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Kofler XV, Grossniklaus U, Schiestl FP, Frachon L. Uncovering genes involved in pollinator-driven mating system shifts and selfing syndrome evolution in Brassica rapa. THE NEW PHYTOLOGIST 2024; 243:1220-1230. [PMID: 38853408 DOI: 10.1111/nph.19880] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Accepted: 05/14/2024] [Indexed: 06/11/2024]
Abstract
Shifts in pollinator occurrence and their pollen transport effectiveness drive the evolution of mating systems in flowering plants. Understanding the genomic basis of these changes is essential for predicting the persistence of a species under environmental changes. We investigated the genomic changes in Brassica rapa over nine generations of pollination by hoverflies associated with rapid morphological evolution toward the selfing syndrome. We combined a genotyping-by-sequencing (GBS) approach with a genome-wide association study (GWAS) to identify candidate genes, and assessed their functional role in the observed morphological changes by studying mutations of orthologous genes in the model plant Arabidopsis thaliana. We found 31 candidate genes involved in a wide range of functions from DNA/RNA binding to transport. Our functional assessment of orthologous genes in A. thaliana revealed that two of the identified genes in B. rapa are involved in regulating the size of floral organs. We found a protein kinase superfamily protein involved in petal width, an important trait in plant attractiveness to pollinators. Moreover, we found a histone lysine methyltransferase (HKMT) associated with stamen length. Altogether, our study shows that hoverfly pollination leads to rapid evolution toward the selfing syndrome mediated by polygenic changes.
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Affiliation(s)
- Xeniya V Kofler
- Department of Systematic and Evolutionary Botany, University of Zurich, Zollikerstrasse 107, 8008, Zürich, Switzerland
- Zurich-Basel Plant Science Center, University of Zurich, ETH Zurich, University of Basel, Tannenstrasse 1, 8092, Zürich, Switzerland
- Department of Plant and Microbial Biology, University of Zurich, Zollikerstrasse 107, 8008, Zürich, Switzerland
| | - Ueli Grossniklaus
- Zurich-Basel Plant Science Center, University of Zurich, ETH Zurich, University of Basel, Tannenstrasse 1, 8092, Zürich, Switzerland
- Department of Plant and Microbial Biology, University of Zurich, Zollikerstrasse 107, 8008, Zürich, Switzerland
| | - Florian P Schiestl
- Department of Systematic and Evolutionary Botany, University of Zurich, Zollikerstrasse 107, 8008, Zürich, Switzerland
- Zurich-Basel Plant Science Center, University of Zurich, ETH Zurich, University of Basel, Tannenstrasse 1, 8092, Zürich, Switzerland
| | - Léa Frachon
- Department of Systematic and Evolutionary Botany, University of Zurich, Zollikerstrasse 107, 8008, Zürich, Switzerland
- Zurich-Basel Plant Science Center, University of Zurich, ETH Zurich, University of Basel, Tannenstrasse 1, 8092, Zürich, Switzerland
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Kreling SES, Reese EM, Cavalluzzi OM, Bozzi NB, Messinger R, Schell CJ, Long RA, Prugh LR. City divided: Unveiling family ties and genetic structuring of coyotes in Seattle. Mol Ecol 2024; 33:e17427. [PMID: 38837263 DOI: 10.1111/mec.17427] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2024] [Revised: 05/02/2024] [Accepted: 05/13/2024] [Indexed: 06/07/2024]
Abstract
Linear barriers pose significant challenges for wildlife gene flow, impacting species persistence, adaptation, and evolution. While numerous studies have examined the effects of linear barriers (e.g., fences and roadways) on partitioning urban and non-urban areas, understanding their influence on gene flow within cities remains limited. Here, we investigated the impact of linear barriers on coyote (Canis latrans) population structure in Seattle, Washington, where major barriers (i.e., interstate highways and bodies of water) divide the city into distinct quadrants. Just under 1000 scats were collected to obtain genetic data between January 2021 and December 2022, allowing us to identify 73 individual coyotes. Notably, private allele analysis underscored limited interbreeding among quadrants. When comparing one quadrant to each other, there were up to 16 private alleles within a single quadrant, representing nearly 22% of the population allelic diversity. Our analysis revealed weak isolation by distance, and despite being a highly mobile species, genetic structuring was apparent between quadrants even with extremely short geographic distance between individual coyotes, implying that Interstate 5 and the Ship Canal act as major barriers. This study uses coyotes as a model species for understanding urban gene flow and its consequences in cities, a crucial component for bolstering conservation of rarer species and developing wildlife friendly cities.
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Affiliation(s)
- Samantha E S Kreling
- School of Environmental and Forest Sciences, University of Washington, Seattle, Washington, USA
| | - Ellen M Reese
- School of Environmental and Forest Sciences, University of Washington, Seattle, Washington, USA
| | - Olivia M Cavalluzzi
- School of Environmental and Forest Sciences, University of Washington, Seattle, Washington, USA
| | - Natalee B Bozzi
- School of Environmental and Forest Sciences, University of Washington, Seattle, Washington, USA
| | - Riley Messinger
- School of Environmental and Forest Sciences, University of Washington, Seattle, Washington, USA
| | - Christopher J Schell
- Department of Environmental Science, Policy, and Management, University of California-Berkeley, Berkeley, California, USA
| | | | - Laura R Prugh
- School of Environmental and Forest Sciences, University of Washington, Seattle, Washington, USA
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García-Castro KL, Márquez EJ. Temporal analysis of genetic diversity and gene flow in the threatened catfish Pseudoplatystoma magdaleniatum from a dammed neotropical river. PLoS One 2024; 19:e0301577. [PMID: 38635781 PMCID: PMC11025948 DOI: 10.1371/journal.pone.0301577] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Accepted: 03/19/2024] [Indexed: 04/20/2024] Open
Abstract
The striped catfish Pseudoplatystoma magdaleniatum is a large-sized migratory species from the north Andes region, endemic to Magdalena basin and one of the major fishery resources. Despite the estimated reduction of over 80% of the fisheries production of this species throughout the basin in recent decades, its population in the lower Magdalena-Cauca basin showed healthy genetics after molecular analyses. However, the current conservation status of this species and several habitat disturbances demand the re-evaluation of its population genetics to infer evolutionary risks and assess potential changes. This work analyzed a total of 164 samples from the Cauca River collected downstream the Ituango Dam between 2019-2021 using species-specific microsatellite markers to compare the genetic diversity and structure in samples collected between 2010-2014 from the lower Magdalena-Cauca basin, previously analyzed. Our results showed a relatively stable panmictic population over time (4 to 10 years), with high genetic diversity and evidence of recent bottleneck. Promoting habitat connectivity to conserve gene flow, characterizing diversity and genetic structure over the entire basin, and integrating the results with future monitoring are important aspects for the management planning for P. magdaleniatum in the Magdalena-Cauca basin.
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Affiliation(s)
- Kevin León García-Castro
- Facultad de Ciencias Universidad Nacional de Colombia–Sede Medellín, Laboratorio de Biología Molecular y Celular, Escuela de Biociencias, Medellín, Antioquia, Colombia
| | - Edna Judith Márquez
- Facultad de Ciencias Universidad Nacional de Colombia–Sede Medellín, Laboratorio de Biología Molecular y Celular, Escuela de Biociencias, Medellín, Antioquia, Colombia
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Maxwell LM, Clark JD, Walsh J, Conway M, Olsen BJ, Kovach AI. Ecological characteristics explain neutral genetic variation of three coastal sparrow species. Mol Ecol 2024; 33:e17316. [PMID: 38481075 DOI: 10.1111/mec.17316] [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: 09/08/2022] [Revised: 02/15/2024] [Accepted: 02/23/2024] [Indexed: 04/09/2024]
Abstract
Eco-phylogeographic approaches to comparative population genetic analyses allow for the inclusion of intrinsic influences as drivers of intraspecific genetic structure. This insight into microevolutionary processes, including changes within a species or lineage, provides better mechanistic understanding of species-specific interactions and enables predictions of evolutionary responses to environmental change. In this study, we used single nucleotide polymorphisms (SNPs) identified from reduced representation sequencing to compare neutral population structure, isolation by distance (IBD), genetic diversity and effective population size (Ne) across three closely related and co-distributed saltmarsh sparrow species differing along a specialization gradient-Nelson's (Ammospiza nelsoni subvirgata), saltmarsh (A. caudacuta) and seaside sparrows (A. maritima maritima). Using an eco-phylogeographic lens within a conservation management context, we tested predictions about species' degree of evolutionary history and ecological specialization to tidal marshes, habitat, current distribution and population status on population genetic metrics. Population structure differed among the species consistent with their current distribution and habitat factors, rather than degree of ecological specialization: seaside sparrows were panmictic, saltmarsh sparrows showed hierarchical structure and Nelson's sparrows were differentiated into multiple, genetically distinct populations. Neutral population genetic theory and demographic/evolutionary history predicted patterns of genetic diversity and Ne rather than degree of ecological specialization. Patterns of population variation and evolutionary distinctiveness (Shapely metric) suggest different conservation measures for long-term persistence and evolutionary potential in each species. Our findings contribute to a broader understanding of the complex factors influencing genetic variation, beyond specialist-generalist status and support the role of an eco-phylogeographic approach in population and conservation genetics.
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Affiliation(s)
- Logan M Maxwell
- Department of Natural Resources and the Environment, University of New Hampshire, Durham, New Hampshire, USA
| | - Jonathan D Clark
- Department of Natural Resources and the Environment, University of New Hampshire, Durham, New Hampshire, USA
| | - Jennifer Walsh
- Department of Natural Resources and the Environment, University of New Hampshire, Durham, New Hampshire, USA
- Fuller Evolutionary Biology Program, Cornell Laboratory of Ornithology, Ithaca, New York, USA
| | - Meaghan Conway
- School of Biology and Ecology, University of Maine, Orono, Maine, USA
| | - Brian J Olsen
- School of Biology and Ecology, University of Maine, Orono, Maine, USA
| | - Adrienne I Kovach
- Department of Natural Resources and the Environment, University of New Hampshire, Durham, New Hampshire, USA
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Tapia HJ, Dávila P. Continuity and discontinuity in evolutionary processes with emphasis on plants. Biosystems 2024; 236:105108. [PMID: 38159673 DOI: 10.1016/j.biosystems.2023.105108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Revised: 12/20/2023] [Accepted: 12/21/2023] [Indexed: 01/03/2024]
Abstract
The present work is aimed to review the concepts of continuity and discontinuity in the reproductive processes and their impact on the evolutionary outcome, emphasizing on the plant model. Let be stated that evolutionary changes need to pass down generation after generation through the cellular reproductive mechanisms, and these mechanisms can account for changes from single nucleotide to genome-wide mutations. Patterns of continuity and discontinuity in sexual and asexual species pose notorious differences as the involvement of the cellular genetic material from single or different individuals, the changes in the ploidy level, or the independence between nuclear and plastid genomes. One relevant aspect of the plant model is the open system for pollen donation, which can be driven from every male flower to every female flower in the neighborhood, as well as the facilitated seed dispersal patterns, that may break or restore the contact between populations. Three significative processes are distinguishable, syngenesis, anagenesis, and cladogenesis. The syngenesis refers to the reproduction between individuals, either if they pertain to the same species, from different populations or even from different species. The anagenesis refers to the pursuit of all the possible rearrangements of genes and alleles pooled in a population of individuals, and the cladogenesis represents the absence of reproduction that leads to differentiation. Recent developments on the genomic analysis of single cells, single chromosomes and fragments of homologous chromosomes could bring new insights into the processes of the evolution, in generational time and in a broad spectrum of spatial/geographic extents.
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Affiliation(s)
- Hector J Tapia
- Laboratorio de Recursos Naturales, UBIPRO, FES Iztacala, Universidad Nacional Autónoma de México (UNAM), Tlalnepantla, 54090, Estado de México, Mexico.
| | - Patricia Dávila
- Laboratorio de Recursos Naturales, UBIPRO, FES Iztacala, Universidad Nacional Autónoma de México (UNAM), Tlalnepantla, 54090, Estado de México, Mexico
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Dayton TL, Alcala N, Moonen L, den Hartigh L, Geurts V, Mangiante L, Lap L, Dost AFM, Beumer J, Levy S, van Leeuwaarde RS, Hackeng WM, Samsom K, Voegele C, Sexton-Oates A, Begthel H, Korving J, Hillen L, Brosens LAA, Lantuejoul S, Jaksani S, Kok NFM, Hartemink KJ, Klomp HM, Borel Rinkes IHM, Dingemans AM, Valk GD, Vriens MR, Buikhuisen W, van den Berg J, Tesselaar M, Derks J, Speel EJ, Foll M, Fernández-Cuesta L, Clevers H. Druggable growth dependencies and tumor evolution analysis in patient-derived organoids of neuroendocrine neoplasms from multiple body sites. Cancer Cell 2023; 41:2083-2099.e9. [PMID: 38086335 DOI: 10.1016/j.ccell.2023.11.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Revised: 09/06/2023] [Accepted: 11/08/2023] [Indexed: 12/18/2023]
Abstract
Neuroendocrine neoplasms (NENs) comprise well-differentiated neuroendocrine tumors (NETs) and poorly differentiated neuroendocrine carcinomas (NECs). Treatment options for patients with NENs are limited, in part due to lack of accurate models. We establish patient-derived tumor organoids (PDTOs) from pulmonary NETs and derive PDTOs from an understudied subtype of NEC, large cell neuroendocrine carcinoma (LCNEC), arising from multiple body sites. PDTOs maintain the gene expression patterns, intra-tumoral heterogeneity, and evolutionary processes of parental tumors. Through hypothesis-driven drug sensitivity analyses, we identify ASCL1 as a potential biomarker for response of LCNEC to treatment with BCL-2 inhibitors. Additionally, we discover a dependency on EGF in pulmonary NET PDTOs. Consistent with these findings, we find that, in an independent cohort, approximately 50% of pulmonary NETs express EGFR. This study identifies an actionable vulnerability for a subset of pulmonary NETs, emphasizing the utility of these PDTO models.
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Affiliation(s)
- Talya L Dayton
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and UMC Utrecht, 3584 CT Utrecht, the Netherlands; Oncode Institute, Hubrecht Institute, 3584 CT Utrecht, the Netherlands.
| | - Nicolas Alcala
- Rare Cancers Genomics Team (RCG), Genomic Epidemiology Branch (GEM), International Agency for Research on Cancer/World Health Organisation (IARC/WHO), 69007 Lyon, France
| | - Laura Moonen
- Department of Pathology, GROW School for Oncology and Reproduction, Maastricht University Medical Centre, 6229 ER Maastricht, the Netherlands
| | - Lisanne den Hartigh
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and UMC Utrecht, 3584 CT Utrecht, the Netherlands
| | - Veerle Geurts
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and UMC Utrecht, 3584 CT Utrecht, the Netherlands
| | - Lise Mangiante
- Rare Cancers Genomics Team (RCG), Genomic Epidemiology Branch (GEM), International Agency for Research on Cancer/World Health Organisation (IARC/WHO), 69007 Lyon, France
| | - Lisa Lap
- Department of Pathology, GROW School for Oncology and Reproduction, Maastricht University Medical Centre, 6229 ER Maastricht, the Netherlands
| | - Antonella F M Dost
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and UMC Utrecht, 3584 CT Utrecht, the Netherlands; Oncode Institute, Hubrecht Institute, 3584 CT Utrecht, the Netherlands
| | - Joep Beumer
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and UMC Utrecht, 3584 CT Utrecht, the Netherlands; Oncode Institute, Hubrecht Institute, 3584 CT Utrecht, the Netherlands
| | - Sonja Levy
- Department of Medical Oncology, Netherlands Cancer Institute, 1066 CX Amsterdam, the Netherlands
| | - Rachel S van Leeuwaarde
- Department of Endocrine Oncology, University Medical Center Utrecht, 3584 CX Utrecht, the Netherlands
| | - Wenzel M Hackeng
- Department of Pathology, University Medical Center Utrecht, Utrecht University, 3584 CX Utrecht, the Netherlands
| | - Kris Samsom
- Department of Pathology, Netherlands Cancer Institute, Amsterdam 1066 CX, the Netherlands
| | - Catherine Voegele
- Rare Cancers Genomics Team (RCG), Genomic Epidemiology Branch (GEM), International Agency for Research on Cancer/World Health Organisation (IARC/WHO), 69007 Lyon, France
| | - Alexandra Sexton-Oates
- Rare Cancers Genomics Team (RCG), Genomic Epidemiology Branch (GEM), International Agency for Research on Cancer/World Health Organisation (IARC/WHO), 69007 Lyon, France
| | - Harry Begthel
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and UMC Utrecht, 3584 CT Utrecht, the Netherlands
| | - Jeroen Korving
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and UMC Utrecht, 3584 CT Utrecht, the Netherlands
| | - Lisa Hillen
- Department of Pathology, GROW School for Oncology and Reproduction, Maastricht University Medical Centre, 6229 ER Maastricht, the Netherlands
| | - Lodewijk A A Brosens
- Department of Pathology, University Medical Center Utrecht, Utrecht University, 3584 CX Utrecht, the Netherlands
| | - Sylvie Lantuejoul
- Department of Biopathology, Pathology Research Platform- Synergie Lyon Cancer- CRCL, Centre Léon Bérard Unicancer, 69008 Lyon, France; Université Grenoble Alpes, Grenoble, France
| | - Sridevi Jaksani
- Hubrecht Organoid Technology, Utrecht 3584 CM, the Netherlands
| | - Niels F M Kok
- Department of Surgery, Netherlands Cancer Institute, Amsterdam 1066 CX, the Netherlands
| | - Koen J Hartemink
- Department of Surgery, Netherlands Cancer Institute, Amsterdam 1066 CX, the Netherlands
| | - Houke M Klomp
- Department of Surgery, Netherlands Cancer Institute, Amsterdam 1066 CX, the Netherlands
| | - Inne H M Borel Rinkes
- Department of Endocrine Surgical Oncology, University Medical Center Utrecht, Utrecht 3508 GA, the Netherlands
| | - Anne-Marie Dingemans
- Department of Pulmonary Diseases, GROW School for Oncology and and Reproduction, Maastricht University Medical Centre, Maastricht, the Netherlands; Department of Pulmonary Medicine, Erasmus MC Cancer Institute, University Medical Center, Rotterdam 3015 GD, the Netherlands
| | - Gerlof D Valk
- Department of Endocrine Oncology, University Medical Center Utrecht, 3584 CX Utrecht, the Netherlands
| | - Menno R Vriens
- Department of Endocrine Surgical Oncology, University Medical Center Utrecht, Utrecht 3508 GA, the Netherlands
| | - Wieneke Buikhuisen
- Department of Thoracic Oncology, Netherlands Cancer Institute, Amsterdam 1066 CX, the Netherlands
| | - José van den Berg
- Department of Pathology, Netherlands Cancer Institute, Amsterdam 1066 CX, the Netherlands
| | - Margot Tesselaar
- Department of Medical Oncology, Netherlands Cancer Institute, 1066 CX Amsterdam, the Netherlands
| | - Jules Derks
- Department of Pulmonary Diseases, GROW School for Oncology and and Reproduction, Maastricht University Medical Centre, Maastricht, the Netherlands
| | - Ernst Jan Speel
- Department of Pathology, GROW School for Oncology and Reproduction, Maastricht University Medical Centre, 6229 ER Maastricht, the Netherlands
| | - Matthieu Foll
- Rare Cancers Genomics Team (RCG), Genomic Epidemiology Branch (GEM), International Agency for Research on Cancer/World Health Organisation (IARC/WHO), 69007 Lyon, France
| | - Lynnette Fernández-Cuesta
- Rare Cancers Genomics Team (RCG), Genomic Epidemiology Branch (GEM), International Agency for Research on Cancer/World Health Organisation (IARC/WHO), 69007 Lyon, France.
| | - Hans Clevers
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and UMC Utrecht, 3584 CT Utrecht, the Netherlands; Oncode Institute, Hubrecht Institute, 3584 CT Utrecht, the Netherlands.
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Cole R, Holroyd N, Tracey A, Berriman M, Viney M. The parasitic nematode Strongyloides ratti exists predominantly as populations of long-lived asexual lineages. Nat Commun 2023; 14:6427. [PMID: 37833369 PMCID: PMC10575991 DOI: 10.1038/s41467-023-42250-1] [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: 02/21/2022] [Accepted: 10/05/2023] [Indexed: 10/15/2023] Open
Abstract
Nematodes are important parasites of people and animals, and in natural ecosystems they are a major ecological force. Strongyloides ratti is a common parasitic nematode of wild rats and we have investigated its population genetics using single-worm, whole-genome sequencing. We find that S. ratti populations in the UK consist of mixtures of mainly asexual lineages that are widely dispersed across a host population. These parasite lineages are likely very old and may have originated in Asia from where rats originated. Genes that underly the parasitic phase of the parasite's life cycle are hyperdiverse compared with the rest of the genome, and this may allow the parasites to maximise their fitness in a diverse host population. These patterns of parasitic nematode population genetics have not been found before and may also apply to Strongyloides spp. that infect people, which will affect how we should approach their control.
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Affiliation(s)
- Rebecca Cole
- School of Biological Sciences, University of Bristol, Bristol, BS8 1TQ, UK
| | - Nancy Holroyd
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, UK
| | - Alan Tracey
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, UK
| | - Matt Berriman
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, UK
- School of Infection & Immunity, University of Glasgow, 120 University Place, Glasgow, G12 8TA, UK
| | - Mark Viney
- School of Biological Sciences, University of Bristol, Bristol, BS8 1TQ, UK.
- Department of Evolution, Ecology and Behaviour, University of Liverpool, Liverpool, L69 7ZB, UK.
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Argyropoulos DC, Tan MH, Adobor C, Mensah B, Labbé F, Tiedje KE, Koram KA, Ghansah A, Day KP. Performance of SNP barcodes to determine genetic diversity and population structure of Plasmodium falciparum in Africa. Front Genet 2023; 14:1071896. [PMID: 37323661 PMCID: PMC10267394 DOI: 10.3389/fgene.2023.1071896] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Accepted: 05/17/2023] [Indexed: 06/17/2023] Open
Abstract
Panels of informative biallelic single nucleotide polymorphisms (SNPs) have been proposed to be an economical method to fast-track the population genetic analysis of Plasmodium falciparum in malaria-endemic areas. Whilst used successfully in low-transmission areas where infections are monoclonal and highly related, we present the first study to evaluate the performance of these 24- and 96-SNP molecular barcodes in African countries, characterised by moderate-to-high transmission, where multiclonal infections are prevalent. For SNP barcodes it is generally recommended that the SNPs chosen i) are biallelic, ii) have a minor allele frequency greater than 0.10, and iii) are independently segregating, to minimise bias in the analysis of genetic diversity and population structure. Further, to be standardised and used in many population genetic studies, these barcodes should maintain characteristics i) to iii) across various iv) geographies and v) time points. Using haplotypes generated from the MalariaGEN P. falciparum Community Project version six database, we investigated the ability of these two barcodes to fulfil these criteria in moderate-to-high transmission African populations in 25 sites across 10 countries. Predominantly clinical infections were analysed, with 52.3% found to be multiclonal, generating high proportions of mixed-allele calls (MACs) per isolate thereby impeding haplotype construction. Of the 24- and 96-SNPs, loci were removed if they were not biallelic and had low minor allele frequencies in all study populations, resulting in 20- and 75-SNP barcodes respectively for downstream population genetics analysis. Both SNP barcodes had low expected heterozygosity estimates in these African settings and consequently biased analyses of similarity. Both minor and major allele frequencies were temporally unstable. These SNP barcodes were also shown to identify weak genetic differentiation across large geographic distances based on Mantel Test and DAPC. These results demonstrate that these SNP barcodes are vulnerable to ascertainment bias and as such cannot be used as a standardised approach for malaria surveillance in moderate-to-high transmission areas in Africa, where the greatest genomic diversity of P. falciparum exists at local, regional and country levels.
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Affiliation(s)
- Dionne C. Argyropoulos
- Department of Microbiology and Immunology, Bio21 Institute and Peter Doherty Institute, The University of Melbourne, Melbourne, VIC, Australia
| | - Mun Hua Tan
- Department of Microbiology and Immunology, Bio21 Institute and Peter Doherty Institute, The University of Melbourne, Melbourne, VIC, Australia
| | - Courage Adobor
- Department of Parasitology, Noguchi Memorial Institute for Medical Research, College of Health Sciences, University of Ghana, Accra, Ghana
| | - Benedicta Mensah
- Department of Parasitology, Noguchi Memorial Institute for Medical Research, College of Health Sciences, University of Ghana, Accra, Ghana
| | - Frédéric Labbé
- Department of Ecology and Evolution, The University of Chicago, Chicago, IL, United States
| | - Kathryn E. Tiedje
- Department of Microbiology and Immunology, Bio21 Institute and Peter Doherty Institute, The University of Melbourne, Melbourne, VIC, Australia
| | - Kwadwo A. Koram
- Epidemiology Department, Noguchi Memorial Institute for Medical Research, University of Ghana, Accra, Ghana
| | - Anita Ghansah
- Department of Parasitology, Noguchi Memorial Institute for Medical Research, College of Health Sciences, University of Ghana, Accra, Ghana
| | - Karen P. Day
- Department of Microbiology and Immunology, Bio21 Institute and Peter Doherty Institute, The University of Melbourne, Melbourne, VIC, Australia
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9
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Karlin EF. A Comparison of Entropic Diversity and Variance in the Study of Population Structure. ENTROPY (BASEL, SWITZERLAND) 2023; 25:492. [PMID: 36981380 PMCID: PMC10048111 DOI: 10.3390/e25030492] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Revised: 01/10/2023] [Accepted: 03/06/2023] [Indexed: 06/18/2023]
Abstract
AMOVA is a widely used approach that focuses on variance within and among strata to study the hierarchical genetic structure of populations. The recently developed Shannon Informational Diversity Translation Analysis (SIDTA) instead tackles exploration of hierarchical genetic structure using entropic allelic diversity. A mix of artificial and natural population data sets (including allopolyploids) is used to compare the performance of SIDTA (a 'q = 1' diversity measure) vs. AMOVA (a 'q = 2' measure) under different conditions. An additive allelic differentiation index based on entropic allelic diversity measuring the mean difference among populations (ΩAP) was developed to facilitate the comparison of SIDTA with AMOVA. These analyses show that the genetic population structure seen by AMOVA is notably different in many ways from that provided by SIDTA, and the extent of this difference is greatly affected by the stability of the markers employed. Negative among group values are lacking with SIDTA but occur with AMOVA, especially with allopolyploids. To provide more focus on measuring allelic differentiation among populations, additional measures were also tested including Bray-Curtis Genetic Differentiation (BCGD) and several expected heterozygosity-based indices (e.g., GST, G″ST, Jost's D, and DEST). Corrections, such as almost unbiased estimators, that were designed to work with heterozygosity-based fixation indices (e.g., FST, GST) are problematic when applied to differentiation indices (eg., DEST, G″ST, G'STH).
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Affiliation(s)
- Eric F Karlin
- School of Theoretical & Applied Science, Ramapo College, Mahwah, NJ 07430, USA
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10
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Martínez-Gil H, Sánchez-Montes G, Montes-Gavilán P, Ugarte G, Martínez-Solano Í. Fine-scale functional connectivity of two syntopic pond-breeding amphibians with contrasting life-history traits: an integrative assessment of direct and indirect estimates of dispersal. CONSERV GENET 2023. [DOI: 10.1007/s10592-023-01506-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/27/2023]
Abstract
AbstractAssessing patterns of functional connectivity among amphibian demes is crucial to unravel their population dynamics and prevent their isolation and eventual extinction. Integrative studies based on direct (capture-mark-recapture) and indirect (genetic) estimates of dispersal provide robust, biologically realistic inferences on population structure and connectivity, with applications for conservation efforts. We focused on two pond-breeding amphibians with contrasting life-history traits: the short-lived, semi-arboreal Hyla molleri and the long-lived, fossorial Pelobates cultripes. We PIT-tagged 2150 individuals of both species in two ponds (Laguna and Gravera, separated by 700 m) and monitored them from 2009 to 2021 to document the frequency and spatial extent of dispersal events. In addition, we genotyped individuals from these and two additional breeding populations at a maximum distance of 5 km with 15–16 microsatellites to characterize fine-scale patterns of genetic structure. We detected dispersal events connecting Laguna and Gravera in both species, albeit at low frequencies (4.8% and 7.7% of recaptured individuals of H. molleri and P. cultripes, respectively). However, both species were capable of covering long distances, with individual accumulated displacements up to 3.5 km (Hyla) and 1.8 km (Pelobates). Breeding populations > 2 km apart were genetically differentiated, indicating lower connectivity at this spatial scale. Estimates of pairwise migration rates differed between species and were asymmetrical, with different ponds representing “source” populations contributing more migrants to other populations in each species. We discuss the role of differences in life history traits and ecological preferences in shaping population dynamics in the two species and highlight management implications of our results.
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11
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Chung MY, Merilä J, Li J, Mao K, López-Pujol J, Tsumura Y, Chung MG. Neutral and adaptive genetic diversity in plants: An overview. Front Ecol Evol 2023. [DOI: 10.3389/fevo.2023.1116814] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/18/2023] Open
Abstract
Genetic diversity is a prerequisite for evolutionary change in all kinds of organisms. It is generally acknowledged that populations lacking genetic variation are unable to evolve in response to new environmental conditions (e.g., climate change) and thus may face an increased risk of extinction. Although the importance of incorporating genetic diversity into the design of conservation measures is now well understood, less attention has been paid to the distinction between neutral (NGV) and adaptive (AGV) genetic variation. In this review, we first focus on the utility of NGV by examining the ways to quantify it, reviewing applications of NGV to infer ecological and evolutionary processes, and by exploring its utility in designing conservation measures for plant populations and species. Against this background, we then summarize the ways to identify and estimate AGV and discuss its potential use in plant conservation. After comparing NGV and AGV and considering their pros and cons in a conservation context, we conclude that there is an urgent need for a better understanding of AGV and its role in climate change adaptation. To date, however, there are only a few AGV studies on non-model plant species aimed at deciphering the genetic and genomic basis of complex trait variation. Therefore, conservation researchers and practitioners should keep utilizing NGV to develop relevant strategies for rare and endangered plant species until more estimates of AGV are available.
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12
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Frère CH, O'Reilly GD, Strickland K, Schultz A, Hohwieler K, Hanger J, de Villiers D, Cristescu R, Powell D, Sherwin W. Evaluating the genetic consequences of population subdivision as it unfolds and how to best mitigate them: A rare story about koalas. Mol Ecol 2023; 32:2174-2185. [PMID: 36756702 DOI: 10.1111/mec.16877] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2022] [Revised: 01/23/2023] [Accepted: 01/25/2023] [Indexed: 02/10/2023]
Abstract
The genetic consequences of the subdivision of populations are regarded as significant to long-term evolution, and research has shown that the scale and speed at which this is now occurring is critically reducing the adaptive potential of most species which inhabit human-impacted landscapes. Here, we provide a rare and, to our knowledge, the first analysis of this process while it is happening and demonstrate a method of evaluating the effect of mitigation measures such as fauna crossings. We did this by using an extensive genetic data set collected from a koala population which was intensely monitored during the construction of linear transport infrastructure which resulted in the subdivision of their population. First, we found that both allelic richness and effective population size decreased through the process of population subdivision. Second, we predicted the extent to which genetic drift could impact genetic diversity over time and showed that after only 10 generations the resulting two subdivided populations could experience between 12% and 69% loss in genetic diversity. Lastly, using forward simulations we estimated that a minimum of eight koalas would need to disperse from each side of the subdivision per generation to maintain genetic connectivity close to zero but that 16 koalas would ensure that both genetic connectivity and diversity remained unchanged. These results have important consequences for the genetic management of species in human-impacted landscapes by showing which genetic metrics are best to identify immediate loss in genetic diversity and how to evaluate the effectiveness of any mitigation measures.
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Affiliation(s)
- C H Frère
- School of Biological Sciences, University of Queensland, St Lucia, Queensland, Australia
| | - G D O'Reilly
- The School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - K Strickland
- Institute of Ecology and Evolution, University of Edinburgh, Edinburgh, UK
| | - A Schultz
- Icelandic Museum of Natural History (Náttúruminjasafn Íslands), Reykjavik, Iceland
| | - K Hohwieler
- School of Science, Technology and Engineering, University of the Sunshine Coast, Queensland, Australia
| | - J Hanger
- Endeavour Veterinary Ecology Pty Ltd, Toorbul, Queensland, Australia
| | - D de Villiers
- Endeavour Veterinary Ecology Pty Ltd, Toorbul, Queensland, Australia
| | - R Cristescu
- School of Science, Technology and Engineering, University of the Sunshine Coast, Queensland, Australia
| | - D Powell
- School of Science, Technology and Engineering, University of the Sunshine Coast, Queensland, Australia
| | - W Sherwin
- The School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, New South Wales, Australia
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13
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Coelho MAG, Pearson GA, Boavida JRH, Paulo D, Aurelle D, Arnaud‐Haond S, Gómez‐Gras D, Bensoussan N, López‐Sendino P, Cerrano C, Kipson S, Bakran‐Petricioli T, Ferretti E, Linares C, Garrabou J, Serrão EA, Ledoux J. Not out of the Mediterranean: Atlantic populations of the gorgonian Paramuricea clavata are a separate sister species under further lineage diversification. Ecol Evol 2023; 13:e9740. [PMID: 36789139 PMCID: PMC9912747 DOI: 10.1002/ece3.9740] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 12/22/2022] [Accepted: 12/27/2022] [Indexed: 01/31/2023] Open
Abstract
The accurate delimitation of species boundaries in nonbilaterian marine taxa is notoriously difficult, with consequences for many studies in ecology and evolution. Anthozoans are a diverse group of key structural organisms worldwide, but the lack of reliable morphological characters and informative genetic markers hampers our ability to understand species diversification. We investigated population differentiation and species limits in Atlantic (Iberian Peninsula) and Mediterranean lineages of the octocoral genus Paramuricea previously identified as P. clavata. We used a diverse set of molecular markers (microsatellites, RNA-seq derived single-copy orthologues [SCO] and mt-mutS [mitochondrial barcode]) at 49 locations. Clear segregation of Atlantic and Mediterranean lineages was found with all markers. Species-tree estimations based on SCO strongly supported these two clades as distinct, recently diverged sister species with incomplete lineage sorting, P. cf. grayi and P. clavata, respectively. Furthermore, a second putative (or ongoing) speciation event was detected in the Atlantic between two P. cf. grayi color morphotypes (yellow and purple) using SCO and supported by microsatellites. While segregating P. cf. grayi lineages showed considerable geographic structure, dominating circalittoral communities in southern (yellow) and western (purple) Portugal, their occurrence in sympatry at some localities suggests a degree of reproductive isolation. Overall, our results show that previous molecular and morphological studies have underestimated species diversity in Paramuricea occurring in the Iberian Peninsula, which has important implications for conservation planning. Finally, our findings validate the usefulness of phylotranscriptomics for resolving evolutionary relationships in octocorals.
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Affiliation(s)
- Márcio A. G. Coelho
- Centre for Marine Sciences (CCMAR)University of AlgarveFaroPortugal,MARE – Marine and Environmental Sciences CentreISPA‐Instituto UniversitárioLisboaPortugal
| | | | | | - Diogo Paulo
- Centre for Marine Sciences (CCMAR)University of AlgarveFaroPortugal
| | - Didier Aurelle
- Aix Marseille Univ., Université de Toulon, CNRS, IRD, MIOMarseilleFrance,Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum National d'Histoire Naturelle, CNRSSorbonne UniversitéParisFrance
| | - Sophie Arnaud‐Haond
- MARBEC (Marine Biodiversity, Exploitation and Conservation)Univ. Montpellier, IFREMER, CNRS, IRDSète CedexFrance
| | - Daniel Gómez‐Gras
- Hawai‘i Institute of Marine BiologyUniversity of Hawai‘i at MānoaKaneoheHawaiiUSA,Departament de Biologia Evolutiva, Ecologia i Ciències AmbientalsUniversitat de Barcelona (UB)BarcelonaSpain,Institut de Recerca de la Biodiversitat (IRBio)Universitat de Barcelona (UB)BarcelonaSpain
| | - Nathaniel Bensoussan
- Aix Marseille Univ., Université de Toulon, CNRS, IRD, MIOMarseilleFrance,Departament de Biologia MarinaInstitut de Ciències del Mar (CSIC)BarcelonaSpain
| | - Paula López‐Sendino
- Departament de Biologia MarinaInstitut de Ciències del Mar (CSIC)BarcelonaSpain
| | - Carlo Cerrano
- Dipartimento di Scienze della Vita e dell’Ambiente (DiSVA)Università Politecnica delle MarcheAnconaItaly,Consorzio Nazionale Interuniversitario per le Scienze del Mare (CoNISMa)RomeItaly,Stazione Zoologica Anton DohrnNaplesItaly,Fano Marine CenterFanoItaly
| | - Silvija Kipson
- Department of Biology, Faculty of ScienceUniversity of ZagrebZagrebCroatia,SEAFAN – Marine Research & ConsultancyZagrebCroatia
| | | | - Eliana Ferretti
- Studio Associato GAIA s.n.c.GenoaItaly,Institute of Marine ScienceThe University of AucklandAucklandNew Zealand
| | - Cristina Linares
- Departament de Biologia Evolutiva, Ecologia i Ciències AmbientalsUniversitat de Barcelona (UB)BarcelonaSpain,Institut de Recerca de la Biodiversitat (IRBio)Universitat de Barcelona (UB)BarcelonaSpain
| | - Joaquim Garrabou
- Aix Marseille Univ., Université de Toulon, CNRS, IRD, MIOMarseilleFrance,Departament de Biologia MarinaInstitut de Ciències del Mar (CSIC)BarcelonaSpain
| | - Ester A. Serrão
- Centre for Marine Sciences (CCMAR)University of AlgarveFaroPortugal,CIBIO/InBIO‐Centro de Investigação em Biodiversidade e Recursos GenéticosVairãoPortugal
| | - Jean‐Baptiste Ledoux
- CIIMAR/CIMAR, Centro Interdisciplinar de Investigação Marinha e AmbientalUniversidade do PortoPortoPortugal
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14
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Li X, Liu T, Li A, Xiao Y, Sun K, Feng J. Diversifying selection and climatic effects on major histocompatibility complex class
II
gene diversity in the greater horseshoe bat. Evol Appl 2023; 16:688-704. [PMID: 36969140 PMCID: PMC10033860 DOI: 10.1111/eva.13528] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2022] [Revised: 12/19/2022] [Accepted: 12/21/2022] [Indexed: 01/09/2023] Open
Abstract
Heterogeneous pathogenic stress can shape major histocompatibility complex (MHC) diversity by influencing the functional plasticity of the immune response. Therefore, MHC diversity could reflect environmental stress, demonstrating its importance in uncovering the mechanisms of adaptive genetic variation. In this study, we combined neutral microsatellite loci, an immune-related MHC II-DRB locus, and climatic factors to unravel the mechanisms affecting the diversity and genetic differentiation of MHC genes in the greater horseshoe bat (Rhinolophus ferrumequinum), a species with a wide geographical distribution that has three distinct genetic lineages in China. First, increased genetic differentiation at the MHC locus among populations compared using microsatellites indicated diversifying selection. Second, the genetic differentiation of MHC and microsatellites were significantly correlated, suggesting that demographic processes exist. However, MHC genetic differentiation was significantly correlated with geographical distance among populations, even after controlling for the neutral markers, suggesting a major effect of selection. Third, although the MHC genetic differentiation was larger than that for microsatellites, there was no significant difference in the genetic differentiation between the two markers among genetic lineages, indicating the effect of balancing selection. Fourth, combined with climatic factors, MHC diversity and supertypes showed significant correlations with temperature and precipitation, but not with the phylogeographic structure of R. ferrumequinum, suggesting an effect of local adaptation driven by climate on MHC diversity. Moreover, the number of MHC supertypes varied between populations and lineages, suggesting regional characteristics and support for local adaptation. Taken together, the results of our study provide insights into the adaptive evolutionary driving forces at different geographic scales in R. ferrumequinum. In addition, climate factors may have played a vital role in driving adaptive evolution in this species.
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Affiliation(s)
- Xiaolin Li
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization Northeast Normal University Changchun China
- Key Laboratory of Vegetation Ecology, Ministry of Education Changchun China
| | - Tong Liu
- College of Life Science, Jilin Agricultural University Changchun China
| | - Aoqiang Li
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization Northeast Normal University Changchun China
| | - Yanhong Xiao
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization Northeast Normal University Changchun China
| | - Keping Sun
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization Northeast Normal University Changchun China
- Key Laboratory of Vegetation Ecology, Ministry of Education Changchun China
| | - Jiang Feng
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization Northeast Normal University Changchun China
- College of Life Science, Jilin Agricultural University Changchun China
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15
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Phylogeography and population genetics of a headwater-stream adapted crayfish, Cambarus pristinus (Decapoda: Cambaridae), from the Cumberland Plateau in Tennessee. CONSERV GENET 2022. [DOI: 10.1007/s10592-022-01477-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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16
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Andrello M, D'Aloia C, Dalongeville A, Escalante MA, Guerrero J, Perrier C, Torres-Florez JP, Xuereb A, Manel S. Evolving spatial conservation prioritization with intraspecific genetic data. Trends Ecol Evol 2022; 37:553-564. [PMID: 35450706 DOI: 10.1016/j.tree.2022.03.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Revised: 03/09/2022] [Accepted: 03/11/2022] [Indexed: 12/15/2022]
Abstract
Spatial conservation prioritization (SCP) is a planning framework used to identify new conservation areas on the basis of the spatial distribution of species, ecosystems, and their services to human societies. The ongoing accumulation of intraspecific genetic data on a variety of species offers a way to gain knowledge of intraspecific genetic diversity and to estimate several population characteristics useful in conservation, such as dispersal and population size. Here, we review how intraspecific genetic data have been integrated into SCP and highlight their potential for identifying conservation area networks that represent intraspecific genetic diversity comprehensively and that ensure the long-term persistence of biodiversity in the face of global change.
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Affiliation(s)
- Marco Andrello
- Institute for the study of Anthropic impacts and Sustainability in the marine environment, National Research Council, CNR-IAS, Rome, Italy.
| | - Cassidy D'Aloia
- Department of Biology, University of Toronto Mississauga, Mississauga, ON, Canada
| | | | - Marco A Escalante
- Laboratory of Molecular Ecology, Institute of Animal Physiology and Genetics of the Czech Academy of Sciences, Liběchov, Czech Republic
| | - Jimena Guerrero
- Sociedad Científica de Investigación Transdisciplinaria y Especialización (SCITE), Calimaya, México
| | - Charles Perrier
- CBGP, INRAe, CIRAD, IRD, Montpellier SupAgro, University of Montpellier, Montpellier, France
| | - Juan Pablo Torres-Florez
- Instituto Chico Mendes de Conservação da Biodiversidade, Centro Nacional de Pesquisa e Conservação de Mamíferos Aquáticos, Santos, Brazil
| | - Amanda Xuereb
- Département de Biologie, Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, QC, Canada
| | - Stéphanie Manel
- CEFE, Univ Montpellier, CNRS, EPHE-PSL University, IRD, Montpellier, France
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17
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Hoban S, Archer FI, Bertola LD, Bragg JG, Breed MF, Bruford MW, Coleman MA, Ekblom R, Funk WC, Grueber CE, Hand BK, Jaffé R, Jensen E, Johnson JS, Kershaw F, Liggins L, MacDonald AJ, Mergeay J, Miller JM, Muller-Karger F, O'Brien D, Paz-Vinas I, Potter KM, Razgour O, Vernesi C, Hunter ME. Global genetic diversity status and trends: towards a suite of Essential Biodiversity Variables (EBVs) for genetic composition. Biol Rev Camb Philos Soc 2022; 97:1511-1538. [PMID: 35415952 PMCID: PMC9545166 DOI: 10.1111/brv.12852] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Revised: 02/25/2022] [Accepted: 03/02/2022] [Indexed: 12/14/2022]
Abstract
Biodiversity underlies ecosystem resilience, ecosystem function, sustainable economies, and human well‐being. Understanding how biodiversity sustains ecosystems under anthropogenic stressors and global environmental change will require new ways of deriving and applying biodiversity data. A major challenge is that biodiversity data and knowledge are scattered, biased, collected with numerous methods, and stored in inconsistent ways. The Group on Earth Observations Biodiversity Observation Network (GEO BON) has developed the Essential Biodiversity Variables (EBVs) as fundamental metrics to help aggregate, harmonize, and interpret biodiversity observation data from diverse sources. Mapping and analyzing EBVs can help to evaluate how aspects of biodiversity are distributed geographically and how they change over time. EBVs are also intended to serve as inputs and validation to forecast the status and trends of biodiversity, and to support policy and decision making. Here, we assess the feasibility of implementing Genetic Composition EBVs (Genetic EBVs), which are metrics of within‐species genetic variation. We review and bring together numerous areas of the field of genetics and evaluate how each contributes to global and regional genetic biodiversity monitoring with respect to theory, sampling logistics, metadata, archiving, data aggregation, modeling, and technological advances. We propose four Genetic EBVs: (i) Genetic Diversity; (ii) Genetic Differentiation; (iii) Inbreeding; and (iv) Effective Population Size (Ne). We rank Genetic EBVs according to their relevance, sensitivity to change, generalizability, scalability, feasibility and data availability. We outline the workflow for generating genetic data underlying the Genetic EBVs, and review advances and needs in archiving genetic composition data and metadata. We discuss how Genetic EBVs can be operationalized by visualizing EBVs in space and time across species and by forecasting Genetic EBVs beyond current observations using various modeling approaches. Our review then explores challenges of aggregation, standardization, and costs of operationalizing the Genetic EBVs, as well as future directions and opportunities to maximize their uptake globally in research and policy. The collection, annotation, and availability of genetic data has made major advances in the past decade, each of which contributes to the practical and standardized framework for large‐scale genetic observation reporting. Rapid advances in DNA sequencing technology present new opportunities, but also challenges for operationalizing Genetic EBVs for biodiversity monitoring regionally and globally. With these advances, genetic composition monitoring is starting to be integrated into global conservation policy, which can help support the foundation of all biodiversity and species' long‐term persistence in the face of environmental change. We conclude with a summary of concrete steps for researchers and policy makers for advancing operationalization of Genetic EBVs. The technical and analytical foundations of Genetic EBVs are well developed, and conservation practitioners should anticipate their increasing application as efforts emerge to scale up genetic biodiversity monitoring regionally and globally.
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Affiliation(s)
- Sean Hoban
- Center for Tree Science, The Morton Arboretum, 4100 Illinois Rt 53, Lisle, IL, 60532, USA
| | - Frederick I Archer
- Southwest Fisheries Science Center, NOAA/NMFS, 8901 La Jolla Shores Drive, La Jolla, CA, 92037, USA
| | - Laura D Bertola
- City College of New York, 160 Convent Avenue, New York, NY, 10031, USA
| | - Jason G Bragg
- Research Centre for Ecosystem Resilience, Australian Institute of Botanical Science, The Royal Botanic Garden Sydney, Mrs Macquaries Rd, Sydney, NSW, 2000, Australia
| | - Martin F Breed
- College of Science and Engineering, Flinders University, University Drive, Bedford Park, SA, 5042, Australia
| | - Michael W Bruford
- School of Biosciences, Cardiff University, Cathays Park, Cardiff, CF10 3AX, Wales, UK
| | - Melinda A Coleman
- Department of Primary Industries, New South Wales Fisheries, National Marine Science Centre, 2 Bay Drive, Coffs Harbour, NSW, 2450, Australia
| | - Robert Ekblom
- Wildlife Analysis Unit, Swedish Environmental Protection Agency, Blekholmsterrassen 36, Stockholm, SE-106 48, Sweden
| | - W Chris Funk
- Department of Biology, Graduate Degree in Ecology, Colorado State University, 1878 Campus Delivery, Fort Collins, CO, 80523-1878, USA
| | - Catherine E Grueber
- School of Life and Environmental Sciences, Faculty of Science, The University of Sydney, Carslaw Building, Sydney, NSW, 2006, Australia
| | - Brian K Hand
- Flathead Lake Biological Station, 32125 Bio Station Ln, Polson, MT, 59860, USA
| | - Rodolfo Jaffé
- Exponent, 15375 SE 30th Place, Suite 250, Bellevue, WA, 98007, USA
| | - Evelyn Jensen
- School of Natural and Environmental Sciences, Newcastle University, Agriculture Building, Newcastle Upon Tyne, NE1 7RU, UK
| | - Jeremy S Johnson
- Department of Environmental Studies, Prescott College, 220 Grove Avenue, Prescott, AZ, 86303, USA
| | - Francine Kershaw
- Natural Resources Defense Council, 40 West 20th Street, New York, NY, 10011, USA
| | - Libby Liggins
- School of Natural Sciences, Massey University, Ōtehā Rohe campus, Gate 4 Albany Highway, Auckland, Aotearoa, 0745, New Zealand
| | - Anna J MacDonald
- Research School of Biology, The Australian National University, Acton, ACT, 2601, Australia
| | - Joachim Mergeay
- Research Institute for Nature and Forest, Gaverstraat 4, 9500, Geraardsbergen, Belgium.,Aquatic Ecology, Evolution and Conservation, KULeuven, Charles Deberiotstraat 32, box 2439, 3000, Leuven, Belgium
| | - Joshua M Miller
- Department of Biological Sciences, MacEwan University, 10700 104 Avenue, Edmonton, AB, T5J 4S2, Canada
| | - Frank Muller-Karger
- College of Marine Science, University of South Florida, 140 7th Avenue South, Saint Petersburg, Florida, 33701, USA
| | - David O'Brien
- NatureScot, Great Glen House, Leachkin Road, Inverness, IV3 8NW, UK
| | - Ivan Paz-Vinas
- Laboratoire Evolution et Diversité Biologique, Université de Toulouse, CNRS, IRD, UPS, UMR-5174 EDB, 118 route de Narbonne, Toulouse, 31062, France
| | - Kevin M Potter
- Department of Forestry and Environmental Resources, North Carolina State University, 3041 Cornwallis Road, Research Triangle Park, NC, 27709, USA
| | - Orly Razgour
- Biosciences, University of Exeter, Streatham Campus, Hatherly Laboratories, Prince of Wales Road, Exeter, EX4 4PS, UK
| | - Cristiano Vernesi
- Forest Ecology Unit, Research and Innovation Centre- Fondazione Edmund Mach, Via E. Mach, 1, San Michele all'Adige, 38010, (TN), Italy
| | - Margaret E Hunter
- U.S. Geological Survey, Wetland and Aquatic Research Center, 7920 NW 71st Street, Gainesville, FL, 32653, USA
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18
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Damm E, Ullrich KK, Amos WB, Odenthal-Hesse L. Evolution of the recombination regulator PRDM9 in minke whales. BMC Genomics 2022; 23:212. [PMID: 35296233 PMCID: PMC8925151 DOI: 10.1186/s12864-022-08305-1] [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: 04/13/2021] [Accepted: 01/11/2022] [Indexed: 11/16/2022] Open
Abstract
Background PRDM9 is a key regulator of meiotic recombination in most metazoans, responsible for reshuffling parental genomes. During meiosis, the PRDM9 protein recognizes and binds specific target motifs via its array of C2H2 zinc-fingers encoded by a rapidly evolving minisatellite. The gene coding for PRDM9 is the only speciation gene identified in vertebrates to date and shows high variation, particularly in the DNA-recognizing positions of the zinc-finger array, within and between species. Across all vertebrate genomes studied for PRDM9 evolution, only one genome lacks variability between repeat types – that of the North Pacific minke whale. This study aims to understand the evolution and diversity of Prdm9 in minke whales, which display the most unusual genome reference allele of Prdm9 so far discovered in mammals. Results Minke whales possess all the features characteristic of PRDM9-directed recombination, including complete KRAB, SSXRD and SET domains and a rapidly evolving array of C2H2-type-Zincfingers (ZnF) with evidence of rapid evolution, particularly at DNA-recognizing positions that evolve under positive diversifying selection. Seventeen novel PRDM9 variants were identified within the Antarctic minke whale species, plus a single distinct PRDM9 variant in Common minke whales – shared across North Atlantic and North Pacific minke whale subspecies boundaries. Conclusion The PRDM9 ZnF array evolves rapidly, in minke whales, with at least one DNA-recognizing position under positive selection. Extensive PRDM9 diversity is observed, particularly in the Antarctic in minke whales. Common minke whales shared a specific Prdm9 allele across subspecies boundaries, suggesting incomplete speciation by the mechanisms associated with PRDM9 hybrid sterility. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08305-1.
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Affiliation(s)
- Elena Damm
- Department Evolutionary Genetics, Research Group Meiotic Recombination and Genome Instability, Max Planck Institute for Evolutionary Biology, August-Thienemann Str. 2, D-24306, Plön, Germany
| | - Kristian K Ullrich
- Department Evolutionary Genetics, Research Group Meiotic Recombination and Genome Instability, Max Planck Institute for Evolutionary Biology, August-Thienemann Str. 2, D-24306, Plön, Germany
| | - William B Amos
- Department of Zoology, University of Cambridge, Cambridge, UK
| | - Linda Odenthal-Hesse
- Department Evolutionary Genetics, Research Group Meiotic Recombination and Genome Instability, Max Planck Institute for Evolutionary Biology, August-Thienemann Str. 2, D-24306, Plön, Germany.
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19
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Sentinella AT, Moles AT, Bragg JG, Rossetto M, Sherwin WB. Detecting steps in spatial genetic data: Which diversity measures are best? PLoS One 2022; 17:e0265110. [PMID: 35287164 PMCID: PMC8920294 DOI: 10.1371/journal.pone.0265110] [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: 09/08/2021] [Accepted: 02/23/2022] [Indexed: 12/05/2022] Open
Abstract
Accurately detecting sudden changes, or steps, in genetic diversity across landscapes is important for locating barriers to gene flow, identifying selectively important loci, and defining management units. However, there are many metrics that researchers could use to detect steps and little information on which might be the most robust. Our study aimed to determine the best measure/s for genetic step detection along linear gradients using biallelic single nucleotide polymorphism (SNP) data. We tested the ability to differentiate between linear and step-like gradients in genetic diversity, using a range of diversity measures derived from the q-profile, including allelic richness, Shannon Information, GST, and Jost-D, as well as Bray-Curtis dissimilarity. To determine the properties of each measure, we repeated simulations of different intensities of step and allele proportion ranges, with varying genome sample size, number of loci, and number of localities. We found that alpha diversity (within-locality) based measures were ineffective at detecting steps. Further, allelic richness-based beta (between-locality) measures (e.g., Jaccard and Sørensen dissimilarity) were not reliable for detecting steps, but instead detected departures from fixation. The beta diversity measures best able to detect steps were: Shannon Information based measures, GST based measures, a Jost-D related measure, and Bray-Curtis dissimilarity. No one measure was best overall, with a trade-off between those measures with high step detection sensitivity (GST and Bray-Curtis) and those that minimised false positives (a variant of Shannon Information). Therefore, when detecting steps, we recommend understanding the differences between measures and using a combination of approaches.
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Affiliation(s)
- Alexander T. Sentinella
- Evolution & Ecology Research Centre, School of Biological, Earth and Environmental Sciences, UNSW Sydney, Sydney, NSW, Australia
- * E-mail:
| | - Angela T. Moles
- Evolution & Ecology Research Centre, School of Biological, Earth and Environmental Sciences, UNSW Sydney, Sydney, NSW, Australia
| | - Jason G. Bragg
- Evolution & Ecology Research Centre, School of Biological, Earth and Environmental Sciences, UNSW Sydney, Sydney, NSW, Australia
- Research Centre for Ecosystem Resilience, Australian Institute of Botanical Science, The Royal Botanic Garden Sydney, Sydney, NSW, Australia
| | - Maurizio Rossetto
- Research Centre for Ecosystem Resilience, Australian Institute of Botanical Science, The Royal Botanic Garden Sydney, Sydney, NSW, Australia
| | - William B. Sherwin
- Evolution & Ecology Research Centre, School of Biological, Earth and Environmental Sciences, UNSW Sydney, Sydney, NSW, Australia
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Scandura M, Fabbri G, Caniglia R, Iacolina L, Mattucci F, Mengoni C, Pante G, Apollonio M, Mucci N. Resilience to Historical Human Manipulations in the Genomic Variation of Italian Wild Boar Populations. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.833081] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Human activities can globally modify natural ecosystems determining ecological, demographic and range perturbations for several animal species. These changes can jeopardize native gene pools in different ways, leading either to genetic homogenization, or conversely, to the split into genetically divergent demes. In the past decades, most European wild boar (Sus scrofa) populations were heavily managed by humans. Anthropic manipulations have strongly affected also Italian populations through heavy hunting, translocations and reintroductions that might have deeply modified their original gene pools. In this study, exploiting the availability of the well-mapped porcine genome, we applied genomic tools to explore genome-wide variability in Italian wild boar populations, investigate their genetic structure and detect signatures of possible introgression from domestic pigs and non-native wild boar. Genomic data from 134 wild boar sampled in six areas of peninsular Italy and in Sardinia were gathered using the Illumina Porcine SNP60 BeadChip (60k Single Nucleotide Polymorphisms – SNPs) and compared with reference genotypes from European specimens and from domestic pigs (both commercial and Italian local breeds), using multivariate and maximum-likelihood approaches. Pairwise FST values, multivariate analysis and assignment procedures indicated that Italian populations were highly differentiated from all the other analyzed European wild boar populations. Overall, a lower heterozygosity was found in the Italian population than in the other European regions. The most diverging populations in Castelporziano Presidential Estate and Maremma Regional Park can be the result of long-lasting isolation, reduced population size and genetic drift. Conversely, an unexpected similarity was found among Apennine populations, even at high distances. Signatures of introgression from both non-Italian wild boar and domestic breeds were very limited. To summarize, we successfully applied genome-wide procedures to explore, for the first time, the genomic diversity of Italian wild boar, demonstrating that they represent a strongly heterogeneous assemblage of demes with different demographic and manipulation histories. Nonetheless, our results suggest that a native component of genomic variation is predominant over exogenous ones in most populations.
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Nowicki M, Hadziabdic D, Trigiano RN, Runge F, Thines M, Boggess SL, Ristaino J, Spring O. Microsatellite Markers from Peronospora tabacina, the Cause of Blue Mold of Tobacco, Reveal Species Origin, Population Structure, and High Gene Flow. PHYTOPATHOLOGY 2022; 112:422-434. [PMID: 34058860 DOI: 10.1094/phyto-03-21-0092-r] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Peronospora tabacina is an obligate parasite that causes blue mold of tobacco. The pathogen reproduces primarily by sporangia, whereas the sexual oospores are rarely observed. A collection of 122 isolates of P. tabacina was genotyped using nine microsatellites to assess the population structure of individuals from subpopulations collected from central, southern, and western Europe; the Middle East; Central America; North America; and Australia. Genetic variations among the six subpopulations accounted for ∼8% of the total variation, including moderate levels of genetic differentiation, high gene flow among these subpopulations, and a positive correlation between geographic and genetic distance (r = 0.225; P < 0.001). Evidence of linkage disequilibrium (P < 0.001) showed that populations contained partially clonal subpopulations but that subpopulations from Australia and Mediterranean Europe did not. High genetic variation and population structure among samples could be explained by continuous gene flow across continents via infected transplant exchange and/or long-distance dispersal of sporangia via wind currents. This study analyzed the most numerous P. tabacina collection and allowed conclusions regarding the migration, mutation, and evolutionary history of this obligate biotrophic oomycete. The evidence pointed to the species origin in Australia and identified intracontinental and intercontinental migration patterns of this important pathogen.[Formula: see text] Copyright © 2022 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.
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Affiliation(s)
- Marcin Nowicki
- Department of Entomology and Plant Pathology, University of Tennessee, Knoxville 37996-4560, U.S.A
| | - Denita Hadziabdic
- Department of Entomology and Plant Pathology, University of Tennessee, Knoxville 37996-4560, U.S.A
| | - Robert N Trigiano
- Department of Entomology and Plant Pathology, University of Tennessee, Knoxville 37996-4560, U.S.A
| | - Fabian Runge
- Institute of Botany 210, University of Hohenheim, D-70593 Stuttgart, Germany
- Biodiversity and Climate Research Centre, Senckenberg Gesellschaft für Naturforschung, D-60325 Frankfurt am Main, Germany
| | - Marco Thines
- Biodiversity and Climate Research Centre, Senckenberg Gesellschaft für Naturforschung, D-60325 Frankfurt am Main, Germany
- Department of Life Sciences, Institute of Ecology, Evolution and Diversity, Goethe University Frankfurt, D-60323 Frankfurt am Main, Germany
| | - Sarah L Boggess
- Department of Entomology and Plant Pathology, University of Tennessee, Knoxville 37996-4560, U.S.A
| | - Jean Ristaino
- Department of Entomology and Plant Pathology, Emerging Plant Disease and Global Food Security Cluster, North Carolina State University, Raleigh 27650, U.S.A
| | - Otmar Spring
- Institute of Botany 210, University of Hohenheim, D-70593 Stuttgart, Germany
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22
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Aitnazarov RB, Mishakova TM, Yudin NS. Assessment of genetic diversity and phylogenetic relationships in Black Pied cattle in the Novosibirsk Region using microsatellite markers. Vavilovskii Zhurnal Genet Selektsii 2022; 25:831-838. [PMID: 35088018 PMCID: PMC8761576 DOI: 10.18699/vj21.096] [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: 09/06/2021] [Revised: 10/17/2021] [Accepted: 10/17/2021] [Indexed: 12/02/2022] Open
Abstract
There are currently over a thousand indigenous cattle breeds well adapted to local habitat conditions thanks
to their long history of evolution and breeding. Identification of the genetic variations controlling the adaptation of
local cattle breeds for their further introduction into the genome of highly productive global breeds is a matter of great
relevance. Studying individual populations of the same breed with the use of microsatellite markers makes it possible
to assess their genetic diversity, relationships, and breed improvement potential. Although the Black Pied breed is the
most common dairy cattle breed in Russia, there are only a few studies on genetic diversity in local Black Pied populations
in some Russian regions. The goal of the present study was to analyze the genetic diversity in Black Pied cattle
populations in the Novosibirsk Region and compare them with other Russian populations; to identify significantly divergent
populations with a view to preserving them under the programs aimed at maintaining the genetic diversity of
the domestic Black Pied breed. DNA samples from 4788 animals of the Black Pied breed from six breeding enterprises
in the Novosibirsk Region have been studied using 11 microsatellite markers. No significant differences in genetic
variability parameters were found between individual populations. Private alleles have been identified in five out of
six populations. Five populations have shown inbreeding coefficient values (FIS) below zero, which indicates heterozygosity
excess. The population distribution test, principal component analysis, FST and DEST values, cluster analysis,
and phylogenetic analysis have revealed two populations genetically distinct from the others. Essentially, the genetic
diversity parameters of the six studied Black Pied cattle populations from the Novosibirsk Region show no significant
differences from other Russian populations of the breed. Excess heterozygosity is observed in most breeding enterprises,
which is a sign of a low inbreeding rate. To maintain the genetic diversity of the Russian Black Pied cattle, we
recommend focusing on the two populations with significant genetic distinctions from the others.
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Affiliation(s)
- R. B. Aitnazarov
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences
| | - T. M. Mishakova
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences
| | - N. S. Yudin
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences
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23
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Kunz F, Klinga P, Sittenthaler M, Schebeck M, Stauffer C, Grünschachner‐Berger V, Hackländer K, Nopp‐Mayr U. Assessment of drivers of spatial genetic variation of a ground-dwelling bird species and its implications for conservation. Ecol Evol 2022; 12:e8460. [PMID: 35127012 PMCID: PMC8796917 DOI: 10.1002/ece3.8460] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Revised: 11/29/2021] [Accepted: 11/30/2021] [Indexed: 11/29/2022] Open
Abstract
In modern wildlife ecology, spatial population genetic methods are becoming increasingly applied. Especially for animal species in fragmented landscapes, preservation of gene flow becomes a high priority target in order to restore genetic diversity and prevent local extinction. Within Central Europe, the Alps represent the core distribution area of the black grouse, Lyrurus tetrix. At its easternmost Alpine range, events of subpopulation extinction have already been documented in the past decades. Molecular data combined with spatial analyses can help to assess landscape effects on genetic variation and therefore can be informative for conservation management. Here, we addressed whether the genetic pattern of the easternmost Alpine black grouse metapopulation system is driven by isolation by distance or isolation by resistance. Correlative ecological niche modeling was used to assess geographic distances and landscape resistances. We then applied regression-based approaches combined with population genetic analyses based on microsatellite data to disentangle effects of isolation by distance and isolation by resistance among individuals and subpopulations. Although population genetic analyses revealed overall low levels of genetic differentiation, the ecological niche modeling showed subpopulations to be clearly delimited by habitat structures. Spatial genetic variation could be attributed to effects of isolation by distance among individuals and isolation by resistance among subpopulations, yet unknown effects might factor in. The easternmost subpopulation was the most differentiated, and at the same time, immigration was not detected; hence, its long-term survival might be threatened. Our study provides valuable insights into the spatial genetic variation of this small-scale metapopulation system of Alpine black grouse.
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Affiliation(s)
- Florian Kunz
- Department of Integrative Biology and Biodiversity ResearchInstitute of Wildlife Biology and Game ManagementUniversity of Natural Resources and Life Sciences, ViennaViennaAustria
| | - Peter Klinga
- Faculty of ForestryTechnical University in ZvolenZvolenSlovakia
- DIANA ‐ Carpathian Wildlife ResearchBanská BystricaSlovakia
| | - Marcia Sittenthaler
- Department of Integrative Biology and Biodiversity ResearchInstitute of Wildlife Biology and Game ManagementUniversity of Natural Resources and Life Sciences, ViennaViennaAustria
- Central Research LaboratoriesNatural History Museum ViennaViennaAustria
| | - Martin Schebeck
- Department of Forest and Soil SciencesInstitute of Forest Entomology, Forest Pathology and Forest ProtectionUniversity of Natural Resources and Life Sciences, ViennaViennaAustria
| | - Christian Stauffer
- Department of Forest and Soil SciencesInstitute of Forest Entomology, Forest Pathology and Forest ProtectionUniversity of Natural Resources and Life Sciences, ViennaViennaAustria
| | | | - Klaus Hackländer
- Department of Integrative Biology and Biodiversity ResearchInstitute of Wildlife Biology and Game ManagementUniversity of Natural Resources and Life Sciences, ViennaViennaAustria
- German Wildlife FoundationHamburgGermany
| | - Ursula Nopp‐Mayr
- Department of Integrative Biology and Biodiversity ResearchInstitute of Wildlife Biology and Game ManagementUniversity of Natural Resources and Life Sciences, ViennaViennaAustria
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24
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The history of genetic diversity and effective population size of an isolated Microtus oeconomus population on Kis Balaton. Mamm Biol 2021. [DOI: 10.1007/s42991-021-00199-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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25
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Petry VS, Stefenon VM, Machado LO, Costa NCFDA, Klabunde GHF, Nodari RO. Patterns of genetic diversity, spatial genetic structure and gene flow in Campomanesia xanthocarpa: insights from SSR markers of different genomic origins. AN ACAD BRAS CIENC 2021; 93:e20210134. [PMID: 34787172 DOI: 10.1590/0001-3765202120210134] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Accepted: 03/17/2021] [Indexed: 11/21/2022] Open
Abstract
Campomanesia xanthocarpa (Mart.) O. Berg is a South American fruit tree species with important ecological and medicinal properties, which remnants are currently found mainly in isolated forest fragments. In this study, SSR markers from three different genomic origins (gene-linked, nuclear neutral, and organellar) were used to evaluate the patterns of genetic diversity, fine-scale spatial genetic structure and historical gene flow in fragmented forest formations of C. xanthocarpa from the Atlantic Forest in southern Brazil. Our results show that the forest fragments present moderate to high levels of genetic diversity in comparison to species presenting similar life traits, although a trend opposite to expected was observed concerning gene-linked and neutral SSR markers. The fine-scale spatial genetic structure revealed different patterns in short and large distance classes, with a distinct influence of gene-linked and neutral markers in driving the genetic structure in each distance class. The presence of an isolation-by-adaptation pattern implies the need for maintenance of the current remnants to assure the conservation of the private alleles. Finally, as the genetic diversity is found predominantly within forest fragments, programs of seed collection and/or genetic rescue should prioritize a larger number of individuals within each fragment, to increase the sampled diversity.
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Affiliation(s)
- Vanessa S Petry
- Programa de Pós-Graduação em Recursos Genéticos Vegetais, Universidade Federal de Santa Catarina, Departamento de Fitotecnia, Rod. Admar Gonzaga 1346, 88034-000 Florianópolis, SC, Brazil
| | - Valdir M Stefenon
- Programa de Pós-Graduação em Recursos Genéticos Vegetais, Universidade Federal de Santa Catarina, Departamento de Fitotecnia, Rod. Admar Gonzaga 1346, 88034-000 Florianópolis, SC, Brazil.,Programa de Pós-Graduação em Ciências Biológicas, Universidade Federal do Pampa, Rodovia Osvaldo Aranha, BR 290, Km 423, 97307-020 São Gabriel, RS, Brazil
| | - Lilian O Machado
- Programa de Pós-Graduação em Recursos Genéticos Vegetais, Universidade Federal de Santa Catarina, Departamento de Fitotecnia, Rod. Admar Gonzaga 1346, 88034-000 Florianópolis, SC, Brazil
| | - Newton C F DA Costa
- Universidade do Estado de Santa Catarina, Centro de Ciências Agrárias, Av. Luiz de Camões, 2090, 88520-000 Lages, SC, Brazil
| | - Gustavo H F Klabunde
- Empresa de Pesquisa Agropecuária e Extensão Rural de Santa Catarina (EPAGRI), Rod. Antônio Heil, 6800, 88318-112 Itajaí, SC, Brazil
| | - Rubens O Nodari
- Programa de Pós-Graduação em Recursos Genéticos Vegetais, Universidade Federal de Santa Catarina, Departamento de Fitotecnia, Rod. Admar Gonzaga 1346, 88034-000 Florianópolis, SC, Brazil
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26
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Ledoux J, Ghanem R, Horaud M, López‐Sendino P, Romero‐Soriano V, Antunes A, Bensoussan N, Gómez‐Gras D, Linares C, Machordom A, Ocaña O, Templado J, Leblois R, Ben Souissi J, Garrabou J. Gradients of genetic diversity and differentiation across the distribution range of a Mediterranean coral: Patterns, processes and conservation implications. DIVERS DISTRIB 2021. [DOI: 10.1111/ddi.13382] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Affiliation(s)
- Jean‐Baptiste Ledoux
- CIIMAR/CIMAR Centro Interdisciplinar de Investigação Marinha e Ambiental Universidade do Porto Porto Portugal
- Institut de Ciències del Mar CSIC Barcelona Spain
| | - Raouia Ghanem
- Institut National Agronomique de Tunisie Université de Carthage Tunis Tunisie
- Laboratoire de Biodiversité, Biotechnologies et Changements Climatiques (LR11ES09) Université Tunis El Manar Tunis Tunisie
| | | | | | | | - Agostinho Antunes
- CIIMAR/CIMAR Centro Interdisciplinar de Investigação Marinha e Ambiental Universidade do Porto Porto Portugal
- Departamento de Biologia Faculdade de Ciências Universidade do Porto Porto Portugal
| | | | | | - Cristina Linares
- Departament de Biologia Evolutiva, Ecologia i Ciències Ambientals Institut de Recerca de la Biodiversitat (IRBIO) Universitat de Barcelona Barcelona Spain
| | - Annie Machordom
- Museo Nacional de Ciencias Naturales (MNCN‐CSIC) Madrid Spain
| | - Oscar Ocaña
- Departamento de Oceanografía Biológica y Biodiversidad Fundación Museo del Mar de Ceuta Ceuta Spain
| | - José Templado
- Museo Nacional de Ciencias Naturales (MNCN‐CSIC) Madrid Spain
| | - Raphaêl Leblois
- CBGP INRAE CIRAD IRD Montpellier SupAgro University of Montpellier Montpellier France
- Institut de Biologie Computationnelle University of Montpellier Montpellier France
| | - Jamila Ben Souissi
- Institut National Agronomique de Tunisie Université de Carthage Tunis Tunisie
- Laboratoire de Biodiversité, Biotechnologies et Changements Climatiques (LR11ES09) Université Tunis El Manar Tunis Tunisie
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27
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Morrison CL, Johnson NA, Jones JW, Eackles MS, Aunins AW, Fitzgerald DB, Hallerman EM, King TL. Genetic and morphological characterization of the freshwater mussel clubshell species complex ( Pleurobema clava and Pleurobema oviforme) to inform conservation planning. Ecol Evol 2021; 11:15325-15350. [PMID: 34765181 PMCID: PMC8571583 DOI: 10.1002/ece3.8219] [Citation(s) in RCA: 3] [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: 04/02/2021] [Revised: 08/14/2021] [Accepted: 08/26/2021] [Indexed: 11/09/2022] Open
Abstract
The shell morphologies of the freshwater mussel species Pleurobema clava (federally endangered) and Pleurobema oviforme (species of concern) are similar, causing considerable taxonomic confusion between the two species over the last 100 years. While P. clava was historically widespread throughout the Ohio River basin and tributaries to the lower Laurentian Great Lakes, P. oviforme was confined to the Tennessee and the upper Cumberland River basins. We used two mitochondrial DNA (mtDNA) genes, 13 novel nuclear DNA microsatellite markers, and shell morphometrics to help resolve this taxonomic confusion. Evidence for a single species was apparent in phylogenetic analyses of each mtDNA gene, revealing monophyletic relationships with minimal differentiation and shared haplotypes. Analyses of microsatellites showed significant genetic structuring, with four main genetic clusters detected, respectively, in the upper Ohio River basin, the lower Ohio River and Great Lakes, and upper Tennessee River basin, and a fourth genetic cluster, which included geographically intermediate populations in the Ohio and Tennessee river basins. While principal components analysis (PCA) of morphometric variables (i.e., length, height, width, and weight) showed significant differences in shell shape, only 3% of the variance in shell shape was explained by nominal species. Using Linear Discriminant and Random Forest (RF) analyses, correct classification rates for the two species' shell forms were 65.5% and 83.2%, respectively. Random Forest classification rates for some populations were higher; for example, for North Fork Holston (HOLS), it was >90%. While nuclear DNA and shell morphology indicate that the HOLS population is strongly differentiated, perhaps indicative of cryptic biodiversity, we consider the presence of a single widespread species the most likely biological scenario for many of the investigated populations based on our mtDNA dataset. However, additional sampling of P. oviforme populations at nuclear loci is needed to corroborate this finding.
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Affiliation(s)
- Cheryl L. Morrison
- U.S. Geological Survey, Eastern Ecological Science Center, Leetown Research LaboratoryKearneysvilleWest VirginiaUSA
| | - Nathan A. Johnson
- U.S. Geological Survey, Wetland and Aquatic Research CenterGainesvilleFloridaUSA
| | - Jess W. Jones
- U.S. Fish and Wildlife Service, Department of Fish and Wildlife Conservation, Virginia Polytechnic Institute and State UniversityBlacksburgVirginiaUSA
| | - Michael S. Eackles
- U.S. Geological Survey, Eastern Ecological Science Center, Leetown Research LaboratoryKearneysvilleWest VirginiaUSA
| | - Aaron W. Aunins
- U.S. Geological Survey, Eastern Ecological Science Center, Leetown Research LaboratoryKearneysvilleWest VirginiaUSA
| | - Daniel B. Fitzgerald
- U.S. Geological Survey, Eastern Ecological Science Center, Leetown Research LaboratoryKearneysvilleWest VirginiaUSA
| | - Eric M. Hallerman
- Department of Fish and Wildlife ConservationVirginia Polytechnic Institute and State UniversityBlacksburgVirginiaUSA
| | - Tim L. King
- U.S. Geological Survey, Eastern Ecological Science Center, Leetown Research LaboratoryKearneysvilleWest VirginiaUSA
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28
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Donati GFA, Zemp N, Manel S, Poirier M, Claverie T, Ferraton F, Gaboriau T, Govinden R, Hagen O, Ibrahim S, Mouillot D, Leblond J, Julius P, Velez L, Zareer I, Ziyad A, Leprieur F, Albouy C, Pellissier L. Species ecology explains the spatial components of genetic diversity in tropical reef fishes. Proc Biol Sci 2021; 288:20211574. [PMID: 34583586 PMCID: PMC8479362 DOI: 10.1098/rspb.2021.1574] [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: 07/14/2021] [Accepted: 09/03/2021] [Indexed: 11/12/2022] Open
Abstract
Generating genomic data for 19 tropical reef fish species of the Western Indian Ocean, we investigate how species ecology influences genetic diversity patterns from local to regional scales. We distinguish between the α, β and γ components of genetic diversity, which we subsequently link to six ecological traits. We find that the α and γ components of genetic diversity are strongly correlated so that species with a high total regional genetic diversity display systematically high local diversity. The α and γ diversity components are negatively associated with species abundance recorded using underwater visual surveys and positively associated with body size. Pelagic larval duration is found to be negatively related to genetic β diversity supporting its role as a dispersal trait in marine fishes. Deviation from the neutral theory of molecular evolution motivates further effort to understand the processes shaping genetic diversity and ultimately the diversification of the exceptional diversity of tropical reef fishes.
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Affiliation(s)
- Giulia Francesca Azzurra Donati
- Landscape Ecology, Institute of Terrestrial Ecosystems, ETH Zürich, CH8092 Zürich, Switzerland
- Swiss Federal Institute for Forest, Snow and Landscape Research WSL, CH8903 Birmensdorf, Switzerland
| | - Niklaus Zemp
- Genetic Diversity Centre (GDC), ETH Zürich, CH8092 Zürich, Switzerland
| | - Stéphanie Manel
- CEFE, Univ Montpellier, CNRS EPHE-PSL University, IRD, Montpellier, France
| | - Maude Poirier
- Landscape Ecology, Institute of Terrestrial Ecosystems, ETH Zürich, CH8092 Zürich, Switzerland
- Swiss Federal Institute for Forest, Snow and Landscape Research WSL, CH8903 Birmensdorf, Switzerland
| | - Thomas Claverie
- MARBEC, Univ Montpellier, CNRS, IFREMER, IRD, Montpellier 34095, France
- Centre Universitaire de formation et de recherche de Mayotte, Dembeni 97660, France
| | - Franck Ferraton
- Centre National de la Recherche Scientifique (CNRS), UMR 248 MARBEC, Montpellier, France
| | - Théo Gaboriau
- Department of Computational Biology, University of Lausanne, 1015 Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Quartier Sorge, 1015 Lausanne, Switzerland
| | | | - Oskar Hagen
- Landscape Ecology, Institute of Terrestrial Ecosystems, ETH Zürich, CH8092 Zürich, Switzerland
- Swiss Federal Institute for Forest, Snow and Landscape Research WSL, CH8903 Birmensdorf, Switzerland
| | - Shameel Ibrahim
- Maldives Whale Shark Research Programme, Popeshead Court Offices, Peter Lane, York, Yorkshire Y01 8SU, UK
| | - David Mouillot
- CEFE, Univ Montpellier, CNRS EPHE-PSL University, IRD, Montpellier, France
- Institut Universitaire de France, Paris, France
| | - Julien Leblond
- Wildlife Conservation Society, Madagascar Program, Antananarivo, Madagascar
| | | | - Laure Velez
- MARBEC, Univ Montpellier, CNRS, IFREMER, IRD, Montpellier 34095, France
| | - Irthisham Zareer
- Maldives Whale Shark Research Programme, Popeshead Court Offices, Peter Lane, York, Yorkshire Y01 8SU, UK
| | - Adam Ziyad
- Ministry of Fisheries and Agriculture, Malé, Republic of Maldives
| | - Fabien Leprieur
- MARBEC, Univ Montpellier, CNRS, IFREMER, IRD, Montpellier 34095, France
- Institut Universitaire de France, Paris, France
| | - Camille Albouy
- IFREMER, Unité Écologie et Modèles pour l'Halieutique, rue de l'Ile d'Yeu, BP21105, 44311 Nantes cedex 3, France
| | - Loïc Pellissier
- Landscape Ecology, Institute of Terrestrial Ecosystems, ETH Zürich, CH8092 Zürich, Switzerland
- Swiss Federal Institute for Forest, Snow and Landscape Research WSL, CH8903 Birmensdorf, Switzerland
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29
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Chromosome-Level Genome Assemblies Expand Capabilities of Genomics for Conservation Biology. Genes (Basel) 2021; 12:genes12091336. [PMID: 34573318 PMCID: PMC8466942 DOI: 10.3390/genes12091336] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 08/20/2021] [Accepted: 08/25/2021] [Indexed: 11/26/2022] Open
Abstract
Genome assemblies are in the process of becoming an increasingly important tool for understanding genetic diversity in threatened species. Unfortunately, due to limited budgets typical for the area of conservation biology, genome assemblies of threatened species, when available, tend to be highly fragmented, represented by tens of thousands of scaffolds not assigned to chromosomal locations. The recent advent of high-throughput chromosome conformation capture (Hi-C) enables more contiguous assemblies containing scaffolds spanning the length of entire chromosomes for little additional cost. These inexpensive contiguous assemblies can be generated using Hi-C scaffolding of existing short-read draft assemblies, where N50 of the draft contigs is larger than 0.1% of the estimated genome size and can greatly improve analyses and facilitate visualization of genome-wide features including distribution of genetic diversity in markers along chromosomes or chromosome-length scaffolds. We compared distribution of genetic diversity along chromosomes of eight mammalian species, including six listed as threatened by IUCN, where both draft genome assemblies and newer chromosome-level assemblies were available. The chromosome-level assemblies showed marked improvement in localization and visualization of genetic diversity, especially where the distribution of low heterozygosity across the genomes of threatened species was not uniform.
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Argyropoulos DC, Ruybal‐Pesántez S, Deed SL, Oduro AR, Dadzie SK, Appawu MA, Asoala V, Pascual M, Koram KA, Day KP, Tiedje KE. The impact of indoor residual spraying on Plasmodium falciparum microsatellite variation in an area of high seasonal malaria transmission in Ghana, West Africa. Mol Ecol 2021; 30:3974-3992. [PMID: 34143538 PMCID: PMC8456823 DOI: 10.1111/mec.16029] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Revised: 05/26/2021] [Accepted: 06/01/2021] [Indexed: 01/16/2023]
Abstract
Here, we report the first population genetic study to examine the impact of indoor residual spraying (IRS) on Plasmodium falciparum in humans. This study was conducted in an area of high seasonal malaria transmission in Bongo District, Ghana. IRS was implemented during the dry season (November-May) in three consecutive years between 2013 and 2015 to reduce transmission and attempt to bottleneck the parasite population in humans towards lower diversity with greater linkage disequilibrium. The study was done against a background of widespread use of long-lasting insecticidal nets, typical for contemporary malaria control in West Africa. Microsatellite genotyping with 10 loci was used to construct 392 P. falciparum multilocus infection haplotypes collected from two age-stratified cross-sectional surveys at the end of the wet seasons pre- and post-IRS. Three-rounds of IRS, under operational conditions, led to a >90% reduction in transmission intensity and a 35.7% reduction in the P. falciparum prevalence (p < .001). Despite these declines, population genetic analysis of the infection haplotypes revealed no dramatic changes with only a slight, but significant increase in genetic diversity (He : pre-IRS = 0.79 vs. post-IRS = 0.81, p = .048). Reduced relatedness of the parasite population (p < .001) was observed post-IRS, probably due to decreased opportunities for outcrossing. Spatiotemporal genetic differentiation between the pre- and post-IRS surveys (D = 0.0329 [95% CI: 0.0209 - 0.0473], p = .034) was identified. These data provide a genetic explanation for the resilience of P. falciparum to short-term IRS programmes in high-transmission settings in sub-Saharan Africa.
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Affiliation(s)
- Dionne C. Argyropoulos
- School of BioSciencesBio21 InstituteThe University of MelbourneMelbourneVic.Australia
- Department of Microbiology and ImmunologyBio21 Institute and Peter Doherty InstituteThe University of MelbourneMelbourneVic.Australia
| | - Shazia Ruybal‐Pesántez
- School of BioSciencesBio21 InstituteThe University of MelbourneMelbourneVic.Australia
- Present address:
Population Health and Immunity Division, Walter and Eliza Hall Institute of Medical ResearchMelbourneVic.Australia
- Present address:
Department of Medical Biology and Bio21 InstituteThe University of MelbourneMelbourneVic.Australia
- Present address:
Burnet InstituteMelbourneVic.Australia
| | - Samantha L. Deed
- School of BioSciencesBio21 InstituteThe University of MelbourneMelbourneVic.Australia
- Department of Microbiology and ImmunologyBio21 Institute and Peter Doherty InstituteThe University of MelbourneMelbourneVic.Australia
| | - Abraham R. Oduro
- Navrongo Health Research CentreGhana Health ServiceNavrongoGhana
| | - Samuel K. Dadzie
- Noguchi Memorial Institute for Medical ResearchUniversity of GhanaLegonGhana
| | - Maxwell A. Appawu
- Noguchi Memorial Institute for Medical ResearchUniversity of GhanaLegonGhana
| | - Victor Asoala
- Navrongo Health Research CentreGhana Health ServiceNavrongoGhana
| | - Mercedes Pascual
- Department of Ecology and EvolutionUniversity of ChicagoChicagoUSA
| | - Kwadwo A. Koram
- Noguchi Memorial Institute for Medical ResearchUniversity of GhanaLegonGhana
| | - Karen P. Day
- School of BioSciencesBio21 InstituteThe University of MelbourneMelbourneVic.Australia
- Department of Microbiology and ImmunologyBio21 Institute and Peter Doherty InstituteThe University of MelbourneMelbourneVic.Australia
| | - Kathryn E. Tiedje
- School of BioSciencesBio21 InstituteThe University of MelbourneMelbourneVic.Australia
- Department of Microbiology and ImmunologyBio21 Institute and Peter Doherty InstituteThe University of MelbourneMelbourneVic.Australia
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Johnstone C, Pérez M, Malca E, Quintanilla JM, Gerard T, Lozano-Peral D, Alemany F, Lamkin J, García A, Laiz-Carrión R. Genetic connectivity between Atlantic bluefin tuna larvae spawned in the Gulf of Mexico and in the Mediterranean Sea. PeerJ 2021; 9:e11568. [PMID: 34178457 PMCID: PMC8210807 DOI: 10.7717/peerj.11568] [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: 10/16/2020] [Accepted: 05/16/2021] [Indexed: 12/11/2022] Open
Abstract
The highly migratory Atlantic bluefin tuna (ABFT) is currently managed as two distinct stocks, in accordance with natal homing behavior and population structuring despite the absence of barriers to gene flow. Larval fish are valuable biological material for tuna molecular ecology. However, they have hardly been used to decipher the ABFT population structure, although providing the genetic signal from successful breeders. For the first time, cooperative field collection of tuna larvae during 2014 in the main spawning area for each stock, the Gulf of Mexico (GOM) and the Mediterranean Sea (MED), enabled us to assess the ABFT genetic structure in a precise temporal and spatial frame exclusively through larvae. Partitioning of genetic diversity at nuclear microsatellite loci and in the mitochondrial control region in larvae spawned contemporarily resulted in low significant fixation indices supporting connectivity between spawners in the main reproduction area for each population. No structuring was detected within the GOM after segregating nuclear diversity in larvae spawned in two hydrographically distinct regions, the eastern GOM (eGOM) and the western GOM (wGOM), with the larvae from eGOM being more similar to those collected in the MED than the larvae from wGOM. We performed clustering of genetically characterized ABFT larvae through Bayesian analysis and by Discriminant Analysis of Principal Components (DAPC) supporting the existence of favorable areas for mixing of ABFT spawners from Western and Eastern stocks, leading to gene flow and apparent connectivity between weakly structured populations. Our findings suggest that the eastern GOM is more prone for the mixing of breeders from the two ABFT populations. Conservation of this valuable resource exploited for centuries calls for intensification of tuna ichthyoplankton research and standardization of genetic tools for monitoring population dynamics.
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Affiliation(s)
- Carolina Johnstone
- Centro Oceanográfico de Málaga, Instituto Español de Oceanografía, Consejo Superior de Investigaciones Científicas, Fuengirola, Málaga, Spain
| | - Montse Pérez
- Centro Oceanográfico de Vigo, Instituto Español de Oceanografía, Consejo Superior de Investigaciones Científicas, Vigo, Pontevedra, Spain
| | - Estrella Malca
- Cooperative Institute for Marine and Atmospheric Studies, University of Miami, Miami, Florida, United States of America.,Southeast Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, Miami, Florida, United States of America
| | - José María Quintanilla
- Centro Oceanográfico de Málaga, Instituto Español de Oceanografía, Consejo Superior de Investigaciones Científicas, Fuengirola, Málaga, Spain
| | - Trika Gerard
- Southeast Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, Miami, Florida, United States of America
| | - Diego Lozano-Peral
- Centro de Supercomputación y Bioinnovación, Servicios Centrales de Apoyo a la Investigación, Universidad de Málaga, Málaga, Spain
| | - Francisco Alemany
- International Commision for the Conservation of Atlantic Tunas, Madrid, Spain
| | - John Lamkin
- Southeast Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, Miami, Florida, United States of America
| | - Alberto García
- Centro Oceanográfico de Málaga, Instituto Español de Oceanografía, Consejo Superior de Investigaciones Científicas, Fuengirola, Málaga, Spain
| | - Raúl Laiz-Carrión
- Centro Oceanográfico de Málaga, Instituto Español de Oceanografía, Consejo Superior de Investigaciones Científicas, Fuengirola, Málaga, Spain
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Hardy BM, Pope KL, Latch EK. Genomic signatures of demographic declines in an imperiled amphibian inform conservation action. Anim Conserv 2021. [DOI: 10.1111/acv.12695] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- B. M. Hardy
- Behavioral and Molecular Ecology Research Group Department of Biological Sciences University of Wisconsin‐Milwaukee Milwaukee WI USA
- Graduate Degree Program in Ecology Colorado State University Fort Collins CO USA
| | - K. L. Pope
- United States Forest Service Pacific Southwest Research Station Arcata CA USA
| | - E. K. Latch
- Behavioral and Molecular Ecology Research Group Department of Biological Sciences University of Wisconsin‐Milwaukee Milwaukee WI USA
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Reiner G, Klein C, Lang M, Willems H. Human-driven genetic differentiation in a managed red deer population. EUR J WILDLIFE RES 2021. [DOI: 10.1007/s10344-021-01472-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
AbstractNineteen red deer areas in a densely populated region with a huge network of fenced motorways and the division into administrative management units (AMUs) with restricted ecological connectivity were investigated. In the season 2018/2019, a total of 1291 red deer samples (on average 68 per area) were collected and genotyped using 16 microsatellite markers. The results show a clear genetic differentiation between most of the AMUs. Fourteen AMUs may be combined into four regions with a considerable internal genetic exchange. Five areas were largely isolated or showed only a limited gene flow with neighbouring areas. Ten of the 19 AMUs had an effective population size below 100. Effective population sizes greater than 500–1000, required to maintain the evolutionary potential and a long-term adaptation potential, were not achieved by any of the studied AMUs, even when AMUs with an appreciable genetic exchange were aggregated. Substantial genetic differentiation between areas can be associated with the presence of landscape barriers hindering gene flow, but also with the maintenance of ‘red deer–free’ areas. Efforts to sustainably preserve the genetic diversity of the entire region should therefore focus on measures ensuring genetic connectivity. Opportunities for this goal arise from the establishment of game bridges over motorways and from the protection of young male stags migrating through the statutory ‘red deer–free’ areas.
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Negisho K, Shibru S, Pillen K, Ordon F, Wehner G. Genetic diversity of Ethiopian durum wheat landraces. PLoS One 2021; 16:e0247016. [PMID: 33596260 PMCID: PMC7888639 DOI: 10.1371/journal.pone.0247016] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Accepted: 01/30/2021] [Indexed: 01/27/2023] Open
Abstract
Genetic diversity and population structure assessment in crops is essential for marker trait association, marker assisted breeding and crop germplasm conservation. We analyzed a set of 285 durum wheat accessions comprising 215 Ethiopian durum wheat landraces, 10 released durum wheat varieties, 10 advanced durum wheat lines from Ethiopia, and 50 durum wheat lines from CIMMYT. We investigated the genetic diversity and population structure for the complete panel as well as for the 215 landraces, separately based on 11,919 SNP markers with known physical positions. The whole panel was clustered into two populations representing on the one hand mainly the landraces, and on the other hand mainly released, advanced and CIMMYT lines. Further population structure analysis of the landraces uncovered 4 subgroups emphasizing the high degree of genetic diversity within Ethiopian durum landraces. Population structure based AMOVA for both sets unveiled significant (P < 0.001) variation between populations and within populations. Total variation within population accessions (81%, 76%) was higher than total variation between populations (19%, 24%) for both sets. Population structure analysis based genetic differentiation (FST) and gene flow (Nm) for the whole set and the Ethiopian landraces were 0.19 and 0.24, 1.04, and 0.81, respectively indicating high genetic differentiation and limited gene flow. Diversity indices verify that the landrace panel was more diverse with (I = 0.7, He = 0.46, uHe = 0.46) than the advanced lines (I = 0.6, He = 0.42, uHe = 0.42). Similarly, differences within the landrace clusters were observed. In summary a high genetic diversity within Ethiopian durum wheat landraces was detected, which may be a target for national and international wheat improvement programs to exploit valuable traits for biotic and abiotic stresses.
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Affiliation(s)
- Kefyalew Negisho
- Ethiopian Institute of Agricultural Research (EIAR), National Agricultural Biotechnology Research Center, Holeta, Ethiopia
| | - Surafel Shibru
- Ethiopian Institute of Agricultural Research (EIAR), Melkassa Research Center, Melkassa, Ethiopia
| | - Klaus Pillen
- Martin-Luther-University, Institute of Agricultural and Nutritional Sciences, Halle (Saale), Germany
| | - Frank Ordon
- Julius Kühn Institute (JKI), Institute for Resistance Research and Stress Tolerance, Quedlinburg, Germany
| | - Gwendolin Wehner
- Julius Kühn Institute (JKI), Institute for Resistance Research and Stress Tolerance, Quedlinburg, Germany
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Neal KM, Fisher RN, Mitrovich MJ, Shaffer HB. Conservation Genomics of the Threatened Western Spadefoot, Spea hammondii, in Urbanized Southern California. J Hered 2021; 111:613-627. [PMID: 33245338 DOI: 10.1093/jhered/esaa049] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Revised: 02/17/2020] [Accepted: 11/19/2020] [Indexed: 11/14/2022] Open
Abstract
Populations of the western spadefoot (Spea hammondii) in southern California occur in one of the most urbanized and fragmented landscapes on the planet and have lost up to 80% of their native habitat. Orange County is one of the last strongholds for this pond-breeding amphibian in the region, and ongoing restoration efforts targeting S. hammondii have involved habitat protection and the construction of artificial breeding ponds. These efforts have successfully increased breeding activity, but genetic characterization of the populations, including estimates of effective population size and admixture between the gene pools of constructed artificial and natural ponds, has never been undertaken. Using thousands of genome-wide single-nucleotide polymorphisms, we characterized the population structure, genetic diversity, and genetic connectivity of spadefoots in Orange County to guide ongoing and future management efforts. We identified at least 2, and possibly 3 major genetic clusters, with additional substructure within clusters indicating that individual ponds are often genetically distinct. Estimates of landscape resistance suggest that ponds on either side of the Los Angeles Basin were likely interconnected historically, but intense urban development has rendered them essentially isolated, and the resulting risk of interruption to natural metapopulation dynamics appears to be high. Resistance surfaces show that the existing artificial ponds were well-placed and connected to natural populations by low-resistance corridors. Toad samples from all ponds (natural and artificial) returned extremely low estimates of effective population size, possibly due to a bottleneck caused by a recent multi-year drought. Management efforts should focus on maintaining gene flow among natural and artificial ponds by both assisted migration and construction of new ponds to bolster the existing pond network in the region.
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Affiliation(s)
- Kevin M Neal
- Department of Ecology and Evolutionary Biology, and La Kretz Center for California Conservation Science, University of California Los Angeles, Los Angeles, CA
| | - Robert N Fisher
- Western Ecological Research Center, U.S. Geological Survey, San Diego, CA
| | | | - H Bradley Shaffer
- Department of Ecology and Evolutionary Biology, and La Kretz Center for California Conservation Science, University of California Los Angeles, Los Angeles, CA
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High genomic diversity maintained by populations of Carex scirpoidea subsp. convoluta, a paraphyletic Great Lakes ecotype. CONSERV GENET 2021. [DOI: 10.1007/s10592-020-01326-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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Reforestation or Genetic Disturbance: A Case Study of Pinus thunbergii in the Iki-no-Matsubara Coastal Forest (Japan). FORESTS 2021. [DOI: 10.3390/f12010072] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
In the twentieth century, a substantial decline in Pinus thunbergii populations in Japan occurred due to the outbreak of pine wood nematode (PWN), Burshaphelencus xylophilus. A PWN-P. thunbergii resistant trees-breeding project was developed in the 1980s to provide reforestation materials to minimalize the pest damage within the population. Since climate change can also contribute to PWN outbreaks, an intensive reforestation plan instated without much consideration can impact on the genetic diversity of P. thunbergii populations. The usage and deployment of PWN-P. thunbergii resistant trees to a given site without genetic management can lead to a genetic disturbance. The Iki-no-Matsubara population was used as a model to design an approach for the deployment management. This research aimed to preserve local genetic diversity, genetic structure, and relatedness by developing a method for deploying Kyushu PWN-P. thunbergii resistant trees as reforestation-material plants into Iki-no-Matsubara. The local genotypes of the Iki-no-Matsubara population and the Kyushu PWN-P. thunbergii resistant trees were analyzed using six microsatellite markers. Genotype origins, relatedness, diversity, and structure of both were investigated and compared with the genetic results previously obtained for old populations of P. thunbergii throughout Japan. A sufficient number of Kyushu PWN-P. thunbergii resistant trees, as mother trees, within seed orchards and sufficient status number of the seedlings to deploy are needed when deploying the Kyushu PWN-P. thunbergii resistant trees as reforestation material planting into Iki-no-Matsubara population. This approach not only be used to preserve Iki-no-Matsubara population (genetic diversity, genetic structure, relatedness, and resilience of the forests) but can also be applied to minimize PWN damage. These results provide a baseline for further seed sourcing as well as develop genetic management strategies within P. thunbergii populations, including Kyushu PWN-P. thunbergii resistant trees.
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Kharzinova VR, Zinovieva NA. The pattern of genetic diversity of different breeds of pigs based on microsatellite analysis. Vavilovskii Zhurnal Genet Selektsii 2020; 24:747-754. [PMID: 33738391 PMCID: PMC7960447 DOI: 10.18699/vj20.669] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
One of the main tasks of genetics and animal breeding is the assessment of genetic diversity and the
study of genetic relationships between different breeds and populations using molecular genetic analysis methods.
We analysed the polymorphism of microsatellites and the information on the state of genetic diversity and
the population structure of local breeds in Russia: the Kemerovo, the Berkshire, the Liven, the Mangalitsa, and the
Civilian; in the Republic of Belarus: the Large White and the Black-and-White; and in Ukraine: the White Steppe, as
well as commercial breeds of imported origin of domestic reproduction: the Large White, the Landrace, and the
Duroc. The materials used for this study were the tissue and DNA samples extracted from 1,194 pigs and DNA of
the UNU “Genetic material bank of domestic and wild animal species and birds” of the L.K. Ernst Federal Research
Center for Animal Husbandry. Polymorphisms of 10 microsatellites (S0155, S0355, S0386, SW24, SO005, SW72,
SW951, S0101, SW240, and SW857) were determined according to the previously developed technique using DNA
analyser ABI3130xl. To estimate the allele pool of each population, the average number of alleles (NA), the effective
number of alleles (NE ) based on the locus, the rarified allelic richness (AR), the observed (HO ) and expected (HE )
heterozygosity,
and the fixation index (FIS) were calculated. The degree of genetic differentiation of the breeds was
assessed based on the pairwise values of FST and D. The analysis of the allelic and genetic diversity parameters of
the local breeds showed that the maximum and minimum levels of polymorphism were observed in pigs of the
Ukrainian White Steppe breed (NA = 6.500, NE = 3.709, and AR = 6.020) and in pigs of the Duroc breed (NA = 4.875,
NE = 2.119, and AR = 3.821), respectively. The highest level of genetic diversity was found in the Large White breed
of the Republic of Belarus (HO = 0.707 and NE = 0.702). The minimum level of genetic diversity was found in pigs of
the imported breeds – the Landrace (HO = 0.459, HE = 0.400) and the Duroc (HO = 0.480, HE = 0.469) – indicating a
high selection pressure in these breeds. Based on the results of phylogenetic analysis, the genetic origin of Large
White pigs, the breeds, from which the Berkshire pigs originated, and the genetic detachment of the Landrace from
the Mangalitsa breeds were revealed. The cluster analysis showed a genetic consolidation of the Black-and-White,
the Berkshire, and the Mangalitsa pigs. Additionally, the imported breeds with clustering depending on the origin
were characterised by a genetic structure different from that of the other breeds. The information obtained from
these studies can serve as a guide for the management and breeding strategies of the pig breeds studied, to allow
their better use and conservation.
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Affiliation(s)
- V R Kharzinova
- L.K. Ernst Federal Research Center for Animal Husbandry, Dubrovitsy, Moscow region, Russia
| | - N A Zinovieva
- L.K. Ernst Federal Research Center for Animal Husbandry, Dubrovitsy, Moscow region, Russia
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Djuicy DD, Hearn J, Tchouakui M, Wondji MJ, Irving H, Okumu FO, Wondji CS. CYP6P9-Driven Signatures of Selective Sweep of Metabolic Resistance to Pyrethroids in the Malaria Vector Anopheles funestus Reveal Contemporary Barriers to Gene Flow. Genes (Basel) 2020; 11:E1314. [PMID: 33167550 PMCID: PMC7694540 DOI: 10.3390/genes11111314] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Revised: 10/24/2020] [Accepted: 10/31/2020] [Indexed: 11/16/2022] Open
Abstract
Pyrethroid resistance in major malaria vectors such as Anopheles funestus threatens malaria control efforts in Africa. Cytochrome P450-mediated metabolic resistance is best understood for CYP6P9 genes in southern Africa in An. funestus. However, we do not know if this resistance mechanism is spreading across Africa and how it relates to broader patterns of gene flow across the continent. Nucleotide diversity of the CYP6P9a gene and the diversity pattern of five gene fragments spanning a region of 120 kb around the CYP6P9a gene were surveyed in mosquitoes from southern, eastern and central Africa. These analyses revealed that a Cyp6P9a resistance-associated allele has swept through southern and eastern Africa and is now fixed in these regions. A similar diversity profile was observed when analysing genomic regions located 34 kb upstream to 86 kb downstream of the CYP6P9a locus, concordant with a selective sweep throughout the rp1 locus. We identify reduced gene flow between southern/eastern Africa and central Africa, which we hypothesise is due to the Great Rift Valley. These potential barriers to gene flow are likely to prevent or slow the spread of CYP6P9-based resistance mechanism to other parts of Africa and would to be considered in future vector control interventions such as gene drive.
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Affiliation(s)
- Delia Doreen Djuicy
- LSTM Research Unit, Centre for Research in Infectious Diseases (CRID), P.O. Box 13591 Yaoundé, Cameroon; (M.T.); (M.J.W.)
| | - Jack Hearn
- Department of Vector Biology, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool L3 5QA, UK; (J.H.); (H.I.)
| | - Magellan Tchouakui
- LSTM Research Unit, Centre for Research in Infectious Diseases (CRID), P.O. Box 13591 Yaoundé, Cameroon; (M.T.); (M.J.W.)
| | - Murielle J. Wondji
- LSTM Research Unit, Centre for Research in Infectious Diseases (CRID), P.O. Box 13591 Yaoundé, Cameroon; (M.T.); (M.J.W.)
- Department of Vector Biology, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool L3 5QA, UK; (J.H.); (H.I.)
| | - Helen Irving
- Department of Vector Biology, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool L3 5QA, UK; (J.H.); (H.I.)
| | - Fredros O. Okumu
- Environmental Health and Ecological Sciences Department, Ifakara Health Institute, PO Box 53 Ifakara 67501, Tanzania;
| | - Charles S. Wondji
- LSTM Research Unit, Centre for Research in Infectious Diseases (CRID), P.O. Box 13591 Yaoundé, Cameroon; (M.T.); (M.J.W.)
- Department of Vector Biology, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool L3 5QA, UK; (J.H.); (H.I.)
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The Genetic Diversity of Cranberry Crop Wild Relatives, Vaccinium macrocarpon Aiton and V. oxycoccos L., in the US, with Special Emphasis on National Forests. PLANTS 2020; 9:plants9111446. [PMID: 33114692 PMCID: PMC7716231 DOI: 10.3390/plants9111446] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Revised: 10/12/2020] [Accepted: 10/12/2020] [Indexed: 12/03/2022]
Abstract
Knowledge of the genetic diversity in populations of crop wild relatives (CWR) can inform effective strategies for their conservation and facilitate utilization to solve agricultural challenges. Two crop wild relatives of the cultivated cranberry are widely distributed in the US. We studied 21 populations of Vaccinium macrocarpon Aiton and 24 populations of Vaccinium oxycoccos L. across much of their native ranges in the US using 32 simple sequence repeat (SSR) markers. We observed high levels of heterozygosity for both species across populations with private alleles ranging from 0 to 26. For V. macrocarpon, we found a total of 613 alleles and high levels of heterozygosity (HO = 0.99, HT = 0.75). We also observed high numbers of alleles (881) and levels of heterozygosity (HO = 0.71, HT = 0.80) in V. oxycoccos (4x). Our genetic analyses confirmed the field identification of a native population of V. macrocarpon on the Okanogan-Wenatchee National Forest in the state of Washington, far outside the previously reported range for the species. Our results will help to inform efforts of the United States Department of Agriculture Agricultural Research Service (USDA-ARS) and the United States Forest Service (USFS) to conserve the most diverse and unique wild cranberry populations through ex situ preservation of germplasm and in situ conservation in designated sites on National Forests.
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Yi X, Donner DM, Marquardt PE, Palmer JM, Jusino MA, Frair J, Lindner DL, Latch EK. Major histocompatibility complex variation is similar in little brown bats before and after white-nose syndrome outbreak. Ecol Evol 2020; 10:10031-10043. [PMID: 33005361 PMCID: PMC7520216 DOI: 10.1002/ece3.6662] [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: 07/13/2020] [Revised: 07/18/2020] [Accepted: 07/19/2020] [Indexed: 12/28/2022] Open
Abstract
White-nose syndrome (WNS), caused by the fungal pathogen Pseudogymnoascus destructans (Pd), has driven alarming declines in North American hibernating bats, such as little brown bat (Myotis lucifugus). During hibernation, infected little brown bats are able to initiate anti-Pd immune responses, indicating pathogen-mediated selection on the major histocompatibility complex (MHC) genes. However, such immune responses may not be protective as they interrupt torpor, elevate energy costs, and potentially lead to higher mortality rates. To assess whether WNS drives selection on MHC genes, we compared the MHC DRB gene in little brown bats pre- (Wisconsin) and post- (Michigan, New York, Vermont, and Pennsylvania) WNS (detection spanning 2014-2015). We genotyped 131 individuals and found 45 nucleotide alleles (27 amino acid alleles) indicating a maximum of 3 loci (1-5 alleles per individual). We observed high allelic admixture and a lack of genetic differentiation both among sampling sites and between pre- and post-WNS populations, indicating no signal of selection on MHC genes. However, post-WNS populations exhibited decreased allelic richness, reflecting effects from bottleneck and drift following rapid population declines. We propose that mechanisms other than adaptive immunity are more likely driving current persistence of little brown bats in affected regions.
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Affiliation(s)
- Xueling Yi
- Department of Biological SciencesUniversity of Wisconsin‐MilwaukeeMilwaukeeWIUSA
| | - Deahn M. Donner
- Northern Research StationUSDA Forest ServiceRhinelanderWIUSA
| | | | | | - Michelle A. Jusino
- Northern Research StationUSDA Forest ServiceMadisonWIUSA
- Department of Plant PathologyUniversity of FloridaGainesvilleFLUSA
| | - Jacqueline Frair
- Roosevelt Wild Life StationSUNY College of Environmental Science and ForestrySyracuseNYUSA
| | | | - Emily K. Latch
- Department of Biological SciencesUniversity of Wisconsin‐MilwaukeeMilwaukeeWIUSA
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Nowicki M, Houston LC, Boggess SL, Aiello AS, Payá‐Milans M, Staton ME, Hayashida M, Yamanaka M, Eda S, Trigiano RN. Species diversity and phylogeography of Cornus kousa (Asian dogwood) captured by genomic and genic microsatellites. Ecol Evol 2020; 10:8299-8312. [PMID: 32788980 PMCID: PMC7417245 DOI: 10.1002/ece3.6537] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Accepted: 06/09/2020] [Indexed: 01/01/2023] Open
Abstract
Cornus kousa (Asian dogwood), an East Asia native tree, is the most economically important species of the dogwood genus, owing to its desirable horticultural traits and ability to hybridize with North America-native dogwoods. To assess the species genetic diversity and to better inform the ongoing and future breeding efforts, we assembled an herbarium and arboretum collection of 131 noncultivated C. kousa specimens. Genotyping and capillary electrophoresis analyses of our C. kousa collection with the newly developed genic and published nuclear genomic microsatellites permitted assessment of genetic diversity and evolutionary history of the species. Regardless of the microsatellite type used, the study yielded generally similar insights into the C. kousa diversity with subtle differences deriving from and underlining the marker used. The accrued evidence pointed to the species distinct genetic pools related to the plant country of origin. This can be helpful in the development of the commercial cultivars for this important ornamental crop with increased pyramided utility traits. Analyses of the C. kousa evolutionary history using the accrued genotyping datasets pointed to an unsampled ancestor population, possibly now extinct, as per the phylogeography of the region. To our knowledge, there are few studies utilizing the same gDNA collection to compare performance of genomic and genic microsatellites. This is the first detailed report on C. kousa species diversity and evolutionary history inference.
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Affiliation(s)
- Marcin Nowicki
- Department of Entomology and Plant PathologyThe University of TennesseeKnoxvilleTNUSA
| | - Logan C. Houston
- Department of Entomology and Plant PathologyThe University of TennesseeKnoxvilleTNUSA
| | - Sarah L. Boggess
- Department of Entomology and Plant PathologyThe University of TennesseeKnoxvilleTNUSA
| | | | - Miriam Payá‐Milans
- Department of Entomology and Plant PathologyThe University of TennesseeKnoxvilleTNUSA
- Present address:
Centro de Biotecnología y Genómica de PlantasUPM‐INIAMadridSpain
| | - Margaret E. Staton
- Department of Entomology and Plant PathologyThe University of TennesseeKnoxvilleTNUSA
| | | | - Masahiro Yamanaka
- Department of Pharmaceytical SciencesInternational University of Health and WelfareOhtawaraJapan
| | - Shigetoshi Eda
- Department of Forestry, Wildlife and FisheriesCenter for Wildlife Health ORUKnoxvilleTNUSA
- Department of MicrobiologyCenter for Wildlife Health ORUKnoxvilleTNUSA
| | - Robert N. Trigiano
- Department of Entomology and Plant PathologyThe University of TennesseeKnoxvilleTNUSA
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Against all odds: a tale of marine range expansion with maintenance of extremely high genetic diversity. Sci Rep 2020; 10:12707. [PMID: 32728141 PMCID: PMC7391780 DOI: 10.1038/s41598-020-69374-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Accepted: 07/07/2020] [Indexed: 02/07/2023] Open
Abstract
The displacement of species from equatorial latitudes to temperate locations following the increase in sea surface temperatures is among the significant reported consequences of climate change. Shifts in the distributional ranges of species result in fish communities tropicalisation, i.e., high latitude colonisations by typically low latitude distribution species. These movements create new interactions between species and new trophic assemblages. The Senegal seabream, Diplodus bellottii, may be used as a model to understand the population genetics of these invasions. In the last decades, this species has undergone an outstanding range expansion from its African area of origin to the Atlantic coast of the Iberian Peninsula, where now occurs abundantly. Mitochondrial and nuclear markers revealed a striking high haplotypic nucleotide and genetic diversity values, along with significant population differentiation throughout the present-day geographical range of the Senegal seabream. These results are not consistent with the central-marginal hypothesis, nor with the expectations of a leptokurtic distribution of individuals, as D. bellottii seems to be able to retain exceptional levels of diversity in marginal and recently colonised areas. We discuss possible causes for hyperdiversity and lack of geographical structure and subsequent implications for fisheries.
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Millar MA, Byrne M. Variable clonality and genetic structure among disjunct populations of Banksia mimica. CONSERV GENET 2020. [DOI: 10.1007/s10592-020-01288-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Zimmerman SJ, Aldridge CL, Oyler-McCance SJ. An empirical comparison of population genetic analyses using microsatellite and SNP data for a species of conservation concern. BMC Genomics 2020; 21:382. [PMID: 32487020 PMCID: PMC7268520 DOI: 10.1186/s12864-020-06783-9] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Accepted: 05/14/2020] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Use of genomic tools to characterize wildlife populations has increased in recent years. In the past, genetic characterization has been accomplished with more traditional genetic tools (e.g., microsatellites). The explosion of genomic methods and the subsequent creation of large SNP datasets has led to the promise of increased precision in population genetic parameter estimates and identification of demographically and evolutionarily independent groups, as well as questions about the future usefulness of the more traditional genetic tools. At present, few empirical comparisons of population genetic parameters and clustering analyses performed with microsatellites and SNPs have been conducted. RESULTS Here we used microsatellite and SNP data generated from Gunnison sage-grouse (Centrocercus minimus) samples to evaluate concordance of the results obtained from each dataset for common metrics of genetic diversity (HO, HE, FIS, AR) and differentiation (FST, GST, DJost). Additionally, we evaluated clustering of individuals using putatively neutral (SNPs and microsatellites), putatively adaptive, and a combined dataset of putatively neutral and adaptive loci. We took particular interest in the conservation implications of any differences. Generally, we found high concordance between microsatellites and SNPs for HE, FIS, AR, and all differentiation estimates. Although there was strong correlation between metrics from SNPs and microsatellites, the magnitude of the diversity and differentiation metrics were quite different in some cases. Clustering analyses also showed similar patterns, though SNP data was able to cluster individuals into more distinct groups. Importantly, clustering analyses with SNP data suggest strong demographic independence among the six distinct populations of Gunnison sage-grouse with some indication of evolutionary independence in two or three populations; a finding that was not revealed by microsatellite data. CONCLUSION We demonstrate that SNPs have three main advantages over microsatellites: more precise estimates of population-level diversity, higher power to identify groups in clustering methods, and the ability to consider local adaptation. This study adds to a growing body of work comparing the use of SNPs and microsatellites to evaluate genetic diversity and differentiation for a species of conservation concern with relatively high population structure and using the most common method of obtaining SNP genotypes for non-model organisms.
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Affiliation(s)
- Shawna J Zimmerman
- U.S. Geological Survey, Fort Collins Science Center, 2150 Centre Avenue, Bldg. C, Fort Collins, CO, 80526, USA.
- Department of Ecosystem Science and Sustainability and Natural Resource Ecology Laboratory, Colorado State University, Fort Collins, CO, 80526, USA.
| | - Cameron L Aldridge
- U.S. Geological Survey, Fort Collins Science Center, 2150 Centre Avenue, Bldg. C, Fort Collins, CO, 80526, USA
- Department of Ecosystem Science and Sustainability and Natural Resource Ecology Laboratory, Colorado State University, Fort Collins, CO, 80526, USA
| | - Sara J Oyler-McCance
- U.S. Geological Survey, Fort Collins Science Center, 2150 Centre Avenue, Bldg. C, Fort Collins, CO, 80526, USA
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Galuszynski NC, Potts AJ. Application of High Resolution Melt analysis (HRM) for screening haplotype variation in a non-model plant genus: Cyclopia (Honeybush). PeerJ 2020; 8:e9187. [PMID: 32461839 PMCID: PMC7233275 DOI: 10.7717/peerj.9187] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Accepted: 04/23/2020] [Indexed: 12/25/2022] Open
Abstract
Aim This study has three broad aims: to (a) develop genus-specific primers for High Resolution Melt analysis (HRM) of members of Cyclopia Vent., (b) test the haplotype discrimination of HRM compared to Sanger sequencing, and (c) provide an example of using HRM to detect novel haplotype variation in wild C. subternata Vogel. populations. Location The Cape Floristic Region (CFR), located along the southern Cape of South Africa. Methods Polymorphic loci were detected through a screening process of sequencing 12 non-coding chloroplast DNA segments across 14 Cyclopia species. Twelve genus-specific primer combinations were designed around variable cpDNA loci, four of which failed to amplify under PCR; the eight remaining were applied to test the specificity, sensitivity and accuracy of HRM. The three top performing HRM Primer combinations were then applied to detect novel haplotypes in wild C. subternata populations, and phylogeographic patterns of C. subternata were explored. Results We present a framework for applying HRM to non-model systems. HRM accuracy varied across the PCR products screened using the genus-specific primers developed, ranging between 56 and 100%. The nucleotide variation failing to produce distinct melt curves is discussed. The top three performing regions, having 100% specificity (i.e. different haplotypes were never grouped into the same cluster, no false negatives), were able to detect novel haplotypes in wild C. subternata populations with high accuracy (96%). Sensitivity below 100% (i.e. a single haplotype being clustered into multiple unique groups during HRM curve analysis, false positives) was resolved through sequence confirmation of each cluster resulting in a final accuracy of 100%. Phylogeographic analyses revealed that wild C. subternata populations tend to exhibit phylogeographic structuring across mountain ranges (accounting for 73.8% of genetic variation base on an AMOVA), and genetic differentiation between populations increases with distance (p < 0.05 for IBD analyses). Conclusions After screening for regions with high HRM clustering specificity-akin to the screening process associated with most PCR based markers-the technology was found to be a high throughput tool for detecting genetic variation in non-model plants.
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Affiliation(s)
- Nicholas C Galuszynski
- Department of Botany, Nelson Mandela University, Port Elizabeth, Eastern Cape, South Africa
| | - Alastair J Potts
- Department of Botany, Nelson Mandela University, Port Elizabeth, Eastern Cape, South Africa
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CapellÀ-Marzo B, SÁnchez-Montes G, MartÍnez-Solano I. Contrasting demographic trends and asymmetric migration rates in a spatially structured amphibian population. Integr Zool 2020; 15:482-497. [PMID: 32329558 DOI: 10.1111/1749-4877.12449] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Natural populations often persist at the landscape scale as metapopulations, with breeding units (subpopulations) experiencing temporal extinction and recolonization events. Important parameters to forecast population viability in these systems include the ratio of the effective number of breeders (Nb ) to the total number of adults (Na ) and migration rates among subpopulations. Here, we present the results of a 10-year integrative monitoring program of a metapopulation of the Iberian green frog (Pelophylax perezi) in central Spain. We characterized population dynamics at two main breeding ponds (Gravera and Laguna) using capture-mark-recapture data to estimate Na in each breeding season, and multilocus genotypes to estimate the effective population size (Ne ), Nb , individual breeding success, and migration rates. Both ponds experienced population decline after a dry season, with Gravera subsequently recovering and Laguna suffering a bottleneck associated with genetic impoverishment. In this subpopulation, average allelic richness and private alleles decreased from 2010 (10.87 and 1.67, respectively) to 2018 (8.0 and 0.20). The Nb /Na ratio in Laguna in 2018 was twice as high (0.95) than in Gravera (0.41) or in pre-bottleneck Laguna (0.50), suggesting plasticity or genetic compensation through increased individual breeding success. Migration rates were asymmetric between ponds, with a stronger contribution from Gravera to Laguna (29.9% vs. 16.2% in the opposite direction) that may result in a rescue effect. This study emphasizes the importance of integrative demographic approaches for the monitoring of natural populations based on a better understanding of their spatio-temporal dynamics, which provides valuable information for conservation actions.
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Affiliation(s)
- Berta CapellÀ-Marzo
- Department of Biodiversity and Evolutionary Biology, Museo Nacional de Ciencias Naturales, CSIC, Madrid, Spain
| | - Gregorio SÁnchez-Montes
- Department of Biodiversity and Evolutionary Biology, Museo Nacional de Ciencias Naturales, CSIC, Madrid, Spain
| | - Iñigo MartÍnez-Solano
- Department of Biodiversity and Evolutionary Biology, Museo Nacional de Ciencias Naturales, CSIC, Madrid, Spain
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Ayala-Burbano PA, Galetti Junior PM, Wormell D, Pissinatti A, Marques MC, de Freitas PD. Studbook and molecular analyses for the endangered black-lion-tamarin; an integrative approach for assessing genetic diversity and driving management in captivity. Sci Rep 2020; 10:6781. [PMID: 32321949 PMCID: PMC7176676 DOI: 10.1038/s41598-020-63542-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Accepted: 03/10/2020] [Indexed: 11/09/2022] Open
Abstract
Breeding strategies based on molecular markers have been adopted by ex-situ conservation programs to assess alternative parameters for the genetic diversity estimates. In this work we evaluated molecular and studbook data for captive populations of black-lion-tamarin (BLT), an endangered primate endemic to Brazil's Atlantic Forest. Pedigree analyses were performed using BLT studbook information collected from 1973 to 2018. We analyzed the whole captive population since its foundation; the current captive population (CCP); and all extant BLTs in the Brazilian captive population (BCP), separately. Microsatellite analyses were implemented on the BCP individuals from the eighth generation (BCP-F8) only to avoid generation overlap. The expected heterozygosity for BCP-F8, using molecular, data was 0.45, and the initial expected heterozygosity was 0.69. Kinship parameters showed high genetic relationships in both pedigree and molecular analyses. The genealogy-based endogamy evidenced a high inbreeding coefficient, while the molecular analyses suggested a non-inbreeding signature. The Mate Suitability Index showed detrimental values for the majority of potential pairs in the CCP. Nevertheless, some individuals evidenced high individual heterozygosity and allele representation, demonstrating good potential to be used as breeders. Thus, we propose the use of molecular data as a complementary parameter to evaluate mating-pairs and to aid management decision-making.
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Affiliation(s)
| | | | - Dominic Wormell
- Durrell Wildlife Conservation Trust, Trinity, Jersey, England
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Mamoozadeh NR, Graves JE, McDowell JR. Genome-wide SNPs resolve spatiotemporal patterns of connectivity within striped marlin ( Kajikia audax), a broadly distributed and highly migratory pelagic species. Evol Appl 2020; 13:677-698. [PMID: 32211060 PMCID: PMC7086058 DOI: 10.1111/eva.12892] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Revised: 09/23/2019] [Accepted: 10/16/2019] [Indexed: 01/04/2023] Open
Abstract
Genomic methodologies offer unprecedented opportunities for statistically robust studies of species broadly distributed in environments conducive to high gene flow, providing valuable information for wildlife conservation and management. Here, we sequence restriction site-associated DNA to characterize genome-wide single nucleotide polymorphisms (SNPs) in a broadly distributed and highly migratory large pelagic fish, striped marlin (Kajikia audax). Assessment of over 4,000 SNPs resolved spatiotemporal patterns of genetic connectivity throughout the species range in the Pacific and, for the first time, Indian oceans. Individual-based cluster analyses identified six genetically distinct populations corresponding with the western Indian, eastern Indian, western South Pacific, and eastern central Pacific oceans, as well as two populations in the North Pacific Ocean (F ST = 0.0137-0.0819). F ST outlier analyses identified a subset of SNPs (n = 59) putatively under the influence of natural selection and capable of resolving populations separated by comparatively high degrees of genetic differentiation. Temporal collections available for some regions demonstrated the stability of allele frequencies over three to five generations of striped marlin. Relative migration rates reflected lower levels of genetic connectivity between Indian Ocean populations (m R ≤ 0.37) compared with most populations in the Pacific Ocean (m R ≥ 0.57) and highlight the importance of the western South Pacific in facilitating gene flow between ocean basins. Collectively, our results provide novel insights into rangewide population structure for striped marlin and highlight substantial inconsistencies between genetically distinct populations and stocks currently recognized for fisheries management. More broadly, we demonstrate that species capable of long-distance dispersal in environments lacking obvious physical barriers to movement can display substantial population subdivision that persists over multiple generations and that may be facilitated by both neutral and adaptive processes. Importantly, surveys of genome-wide markers enable inference of population-level relationships using sample sizes practical for large pelagic fishes of conservation concern.
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Affiliation(s)
- Nadya R. Mamoozadeh
- Department of Fisheries ScienceVirginia Institute of Marine ScienceWilliam & MaryGloucester PointVirginia
| | - John E. Graves
- Department of Fisheries ScienceVirginia Institute of Marine ScienceWilliam & MaryGloucester PointVirginia
| | - Jan R. McDowell
- Department of Fisheries ScienceVirginia Institute of Marine ScienceWilliam & MaryGloucester PointVirginia
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Ony MA, Nowicki M, Boggess SL, Klingeman WE, Zobel JM, Trigiano RN, Hadziabdic D. Habitat fragmentation influences genetic diversity and differentiation: Fine-scale population structure of Cercis canadensis (eastern redbud). Ecol Evol 2020; 10:3655-3670. [PMID: 32313625 PMCID: PMC7160182 DOI: 10.1002/ece3.6141] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Revised: 01/31/2020] [Accepted: 02/05/2020] [Indexed: 02/05/2023] Open
Abstract
Forest fragmentation may negatively affect plants through reduced genetic diversity and increased population structure due to habitat isolation, decreased population size, and disturbance of pollen-seed dispersal mechanisms. However, in the case of tree species, effective pollen-seed dispersal, mating system, and ecological dynamics may help the species overcome the negative effect of forest fragmentation. A fine-scale population genetics study can shed light on the postfragmentation genetic diversity and structure of a species. Here, we present the genetic diversity and population structure of Cercis canadensis L. (eastern redbud) wild populations on a fine scale within fragmented areas centered around the borders of Georgia-Tennessee, USA. We hypothesized high genetic diversity among the collections of C. canadensis distributed across smaller geographical ranges. Fifteen microsatellite loci were used to genotype 172 individuals from 18 unmanaged and naturally occurring collection sites. Our results indicated presence of population structure, overall high genetic diversity (H E = 0.63, H O = 0.34), and moderate genetic differentiation (F ST = 0.14) among the collection sites. Two major genetic clusters within the smaller geographical distribution were revealed by STRUCTURE. Our data suggest that native C. canadensis populations in the fragmented area around the Georgia-Tennessee border were able to maintain high levels of genetic diversity, despite the presence of considerable spatial genetic structure. As habitat isolation may negatively affect gene flow of outcrossing species across time, consequences of habitat fragmentation should be regularly monitored for this and other forest species. This study also has important implications for habitat management efforts and future breeding programs.
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Affiliation(s)
- Meher A. Ony
- Department of Entomology and Plant PathologyUniversity of TennesseeKnoxvilleTNUSA
| | - Marcin Nowicki
- Department of Entomology and Plant PathologyUniversity of TennesseeKnoxvilleTNUSA
| | - Sarah L. Boggess
- Department of Entomology and Plant PathologyUniversity of TennesseeKnoxvilleTNUSA
| | | | - John M. Zobel
- Department of Forest ResourcesUniversity of MinnesotaSt. PaulMNUSA
| | - Robert N. Trigiano
- Department of Entomology and Plant PathologyUniversity of TennesseeKnoxvilleTNUSA
| | - Denita Hadziabdic
- Department of Entomology and Plant PathologyUniversity of TennesseeKnoxvilleTNUSA
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