | - Yoshiaki Tsuda
- Sugadaira Research Station, Mountain Science Center, University of Tsukuba, Nagano, Japan
| | - Yukio Nagano
- Analytical Research Center for Experimental Sciences, Saga University, Saga, Japan
- The United Graduate School of Agricultural Sciences, Kagoshima University, Kagoshima, Japan
| | | | | | - Tadashi Kajita
- The United Graduate School of Agricultural Sciences, Kagoshima University, Kagoshima, Japan
- Iriomote Station, Tropical Biosphere Research Center, University of the Ryukyus, Nishihara, Okinawa, Japan
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5
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Lu-Irving P, Bragg JG, Rossetto M, King K, O’Brien M, van der Merwe MM. Capturing Genetic Diversity in Seed Collections: An Empirical Study of Two Congeners with Contrasting Mating Systems. PLANTS (BASEL, SWITZERLAND) 2023; 12:522. [PMID: 36771606 PMCID: PMC9921034 DOI: 10.3390/plants12030522] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Revised: 01/10/2023] [Accepted: 01/13/2023] [Indexed: 06/18/2023]
Abstract
Plant mating systems shape patterns of genetic diversity and impact the long-term success of populations. As such, they are relevant to the design of seed collections aiming to maximise genetic diversity (e.g., germplasm conservation, ecological restoration). However, for most species, little is known empirically about how variation in mating systems and genetic diversity is distributed. We investigated the relationship between genetic diversity and mating systems in two functionally similar, co-occurring species of Hakea (Proteaceae), and evaluated the extent to which genetic diversity was captured in seeds. We genotyped hundreds of seedlings and mother plants via DArTseq, and developed novel implementations of two approaches to inferring the mating system from SNP data. A striking contrast in patterns of genetic diversity between H. sericea and H. teretifolia was revealed, consistent with a contrast in their mating systems. While both species had mixed mating systems, H. sericea was found to be habitually selfing, while H. teretifolia more evenly employed both selfing and outcrossing. In both species, seed collection schemes maximised genetic diversity by increasing the number of maternal lines and sites sampled, but twice as many sites were needed for the selfing species to capture equivalent levels of genetic variation at a regional scale.
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Affiliation(s)
- Patricia Lu-Irving
- Research Centre for Ecosystem Resilience, Australian Institute of Botanical Science, Royal Botanic Gardens Sydney, Mrs Macquaries Rd., Sydney, NSW 2000, Australia
| | - Jason G. Bragg
- Research Centre for Ecosystem Resilience, Australian Institute of Botanical Science, Royal Botanic Gardens Sydney, Mrs Macquaries Rd., Sydney, NSW 2000, Australia
| | - Maurizio Rossetto
- Research Centre for Ecosystem Resilience, Australian Institute of Botanical Science, Royal Botanic Gardens Sydney, Mrs Macquaries Rd., Sydney, NSW 2000, Australia
| | - Kit King
- Research Centre for Ecosystem Resilience, Australian Institute of Botanical Science, Royal Botanic Gardens Sydney, Mrs Macquaries Rd., Sydney, NSW 2000, Australia
| | - Mitchell O’Brien
- Research Centre for Ecosystem Resilience, Australian Institute of Botanical Science, Royal Botanic Gardens Sydney, Mrs Macquaries Rd., Sydney, NSW 2000, Australia
- Commonwealth Scientific and Industrial Research Organisation (CSIRO), Innovation Quarter Westmead, Level 3, East Tower, 158-164 Hawkesbury Rd., Westmead, NSW 2145, Australia
| | - Marlien M. van der Merwe
- Research Centre for Ecosystem Resilience, Australian Institute of Botanical Science, Royal Botanic Gardens Sydney, Mrs Macquaries Rd., Sydney, NSW 2000, Australia
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6
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Tidière M, Portanier E, Jacquet S, Goodman SM, Monnier G, Beuneux G, Desmet J, Kaerle C, Queney G, Barataud M, Pontier D. Species delineation and genetic structure of two
Chaerephon
species (
C. pusillus
and
C. leucogaster
) on Madagascar and the Comoro archipelago. Ecol Evol 2022; 12:e9566. [DOI: 10.1002/ece3.9566] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Revised: 11/03/2022] [Accepted: 11/14/2022] [Indexed: 12/04/2022] Open
Affiliation(s)
- Morgane Tidière
- LabEx ECOFECT Université de Lyon Lyon France
- LBBE UMR5558 CNRS Université de Lyon 1 Villeurbanne France
| | | | - Stéphanie Jacquet
- LabEx ECOFECT Université de Lyon Lyon France
- LBBE UMR5558 CNRS Université de Lyon 1 Villeurbanne France
| | - Steven M. Goodman
- Field Museum of Natural History Chicago Illinois USA
- Association Vahatra Antananarivo Madagascar
| | | | - Gregory Beuneux
- Société Française pour l'Etude et la Protection des Mammifères Bourges France
| | | | | | | | - Michel Barataud
- Société Française pour l'Etude et la Protection des Mammifères Bourges France
| | - Dominique Pontier
- LabEx ECOFECT Université de Lyon Lyon France
- LBBE UMR5558 CNRS Université de Lyon 1 Villeurbanne France
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7
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Martínez de León R, Castellanos-Morales G, Moreno-Letelier A. Incipient speciation, high genetic diversity, and ecological divergence in the alligator bark juniper suggest complex demographic changes during the Pleistocene. PeerJ 2022; 10:e13802. [PMID: 35910768 PMCID: PMC9336613 DOI: 10.7717/peerj.13802] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Accepted: 07/07/2022] [Indexed: 01/18/2023] Open
Abstract
The most recent glacial cycles of the Pleistocene affected the distribution, population sizes, and levels of genetic structure of temperate-forest species in the main Mexican mountain systems. Our objective was to investigate the effects these cycles had on the genetic structure and distribution of a dominant species of the "mexical" vegetation across North and Central America. We studied the genetic diversity of Juniperus deppeana, a conifer distributed from the Southwestern United States to the highlands of Central America. We combined information of one plastid marker and two nuclear markers to infer phylogeographic structure, genetic diversity and demographic changes. We also characterized the climatic niche for each variety to infer the plausible area of suitability during past climatic conditions and to evaluate climatic niche discontinuities along with the species distribution. We found a marked phylogeographic structure separating the populations North and South of the Isthmus of Tehuantepec, with populations to the South of this barrier forming a distinct genetic cluster corresponding to Juniperus deppeana var. gamboana. We also found signals of population expansion in the Northern genetic cluster. Ecological niche modeling results confirmed climatic niche differences and discontinuities among J. deppeana varieties and heterogeneous responses to climatic oscillations. Overall, J. deppeana's genetic diversity has been marked by distribution shifts, population growth and secondary contact the North, and in situ permanence in the South since the last interglacial to the present. High genetic variation suggests a wide and climatically diverse distribution during climatic oscillations. We detected the existence of two main genetic clusters, supporting previous proposals that Juniperus deppeana and Juniperus gamboana may be considered two separate species.
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Affiliation(s)
- Rodrigo Martínez de León
- Posgrado en Ciencias Biológicas, Universidad Nacional Autónoma de México, Ciudad de México, Mexico,Jardín Botánico, Instituto de Biología, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | | | - Alejandra Moreno-Letelier
- Jardín Botánico, Instituto de Biología, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
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8
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Stabilizing selection on Atlantic cod supergenes through a millennium of extensive exploitation. Proc Natl Acad Sci U S A 2022; 119:2114904119. [PMID: 35165196 PMCID: PMC8872764 DOI: 10.1073/pnas.2114904119] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/04/2022] [Indexed: 12/21/2022] Open
Abstract
Ecological disruption due to human impacts is evident worldwide, and a key to mitigation lies in characterizing the underlying mechanisms of species and ecosystem stability. Here we show that three extensive “supergenes” are maintained in Atlantic cod by stabilizing selection, tying these genes to the persistence of a keystone species distributed across the northern Atlantic Ocean. Removal of this species has caused severe ecosystem reshuffling in several areas of its range. Genomic inference of historic stock sizes further shows that cod has been under pressure in the North Sea system since the Viking period, in line with zooarchaeological records. Expansion of fisheries in Northern Europe through the past millennium is well documented and supports the inferred long-term declines. Life on Earth has been characterized by recurring cycles of ecological stasis and disruption, relating biological eras to geological and climatic transitions through the history of our planet. Due to the increasing degree of ecological abruption caused by human influences many advocate that we now have entered the geological era of the Anthropocene, or “the age of man.” Considering the ongoing mass extinction and ecosystem reshuffling observed worldwide, a better understanding of the drivers of ecological stasis will be a requisite for identifying routes of intervention and mitigation. Ecosystem stability may rely on one or a few keystone species, and the loss of such species could potentially have detrimental effects. The Atlantic cod (Gadus morhua) has historically been highly abundant and is considered a keystone species in ecosystems of the northern Atlantic Ocean. Collapses of cod stocks have been observed on both sides of the Atlantic and reported to have detrimental effects that include vast ecosystem reshuffling. By whole-genome resequencing we demonstrate that stabilizing selection maintains three extensive “supergenes” in Atlantic cod, linking these genes to species persistence and ecological stasis. Genomic inference of historic effective population sizes shows continued declines for cod in the North Sea–Skagerrak–Kattegat system through the past millennia, consistent with an early onset of the marine Anthropocene through industrialization and commercialization of fisheries throughout the medieval period.
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9
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Foster SD, Feutry P, Grewe P, Davies C. Sample size requirements for genetic studies on yellowfin tuna. PLoS One 2021; 16:e0259113. [PMID: 34735482 PMCID: PMC8568148 DOI: 10.1371/journal.pone.0259113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Accepted: 10/12/2021] [Indexed: 12/02/2022] Open
Abstract
In population genetics, the amount of information for an analytical task is governed by the number of individuals sampled and the amount of genetic information measured on each of those individuals. In this work, we assessed the numbers of individual yellowfin tuna (Thunnus albacares) and genetic markers required for ocean-basin scale inferences. We assessed this for three distinct data analysis tasks that are often employed: testing for differences between genetic profiles; stock delineation, and; assignment of individuals to stocks. For all analytical tasks, we used real (not simulated) data from four sampling locations that span the tropical Pacific Ocean. Whilst spatially separated, the genetic differences between the sampling sites were not substantial, a maximum of approximately Fst = 0.02, which is quite typical of large pelagic fish. We repeatedly sub-sampled the data, mimicking a new survey, and performed the analyses. False positive rates were also assessed by re-sampling and randomly assigning fish to groups. Varying the sample sizes indicated that some analytical tasks, namely profile testing, required relatively few individuals per sampling location (n ≳ 10) and single nucleotide polymorphisms (SNPs, m ≳ 256). Stock delineation required more individuals per sampling location (n ≳ 25). Assignment of fish to sampling locations required substantially more individuals, more in fact than we had available (n > 50), although this sample size could be reduced to n ≳ 30 when individual fish were assumed to belong to one of the groups sampled. With these results, designers of molecular ecological surveys for yellowfin tuna, and users of information from them, can assess whether the information content is adequate for the required inferential task.
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Affiliation(s)
| | - Pierre Feutry
- CSIRO’s Oceans and Atmospheres, Hobart, Tasmania, Australia
| | - Peter Grewe
- CSIRO’s Oceans and Atmospheres, Hobart, Tasmania, Australia
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10
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Sagar V, Kaelin CB, Natesh M, Reddy PA, Mohapatra RK, Chhattani H, Thatte P, Vaidyanathan S, Biswas S, Bhatt S, Paul S, Jhala YV, Verma MM, Pandav B, Mondol S, Barsh GS, Swain D, Ramakrishnan U. High frequency of an otherwise rare phenotype in a small and isolated tiger population. Proc Natl Acad Sci U S A 2021; 118:e2025273118. [PMID: 34518374 PMCID: PMC8488692 DOI: 10.1073/pnas.2025273118] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/09/2021] [Indexed: 11/18/2022] Open
Abstract
Most endangered species exist today in small populations, many of which are isolated. Evolution in such populations is largely governed by genetic drift. Empirical evidence for drift affecting striking phenotypes based on substantial genetic data are rare. Approximately 37% of tigers (Panthera tigris) in the Similipal Tiger Reserve (in eastern India) are pseudomelanistic, characterized by wide, merged stripes. Camera trap data across the tiger range revealed the presence of pseudomelanistic tigers only in Similipal. We investigated the genetic basis for pseudomelanism and examined the role of drift in driving this phenotype's frequency. Whole-genome data and pedigree-based association analyses from captive tigers revealed that pseudomelanism cosegregates with a conserved and functionally important coding alteration in Transmembrane Aminopeptidase Q (Taqpep), a gene responsible for similar traits in other felid species. Noninvasive sampling of tigers revealed a high frequency of the Taqpep p.H454Y mutation in Similipal (12 individuals, allele frequency = 0.58) and absence from all other tiger populations (395 individuals). Population genetic analyses confirmed few (minimal number) tigers in Similipal, and its genetic isolation, with poor geneflow. Pairwise FST (0.33) at the mutation site was high but not an outlier. Similipal tigers had low diversity at 81 single nucleotide polymorphisms (mean heterozygosity = 0.28, SD = 0.27). Simulations were consistent with founding events and drift as possible drivers for the observed stark difference of allele frequency. Our results highlight the role of stochastic processes in the evolution of rare phenotypes. We highlight an unusual evolutionary trajectory in a small and isolated population of an endangered species.
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Affiliation(s)
- Vinay Sagar
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore 560065, India;
| | - Christopher B Kaelin
- Department of Genetics, Stanford University, Palo Alto, CA 94309
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806
| | - Meghana Natesh
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore 560065, India
- Biology Department, Indian Institute of Science Education and Research, Tirupati 411008, India
| | - P Anuradha Reddy
- Laboratory for Conservation of Endangered Species, Center for Cellular & Molecular Biology, Hyderabad 500048, India
| | | | - Himanshu Chhattani
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore 560065, India
| | - Prachi Thatte
- World Wide Fund for Nature - India, New Delhi 110003 India
| | - Srinivas Vaidyanathan
- Foundation for Ecological Research, Advocacy and Learning, Auroville Post, Tamil Nadu 605101 India
| | | | | | - Shashi Paul
- Odisha Forest Department, Bhubaneswar 751023, India
| | - Yadavendradev V Jhala
- Wildlife Institute of India, Dehradun 248001, India
- National Tiger Conservation Authority, Wildlife Institute of India Tiger Cell, Wildlife Institute of India, Dehradun 248001, India
| | | | | | | | - Gregory S Barsh
- Department of Genetics, Stanford University, Palo Alto, CA 94309
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806
| | - Debabrata Swain
- Former Member Secretary, National Tiger Conservation Authority, New Delhi 110003, India
- Former Principal Chief Conservator of Forest and Head of Forest Force, Indian Forest Service, Bhubaneswar 751023, India
| | - Uma Ramakrishnan
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore 560065, India;
- DBT - Wellcome Trust India Alliance, Hyderabad 500034, India
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11
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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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12
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Gasca-Pineda J, Gutiérrez-Guerrero YT, Aguirre-Planter E, Eguiarte LE. The role of environment, local adaptation, and past climate fluctuation on the amount and distribution of genetic diversity in two subspecies of Mexican wild Zea mays. AMERICAN JOURNAL OF BOTANY 2020; 107:1542-1554. [PMID: 33205455 DOI: 10.1002/ajb2.1561] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Accepted: 07/09/2020] [Indexed: 06/11/2023]
Abstract
PREMISE Past climate fluctuations during the Holocene and Pleistocene shaped the distribution of several plant species in temperate areas over the world. Wild maize, commonly known as teosinte, is a good system to evaluate the effects of historical climate fluctuations on genetic diversity due to its wide distribution in Mexico with contrasting environmental conditions. We explored the influence of contemporary factors and historical environmental shifts on genetic diversity, including present and three historical periods using neutral markers. METHODS We used 22 nuclear microsatellite loci to examine the genetic diversity of 14 populations of Zea mays subsp. parviglumis and 15 populations of Zea mays subsp. mexicana (527 individuals total). We implemented genetic structure analyses to evaluate genetic differentiation between and within subspecies. We applied coalescent-based demographic analysis and species distribution modeling to evaluate the effects of historical environmental shifts. RESULTS We found 355 alleles in total for the two subspecies and variable levels of diversity in each (Z. mays subsp. parviglumis expected heterozygosity HE = 0.3646-0.7699; Z. mays subsp. mexicana HE = 0.5885-0.7671). We detected significant genetic structure among populations (DEST = 0.4332) with significant heterozygote deficiency (FIS = 0.1796), and variable selfing rates (sg2 = 0.0-0.3090). The Bayesian assignment analysis differentiated four genetic groups. Demographic and species distribution modeling analysis suggested that environmental shifts were influential in the amount of genetic diversity. CONCLUSIONS Our analyses suggest that the current genetic diversity in teosinte is shaped by factors such as local adaptation and genetic isolation, along with historical environmental fluctuations.
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Affiliation(s)
- Jaime Gasca-Pineda
- Laboratorio de Evolución Molecular y Experimental, Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, AP, 70-275 Coyoacán 04510, Ciudad de México, México
| | - Yocelyn T Gutiérrez-Guerrero
- Laboratorio de Evolución Molecular y Experimental, Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, AP, 70-275 Coyoacán 04510, Ciudad de México, México
| | - Erika Aguirre-Planter
- Laboratorio de Evolución Molecular y Experimental, Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, AP, 70-275 Coyoacán 04510, Ciudad de México, México
| | - Luis E Eguiarte
- Laboratorio de Evolución Molecular y Experimental, Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, AP, 70-275 Coyoacán 04510, Ciudad de México, México
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