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Hull KL, Greenwood MP, Lloyd M, Brink-Hull M, Bester-van der Merwe AE, Rhode C. Drivers of genomic diversity and phenotypic development in early phases of domestication in Hermetia illucens. INSECT MOLECULAR BIOLOGY 2024. [PMID: 38963286 DOI: 10.1111/imb.12940] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2023] [Accepted: 06/17/2024] [Indexed: 07/05/2024]
Abstract
The black soldier fly (BSF), Hermetia illucens, has the ability to efficiently bioremediate organic waste into usable bio-compounds. Understanding the impact of domestication and mass rearing on fitness and production traits is therefore important for sustainable production. This study aimed to assess patterns of genomic diversity and its association to phenotypic development across early generations of mass rearing under two selection strategies: selection for greater larval mass (SEL lines) and no direct artificial selection (NS lines). Genome-wide single nucleotide polymorphism (SNP) data were generated using 2bRAD sequencing, while phenotypic traits relating to production and population fitness were measured. Declining patterns of genomic diversity were observed across three generations of captive breeding, with the lowest diversity recorded for the F3 generation of both selection lines, most likely due to founder effects. The SEL cohort displayed statistically significantly greater larval weight com the NS lines with pronounced genetic and phenotypic directional changes across generations. Furthermore, lower genetic and phenotypic diversity, particularly for fitness traits, were evident for SEL lines, illustrating the trade-off between selecting for mass and the resulting decline in population fitness. SNP-based heritability was significant for growth, but was low or non-significant for fitness traits. Genotype-phenotype correlations were observed for traits, but individual locus effect sizes where small and very few of these loci demonstrated a signature for selection. Pronounced genetic drift, due to small effective population sizes, is likely overshadowing the impacts of selection on genomic diversity and consequently phenotypic development. The results hold particular relevance for genetic management and selective breeding for BSF in future.
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Affiliation(s)
- Kelvin L Hull
- Department of Genetics, Stellenbosch University, Stellenbosch, South Africa
| | | | - Melissa Lloyd
- Research and Development Department, Insect Technology Group Holdings UK Ltd., Guildford, UK
| | - Marissa Brink-Hull
- Department of Genetics, Stellenbosch University, Stellenbosch, South Africa
| | | | - Clint Rhode
- Department of Genetics, Stellenbosch University, Stellenbosch, South Africa
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2
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Tyagi A, Yadav N, Pandit A, Ramakrishnan U. On the road to losing connectivity: Faecal samples provide genome-wide insights into anthropogenic impacts on two large herbivore species in central India. Mol Ecol 2024:e17461. [PMID: 38958291 DOI: 10.1111/mec.17461] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Revised: 06/12/2024] [Accepted: 06/24/2024] [Indexed: 07/04/2024]
Abstract
Humans have impacted most of the planet, and the ensuing fragmentation results in small, isolated habitat patches posing a risk of genetic diversity loss, inbreeding, and genetic load. Understanding how natural and anthropogenic landscape features affect gene flow among habitat patches is critical for maintaining connectivity. Genome-wide data are required to comprehend the impacts of recent fragmentation, which can be challenging when only non-invasive samples are available. Here, we build upon advancements in conservation genomics to address connectivity of two large herbivores, gaur (Bos gaurus) and sambar (Rusa unicolor) in central India. Given their habitat associations, we expected these species to respond similarly to habitat fragmentation. We used faecal-DNA and methylation-based host-DNA enrichment with modified ddRAD protocol to generate genome-wide single-nucleotide polymorphism (SNP) data for 124 gaur and 99 sambar individuals. Our findings reveal that gaur populations in central India are fragmented, displaying high genetic differentiation, with drift significantly affecting small populations like Umred Karhandla Wildlife Sanctuary. Although sambar shows low genetic structure, another small population, Bor Tiger Reserve is genetically differentiated. Our results suggest that although land cover change and roads restrict animal movement, the extent of this impact varies across the two species. We show that different species respond differently to landscape features, even with similar habitat associations. We highlight small and isolated populations requiring urgent conservation intervention. Such multi-species approaches enhance our understanding of cross-species connectivity patterns. We suggest shifting from single-species to multi-species holistic conservation approach in rapidly developing landscapes to better manage co-occurring endangered species.
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Affiliation(s)
- Abhinav Tyagi
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore, India
- SASTRA Deemed to be University, Thanjavur, India
| | - Nidhi Yadav
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore, India
| | - Awadhesh Pandit
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore, India
| | - Uma Ramakrishnan
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore, India
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3
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Muharromah AF, Carvajal TM, Regilme MAF, Watanabe K. Fine-scale adaptive divergence and population genetic structure of Aedes aegypti in Metropolitan Manila, Philippines. Parasit Vectors 2024; 17:233. [PMID: 38769579 PMCID: PMC11107013 DOI: 10.1186/s13071-024-06300-x] [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: 02/06/2024] [Accepted: 04/23/2024] [Indexed: 05/22/2024] Open
Abstract
BACKGROUND The adaptive divergence of Aedes aegypti populations to heterogeneous environments can be a driving force behind the recent expansion of their habitat distribution and outbreaks of dengue disease in urbanized areas. In this study, we investigated the population genomics of Ae. aegypti at a regional scale in Metropolitan Manila, Philippines. METHODS We used the Pool-Seq double digestion restriction-site association DNA sequencing (ddRAD-Seq) approach to generate a high number of single nucleotide polymorphisms (SNPs), with the aim to determine local adaptation and compare the population structure with 11 microsatellite markers. A total of 217 Ae. aegypti individuals from seven female and seven male populations collected from Metropolitan Manila were used in the assays. RESULTS We detected 65,473 SNPs across the populations, of which 76 were non-neutral SNPs. Of these non-neutral SNPs, the multivariate regression test associated 50 with eight landscape variables (e.g. open space, forest, etc.) and 29 with five climate variables (e.g. air temperature, humidity, etc.) (P-value range 0.005-0.045) in female and male populations separately. Male and female populations exhibited contrasting spatial divergence, with males exhibiting greater divergence than females, most likely reflecting the different dispersal abilities of male and female mosquitoes. In the comparative analysis of the same Ae. aegypti individuals, the pairwise FST values of 11 microsatellite markers were lower than those of the neutral SNPs, indicating that the neutral SNPs generated via pool ddRAD-Seq were more sensitive in terms of detecting genetic differences between populations at fine-spatial scales. CONCLUSIONS Overall, our study demonstrates the utility of pool ddRAD-Seq for examining genetic differences in Ae. aegypti populations in areas at fine-spatial scales that could inform vector control programs such as Wolbachia-infected mosquito mass-release programs. This in turn would provide information on mosquito population dispersal patterns and the potential barriers to mosquito movement within and around the release area. In addition, the potential of environmental adaptability observed in Ae. aegypti could help population control efforts.
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Affiliation(s)
- Atikah Fitria Muharromah
- Center for Marine Environmental Studies (CMES), Ehime University, Bunkyo-cho 3, Matsuyama, Ehime, 7908577, Japan
- Graduate School of Science and Engineering, Ehime University, Bunkyo-cho 3, Matsuyama, Ehime, 7908577, Japan
- Department of Tropical Biology, Faculty of Biology, Universitas Gadjah Mada, Yogyakarta, 55281, Indonesia
| | - Thaddeus M Carvajal
- Center for Marine Environmental Studies (CMES), Ehime University, Bunkyo-cho 3, Matsuyama, Ehime, 7908577, Japan
- Biological Control Research Unit, Center for Natural Sciences and Environmental Research, De La Salle University, 2401 Taft Avenue, 1004, Manila, Philippines
| | - Maria Angenica F Regilme
- Center for Marine Environmental Studies (CMES), Ehime University, Bunkyo-cho 3, Matsuyama, Ehime, 7908577, Japan
| | - Kozo Watanabe
- Center for Marine Environmental Studies (CMES), Ehime University, Bunkyo-cho 3, Matsuyama, Ehime, 7908577, Japan.
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4
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Pearce DL, Edson JE, Jennelle CS, Walter WD. Evaluation of DNA yield from various tissue and sampling sources for use in single nucleotide polymorphism panels. Sci Rep 2024; 14:11340. [PMID: 38760358 PMCID: PMC11101418 DOI: 10.1038/s41598-024-56128-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Accepted: 03/01/2024] [Indexed: 05/19/2024] Open
Abstract
Genetics studies are used by wildlife managers and researchers to gain inference into a population of a species of interest. To gain these insights, microsatellites have been the primary method; however, there currently is a shift from microsatellites to single nucleotide polymorphisms (SNPs). With the different DNA requirements between microsatellites and SNPs, an investigation into which samples can provide adequate DNA yield is warranted. Using samples that were collected from previous genetic projects from regions in the USA from 2014 to 2021, we investigated the DNA yield of eight sample categories to gain insights into which provided adequate DNA to be used in ddRADseq or already developed high- or medium-density SNP panels. We found seven sample categories that met the DNA requirements for use in all three panels, and one sample category that did not meet any of the three panels requirements; however, DNA integrity was highly variable and not all sample categories that met panel DNA requirements could be considered high quality DNA. Additionally, we used linear random-effects models to determine which covariates would have the greatest influence on DNA yield. We determined that all covariates (tissue type, storage method, preservative, DNA quality, time until DNA extraction and time after DNA extraction) could influence DNA yield.
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Affiliation(s)
- David L Pearce
- Pennsylvania Cooperative Fish and Wildlife Research Unit, The Pennsylvania State University, 413 Forest Resources Building, University Park, PA, 16802, USA
- Department of Rangeland, Wildlife and Fisheries Management, Texas A&M University, College Station, TX, 77843, USA
| | - Jessie E Edson
- Pennsylvania Cooperative Fish and Wildlife Research Unit, The Pennsylvania State University, 413 Forest Resources Building, University Park, PA, 16802, USA
| | - Chris S Jennelle
- Minnesota Department of Natural Resources, 5463 West Broadway Ave., Forest Lake, MN, 55025, USA
- Minnesota Department of Natural Resources, Division of Ecological and Water Resources, Nongame Wildlife Program, St Paul, MN, 55155, USA
| | - W David Walter
- U.S. Geological Survey, Pennsylvania Cooperative Fish and Wildlife Research Unit, The Pennsylvania State University, 403 Forest Resources Building, University Park, PA, 16802, USA.
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Pedrazzini C, Rehner SA, Strasser H, Zemp N, Holderegger R, Widmer F, Enkerli J. Clonal genomic population structure of Beauveria brongniartii and Beauveria pseudobassiana: Pathogens of the common European cockchafer (Melolontha melolontha L.). Environ Microbiol 2024; 26:e16612. [PMID: 38622804 DOI: 10.1111/1462-2920.16612] [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: 11/11/2023] [Accepted: 03/07/2024] [Indexed: 04/17/2024]
Abstract
Beauveria brongniartii is a fungal pathogen that infects the beetle Melolontha melolontha, a significant agricultural pest in Europe. While research has primarily focused on the use of B. brongniartii for controlling M. melolontha, the genomic structure of the B. brongniartii population remains unknown. This includes whether its structure is influenced by its interaction with M. melolontha, the timing of beetle-swarming flights, geographical factors, or reproductive mode. To address this, we analysed genome-wide SNPs to infer the population genomics of Beauveria spp., which were isolated from infected M. melolontha adults in an Alpine region. Surprisingly, only one-third of the isolates were identified as B. brongniartii, while two-thirds were distributed among cryptic taxa within B. pseudobassiana, a fungal species not previously recognized as a pathogen of M. melolontha. Given the prevalence of B. pseudobassiana, we conducted analyses on both species. We found no spatial or temporal genomic patterns within either species and no correlation with the population structure of M. melolontha, suggesting that the dispersal of the fungi is independent of the beetle. Both species exhibited clonal population structures, with B. brongniartii fixed for one mating type and B. pseudobassiana displaying both mating types. This implies that factors other than mating compatibility limit sexual reproduction. We conclude that the population genomic structure of Beauveria spp. is primarily influenced by predominant asexual reproduction and dispersal.
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Affiliation(s)
- Chiara Pedrazzini
- Molecular Ecology, Agroscope, Zürich, Switzerland
- Institute of Environmental Systems Science, ETH, Zürich, Switzerland
| | - Stephen A Rehner
- Mycology and Nematology Genetic Diversity and Biology Laboratory, United States Department of Agriculture USDA, Beltsville, Maryland, USA
| | - Hermann Strasser
- Institute of Microbiology, Leopold-Franzens University Innsbruck, Innsbruck, Austria
| | - Niklaus Zemp
- Genetic Diversity Centre (GDC), ETH, Zürich, Switzerland
| | - Rolf Holderegger
- Institute of Environmental Systems Science, ETH, Zürich, Switzerland
- Swiss Federal Research Institute WSL, Birmensdorf, Switzerland
| | | | - Jürg Enkerli
- Molecular Ecology, Agroscope, Zürich, Switzerland
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6
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Olah G, Waples RS, Stojanovic D. Influence of molecular marker type on estimating effective population size and other genetic parameters in a critically endangered parrot. Ecol Evol 2024; 14:e11102. [PMID: 38524913 PMCID: PMC10961163 DOI: 10.1002/ece3.11102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Revised: 02/15/2024] [Accepted: 02/20/2024] [Indexed: 03/26/2024] Open
Abstract
Genetics is a fast-moving field, and for conservation practitioners or ecologists, it can be bewildering. The choice of marker used in studies is fundamental; in the literature, preference has recently shifted from microsatellites to single nucleotide polymorphism (SNP) loci. Understanding how marker type affects estimates of population genetic parameters is important in the context of conservation, especially because the accuracy of estimates has a bearing on the actions taken to protect threatened species. We compare parameter estimates between seven microsatellites, 3761 SNP loci, and a random subset of 100 SNPs for the exact same 324 individual swift parrots, Lathamus discolor, and also use 457 additional samples from subsequent years to compare SNP estimates. Both marker types estimated a lower H O than H E. We show that microsatellites and SNPs mainly indicate a lack of spatial genetic structure, except when a priori collection locations were used on the SNP data in a discriminant analysis of principal components (DAPC). The 100-SNP subset gave comparable results to when the full dataset was used. Estimates of effective population size (N e) were comparable between markers when the same individuals were considered, but SNPs had narrower confidence intervals. This is reassuring because conservation assessments that rely on population genetic estimates based on a few microsatellites are unlikely to be nullified by the general shift toward SNPs in the literature. However, estimates between markers and datasets varied considerably when only adult samples were considered; hence, including samples of all age groups is recommended to be used when available. The estimated N e was higher for the full SNP dataset (2010-2019) than the smaller comparison data (2010-2015), which might be a better reflection of the species status. The lower precision of microsatellites may not necessarily be a barrier for most conservation applications; however, SNPs will improve confidence limits, which may be useful for practitioners.
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Affiliation(s)
- George Olah
- Fenner School of Environment and SocietyAustralian National UniversityCanberraAustralian Capital TerritoryAustralia
- King's Forensics, Department of Analytical, Environmental and Forensic Sciences, Faculty of Life Sciences and MedicineKing's College LondonLondonUK
| | - Robin S. Waples
- School of Aquatic and Fishery SciencesUniversity of WashingtonSeattleWashingtonUSA
| | - Dejan Stojanovic
- Fenner School of Environment and SocietyAustralian National UniversityCanberraAustralian Capital TerritoryAustralia
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7
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Koontz AC, Schumacher EK, Spence ES, Hoban SM. Ex situ conservation of two rare oak species using microsatellite and SNP markers. Evol Appl 2024; 17:e13650. [PMID: 38524684 PMCID: PMC10960078 DOI: 10.1111/eva.13650] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Revised: 12/27/2023] [Accepted: 01/14/2024] [Indexed: 03/26/2024] Open
Abstract
Plant collections held by botanic gardens and arboreta are key components of ex situ conservation. Maintaining genetic diversity in such collections allows them to be used as resources for supplementing wild populations. However, most recommended minimum sample sizes for sufficient ex situ genetic diversity are based on microsatellite markers, and it remains unknown whether these sample sizes remain valid in light of more recently developed next-generation sequencing (NGS) approaches. To address this knowledge gap, we examine how ex situ conservation status and sampling recommendations differ when derived from microsatellites and single nucleotide polymorphisms (SNPs) in garden and wild samples of two threatened oak species. For Quercus acerifolia, SNPs show lower ex situ representation of wild allelic diversity and slightly lower minimum sample size estimates than microsatellites, while results for each marker are largely similar for Q. boyntonii. The application of missing data filters tends to lead to higher ex situ representation, while the impact of different SNP calling approaches is dependent on the species being analyzed. Measures of population differentiation within species are broadly similar between markers, but larger numbers of SNP loci allow for greater resolution of population structure and clearer assignment of ex situ individuals to wild source populations. Our results offer guidance for future ex situ conservation assessments utilizing SNP data, such as the application of missing data filters and the usage of a reference genome, and illustrate that both microsatellites and SNPs remain viable options for botanic gardens and arboreta seeking to ensure the genetic diversity of their collections.
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Affiliation(s)
| | | | - Emma S. Spence
- Morton ArboretumCenter for Tree ScienceLisleIllinoisUSA
- Cornell UniversityDepartment of Public and Ecosystem HealthIthacaNew YorkUSA
| | - Sean M. Hoban
- Morton ArboretumCenter for Tree ScienceLisleIllinoisUSA
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8
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Longo A, Kurta K, Vanhala T, Jeuthe H, de Koning DJ, Palaiokostas C. Genetic diversity patterns in farmed rainbow trout (Oncorhynchus mykiss) populations using genome-wide SNP and haplotype data. Anim Genet 2024; 55:87-98. [PMID: 37994156 DOI: 10.1111/age.13378] [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: 02/10/2023] [Revised: 10/25/2023] [Accepted: 11/01/2023] [Indexed: 11/24/2023]
Abstract
Rainbow trout is one of the most popular aquaculture species worldwide, with a long history of domestication. However, limited information exists about the genetic diversity of farmed rainbow trout populations globally, with most available reports relying on low-throughput genotyping technologies. Notably, no information exists about the genetic diversity status of farmed rainbow trout in Sweden. Double-digest restriction-site-associated DNA sequencing was performed on more than 500 broodfish from two leading producers in Sweden and from the country's national breeding program. Following the detection of single nucleotide polymorphisms (SNPs), genetic diversity was studied by using either individual SNPs (n = 8680; one SNP retained per 300 bp sequence reads) or through SNP haplotypes (n = 20 558; all SNPs retained in 300 bp sequence reads). Similar amounts of genetic diversity were found amongst the three populations when individual SNPs were used. Furthermore, principal component analysis and discriminant analysis of principal components suggested two genetic clusters with the two industry populations grouped together. Genetic differentiation based on the FST fixation index was ~0.01 between the industry populations and ~0.05 when those were compared with the breeding program. Preliminary estimates of effective population size (Ne ) and inbreeding (based on runs of homozygosity; FROH ) were similar amongst the three populations (Ne ≈ 50-80; median FROH ≈ 0.11). Finally, the haplotype-based analysis suggested that animals from the breeding program had higher shared coancestry levels than those from the other two populations. Overall, our study provides novel insights into the genetic diversity and structure of Sweden's three main farmed rainbow trout populations, which could guide their future management.
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Affiliation(s)
- Alessio Longo
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Khrystyna Kurta
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Tytti Vanhala
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Henrik Jeuthe
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden
- Aquaculture Center North, Kälarne, Sweden
| | - Dirk-Jan de Koning
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Christos Palaiokostas
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden
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9
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Talavera A, Palmada-Flores M, Burriel-Carranza B, Valbuena-Ureña E, Mochales-Riaño G, Adams DC, Tejero-Cicuéndez H, Soler-Membrives A, Amat F, Guinart D, Carbonell F, Obon E, Marquès-Bonet T, Carranza S. Genomic insights into the Montseny brook newt ( Calotriton arnoldi), a Critically Endangered glacial relict. iScience 2024; 27:108665. [PMID: 38226169 PMCID: PMC10788218 DOI: 10.1016/j.isci.2023.108665] [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: 08/14/2023] [Revised: 10/09/2023] [Accepted: 12/05/2023] [Indexed: 01/17/2024] Open
Abstract
The Montseny brook newt (Calotriton arnoldi), considered the most endangered amphibian in Europe, is a relict salamandrid species endemic to a small massif located in northeastern Spain. Although conservation efforts should always be guided by genomic studies, those are yet scarce among urodeles, hampered by the extreme sizes of their genomes. Here, we present the third available genome assembly for the order Caudata, and the first genomic study of the species and its sister taxon, the Pyrenean brook newt (Calotriton asper), combining whole-genome and ddRADseq data. Our results reveal significant demographic oscillations which accurately mirrored Europe's climatic history. Although severe bottlenecks have led to depauperate genomic diversity and long runs of homozygosity along a gigantic genome, inbreeding might have been avoided by assortative mating strategies. Other life history traits, however, seem to have been less advantageous, and the lack of land dispersal has driven to exceptional levels of population fragmentation.
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Affiliation(s)
- Adrián Talavera
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Barcelona, Spain
| | - Marc Palmada-Flores
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Barcelona, Spain
| | - Bernat Burriel-Carranza
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Barcelona, Spain
- Museu de Ciències Naturals de Barcelona, Pº Picasso s/n, Parc Ciutadella, 08003 Barcelona, Spain
| | | | | | - Dean C. Adams
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA 50010, USA
| | - Héctor Tejero-Cicuéndez
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Barcelona, Spain
- Department of Biodiversity, Ecology and Evolution, Faculty of Biology, Universidad Complutense de Madrid, 28040 Madrid, Spain
| | - Anna Soler-Membrives
- Departament de Biologia Animal, de Biologia Vegetal i d'Ecologia, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Fèlix Amat
- Àrea d’Herpetologia, BiBIO, Museu de Granollers – Ciències Naturals. Palaudàries 102, Granollers, Barcelona, Spain
| | - Daniel Guinart
- Servei de Gestió de Parcs Naturals, Diputació de Barcelona, Spain
| | - Francesc Carbonell
- Centre de fauna salvatge de Torreferrussa (Forestal Catalana, SA), Santa Perpètua de Mogoda, Spain
| | - Elena Obon
- Centre de fauna salvatge de Torreferrussa (Forestal Catalana, SA), Santa Perpètua de Mogoda, Spain
| | - Tomàs Marquès-Bonet
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Barcelona, Spain
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Barcelona, Spain
- Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain
- Catalan Institution of Research and Advanced Studies (ICREA), Barcelona, Spain
| | - Salvador Carranza
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Barcelona, Spain
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10
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Beninde J, Wittische J, Frantz AC. Quantifying uncertainty in inferences of landscape genetic resistance due to choice of individual-based genetic distance metric. Mol Ecol Resour 2024; 24:e13831. [PMID: 37475166 DOI: 10.1111/1755-0998.13831] [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: 03/15/2021] [Revised: 05/12/2023] [Accepted: 06/22/2023] [Indexed: 07/22/2023]
Abstract
Estimates of gene flow resulting from landscape resistance inferences frequently inform conservation management decision-making processes. Therefore, results must be robust across approaches and reflect real-world gene flow instead of methodological artefacts. Here, we tested the impact of 32 individual-based genetic distance metrics on the robustness and accuracy of landscape resistance modelling results. We analysed three empirical microsatellite datasets and 36 simulated datasets that varied in landscape resistance and genetic spatial autocorrelation. We used ResistanceGA to generate optimised multi-feature resistance surfaces for each of these datasets using 32 different genetic distance metrics. Results of the empirical dataset demonstrated that the choice of genetic distance metric can have strong impacts on inferred optimised resistance surfaces. Simulations showed accurate parametrisation of resistance surfaces across most genetic distance metrics only when a small number of environmental features was impacting gene flow. Landscape scenarios with many features impacting gene flow led to a generally poor recovery of true resistance surfaces. Simulation results also emphasise that choosing a genetic distance metric should not be based on marginal R2 -based model fit. Until more robust methods are available, resistance surfaces can be optimised with different genetic distance metrics and the convergence of results needs to be assessed via pairwise matrix correlations. Based on the results presented here, high correlation coefficients across different genetic distance categories likely indicate accurate inference of true landscape resistance. Most importantly, empirical results should be interpreted with great caution, especially when they appear counter-intuitive in light of the ecology of a species.
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Affiliation(s)
- Joscha Beninde
- LA Kretz Center for California Conservation Science, Institute of the Environment and Sustainability, University of California, Los Angeles, California, USA
- IUCN WCPA Connectivity Conservation Specialist Group, Gland, Switzerland
- Amsterdam Institute for Life and Environment (A-LIFE), Section Ecology and Evolution, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Julian Wittische
- Musée National d'Histoire Naturelle, Luxembourg City, Luxembourg
- The Fondation Faune-Flore, Luxembourg City, Luxembourg
| | - Alain C Frantz
- Musée National d'Histoire Naturelle, Luxembourg City, Luxembourg
- The Fondation Faune-Flore, Luxembourg City, Luxembourg
- The University of Sheffield, Sheffield, UK
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11
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Borja Lozano MV, Vigil Santillán B, More Montoya MJ, Morón Barraza JA, García-Serquén AL, Gutiérrez Reynoso G, Yalta-Macedo CE. Genotyping-by-sequencing reveals a high number and quality of single nucleotide polymorphisms in guinea pigs (Cavia porcellus) from the Peruvian Andes. Anim Genet 2023; 54:792-797. [PMID: 37796666 DOI: 10.1111/age.13367] [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: 07/06/2023] [Revised: 07/06/2023] [Accepted: 09/25/2023] [Indexed: 10/07/2023]
Abstract
Guinea pigs are a major source of animal protein for Peruvian Andean families. Despite the economic and cultural relevance of guinea pigs, their genomic characterization has been scarcely addressed. Genotyping-by-sequencing (GBS) has emerged as an affordable alternative to genotyping of livestock and native animals. Here, we report the use of GBS for single nucleotide polymorphism (SNP) discovery of traditionally raised guinea pigs from six regions of the Peruvian Andes and one group of breeding animals. The paired-end (2 × 150 bp) sequencing of 40 guinea pig DNA samples generated a mean of 6.4 million high-quality sequencing reads per sample. We obtained an average sequencing depth of 10× with an 88.5% mapping rate to the Cavia porcellus reference genome. A total of 279 965 SNPs (102 SNPs/Mbp) were identified after variant calling and quality filtering. Based on this SNP set, we assessed the genetic diversity and distance within our selected guinea pig populations. An overall average minor allele frequency of 0.13, an observed heterozygosity of 0.31, an expected heterozygosity of 0.35, and an F-value of 0.1 were obtained, while the SNP-based neighbor-joining tree suggests a closer genetic relationship between individuals from geographically close locations. We showed that GBS is a cost-effective tool for SNP discovery and genetic characterization of Peruvian guinea pig populations. Therefore, it may be considered as a suitable and affordable tool for genomic characterization of poorly studied native animal species.
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Affiliation(s)
- María Victoria Borja Lozano
- Laboratorio de Biología Molecular y Genómica, Dirección de Recursos Genéticos y Biotecnología, Instituto Nacional de Innovación Agraria, Lima, Peru
- Facultad de Zootecnia, Universidad Nacional Agraria La Molina, Lima, Peru
| | - Bianca Vigil Santillán
- Laboratorio de Biología Molecular y Genómica, Dirección de Recursos Genéticos y Biotecnología, Instituto Nacional de Innovación Agraria, Lima, Peru
| | - Manuel J More Montoya
- Facultad de Ciencias Agrarias, Universidad Nacional de San Antonio Abad del Cusco, Cusco, Peru
| | | | - Aura Liz García-Serquén
- Laboratorio de Biología Molecular y Genómica, Dirección de Recursos Genéticos y Biotecnología, Instituto Nacional de Innovación Agraria, Lima, Peru
| | | | - Claudia E Yalta-Macedo
- Laboratorio de Biología Molecular y Genómica, Dirección de Recursos Genéticos y Biotecnología, Instituto Nacional de Innovación Agraria, Lima, Peru
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12
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Coleman JL, Wyffels JT, Penfold LM, Richardson D, Maddox JD. Development of genetic markers for reproductive management of toucans. Zoo Biol 2023; 42:825-833. [PMID: 37338091 DOI: 10.1002/zoo.21792] [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: 05/07/2022] [Revised: 04/26/2023] [Accepted: 06/08/2023] [Indexed: 06/21/2023]
Abstract
Retention of genetic diversity in successive generations is key to successful ex situ programs and will become increasingly important to restore wild populations of threatened animals. When animal genealogy is partly unknown or gaps exist in studbook records, the application of molecular resources facilitates informed breeding. Here, we apply molecular resources to an ex situ breeding population of toucans (Ramphastidae), a bird family zoos commonly maintain. Toucans face population declines from illegal poaching and habitat degradation. We developed novel microsatellite markers using blood samples from 15 Keel-billed Toucans (Ramphastos sulfuratus Lesson 1830). Parentage of two individuals was known a priori, but possible sibship among 13 putative founders-including the parents-was unknown. We compared available avian heterologous and novel microsatellite markers to recover known relationships and reconstruct sibship. Eight of 61 heterologous markers amplified consistently and were polymorphic, but less so than the 18 novel markers. Known sibship (and three sibling pairs whose relatedness was unknown a priori) and paternity-though not maternity except in one case-were well-recovered using both likelihood and pairwise relatedness methods, when incorporating novel but not heterologous markers. Zoo researchers seeking microsatellite primer sets for their breeding toucan populations will likely benefit from our heterologous markers, which can be leveraged both to assess relatedness and select breeding pairs. We recommend that zoo biologists rely on species-specific primers and not optimize heterologous primers for toucan species without molecular resources. We conclude with a brief discussion of modern genotyping methods of interest to zoo researchers.
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Affiliation(s)
- Jeffrey L Coleman
- Negaunee Integrative Research Center, Field Museum of Natural History, Chicago, Illinois, USA
- Department of Integrative Biology, University of Texas at Austin, Austin, Texas, USA
| | - Jennifer T Wyffels
- Center for Bioinformatics & Computational Biology, University of Delaware, Newark, Delaware, USA
- Ripley's Aquariums, Orlando, Florida, USA
| | - Linda M Penfold
- South-East Zoo Alliance for Reproduction & Conservation, Yulee, Florida, USA
| | | | - J Dylan Maddox
- Negaunee Integrative Research Center, Field Museum of Natural History, Chicago, Illinois, USA
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13
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Afonso RO, Pina-Martins F, Friesen V, Sun Z, Campioni L, Madeiros J, Silva MC. No evidence of inbreeding depression despite a historical severe bottleneck in the endangered Bermuda petrel (Pterodroma cahow). J Hered 2023; 114:459-469. [PMID: 37162284 DOI: 10.1093/jhered/esad030] [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: 10/28/2022] [Accepted: 05/08/2023] [Indexed: 05/11/2023] Open
Abstract
The Bermuda petrel Pterodroma cahow is an island endemic seabird that belongs to the Procellariiformes, one of the most endangered orders of birds. Historical records suggest a significant population size decline following human settlement in Bermuda, bringing the species to near extinction. Since the 1950s, the population has been recovering aided by the implementation of an ongoing conservation plan. However, it still faces several threats, and negative genetic effects resulting from that drastic decline are to be expected, including inbreeding and genetic drift. We studied genetic diversity and levels of inbreeding, and their effects on individual fitness and mating choice. We also tested for a genetic signature of the recent demographic bottleneck. For this, we analyzed variation in thousands of nuclear single-nucleotide polymorphisms derived from double digest restriction site-associated DNA sequencing and 1 mitochondrial gene (cytochrome oxidase I). The results revealed that the Bermuda petrel suffered a recent genetic bottleneck and shows low mitochondrial diversity compared with other petrel species. Conversely, nuclear diversity was similar to that of other endangered petrels. Inbreeding levels were not high overall, although some individuals were highly inbred. However, we found no evidence that individual inbreeding or relatedness between mates affected hatching success, or that mate choice is influenced by kinship in this very small population.
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Affiliation(s)
- Rita O Afonso
- cE3c-Centre for Ecology, Evolution and Environmental Changes & CHANGE-Global Change and Sustainability Institute, Departamento de Biologia Animal, Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal
| | - Francisco Pina-Martins
- cE3c-Centre for Ecology, Evolution and Environmental Changes & CHANGE-Global Change and Sustainability Institute, Departamento de Biologia Animal, Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal
| | - Vicki Friesen
- Department of Biology, Queen's University, Kingston, ON, Canada
| | - Zhengxin Sun
- Department of Biology, Queen's University, Kingston, ON, Canada
| | - Letizia Campioni
- MARE-Marine and Environmental Sciences Centre, Ispa-Instituto Universitário, Lisboa, Portugal
| | - Jeremy Madeiros
- Department of Environment and Natural Resources, Government of Bermuda, Hamilton, Bermuda
| | - Mónica C Silva
- cE3c-Centre for Ecology, Evolution and Environmental Changes & CHANGE-Global Change and Sustainability Institute, Departamento de Biologia Animal, Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal
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14
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Thorstensen MJ, Weinrauch AM, Bugg WS, Jeffries KM, Anderson WG. Tissue-specific transcriptomes reveal potential mechanisms of microbiome heterogeneity in an ancient fish. Database (Oxford) 2023; 2023:baad055. [PMID: 37590163 PMCID: PMC10434735 DOI: 10.1093/database/baad055] [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: 10/13/2022] [Revised: 06/16/2023] [Accepted: 07/23/2023] [Indexed: 08/19/2023]
Abstract
The lake sturgeon (Acipenser fulvescens) is an ancient, octoploid fish faced with conservation challenges across its range in North America, but a lack of genomic resources has hindered molecular research in the species. To support such research, we created a transcriptomic database from 13 tissues: brain, esophagus, gill, head kidney, heart, white muscle, liver, glandular stomach, muscular stomach, anterior intestine, pyloric cecum, spiral valve and rectum. The transcriptomes for each tissue were sequenced and assembled individually from a mean of 98.3 million (±38.9 million SD) reads each. In addition, an overall transcriptome was assembled and annotated with all data used for each tissue-specific transcriptome. All assembled transcriptomes and their annotations were made publicly available as a scientific resource. The non-gut transcriptomes provide important resources for many research avenues. However, we focused our analysis on messenger ribonucleic acid (mRNA) observations in the gut because the gut represents a compartmentalized organ system with compartmentalized functions, and seven of the sequenced tissues were from each of these portions. These gut-specific analyses were used to probe evidence of microbiome regulation by studying heterogeneity in microbial genes and genera identified from mRNA annotations. Gene set enrichment analyses were used to reveal the presence of photoperiod and circadian-related transcripts in the pyloric cecum, which may support periodicity in lake sturgeon digestion. Similar analyses were used to identify different types of innate immune regulation across the gut, while analyses of unique transcripts annotated to microbes revealed heterogeneous genera and genes among different gut tissues. The present results provide a scientific resource and information about the mechanisms of compartmentalized function across gut tissues in a phylogenetically ancient vertebrate. Database URL: https://figshare.com/projects/Lake_Sturgeon_Transcriptomes/133143.
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Affiliation(s)
- Matt J Thorstensen
- Department of Biological Sciences, University of Manitoba, 212B Biological Sciences Building, 50 Sifton Road, Winnipeg, MB R3T 2N2, Canada
| | - Alyssa M Weinrauch
- Department of Biological Sciences, University of Manitoba, 212B Biological Sciences Building, 50 Sifton Road, Winnipeg, MB R3T 2N2, Canada
| | - William S Bugg
- Department of Biological Sciences, University of Manitoba, 212B Biological Sciences Building, 50 Sifton Road, Winnipeg, MB R3T 2N2, Canada
| | - Ken M Jeffries
- Department of Biological Sciences, University of Manitoba, 212B Biological Sciences Building, 50 Sifton Road, Winnipeg, MB R3T 2N2, Canada
| | - W Gary Anderson
- Department of Biological Sciences, University of Manitoba, 212B Biological Sciences Building, 50 Sifton Road, Winnipeg, MB R3T 2N2, Canada
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15
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Bonnin N, Piel AK, Brown RP, Li Y, Connell JA, Avitto AN, Boubli JP, Chitayat A, Giles J, Gundlapally MS, Lipende I, Lonsdorf EV, Mjungu D, Mwacha D, Pintea L, Pusey AE, Raphael J, Wich SA, Wilson ML, Wroblewski EE, Hahn BH, Stewart FA. Barriers to chimpanzee gene flow at the south-east edge of their distribution. Mol Ecol 2023; 32:3842-3858. [PMID: 37277946 PMCID: PMC10421595 DOI: 10.1111/mec.16986] [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: 09/12/2022] [Revised: 04/28/2023] [Accepted: 05/02/2023] [Indexed: 06/07/2023]
Abstract
Populations on the edge of a species' distribution may represent an important source of adaptive diversity, yet these populations tend to be more fragmented and are more likely to be geographically isolated. Lack of genetic exchanges between such populations, due to barriers to animal movement, can not only compromise adaptive potential but also lead to the fixation of deleterious alleles. The south-eastern edge of chimpanzee distribution is particularly fragmented, and conflicting hypotheses have been proposed about population connectivity and viability. To address this uncertainty, we generated both mitochondrial and MiSeq-based microsatellite genotypes for 290 individuals ranging across western Tanzania. While shared mitochondrial haplotypes confirmed historical gene flow, our microsatellite analyses revealed two distinct clusters, suggesting two populations currently isolated from one another. However, we found evidence of high levels of gene flow maintained within each of these clusters, one of which covers an 18,000 km2 ecosystem. Landscape genetic analyses confirmed the presence of barriers to gene flow with rivers and bare habitats highly restricting chimpanzee movement. Our study demonstrates how advances in sequencing technologies, combined with the development of landscape genetics approaches, can resolve ambiguities in the genetic history of critical populations and better inform conservation efforts of endangered species.
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Affiliation(s)
- Noémie Bonnin
- School of Biological and Environmental Sciences, Liverpool John Moores University, UK
| | - Alex K. Piel
- Department of Anthropology, University College London, London, UK
| | - Richard P. Brown
- School of Biological and Environmental Sciences, Liverpool John Moores University, UK
| | - Yingying Li
- Departments of Medicine and Microbiology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Jesse A. Connell
- Departments of Medicine and Microbiology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Alexa N. Avitto
- Departments of Medicine and Microbiology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Jean P. Boubli
- School of Science, Engineering & Environment, University of Salford, Salford, UK
| | - Adrienne Chitayat
- Institute of Biodiversity and Ecological Dynamics, University of Amsterdam, The Netherlands
| | - Jasmin Giles
- Departments of Medicine and Microbiology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Madhurima S. Gundlapally
- Departments of Medicine and Microbiology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Iddi Lipende
- Tanzania Wildlife Research Institute (TAWIRI), Arusha, Tanzania
| | - Elizabeth V. Lonsdorf
- Department of Psychology, Franklin and Marshall College, Lancaster, PA 17604, USA
- Department of Anthropology, Emory University, Atlanta, GA 30322, USA
| | - Deus Mjungu
- Gombe Stream Research Centre, The Jane Goodall Institute–Tanzania, P.O. Box 1182, Kigoma, Tanzania
| | - Dismas Mwacha
- Gombe Stream Research Centre, The Jane Goodall Institute–Tanzania, P.O. Box 1182, Kigoma, Tanzania
| | - Lilian Pintea
- Conservation Science Department, the Jane Goodall Institute, Washington, DC, 20036, USA
| | - Anne E. Pusey
- Department of Evolutionary Anthropology, Duke University, Durham, NC, USA
| | | | - Serge A. Wich
- School of Biological and Environmental Sciences, Liverpool John Moores University, UK
- Institute of Biodiversity and Ecological Dynamics, University of Amsterdam, The Netherlands
| | - Michael L. Wilson
- Department of Anthropology, University of Minnesota, Minneapolis, MN 55455, USA
- Department of Ecology, Evolution, and Behavior, University of Minnesota, St. Paul, MN 55108, USA
- Institute on the Environment, University of Minnesota, St. Paul, MN 55108, USA
| | | | - Beatrice H. Hahn
- Departments of Medicine and Microbiology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Fiona A. Stewart
- School of Biological and Environmental Sciences, Liverpool John Moores University, UK
- Department of Anthropology, University College London, London, UK
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16
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Ruperao P, Bajaj P, Subramani R, Yadav R, Reddy Lachagari VB, Lekkala SP, Rathore A, Archak S, Angadi UB, Singh R, Singh K, Mayes S, Rangan P. A pilot-scale comparison between single and double-digest RAD markers generated using GBS strategy in sesame (Sesamum indicum L.). PLoS One 2023; 18:e0286599. [PMID: 37267340 DOI: 10.1371/journal.pone.0286599] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Accepted: 05/19/2023] [Indexed: 06/04/2023] Open
Abstract
To reduce the genome sequence representation, restriction site-associated DNA sequencing (RAD-seq) protocols is being widely used either with single-digest or double-digest methods. In this study, we genotyped the sesame population (48 sample size) in a pilot scale to compare single and double-digest RAD-seq (sd and ddRAD-seq) methods. We analysed the resulting short-read data generated from both protocols and assessed their performance impacting the downstream analysis using various parameters. The distinct k-mer count and gene presence absence variation (PAV) showed a significant difference between the sesame samples studied. Additionally, the variant calling from both datasets (sdRAD-seq and ddRAD-seq) exhibits a significant difference between them. The combined variants from both datasets helped in identifying the most diverse samples and possible sub-groups in the sesame population. The most diverse samples identified from each analysis (k-mer, gene PAV, SNP count, Heterozygosity, NJ and PCA) can possibly be representative samples holding major diversity of the small sesame population used in this study. The best possible strategies with suggested inputs for modifications to utilize the RAD-seq strategy efficiently on a large dataset containing thousands of samples to be subjected to molecular analysis like diversity, population structure and core development studies were discussed.
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Affiliation(s)
- Pradeep Ruperao
- Center of Excellence in Genomics and Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Prasad Bajaj
- Center of Excellence in Genomics and Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Rajkumar Subramani
- ICAR-National Bureau of Plant Genetic Resources, PUSA Campus, New Delhi, India
| | - Rashmi Yadav
- ICAR-National Bureau of Plant Genetic Resources, PUSA Campus, New Delhi, India
| | | | | | | | - Sunil Archak
- ICAR-National Bureau of Plant Genetic Resources, PUSA Campus, New Delhi, India
| | - Ulavappa B Angadi
- ICAR-Indian Agricultural Statistical Research Institute, New Delhi, India
| | - Rakesh Singh
- ICAR-National Bureau of Plant Genetic Resources, PUSA Campus, New Delhi, India
| | - Kuldeep Singh
- Genebank, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Sean Mayes
- Center of Excellence in Genomics and Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Parimalan Rangan
- ICAR-National Bureau of Plant Genetic Resources, PUSA Campus, New Delhi, India
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, Australia
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17
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Li C, Xiao H, Zhang X, Lin H, Elmer KR, Zhao J. Deep genome-wide divergences among species in White Cloud Mountain minnow Tanichthys albonubes (Cypriniformes: Tanichthyidae) complex: Conservation and species management implications. Mol Phylogenet Evol 2023; 182:107734. [PMID: 36804428 DOI: 10.1016/j.ympev.2023.107734] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Revised: 02/09/2023] [Accepted: 02/13/2023] [Indexed: 02/17/2023]
Abstract
Identifying cryptic species is important for the assessments of biodiversity. Further, untangling mechanisms underlying the origins of cryptic species can facilitate our understanding of evolutionary processes. Advancements in genomic approaches for non-model systems have offered unprecedented opportunities to investigate these areas. The White Cloud Mountain minnow (Tanichthys albonubes) is a popular freshwater pet fish worldwide but its wild populations in China are critically endangered. Recent research based on a few molecular markers suggested that this species in fact comprised seven cryptic species, of which six were previously unknown. Here, we tested six of these cryptic species and quantified genomic interspecific divergences between species in the T. albonubes complex by analyzing genome-wide restriction site-associated DNA sequencing (RADseq) data generated from 189 individuals sampled from seven populations (including an outgroup congeneric species, T. micagemmae). We found that six cryptic species previously suggested were well supported by RADseq data. The genetic diversity of each species in the T. albonubes complex was low compared with T. micagemmae and the contemporary effective population sizes (Ne) of each cryptic species were small. Phylogenetic analysis showed seven clades with high support values confirmed with Neighbor-Net trees. The pairwise divergences between species in T. albonubes complex were deep and the highly differentiated loci were evenly distributed across the genome. We proposed that the divergence level of T. albonubes complex is at a late stage of cryptic speciation and lacking gene flow. Our findings provide new insights into cryptic speciation and have important implications for conservation and species management of T. albonubes complex.
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Affiliation(s)
- Chao Li
- Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, Guangdong Provincial Key Laboratory for Healthy and Safe Aquaculture, Guangdong Provincial Engineering Technology Research Center for Environmentally Friendly Aquaculture, School of Life Sciences, South China Normal University, Guangzhou, China; Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | - Han Xiao
- Institute of Life and Environmental Sciences, University of Iceland, Reykjavík, Iceland
| | - Xiuxia Zhang
- Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, Guangdong Provincial Key Laboratory for Healthy and Safe Aquaculture, Guangdong Provincial Engineering Technology Research Center for Environmentally Friendly Aquaculture, School of Life Sciences, South China Normal University, Guangzhou, China
| | - Hungdu Lin
- The Affiliated School of National Tainan First Senior High School, Tainan, Taiwan
| | - Kathryn R Elmer
- Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | - Jun Zhao
- Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, Guangdong Provincial Key Laboratory for Healthy and Safe Aquaculture, Guangdong Provincial Engineering Technology Research Center for Environmentally Friendly Aquaculture, School of Life Sciences, South China Normal University, Guangzhou, China.
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18
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Zimmerman SJ, Aldridge CL, O'Donnell MS, Edmunds DR, Coates PS, Prochazka BG, Fike JA, Cross TB, Fedy BC, Oyler-McCance SJ. A genetic warning system for a hierarchically structured wildlife monitoring framework. ECOLOGICAL APPLICATIONS : A PUBLICATION OF THE ECOLOGICAL SOCIETY OF AMERICA 2023; 33:e2787. [PMID: 36482030 DOI: 10.1002/eap.2787] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2022] [Revised: 10/10/2022] [Accepted: 10/20/2022] [Indexed: 06/17/2023]
Abstract
Genetic variation is a well-known indicator of population fitness yet is not typically included in monitoring programs for sensitive species. Additionally, most programs monitor populations at one scale, which can lead to potential mismatches with ecological processes critical to species' conservation. Recently developed methods generating hierarchically nested population units (i.e., clusters of varying scales) for greater sage-grouse (Centrocercus urophasianus) have identified population trend declines across spatiotemporal scales to help managers target areas for conservation. The same clusters used as a proxy for spatial scale can alert managers to local units (i.e., neighborhood-scale) with low genetic diversity, further facilitating identification of management targets. We developed a genetic warning system utilizing previously developed hierarchical population units to identify management-relevant areas with low genetic diversity within the greater sage-grouse range. Within this warning system we characterized conservation concern thresholds based on values of genetic diversity and developed a statistical model for microsatellite data to robustly estimate these values for hierarchically nested populations. We found that 41 of 224 neighborhood-scale clusters had low genetic diversity, 23 of which were coupled with documented local population trend decline. We also found evidence of cross-scale low genetic diversity in the small and isolated Washington population, unlikely to be reversed through typical local management actions alone. The combination of low genetic diversity and a declining population suggests relatively high conservation concern. Our findings could further facilitate conservation action prioritization in combination with population trend assessments and (or) local information, and act as a base-line of genetic diversity for future comparison. Importantly, the approach we used is broadly applicable across taxa.
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Affiliation(s)
- Shawna J Zimmerman
- U.S. Geological Survey, Fort Collins Science Center, Fort Collins, Colorado, USA
| | - Cameron L Aldridge
- U.S. Geological Survey, Fort Collins Science Center, Fort Collins, Colorado, USA
| | - Michael S O'Donnell
- U.S. Geological Survey, Fort Collins Science Center, Fort Collins, Colorado, USA
| | - David R Edmunds
- U.S. Geological Survey, Fort Collins Science Center, Fort Collins, Colorado, USA
| | - Peter S Coates
- U.S. Geological Survey, Western Ecological Research Center, Dixon Field Station, Dixon, California, USA
| | - Brian G Prochazka
- U.S. Geological Survey, Western Ecological Research Center, Dixon Field Station, Dixon, California, USA
| | - Jennifer A Fike
- U.S. Geological Survey, Fort Collins Science Center, Fort Collins, Colorado, USA
| | - Todd B Cross
- School of Environment, Resources and Sustainability, University of Waterloo, Waterloo, Ontario, Canada
| | - Bradley C Fedy
- School of Environment, Resources and Sustainability, University of Waterloo, Waterloo, Ontario, Canada
| | - Sara J Oyler-McCance
- U.S. Geological Survey, Fort Collins Science Center, Fort Collins, Colorado, USA
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19
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Maas DL, Prost S, de Leeuw CA, Bi K, Smith LL, Purwanto P, Aji LP, Tapilatu RF, Gillespie RG, Becking LE. Sponge diversification in marine lakes: Implications for phylogeography and population genomic studies on sponges. Ecol Evol 2023; 13:e9945. [PMID: 37066063 PMCID: PMC10099488 DOI: 10.1002/ece3.9945] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Revised: 03/06/2023] [Accepted: 03/08/2023] [Indexed: 04/18/2023] Open
Abstract
The relative influence of geography, currents, and environment on gene flow within sessile marine species remains an open question. Detecting subtle genetic differentiation at small scales is challenging in benthic populations due to large effective population sizes, general lack of resolution in genetic markers, and because barriers to dispersal often remain elusive. Marine lakes can circumvent confounding factors by providing discrete and replicated ecosystems. Using high-resolution double digest restriction-site-associated DNA sequencing (4826 Single Nucleotide Polymorphisms, SNPs), we genotyped populations of the sponge Suberites diversicolor (n = 125) to test the relative importance of spatial scales (1-1400 km), local environmental conditions, and permeability of seascape barriers in shaping population genomic structure. With the SNP dataset, we show strong intralineage population structure, even at scales <10 km (average F ST = 0.63), which was not detected previously using single markers. Most variation was explained by differentiation between populations (AMOVA: 48.8%) with signatures of population size declines and bottlenecks per lake. Although the populations were strongly structured, we did not detect significant effects of geographic distance, local environments, or degree of connection to the sea on population structure, suggesting mechanisms such as founder events with subsequent priority effects may be at play. We show that the inclusion of morphologically cryptic lineages that can be detected with the COI marker can reduce the obtained SNP set by around 90%. Future work on sponge genomics should confirm that only one lineage is included. Our results call for a reassessment of poorly dispersing benthic organisms that were previously assumed to be highly connected based on low-resolution markers.
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Affiliation(s)
- Diede L. Maas
- Marine Animal EcologyWageningen University & ResearchWageningenThe Netherlands
| | - Stefan Prost
- LOEWE Centre for Translational Biodiversity GenomicsSenckenberg Natural History MuseumFrankfurt am MainGermany
- South African National Biodiversity InstituteNational Zoological Gardens of South AfricaPretoriaSouth Africa
| | | | - Ke Bi
- Museum of Vertebrate ZoologyUniversity of California BerkeleyBerkeleyCaliforniaUSA
- Computational Genomics Resource Laboratory, California Institute for Quantitative BiosciencesUniversity of California BerkeleyBerkeleyCaliforniaUSA
| | - Lydia L. Smith
- Museum of Vertebrate ZoologyUniversity of California BerkeleyBerkeleyCaliforniaUSA
| | | | - Ludi P. Aji
- Marine Animal EcologyWageningen University & ResearchWageningenThe Netherlands
- Research Centre for Oceanography, Indonesian Institute of SciencesLembaga Ilmu Pengetahuan IndonesiaJakartaIndonesia
| | - Ricardo F. Tapilatu
- Marine Science and Fisheries Departments and Research Center of Pacific Marine ResourcesState University of PapuaManokwariIndonesia
| | - Rosemary G. Gillespie
- Department of Environmental Science, Policy and ManagementUniversity of California BerkeleyBerkeleyCaliforniaUSA
| | - Leontine E. Becking
- Department of Environmental Science, Policy and ManagementUniversity of California BerkeleyBerkeleyCaliforniaUSA
- Aquaculture and Fisheries, Naturalis Biodiversity CenterWageningen University & ResearchWageningenThe Netherlands
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20
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Müller MF, Banks SC, Crewe TL, Campbell HA. The rise of animal biotelemetry and genetics research data integration. Ecol Evol 2023; 13:e9885. [PMID: 36937069 PMCID: PMC10019913 DOI: 10.1002/ece3.9885] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 02/17/2023] [Accepted: 02/20/2023] [Indexed: 03/18/2023] Open
Abstract
The advancement and availability of innovative animal biotelemetry and genomic technologies are improving our understanding of how the movements of individuals influence gene flow within and between populations and ultimately drive evolutionary and ecological processes. There is a growing body of work that is integrating what were once disparate fields of biology, and here, we reviewed the published literature up until January 2023 (139 papers) to better understand the drivers of this research and how it is improving our knowledge of animal biology. The review showed that the predominant drivers for this research were as follows: (1) understanding how individual-based movements affect animal populations, (2) analyzing the relationship between genetic relatedness and social structuring, and (3) studying how the landscape affects the flow of genes, and how this is impacted by environmental change. However, there was a divergence between taxa as to the most prevalent research aim and the methodologies applied. We also found that after 2010 there was an increase in studies that integrated the two data types using innovative statistical techniques instead of analyzing the data independently using traditional statistics from the respective fields. This new approach greatly improved our understanding of the link between the individual, the population, and the environment and is being used to better conserve and manage species. We discuss the challenges and limitations, as well as the potential for growth and diversification of this research approach. The paper provides a guide for researchers who wish to consider applying these disparate disciplines and advance the field.
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Affiliation(s)
- Mara F. Müller
- Research Institute for the Environment and LivelihoodsFaculty of Science and Technology, Charles Darwin UniversityNorthern TerritoryDarwinAustralia
| | - Sam C. Banks
- Research Institute for the Environment and LivelihoodsFaculty of Science and Technology, Charles Darwin UniversityNorthern TerritoryDarwinAustralia
| | - Tara L. Crewe
- Department of Natural Resources and RenewablesGovernment of Nova ScotiaKentvilleNova ScotiaCanada
| | - Hamish A. Campbell
- Research Institute for the Environment and LivelihoodsFaculty of Science and Technology, Charles Darwin UniversityNorthern TerritoryDarwinAustralia
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21
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Dufresnes C, Dutoit L, Brelsford A, Goldstein-Witsenburg F, Clément L, López-Baucells A, Palmeirim J, Pavlinić I, Scaravelli D, Ševčík M, Christe P, Goudet J. Inferring genetic structure when there is little: population genetics versus genomics of the threatened bat Miniopterus schreibersii across Europe. Sci Rep 2023; 13:1523. [PMID: 36707640 PMCID: PMC9883447 DOI: 10.1038/s41598-023-27988-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2022] [Accepted: 01/11/2023] [Indexed: 01/28/2023] Open
Abstract
Despite their paramount importance in molecular ecology and conservation, genetic diversity and structure remain challenging to quantify with traditional genotyping methods. Next-generation sequencing holds great promises, but this has not been properly tested in highly mobile species. In this article, we compared microsatellite and RAD-sequencing (RAD-seq) analyses to investigate population structure in the declining bent-winged bat (Miniopterus schreibersii) across Europe. Both markers retrieved general patterns of weak range-wide differentiation, little sex-biased dispersal, and strong isolation by distance that associated with significant genetic structure between the three Mediterranean Peninsulas, which could have acted as glacial refugia. Microsatellites proved uninformative in individual-based analyses, but the resolution offered by genomic SNPs illuminated on regional substructures within several countries, with colonies sharing migrators of distinct ancestry without admixture. This finding is consistent with a marked philopatry and spatial partitioning between mating and rearing grounds in the species, which was suspected from marked-recaptured data. Our study advocates that genomic data are necessary to properly unveil the genetic footprints left by biogeographic processes and social organization in long-distant flyers, which are otherwise rapidly blurred by their high levels of gene flow.
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Affiliation(s)
- Christophe Dufresnes
- Laboratory for Amphibian Systematic and Evolutionary Research, College of Biology and the Environment, Nanjing Forestry University, Nanjing, People's Republic of China.
| | - Ludovic Dutoit
- Department of Ecology and Evolution, University of Lausanne, 1015, Lausanne, Switzerland.,Department of Zoology, University of Otago, Dunedin, New Zealand
| | - Alan Brelsford
- Department of Evolution, Ecology, and Organismal Biology, University of California Riverside, Riverside, CA, USA
| | | | - Laura Clément
- Department of Ecology and Evolution, University of Lausanne, 1015, Lausanne, Switzerland
| | - Adria López-Baucells
- Bat Research Area, Granollers Museum of Natural Sciences, Carrer Palaudaries 102, 08402, Granollers, Spain
| | - Jorge Palmeirim
- Department of Animal Biology, Centre for Ecology, Evolution and Environmental Change - cE3c, University of Lisbon, 1749-016, Lisbon, Portugal
| | - Igor Pavlinić
- Department of Zoology, Croatian Natural History Museum, Demetrova 1, 10000, Zagreb, Croatia
| | - Dino Scaravelli
- Department of Biological, Geological, and Environmental Sciences, University of Bologna, Via Selmi 3, 40126, Bologna, Italy
| | - Martin Ševčík
- Department of Zoology, Faculty of Science, Charles University in Prague, Viničná 7, 128 44, Prague 2, Czech Republic
| | - Philippe Christe
- Department of Ecology and Evolution, University of Lausanne, 1015, Lausanne, Switzerland.
| | - Jérôme Goudet
- Department of Ecology and Evolution, University of Lausanne, 1015, Lausanne, Switzerland.
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22
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Holmes IA, Grundler MC. Phylogenetically under-dispersed gut microbiomes are not correlated with host genomic heterozygosity in a genetically diverse reptile community. Mol Ecol 2023; 32:258-274. [PMID: 36221927 PMCID: PMC9797449 DOI: 10.1111/mec.16733] [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: 07/20/2021] [Revised: 09/09/2022] [Accepted: 09/15/2022] [Indexed: 12/31/2022]
Abstract
While key elements of fitness in vertebrate animals are impacted by their microbiomes, the host genetic characteristics that factor into microbiome composition are not fully understood. Here, we correlate host genomic heterozygosity and gut microbiome phylogenetic diversity across a community of reptiles in southwestern New Mexico to test hypotheses about the behaviour of host genes that drive microbiome assembly. We find that microbiome communities are phylogenetically under-dispersed relative to random expectations, and that host heterozygosity is not correlated with microbiome diversity. Our analyses reinforce results from functional genomic work that identify conserved host immune and nonimmune genes as key players in microbiome assembly, rather than gene families that rely on heterozygosity for their function.
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Affiliation(s)
- Iris A. Holmes
- Museum of Zoology and Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109 USA
- Cornell Institute of Host Microbe Interactions and Disease and Department of Microbiology, Cornell University, Ithaca, NY 14853 USA
| | - Michael C. Grundler
- Museum of Zoology and Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109 USA
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA 90095 USA
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23
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Osborne MJ, Caeiro-Dias G, Turner TF. Transitioning from microsatellites to SNP-based microhaplotypes in genetic monitoring programmes: Lessons from paired data spanning 20 years. Mol Ecol 2023; 32:316-334. [PMID: 36321869 DOI: 10.1111/mec.16760] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Revised: 10/14/2022] [Accepted: 10/17/2022] [Indexed: 11/18/2022]
Abstract
Many long-term genetic monitoring programmes began before next-generation sequencing became widely available. Older programmes can now transition to new marker systems usually consisting of 1000s of SNP loci, but there are still important questions about comparability, precision, and accuracy of key metrics estimated using SNPs. Ideally, transitioned programmes should capitalize on new information without sacrificing continuity of inference across the time series. We combined existing microsatellite-based genetic monitoring information with SNP-based microhaplotypes obtained from archived samples of Rio Grande silvery minnow (Hybognathus amarus) across a 20-year time series to evaluate point estimates and trajectories of key genetic metrics. Demographic and genetic monitoring bracketed multiple collapses of the wild population and included cases where captive-born repatriates comprised the majority of spawners in the wild. Even with smaller sample sizes, microhaplotypes yielded comparable and in some cases more precise estimates of variance genetic effective population size, multilocus heterozygosity and inbreeding compared to microsatellites because many more microhaplotype loci were available. Microhaplotypes also recorded shifts in allele frequencies associated with population bottlenecks. Trends in microhaplotype-based inbreeding metrics were associated with the fraction of hatchery-reared repatriates to the wild and should be incorporated into future genomic monitoring. Although differences in accuracy and precision of some metrics were observed between marker types, biological inferences and management recommendations were consistent.
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Affiliation(s)
- Megan J Osborne
- Department of Biology and Museum of Southwestern Biology, University of New Mexico, Albuquerque, New Mexico, USA
| | - Guilherme Caeiro-Dias
- Department of Biology and Museum of Southwestern Biology, University of New Mexico, Albuquerque, New Mexico, USA
| | - Thomas F Turner
- Department of Biology and Museum of Southwestern Biology, University of New Mexico, Albuquerque, New Mexico, USA
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24
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Snead AA, Alda F. Time-Series Sequences for Evolutionary Inferences. Integr Comp Biol 2022; 62:1771-1783. [PMID: 36104153 DOI: 10.1093/icb/icac146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 07/28/2022] [Accepted: 07/29/2022] [Indexed: 01/05/2023] Open
Affiliation(s)
- Anthony A Snead
- Department of Biological Sciences, University of Alabama, 300 Hackberry Lane, Tuscaloosa, AL 35487, USA
| | - Fernando Alda
- Department of Biology, Geology and Environmental Science, University of Tennessee at Chattanooga, 615 McCallie Ave, Chattanooga, TN 37403, USA
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25
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Mijangos JL, Bino G, Hawke T, Kolomyjec SH, Kingsford RT, Sidhu H, Grant T, Day J, Dias KN, Gongora J, Sherwin WB. Fragmentation by major dams and implications for the future viability of platypus populations. Commun Biol 2022; 5:1127. [PMID: 36329312 PMCID: PMC9633709 DOI: 10.1038/s42003-022-04038-9] [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: 03/16/2022] [Accepted: 09/27/2022] [Indexed: 11/06/2022] Open
Abstract
The evolutionarily unique platypus (Ornithorhynchus anatinus) has experienced major declines and extinctions from a range of historical and recent interacting human-mediated threats. Although spending most of their time in the water, platypuses can move over land. Nevertheless, uncertainties remain whether dams are barriers to movement, thus limiting gene flow and dispersal, essential to evolution and ecology. Here we examined disruption of gene flow between platypus groups below and above five major dams, matched to four adjacent rivers without major dams. Genetic differentiation (FST) across dams was 4- to 20-fold higher than along similar stretches of adjacent undammed rivers; FST across dams was similar to differentiation between adjacent river systems. This indicates that major dams represent major barriers for platypus movements. Furthermore, FST between groups was correlated with the year in which the dam was built, increasing by 0.011 every generation, reflecting the effects of these barriers on platypus genetics. This study provides evidence of gene flow restriction, which jeopardises the long-term viability of platypus populations when groups are fragmented by major dams. Mitigation strategies, such as building of by-pass structures and translocation between upstream and downstream of the dam, should be considered in conservation and management planning.
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Affiliation(s)
- Jose L. Mijangos
- grid.1005.40000 0004 4902 0432School of Science, UNSW, Canberra, Australia ,grid.1039.b0000 0004 0385 7472Centre for Conservation Ecology and Genomics, Institute for Applied Ecology, University of Canberra, Canberra, Australia
| | - Gilad Bino
- grid.1005.40000 0004 4902 0432Centre for Ecosystem Science, School of Biological, Earth and Environmental Sciences, UNSW, Sydney, Australia
| | - Tahneal Hawke
- grid.1005.40000 0004 4902 0432Centre for Ecosystem Science, School of Biological, Earth and Environmental Sciences, UNSW, Sydney, Australia
| | - Stephen H. Kolomyjec
- grid.258898.60000 0004 0462 9201College of Science and the Environment, Lake Superior State University, Sault Sainte Marie, USA
| | - Richard T. Kingsford
- grid.1005.40000 0004 4902 0432Centre for Ecosystem Science, School of Biological, Earth and Environmental Sciences, UNSW, Sydney, Australia
| | - Harvinder Sidhu
- grid.1005.40000 0004 4902 0432School of Science, UNSW, Canberra, Australia
| | - Tom Grant
- grid.1005.40000 0004 4902 0432Centre for Ecosystem Science, School of Biological, Earth and Environmental Sciences, UNSW, Sydney, Australia
| | - Jenna Day
- grid.1013.30000 0004 1936 834XSydney School of Veterinary Science, Faculty of Science, The University of Sydney, Sydney, Australia
| | - Kimberly N. Dias
- grid.1013.30000 0004 1936 834XSydney School of Veterinary Science, Faculty of Science, The University of Sydney, Sydney, Australia
| | - Jaime Gongora
- grid.1013.30000 0004 1936 834XSydney School of Veterinary Science, Faculty of Science, The University of Sydney, Sydney, Australia
| | - William B. Sherwin
- grid.1005.40000 0004 4902 0432Evolution & Ecology Research Centre, UNSW, Sydney, Australia
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26
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Perea S, Mendes SL, Sousa-Santos C, Ondina P, Amaro R, Castro J, San-Miguel E, Lima CS, Garcia M, Velasquez V, Garcia-Roves P, Fernández D, Araujo R, Sousa VC, Reis J. Applying genomic approaches to delineate conservation strategies using the freshwater mussel Margaritifera margaritifera in the Iberian Peninsula as a model. Sci Rep 2022; 12:16894. [PMID: 36207367 PMCID: PMC9546909 DOI: 10.1038/s41598-022-20947-5] [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: 06/14/2022] [Accepted: 09/21/2022] [Indexed: 11/09/2022] Open
Abstract
Effective conservation actions to counteract the current decline of populations and species require a deep knowledge on their genetic structure. We used Single Nucleotide Polymorphisms (SNPs) to infer the population structure of the highly threatened freshwater pearl mussel Margaritifera margaritifera in the Iberian Peninsula. A total of 130 individuals were collected from 26 locations belonging to 16 basins. We obtained 31,692 SNPs through Genotyping by Sequencing (GBS) and used this dataset to infer population structure. Genetic diversity given as observed heterozygosity was low. Pairwise FST comparisons revealed low levels of genetic differentiation among geographically close populations. Up to 3 major genetic lineages were determined: Atlantic, Cantabrian and Douro. This structure suggests a close co-evolutionary process with brown trout (Salmo trutta), the primordial fish host of this mussel in the studied area. Some sub-basins showed some genetic structuring, whereas in others no intrapopulation differentiation was found. Our results confirm that genetic conservation units do not match individual basins, and that knowledge about the genetic structure is necessary before planning recovery plans that may involve relocation or restocking. The same reasoning should be applied to strictly freshwater species that are sessile or have restricted dispersal abilities and are currently imperiled worldwide.
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Affiliation(s)
- S Perea
- MARE-Marine and Environmental Sciences Centre/ARNET-Aquatic Research Network, Faculdade de Ciências da Universidade de Lisboa, Campo Grande, 1749-016, Lisbon, Portugal.,Instituto de Biología, Departamento de Zoología, Universidad Nacional Autónoma de México, Tercer Circuito Exterior S/N, C.P. 04510, Mexico City, Mexico
| | - S L Mendes
- MARE-Marine and Environmental Sciences Centre/ARNET-Aquatic Research Network, Faculdade de Ciências da Universidade de Lisboa, Campo Grande, 1749-016, Lisbon, Portugal.,cE3c-Centre for Ecology, Evolution and Environmental Changes, Department of Animal Biology, Faculdade de Ciências da Universidade de Lisboa, Campo Grande, 1749-016, Lisbon, Portugal
| | - C Sousa-Santos
- MARE-Marine and Environmental Sciences Centre/ARNET-Aquatic Research Network, ISPA-Instituto Superior de Ciências Psicológicas, Sociais e da Vida, Rua Jardim do Tabaco, 34, 1149-041, Lisbon, Portugal
| | - P Ondina
- Departamento de Zooloxía, Xenética e Antropoloxía Física, Universidade de Santiago de Compostela, Campus Terra, 27002, Lugo, Spain.,IBADER-Instituto de Biodiversidade Agraria E Desenvolvemento Rural, Campus, Universidade de Santiago de Compostela, Campus Terra, 27002, Lugo, Spain
| | - R Amaro
- Departamento de Zooloxía, Xenética e Antropoloxía Física, Universidade de Santiago de Compostela, Campus Terra, 27002, Lugo, Spain.,IBADER-Instituto de Biodiversidade Agraria E Desenvolvemento Rural, Campus, Universidade de Santiago de Compostela, Campus Terra, 27002, Lugo, Spain
| | - J Castro
- Departamento de Zooloxía, Xenética e Antropoloxía Física, Universidade de Santiago de Compostela, Campus Terra, 27002, Lugo, Spain.,IBADER-Instituto de Biodiversidade Agraria E Desenvolvemento Rural, Campus, Universidade de Santiago de Compostela, Campus Terra, 27002, Lugo, Spain
| | - E San-Miguel
- Departamento de Zooloxía, Xenética e Antropoloxía Física, Universidade de Santiago de Compostela, Campus Terra, 27002, Lugo, Spain.,IBADER-Instituto de Biodiversidade Agraria E Desenvolvemento Rural, Campus, Universidade de Santiago de Compostela, Campus Terra, 27002, Lugo, Spain
| | - C S Lima
- MARE-Marine and Environmental Sciences Centre/ARNET-Aquatic Research Network, ISPA-Instituto Superior de Ciências Psicológicas, Sociais e da Vida, Rua Jardim do Tabaco, 34, 1149-041, Lisbon, Portugal
| | - M Garcia
- MARE-Marine and Environmental Sciences Centre/ARNET-Aquatic Research Network, Faculdade de Ciências da Universidade de Lisboa, Campo Grande, 1749-016, Lisbon, Portugal
| | - V Velasquez
- Dirección General del Medio Natural y Desarrollo Rural, Oviedo, Principado de Asturias, Spain
| | - P Garcia-Roves
- Dirección General del Medio Natural y Desarrollo Rural, Oviedo, Principado de Asturias, Spain
| | - D Fernández
- Biosfera-Consultoría Medioambiental, C/Candamo no. 5,, C.P. 33012, Oviedo, Asturias, Spain
| | - R Araujo
- Museo Nacional de Ciencias Naturales - CSIC, C/José Gutierrez Abascal, 2, 28006, Madrid, Spain
| | - V C Sousa
- cE3c-Centre for Ecology, Evolution and Environmental Changes, Department of Animal Biology, Faculdade de Ciências da Universidade de Lisboa, Campo Grande, 1749-016, Lisbon, Portugal
| | - J Reis
- MARE-Marine and Environmental Sciences Centre/ARNET-Aquatic Research Network, Faculdade de Ciências da Universidade de Lisboa, Campo Grande, 1749-016, Lisbon, Portugal.
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27
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Gutiérrez‐Pesquera LM, Tejedo M, Camacho A, Enriquez‐Urzelai U, Katzenberger M, Choda M, Pintanel P, Nicieza AG. Phenology and plasticity can prevent adaptive clines in thermal tolerance across temperate mountains: The importance of the elevation-time axis. Ecol Evol 2022; 12:e9349. [PMID: 36225839 PMCID: PMC9534760 DOI: 10.1002/ece3.9349] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Revised: 09/05/2022] [Accepted: 09/07/2022] [Indexed: 11/10/2022] Open
Abstract
Critical thermal limits (CTmax and CTmin) decrease with elevation, with greater change in CTmin, and the risk to suffer heat and cold stress increasing at the gradient ends. A central prediction is that populations will adapt to the prevailing climatic conditions. Yet, reliable support for such expectation is scant because of the complexity of integrating phenotypic, molecular divergence and organism exposure. We examined intraspecific variation of CTmax and CTmin, neutral variation for 11 microsatellite loci, and micro- and macro-temperatures in larvae from 11 populations of the Galician common frog (Rana parvipalmata) across an elevational gradient, to assess (1) the existence of local adaptation through a PST-FST comparison, (2) the acclimation scope in both thermal limits, and (3) the vulnerability to suffer acute heat and cold thermal stress, measured at both macro- and microclimatic scales. Our study revealed significant microgeographic variation in CTmax and CTmin, and unexpected elevation gradients in pond temperatures. However, variation in CTmax and CTmin could not be attributed to selection because critical thermal limits were not correlated to elevation or temperatures. Differences in breeding phenology among populations resulted in exposure to higher and more variable temperatures at mid and high elevations. Accordingly, mid- and high-elevation populations had higher CTmax and CTmin plasticities than lowland populations, but not more extreme CTmax and CTmin. Thus, our results support the prediction that plasticity and phenological shifts may hinder local adaptation, promoting thermal niche conservatism. This may simply be a consequence of a coupled variation of reproductive timing with elevation (the "elevation-time axis" for temperature variation). Mid and high mountain populations of R. parvipalmata are more vulnerable to heat and cool impacts than lowland populations during the aquatic phase. All of this contradicts some of the existing predictions on adaptive thermal clines and vulnerability to climate change in elevational gradients.
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Affiliation(s)
| | - Miguel Tejedo
- Department of Evolutionary EcologyEstación Biológica de Doñana, CSICSevillaSpain
| | - Agustín Camacho
- Department of Evolutionary EcologyEstación Biológica de Doñana, CSICSevillaSpain
| | | | - Marco Katzenberger
- Department of Evolutionary EcologyEstación Biológica de Doñana, CSICSevillaSpain,Laboratory of Bioinformatics and Evolutionary Biology, Department of GeneticsUniversidade Federal de PernambucoRecifePrince Edward IslandBrazil
| | - Magdalena Choda
- Department of Organisms and Systems BiologyUniversity of OviedoOviedoSpain
| | - Pol Pintanel
- Department of Evolutionary EcologyEstación Biológica de Doñana, CSICSevillaSpain,Laboratorio de Ecofisiología and Museo de Zoología (QCAZ), Escuela de Ciencias BiológicasPontificia Universidad Católica del EcuadorQuitoEcuador
| | - Alfredo G. Nicieza
- Department of Organisms and Systems BiologyUniversity of OviedoOviedoSpain,Biodiversity Research Institute (IMIB)University of Oviedo‐Principality of Asturias‐CSICMieresSpain
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28
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Demartsev V, Haddas-Sasson M, Ilany A, Koren L, Geffen E. Male rock hyraxes that maintain an isochronous song rhythm achieve higher reproductive success. J Anim Ecol 2022. [PMID: 36097377 DOI: 10.1111/1365-2656.13801] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Accepted: 07/26/2022] [Indexed: 11/29/2022]
Abstract
Rhythmic stability (nonrandom temporal structure) is required for many neural and physiological functions, whereas rhythmic irregularities can indicate genetic or developmental deficiencies. Therefore, rhythmic courtship or contest signals are widespread in nature as honest advertisement displays. Examination of bird songs revealed the pervasiveness of categorical rhythmic patterns that can be described as small integer ratios between sequential inter-call intervals. As similar rhythmic profiles are prevalent in human music, it was suggested that a shared functionality could drive both animal songs and human musical rhythms, facilitating synchrony between signallers and enabling easy identification of performance errors. Here we examined whether the rhythmic structure and the rhythmic stability of vocal displays are related to reproductive success in male rock hyraxes (Procavia capensis), which presents an unusual case of a terrestrial singing mammal. We combined long-term parentage analysis of 13 male hyraxes (22 male/years) with an analysis of an audio library of 105 hyrax songs. Male annual reproductive success was determined by the number of offspring that survived to the age of 1 year. The frequency of singing events was used to determine the seasonal singing effort for each male. Songs were analysed for rhythmic structure, focusing on the presence of categorical rhythms and the contribution of rhythmic stability to annual reproductive success. We found that male hyraxes that sing more frequently tend to have more surviving offspring and that the rhythmic profile of hyrax songs is predominantly isochronous with sequential vocal element pairs nearly equally spaced. The ratio of isochronous vocal element transitions (on-integer) to element transitions that deviate from an isochronous pattern (off-integer) in hyrax songs is positively correlated with male reproductive success. Our findings support the notion that isochronous rhythmic stability can serve as an indication of quality in sexually selected signals and is not necessarily driven by the need for multiple caller synchronization. The relative scarcity of nonisochronous rhythmic categories in individually performed hyrax songs raises the question of whether such rhythmic categories could be a product of collective, coordinated signalling, while being selected against in individual performance.
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Affiliation(s)
- Vlad Demartsev
- Department of Biology, University of Konstanz, Konstanz, Germany.,Department for the Ecology of Animal Societies, Max Plank Institute for Animal Behavior, Konstanz, Germany
| | | | - Amiyaal Ilany
- Faculty of Life Sciences, Bar Ilan University, Ramat-Gan, Israel
| | - Lee Koren
- Faculty of Life Sciences, Bar Ilan University, Ramat-Gan, Israel
| | - Eli Geffen
- School of Zoology, Tel Aviv University, Tel Aviv, Israel
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29
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Virrueta Herrera S, Johnson KP, Sweet AD, Ylinen E, Kunnasranta M, Nyman T. High levels of inbreeding with spatial and host-associated structure in lice of an endangered freshwater seal. Mol Ecol 2022; 31:4593-4606. [PMID: 35726520 PMCID: PMC9544963 DOI: 10.1111/mec.16569] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2022] [Revised: 05/12/2022] [Accepted: 05/20/2022] [Indexed: 02/02/2023]
Abstract
Host-specialist parasites of endangered large vertebrates are in many cases more endangered than their hosts. In particular, low host population densities and reduced among-host transmission rates are expected to lead to inbreeding within parasite infrapopulations living on single host individuals. Furthermore, spatial population structures of directly-transmitted parasites should be concordant with those of their hosts. Using population genomic approaches, we investigated inbreeding and population structure in a host-specialist seal louse (Echinophthirius horridus) infesting the Saimaa ringed seal (Phoca hispida saimensis), which is endemic to Lake Saimaa in Finland, and is one of the most endangered pinnipeds in the world. We conducted genome resequencing of pairs of lice collected from 18 individual Saimaa ringed seals throughout the Lake Saimaa complex. Our analyses showed high genetic similarity and inbreeding between lice inhabiting the same individual seal host, indicating low among-host transmission rates. Across the lake, genetic differentiation among individual lice was correlated with their geographic distance, and assignment analyses revealed a marked break in the genetic variation of the lice in the middle of the lake, indicating substantial population structure. These findings indicate that movements of Saimaa ringed seals across the main breeding areas of the fragmented Lake Saimaa complex may in fact be more restricted than suggested by previous population-genetic analyses of the seals themselves.
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Affiliation(s)
- Stephany Virrueta Herrera
- Illinois Natural History Survey, Prairie Research Institute, University of Illinois, Champaign, Illinois, USA.,Program in Ecology, Evolution, and Conservation, University of Illinois, Urbana, Illinois, USA
| | - Kevin P Johnson
- Illinois Natural History Survey, Prairie Research Institute, University of Illinois, Champaign, Illinois, USA
| | - Andrew D Sweet
- Department of Biological Sciences, Arkansas State University, Jonesboro, Arkansas, USA
| | - Eeva Ylinen
- Department of Environmental and Biological Sciences, University of Eastern Finland, Joensuu, Finland
| | - Mervi Kunnasranta
- Department of Environmental and Biological Sciences, University of Eastern Finland, Joensuu, Finland.,Natural Resources Institute Finland, Joensuu, Finland
| | - Tommi Nyman
- Department of Ecosystems in the Barents Region, Svanhovd Research Station, Norwegian Institute of Bioeconomy Research, Svanvik, Norway
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30
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Ruocco M, Jahnke M, Silva J, Procaccini G, Dattolo E. 2b-RAD Genotyping of the Seagrass Cymodocea nodosa Along a Latitudinal Cline Identifies Candidate Genes for Environmental Adaptation. Front Genet 2022; 13:866758. [PMID: 35651946 PMCID: PMC9149362 DOI: 10.3389/fgene.2022.866758] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Accepted: 04/19/2022] [Indexed: 11/18/2022] Open
Abstract
Plant populations distributed along broad latitudinal gradients often show patterns of clinal variation in genotype and phenotype. Differences in photoperiod and temperature cues across latitudes influence major phenological events, such as timing of flowering or seed dormancy. Here, we used an array of 4,941 SNPs derived from 2b-RAD genotyping to characterize population differentiation and levels of genetic and genotypic diversity of three populations of the seagrass Cymodocea nodosa along a latitudinal gradient extending across the Atlantic-Mediterranean boundary (i.e., Gran Canaria—Canary Islands, Faro—Portugal, and Ebro Delta—Spain). Our main goal was to search for potential outlier loci that could underlie adaptive differentiation of populations across the latitudinal distribution of the species. We hypothesized that such polymorphisms could be related to variation in photoperiod-temperature regime occurring across latitudes. The three populations were clearly differentiated and exhibited diverse levels of clonality and genetic diversity. Cymodocea nodosa from the Mediterranean displayed the highest genotypic richness, while the Portuguese population had the highest clonality values. Gran Canaria exhibited the lowest genetic diversity (as observed heterozygosity). Nine SNPs were reliably identified as outliers across the three sites by two different methods (i.e., BayeScan and pcadapt), and three SNPs could be associated to specific protein-coding genes by screening available C. nodosa transcriptomes. Two SNPs-carrying contigs encoded for transcription factors, while the other one encoded for an enzyme specifically involved in the regulation of flowering time, namely Lysine-specific histone demethylase 1 homolog 2. When analyzing biological processes enriched within the whole dataset of outlier SNPs identified by at least one method, “regulation of transcription” and “signalling” were among the most represented. Our results highlight the fundamental importance signal integration and gene-regulatory networks, as well as epigenetic regulation via DNA (de)methylation, could have for enabling adaptation of seagrass populations along environmental gradients.
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Affiliation(s)
| | - Marlene Jahnke
- Department of Marine Sciences, Tjärnö Marine Laboratory, University of Gothenburg, Gothenburg, Sweden
| | - João Silva
- Centre of Marine Sciences, University of Algarve, Faro, Portugal
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31
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Hauser S, Galla SJ, Putnam AS, Steeves TE, Latch EK. Comparing genome-based estimates of relatedness for use in pedigree-based conservation management. Mol Ecol Resour 2022; 22:2546-2558. [PMID: 35510790 DOI: 10.1111/1755-0998.13630] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Revised: 02/28/2022] [Accepted: 03/30/2022] [Indexed: 12/01/2022]
Abstract
Researchers have long debated which estimator of relatedness best captures the degree of relationship between two individuals. In the genomics era, this debate continues, with relatedness estimates being sensitive to the methods used to generate markers, marker quality, and levels of diversity in sampled individuals. Here, we compare six commonly used genome-based relatedness estimators (kinship genetic distance (KGD), Wang Maximum Likelihood (TrioML), Queller and Goodnight (Rxy ), Kinship INference for Genome-wide association studies (KING-robust), and Pairwise Relatedness (RAB ), allele-sharing co-ancestry (AS)) across five species bred in captivity-including three birds and two mammals-with varying degrees of reliable pedigree data, using reduced-representation and whole genome resequencing data. Genome-based relatedness estimates varied widely across estimators, sequencing methods, and species, yet the most consistent results for known first order relationships were found using Rxy , RAB , and AS. However, AS was found to be less consistently correlated with known pedigree relatedness than either Rxy or RAB . Our combined results indicate there is not a single genome-based estimator that is ideal across different species and data types. To determine the most appropriate genome-based relatedness estimator for each new dataset, we recommend assessing the relative: (1) correlation of candidate estimators with known relationships in the pedigree and (2) precision of candidate estimators with known first-order relationships. These recommendations are broadly applicable to conservation breeding programs, particularly where genome-based estimates of relatedness can complement and complete poorly pedigreed populations. Given a growing interest in the application of wild pedigrees, our results are also applicable to in-situ wildlife management.
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Affiliation(s)
- Samantha Hauser
- Department of Biological Sciences, University of Wisconsin, Milwaukee, Wisconsin, USA.,Embark Veterinary, Inc., Boston, Massachusetts, United States of America
| | - Stephanie J Galla
- School of Biological Sciences, University of Canterbury, New Zealand.,Department of Biological Sciences, Boise State University, Boise, Idaho, USA
| | - Andrea S Putnam
- Department of Exhibit-Curators, San Diego Zoo Wildlife Alliance, San Diego, California, USA
| | - Tammy E Steeves
- School of Biological Sciences, University of Canterbury, New Zealand
| | - Emily K Latch
- Department of Biological Sciences, University of Wisconsin, Milwaukee, Wisconsin, USA
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Jafari O, Zeinalabedini M, Robledo D, Fernandes JMO, Hedayati AA, Arefnezhad B. Genotyping-by-Sequencing Reveals the Impact of Restocking on Wild Common Carp Populations of the Southern Caspian Basin. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.872176] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Understanding the population structure and level of genetic diversity of wild populations is fundamental for appropriate stock management and species conservation. The common carp (Cyprinus carpio) is one of the most important bony fish throughout the Southern coastline of the Caspian Sea, but captures of this species have seen a dramatic reduction during the last decade. As a consequence, a restocking program has been put in place to maintain C. carpio populations, but its impact is not clear. In the present study, the population structure and genetic diversity of C. carpio in the Southern Caspian basin was determined using 17,828 single-nucleotide polymorphism (SNP) markers. A total of 117 individuals collected from four different locations in the southern Caspian basin and a farm were genotyped by genotyping-by-sequencing. The overall Fst obtained was 0.04, indicating a low level of differentiation between populations, and most genetic diversity was attributed to within population variation (97%). The low Fst values suggest that frequent migration events between different locations occur, and three migration events were inferred in the present study. However, each population still showed a distinct genetic profile, which allowed distinguishing the origin of the fish. This indicates that the ongoing restocking program is maintaining the differences between populations to some extent. Nonetheless, high inbreeding and low heterozygosity were detected in all populations, suggesting that additional conservation efforts are required to protect C. carpio populations in the Southern coast of the Caspian Sea.
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Range-wide phylogeography of the flightless steppe beetle Lethrus apterus (Geotrupidae) reveals recent arrival to the Pontic Steppes from the west. Sci Rep 2022; 12:5069. [PMID: 35332221 PMCID: PMC8948295 DOI: 10.1038/s41598-022-09007-0] [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: 09/13/2021] [Accepted: 03/10/2022] [Indexed: 11/21/2022] Open
Abstract
The Eurasian Steppe belt is one of the largest biomes in the Northern Hemisphere. We provide here a range-wide phylogeography of the flightless steppe beetle Lethrus apterus that inhabits the western part of the Steppe belt through the study of population-level variance of mitochondrial cytochrome oxidase I sequences and nuclear microsatellites. We detected a concordant geographic structure of genetic data with a significant isolation-by-distance pattern. We found more genetic variation in the western part of the area and identified Northern Bulgaria and the Pannonian Basin as possible refugia. Genetic clusters were separated by main rivers in the eastern part of the area. This implies west-to-east colonisation and argues for an evolutionarily recent arrival of this species to its current main distribution area, the Pontic Steppes. This contradicts the classical biogeographical wisdom that assumed an east-to-west colonisation pattern.
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Genetic and Phenotypic Characteristics of the Salmo trutta Complex in Italy. APPLIED SCIENCES-BASEL 2022. [DOI: 10.3390/app12073219] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Salmonid fish have become ecological and research models of study in the field of conservation genetics and genomics. Over the last decade, brown trout have received a high level of interest in research and publications. The term Salmo trutta complex is used to indicate the large number of geographic forms present in the species Salmo trutta. In Europe, the S. trutta complex consists (based on mitochondrial DNA control region analysis) of seven major evolutionary lineages: Atlantic (AT), Mediterranean (ME), Adriatic (AD), Danubian (DA), Marmoratus (MA), Duero (DU) and Tigris (TI). In several nations, the difficulty of identifying some lineages derives from their wide phenotypic and geographic plasticity and the presence of mixed lineages (due to introgressive hybridization with domestic AT populations). In Italy, the S. trutta complex populations living in the Tyrrhenian area and on the main islands (Sicily, Sardinia and Corsica) showed high genetic diversity. Currently, on the Italian Red List, the protected (near threatened) populations are the AD and ME lineages. Recent studies based on traditional (mitochondrial and nuclear markers) and NGS (next-generation sequencing) analyses have clarified some genetic differences between the populations of the Tyrrhenian region, Sicily, Sardinia and Corsica. Native populations in Sardinia belong to the AD lineage, while those living in Corsica are mainly characterized by the AD, MA and ME haplotypes. In Sicily, in the area of the Iblei mountains, an AT lineage (North African) exists. According to some authors, the term Salmo macrostigma should only be used for populations in North Africa. The use of genotyping methods based on mtDNA and nuclear markers and the latest generation sequencing techniques can improve the study of populations and evolutionary lineages in areas where there are overlaps and hybridization phenomena.
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Tyagi A, Khan A, Thatte P, Ramakrishnan U. Genome‐wide
SNP
markers from fecal samples reveal anthropogenic impacts on connectivity: case of a small carnivore in the central Indian landscape. Anim Conserv 2022. [DOI: 10.1111/acv.12770] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- A. Tyagi
- National Centre for Biological Sciences Tata Institute of Fundamental Research Bangalore India
- SASTRA Deemed to be University Thanjavur India
| | - A. Khan
- National Centre for Biological Sciences Tata Institute of Fundamental Research Bangalore India
| | - P. Thatte
- National Centre for Biological Sciences Tata Institute of Fundamental Research Bangalore India
- World Wide Fund for Nature‐India New Delhi India
| | - U. Ramakrishnan
- National Centre for Biological Sciences Tata Institute of Fundamental Research Bangalore India
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Yang F, Cai L, Dao Z, Sun W. Genomic Data Reveals Population Genetic and Demographic History of Magnolia fistulosa (Magnoliaceae), a Plant Species With Extremely Small Populations in Yunnan Province, China. FRONTIERS IN PLANT SCIENCE 2022; 13:811312. [PMID: 35251084 PMCID: PMC8892343 DOI: 10.3389/fpls.2022.811312] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Accepted: 01/13/2022] [Indexed: 05/11/2023]
Abstract
Elucidating the genetic background of threatened species is fundamental to their management and conservation, and investigating the demographic history of these species is helpful in the determination of the threats facing them. The woody species of the genus Magnolia (Magnoliaceae) have high economic, scientific and ecological values. Although nearly half of all Magnolia species have been evaluated as threatened, to date there has been no population genetic study employing Next Generation Sequencing (NGS) technology in this genus. In the present study, we investigate the conservation genomics of Magnolia fistulosa, a threatened species endemic to the limestone area along the Sino-Vietnamese border, using a double digest restriction-site-associated DNA-sequencing (ddRAD-seq) approach. To increase the reliability of our statistical inferences, we employed two approaches, Stacks and ipyrad, for SNP calling. A total of 15,272 and 18,960, respectively, putatively neutral SNPs were generated by Stacks and ipyrad. Relatively high genetic diversity and large population divergence were detected in M. fistulosa. Although higher absolute values were calculated using the ipyrad data set, the two data sets showed the same trends in genetic diversity (π, H e), population differentiation (F ST) and inbreeding coefficients (F IS). A change in the effective population size of M. fistulosa within the last 1 Ma was detected, including a population decline about 0.5-0.8 Ma ago, a bottleneck event about 0.2-0.3 Ma ago, population fluctuations during the last glacial stage, and the recovery of effective population size after the last glacial maximum. Our findings not only lay the foundation for the future conservation of this species, but also provide new insights into the evolutionary history of the genus Magnolia in southeastern Yunnan, China.
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Affiliation(s)
- Fengmao Yang
- Yunnan Key Laboratory for Integrative Conservation of Plant Species With Extremely Small Populations, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
- University of the Chinese Academy of Sciences, Beijing, China
| | - Lei Cai
- Yunnan Key Laboratory for Integrative Conservation of Plant Species With Extremely Small Populations, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Zhiling Dao
- Yunnan Key Laboratory for Integrative Conservation of Plant Species With Extremely Small Populations, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Weibang Sun
- Yunnan Key Laboratory for Integrative Conservation of Plant Species With Extremely Small Populations, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
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Kardum Hjort C, Paris JR, Olsson P, Herbertsson L, de Miranda JR, Dudaniec RY, Smith HG. Genomic divergence and a lack of recent introgression between commercial and wild bumblebees (
Bombus terrestris
). Evol Appl 2022; 15:365-382. [PMID: 35386397 PMCID: PMC8965379 DOI: 10.1111/eva.13346] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Revised: 12/08/2021] [Accepted: 01/17/2022] [Indexed: 11/27/2022] Open
Abstract
The global movement of bees for agricultural pollination services can affect local pollinator populations via hybridization. When commercial bumblebees are of the same species but of different geographic origin, intraspecific hybridization may result in beneficial integration of new genetic variation, or alternatively may disrupt locally adapted gene complexes. However, neither the existence nor the extent of genomic introgression and evolutionary divergence between wild and commercial bumblebees is fully understood. We obtained whole‐genome sequencing data from wild and commercial Bombus terrestris collected from sites in Southern Sweden with and without long‐term use of commercially imported B. terrestris. We search for evidence of introgression, dispersal and genome‐wide differentiation in a comparative genomic analysis of wild and commercial bumblebees. Commercial B. terrestris were found in natural environments near sites where commercial bumblebees were used, as well as drifting wild B. terrestris in commercial bumblebee colonies. However, we found no evidence for widespread, recent genomic introgression of commercial B. terrestris into local wild conspecific populations. We found that wild B. terrestris had significantly higher nucleotide diversity (Nei's pi, π), while the number of segregating sites (Watterson's theta, θw) was higher in commercial B. terrestris. A highly divergent region on chromosome 11 was identified in commercial B. terrestris and found to be enriched with structural variants. The genes present in this region are involved in flight muscle contraction and structure and pathogen immune response, providing evidence for differing evolutionary processes operating in wild and commercial B. terrestris. We did not find evidence for recent introgression, suggesting that co‐occurring commercial B. terrestris have not disrupted evolutionary processes in wild B. terrestris populations.
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Affiliation(s)
| | - Josephine R. Paris
- College of Life and Environmental Science University of Exeter Exeter EX4 4QD United Kingdom
| | - Peter Olsson
- Department of Biology Lund University SE‐223 62 Lund Sweden
| | - Lina Herbertsson
- Centre for Environmental and Climate Science Lund University SE‐223 62 Lund Sweden
| | - Joachim R. de Miranda
- Department of Ecology Swedish University of Agricultural Sciences Box 7044 SE‐750 07 Uppsala Sweden
| | - Rachael Y. Dudaniec
- Department of Biological Sciences Macquarie University Sydney 2109 NSW Australia
| | - Henrik G. Smith
- Department of Biology Lund University SE‐223 62 Lund Sweden
- Centre for Environmental and Climate Science Lund University SE‐223 62 Lund Sweden
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38
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Conservation genomics of an Australian cycad Cycas calcicola, and the Absence of Key Genotypes in Botanic Gardens. CONSERV GENET 2022. [DOI: 10.1007/s10592-022-01428-8] [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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Scarparo G, Sankovitz M, Loope KJ, Wilson‐Rankin E, Purcell J. Early queen joining and long-term queen associations in polygyne colonies of an invasive wasp revealed by longitudinal genetic analysis. Evol Appl 2021; 14:2901-2914. [PMID: 34950236 PMCID: PMC8674895 DOI: 10.1111/eva.13324] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Revised: 10/30/2021] [Accepted: 11/02/2021] [Indexed: 12/02/2022] Open
Abstract
Invasive social insects rank among the most damaging of terrestrial species. They are responsible for extensive damage and severely threaten the biodiversity of environments where they are introduced. Variation in colony social form commonly occurs in introduced populations of yellowjacket wasps (genus Vespula). In particular, invasive colonies may contain multiple queens (i.e., polygyne) and persist several years, while in the native range, the colonies are usually annual and harbor a single queen (i.e., monogyne). In this study, we used genome-wide loci obtained by double digest restriction site-associated DNA sequencing (RADseq) to investigate the genetic structure and queen turnover in colonies of the western yellowjacket, Vespula pensylvanica, in their introduced range in Hawaii. Of the 27 colonies monitored over four months (October-January), 19 were polygyne and already contained multiple queens on the first day of sampling. Contrary to previous speculation, this finding suggests that polygyny often arises early in the annual colony cycle, before the production of new queens in the fall. Furthermore, polygyne colonies exhibited a prolonged average lifespan relative to those headed by a single queen. As a result, there is no clear window during which colony eradication efforts would be more effective than upon first discovery. The relatedness among nestmate queens was slightly above zero, indicating that these colonies are generally composed of nonrelatives. The queen turnover within each colony was low, and we detected some full-sibling workers sampled up to four months apart. Finally, we did not detect any population structure among colonies, suggesting that queens disperse up to several kilometers. Taken together, our results provide the first insights into the requeening dynamics in this invasive and incipiently polygyne population and illuminate the early establishment of multiple long-lasting queens in these damaging colonies.
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Affiliation(s)
- Giulia Scarparo
- Department of EntomologyUniversity of California RiversideRiversideCaliforniaUSA
| | - Madison Sankovitz
- Department of EntomologyUniversity of California RiversideRiversideCaliforniaUSA
| | - Kevin J. Loope
- Department of EntomologyUniversity of California RiversideRiversideCaliforniaUSA
- Department of Fish and Wildlife ConservationVirginia TechBlacksburgVirginiaUSA
| | - Erin Wilson‐Rankin
- Department of EntomologyUniversity of California RiversideRiversideCaliforniaUSA
| | - Jessica Purcell
- Department of EntomologyUniversity of California RiversideRiversideCaliforniaUSA
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40
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Wolfgramm H, Martens J, Töpfer T, Vamberger M, Pathak A, Stuckas H, Päckert M. Asymmetric allelic introgression across a hybrid zone of the coal tit ( Periparus ater) in the central Himalayas. Ecol Evol 2021; 11:17332-17351. [PMID: 34938512 PMCID: PMC8668783 DOI: 10.1002/ece3.8369] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Revised: 10/26/2021] [Accepted: 11/02/2021] [Indexed: 11/07/2022] Open
Abstract
In the Himalayas, a number of secondary contact zones have been described for vicariant vertebrate taxa. However, analyses of genetic divergence and admixture are missing for most of these examples. In this study, we provide a population genetic analysis for the coal tit (Periparus ater) hybrid zone in Nepal. Intermediate phenotypes between the distinctive western "spot-winged tit" (P. a. melanolophus) and Eastern Himalayan coal tits (P. a. aemodius) occur across a narrow range of <100 km in western Nepal. As a peculiarity, another distinctive cinnamon-bellied form is known from a single population so far. Genetic admixture of western and eastern mitochondrial lineages was restricted to the narrow zone of phenotypically intermediate populations. The cline width was estimated 46 km only with a center close to the population of the cinnamon-bellied phenotype. In contrast, allelic introgression of microsatellite loci was asymmetrical from eastern P. a. aemodius into far western populations of phenotypic P. a. melanolophus but not vice versa. Accordingly, the microsatellite cline was about 3.7 times wider than the mitochondrial one.
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Affiliation(s)
- Hannes Wolfgramm
- Senckenberg Natural History Collections DresdenDresdenGermany
- Present address:
Department of Functional GenomicsInterfaculty Institute of Genetics and Functional GenomicsUniversity Medicine GreifswaldGreifswaldGermany
| | - Jochen Martens
- Institute of Organismic and Molecular Evolution (iomE)Johannes Gutenberg UniversityMainzGermany
| | - Till Töpfer
- Leibniz Institute for the Analysis of Biodiversity ChangeZoological Research Museum Alexander KoenigBonnGermany
| | | | - Abhinaya Pathak
- Department of National Parks and Wildlife ConservationKathmanduNepal
| | - Heiko Stuckas
- Senckenberg Natural History Collections DresdenDresdenGermany
| | - Martin Päckert
- Senckenberg Natural History Collections DresdenDresdenGermany
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41
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Winternitz J. Detangling the mechanisms and timing of MHC-dependent sexual selection using Soay sheep. Mol Ecol 2021; 30:6513-6516. [PMID: 34716950 DOI: 10.1111/mec.16255] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Accepted: 10/25/2021] [Indexed: 11/29/2022]
Abstract
Immune defence is a key component of fitness, and individuals are expected to have evolved preferences for mates that ensure immunocompetent offspring. Potential preferences include those for mates with specific heritable immune gene profiles ("good genes") or for immunogenetically dissimilar mates to increase offspring immune gene diversity. The major histocompatibility complex (MHC) is by far the most investigated immune gene in mate choice studies, but we still know very little about its role in sexual selection for genetic benefits. In this issue of Molecular Ecology, Huang et al. capitalize on the extraordinary wealth of behavioural, life history and genetic/genomic data from the free-living Soay sheep population on the Island of Hirta to address this problem. While the authors find evidence of both pre- and postcopulatory MHC-based sexual selection, postcopulatory MHC-dissimilar mate choice is indistinguishable from genome-wide effects, suggesting it is a byproduct of inbreeding avoidance in Soay sheep. The study's comprehensive sampling ensures that inferences are generalizable to the entire population and provides a gold standard for studies investigating immune gene-based sexual selection.
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Affiliation(s)
- Jamie Winternitz
- Department of Animal Behavior, Bielefeld University, Bielefeld, Germany
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42
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Foster Y, Dutoit L, Grosser S, Dussex N, Foster BJ, Dodds KG, Brauning R, Van Stijn T, Robertson F, McEwan JC, Jacobs JME, Robertson BC. Genomic signatures of inbreeding in a critically endangered parrot, the kākāpō. G3 (BETHESDA, MD.) 2021; 11:jkab307. [PMID: 34542587 PMCID: PMC8527487 DOI: 10.1093/g3journal/jkab307] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Accepted: 08/23/2021] [Indexed: 02/06/2023]
Abstract
Events of inbreeding are inevitable in critically endangered species. Reduced population sizes and unique life-history traits can increase the severity of inbreeding, leading to declines in fitness and increased risk of extinction. Here, we investigate levels of inbreeding in a critically endangered flightless parrot, the kākāpō (Strigops habroptilus), wherein a highly inbred island population and one individual from the mainland of New Zealand founded the entire extant population. Genotyping-by-sequencing (GBS), and a genotype calling approach using a chromosome-level genome assembly, identified a filtered set of 12,241 single-nucleotide polymorphisms (SNPs) among 161 kākāpō, which together encompass the total genetic potential of the extant population. Multiple molecular-based estimates of inbreeding were compared, including genome-wide estimates of heterozygosity (FH), the diagonal elements of a genomic-relatedness matrix (FGRM), and runs of homozygosity (RoH, FRoH). In addition, we compared levels of inbreeding in chicks from a recent breeding season to examine if inbreeding is associated with offspring survival. The density of SNPs generated with GBS was sufficient to identify chromosomes that were largely homozygous with RoH distributed in similar patterns to other inbred species. Measures of inbreeding were largely correlated and differed significantly between descendants of the two founding populations. However, neither inbreeding nor ancestry was found to be associated with reduced survivorship in chicks, owing to unexpected mortality in chicks exhibiting low levels of inbreeding. Our study highlights important considerations for estimating inbreeding in critically endangered species, such as the impacts of small population sizes and admixture between diverse lineages.
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Affiliation(s)
- Yasmin Foster
- Department of Zoology, University of Otago, Dunedin 9054, New Zealand
| | - Ludovic Dutoit
- Department of Zoology, University of Otago, Dunedin 9054, New Zealand
| | - Stefanie Grosser
- Department of Zoology, University of Otago, Dunedin 9054, New Zealand
| | - Nicolas Dussex
- Centre for Palaeogenetics, SE-106 91 Stockholm, Sweden
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, SE-104 05 Stockholm, Sweden
- Department of Zoology, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Brodie J Foster
- Department of Zoology, University of Otago, Dunedin 9054, New Zealand
| | - Ken G Dodds
- AgResearch Invermay Agricultural Centre, Mosgiel 9053, New Zealand
| | - Rudiger Brauning
- AgResearch Invermay Agricultural Centre, Mosgiel 9053, New Zealand
| | - Tracey Van Stijn
- AgResearch Invermay Agricultural Centre, Mosgiel 9053, New Zealand
| | - Fiona Robertson
- Department of Zoology, University of Otago, Dunedin 9054, New Zealand
| | - John C McEwan
- AgResearch Invermay Agricultural Centre, Mosgiel 9053, New Zealand
| | | | - Bruce C Robertson
- Department of Zoology, University of Otago, Dunedin 9054, New Zealand
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43
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Ottenburghs J. The genic view of hybridization in the Anthropocene. Evol Appl 2021; 14:2342-2360. [PMID: 34745330 PMCID: PMC8549621 DOI: 10.1111/eva.13223] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Revised: 03/10/2021] [Accepted: 03/10/2021] [Indexed: 12/24/2022] Open
Abstract
Human impact is noticeable around the globe, indicating that a new era might have begun: the Anthropocene. Continuing human activities, including land-use changes, introduction of non-native species and rapid climate change, are altering the distributions of countless species, often giving rise to human-mediated hybridization events. While the interbreeding of different populations or species can have detrimental effects, such as genetic extinction, it can be beneficial in terms of adaptive introgression or an increase in genetic diversity. In this paper, I first review the different mechanisms and outcomes of anthropogenic hybridization based on literature from the last five years (2016-2020). The most common mechanisms leading to the interbreeding of previously isolated taxa include habitat change (51% of the studies) and introduction of non-native species (34% intentional and 19% unintentional). These human-induced hybridization events most often result in introgression (80%). The high incidence of genetic exchange between the hybridizing taxa indicates that the application of a genic view of speciation (and introgression) can provide crucial insights on how to address hybridization events in the Anthropocene. This perspective considers the genome as a dynamic collection of genetic loci with distinct evolutionary histories, giving rise to a heterogenous genomic landscape in terms of genetic differentiation and introgression. First, understanding this genomic landscape can lead to a better selection of diagnostic genetic markers to characterize hybrid populations. Second, describing how introgression patterns vary across the genome can help to predict the likelihood of negative processes, such as demographic and genetic swamping, as well as positive outcomes, such as adaptive introgression. It is especially important to not only quantify how much genetic material introgressed, but also what has been exchanged. Third, comparing introgression patterns in pre-Anthropocene hybridization events with current human-induced cases might provide novel insights into the likelihood of genetic swamping or species collapse during an anthropogenic hybridization event. However, this comparative approach remains to be tested before it can be applied in practice. Finally, the genic view of introgression can be combined with conservation genomic studies to determine the legal status of hybrids and take appropriate measures to manage anthropogenic hybridization events. The interplay between evolutionary and conservation genomics will result in the constant exchange of ideas between these fields which will not only improve our knowledge on the origin of species, but also how to conserve and protect them.
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Affiliation(s)
- Jente Ottenburghs
- Wildlife Ecology and ConservationWageningen University & ResearchWageningenThe Netherlands
- Forest Ecology and Forest ManagementWageningen University & ResearchWageningenThe Netherlands
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Development of SNP Set for the Marker-Assisted Selection of Guar ( Cyamopsis tetragonoloba (L.) Taub.) Based on a Custom Reference Genome Assembly. PLANTS 2021; 10:plants10102063. [PMID: 34685872 PMCID: PMC8539970 DOI: 10.3390/plants10102063] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Revised: 09/20/2021] [Accepted: 09/27/2021] [Indexed: 12/11/2022]
Abstract
Guar gum, a polysaccharide derived from guar seeds, is widely used in a variety of industrial applications, including oil and gas production. Although guar is mostly propagated in India, interest in guar as a new industrial legume crop is increasing worldwide, demanding the development of effective tools for marker-assisted selection. In this paper, we report a wide-ranging set of 4907 common SNPs and 327 InDels generated from RADseq genotyping data of 166 guar plants of different geographical origin. A custom guar reference genome was assembled and used for variant calling. A consensus set of variants was built using three bioinformatic pipelines for short variant discovery. The developed molecular markers were used for genome-wide association study, resulting in the discovery of six markers linked to the variation of an important agronomic trait—percentage of pods matured to the harvest date under long light day conditions. One of the associated variants was found inside the putative transcript sequence homologous to an ABC transporter in Arabidopsis, which has been shown to play an important role in D-myo-inositol phosphates metabolism. Earlier, we suggested that genes involved in myo-inositol phosphate metabolism have significant impact on the early flowering of guar plants. Hence, we believe that the developed SNP set allows for the identification of confident molecular markers of important agrobiological traits.
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Szatmári L, Cserkész T, Laczkó L, Lanszki J, Pertoldi C, Abramov AV, Elmeros M, Ottlecz B, Hegyeli Z, Sramkó G. A comparison of microsatellites and genome-wide SNPs for the detection of admixture brings the first molecular evidence for hybridization between Mustela eversmanii and M. putorius (Mustelidae, Carnivora). Evol Appl 2021; 14:2286-2304. [PMID: 34603499 PMCID: PMC8477604 DOI: 10.1111/eva.13291] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2021] [Revised: 07/28/2021] [Accepted: 08/02/2021] [Indexed: 11/30/2022] Open
Abstract
Introgressive hybridization can pose a serious threat to endangered species which have an overlapping distribution such as in the case of two polecat species, Mustela eversmanii and M. putorius, in Europe. The population size of steppe polecat is known to continuously shrink, whereas its sister species, the European polecat, is still somehow widespread. In this study, we perform an analysis using microsatellite (SSR) and genomic (SNP) data sets to identify natural hybrids between polecats. Four populations were genotyped for eight polymorphic SSR loci, and thousands of unlinked SNPs were generated using a reduced-representation sequencing approach, RADseq, to characterize the genetic make-up of allopatric populations and to identify hybrids in the sympatric area. We applied standard population genetic analyses to characterize the populations based on their SSR allelic frequency. Only a single sample out of 48 sympatric samples showed exact intermediacy that we identified as an F1 hybrid. Additionally, one specimen was indicated in the genomic data sets as backcrossed. Other backcrosses, indicated by SSRs, were not validated by SNPs, which highlights the higher efficacy of the genomic method to identify backcrossed individuals. The low frequency of hybridization suggests that the difference in habitat preference of the two species may act as a barrier to admixture. Therefore, it is apparently unlikely that polecat populations are threatened by significant introgression. The two species showed a clear genetic differentiation using both techniques. We found higher genetic diversity values in the sympatric steppe polecat population than in the other studies on polecat populations. Although M. putorius is a hunted species in most countries, genetic diversity values indicate worse conditions in Europe than in the protected sibling species M. eversmanii. Suspending hunting and providing protected status of the former seems to be reasonable and timely.
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Affiliation(s)
- Lajos Szatmári
- MTA-DE "Lendület" Evolutionary Phylogenomics Research Group Debrecen Hungary
- Department of Botany University of Debrecen Debrecen Hungary
| | - Tamás Cserkész
- Department of Zoology Hungarian Natural History Museum Budapest Hungary
- Bükk Mammalogical Society Eger Hungary
| | - Levente Laczkó
- MTA-DE "Lendület" Evolutionary Phylogenomics Research Group Debrecen Hungary
- Department of Botany University of Debrecen Debrecen Hungary
| | - József Lanszki
- Carnivore Ecology Research Group Szent István University, Kaposvár Campus Kaposvár Hungary
| | - Cino Pertoldi
- Department of Chemistry and Bioscience Aalborg University Aalborg Øst Denmark
- Aalborg Zoo Aalborg Denmark
| | - Alexei V Abramov
- Zoological Institute Russian Academy of Sciences Saint Petersburg Russia
| | - Morten Elmeros
- Department of Bioscience - Wildlife Ecology Aarhus University Rønde Denmark
| | | | - Zsolt Hegyeli
- Milvus Group Bird and Nature Protection Association Tîrgu Mureș Romania
| | - Gábor Sramkó
- MTA-DE "Lendület" Evolutionary Phylogenomics Research Group Debrecen Hungary
- Department of Botany University of Debrecen Debrecen Hungary
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Barbosa S, Andrews KR, Goldberg AR, Gour DS, Hohenlohe PA, Conway CJ, Waits LP. The role of neutral and adaptive genomic variation in population diversification and speciation in two ground squirrel species of conservation concern. Mol Ecol 2021; 30:4673-4694. [PMID: 34324748 DOI: 10.1111/mec.16096] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Revised: 07/10/2021] [Accepted: 07/19/2021] [Indexed: 11/29/2022]
Abstract
Understanding the neutral (demographic) and adaptive processes leading to the differentiation of species and populations is a critical component of evolutionary and conservation biology. In this context, recently diverged taxa represent a unique opportunity to study the process of genetic differentiation. Northern and southern Idaho ground squirrels (Urocitellus brunneus - NIDGS, and U. endemicus - SIDGS, respectively) are a recently diverged pair of sister species that have undergone dramatic declines in the last 50 years and are currently found in metapopulations across restricted spatial areas with distinct environmental pressures. Here we genotyped single-nucleotide polymorphisms (SNPs) from buccal swabs with restriction site-associated DNA sequencing (RADseq). With these data we evaluated neutral genetic structure at both theinter- and intraspecific level, and identified putatively adaptive SNPs using population structure outlier detection and genotype-environment association (GEA) analyses. At the interspecific level, we detected a clear separation between NIDGS and SIDGS, and evidence for adaptive differentiation putatively linked to torpor patterns. At the intraspecific level, we found evidence of both neutral and adaptive differentiation. For NIDGS, elevation appears to be the main driver of adaptive differentiation, while neutral variation patterns match and expand information on the low connectivity between some populations identified in previous studies using microsatellite markers. For SIDGS, neutral substructure generally reflected natural geographic barriers, while adaptive variation reflected differences in land cover and temperature, as well as elevation. These results clearly highlight the roles of neutral and adaptive processes for understanding the complexity of the processes leading to species and population differentiation, which can have important conservation implications in susceptible and threatened species.
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Affiliation(s)
- Soraia Barbosa
- Department of Fish and Wildlife Sciences, College of Natural Resources, University of Idaho, 875 Perimeter Drive, Moscow, ID, 83844-1136, USA
| | - Kimberly R Andrews
- University of Idaho, Institute for Bioinformatics and Evolutionary Studies (IBEST), Moscow, ID, 83844-1136, USA
| | - Amanda R Goldberg
- Department of Fish and Wildlife Sciences, College of Natural Resources, University of Idaho, 875 Perimeter Drive, Moscow, ID, 83844-1136, USA
| | - Digpal S Gour
- Department of Fish and Wildlife Sciences, College of Natural Resources, University of Idaho, 875 Perimeter Drive, Moscow, ID, 83844-1136, USA
| | - Paul A Hohenlohe
- University of Idaho, Institute for Bioinformatics and Evolutionary Studies (IBEST), Moscow, ID, 83844-1136, USA.,Department of Biological Sciences, College of Science, University of Idaho, 875 Perimeter Drive, Moscow, ID, 83844-3051, USA
| | - Courtney J Conway
- U.S. Geological Survey, Idaho Cooperative Fish & Wildlife Research Unit, Department of Fish and Wildlife Sciences, College of Natural Resources, University of Idaho, Moscow, ID, 83844-1141, USA
| | - Lisette P Waits
- Department of Fish and Wildlife Sciences, College of Natural Resources, University of Idaho, 875 Perimeter Drive, Moscow, ID, 83844-1136, USA
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Dang BT, Truong OT, Tran SQ, Glenner H. Comparative population genetics of swimming crab host ( Portunus pelagicus) and common symbiotic barnacle ( Octolasmis angulata) in Vietnam. PeerJ 2021; 9:e11671. [PMID: 34277149 PMCID: PMC8272463 DOI: 10.7717/peerj.11671] [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: 11/27/2020] [Accepted: 06/03/2021] [Indexed: 11/20/2022] Open
Abstract
Background By comparing spatial geographical structures of host populations with that of their symbionts light can be shed on their biological interactions, and the degree of congruence between host and symbiont phylogeographies should reflect their life histories and especially dispersal mechanisms. Methods Here, we analyzed the genetic diversity and structure of a host, the blue swimming crab, Portunus pelagicus, and its symbiotic pedunculate barnacle Octolasmis angulata from six location sites representing three geographic regions (north, central and south) along the Vietnam coastline. High levels of congruence in their phylogeographic patterns were expected as they both undergo planktonic larval stages. Results Based on the COI mtDNA markers, O. angulata populations showed higher genetic diversity in comparison with their host P. pelagicus (number of haplotype/individuals, haplotype and nucleotide diversity are 119/192, 0.991 ± 0.002 and 0.02; and 89/160, 0.913 ± 0.02 and 0.015, respectively). Pairwise Fst and AMOVA analyses showed a more pronounced population structure in the symbiotic barnacle than in its crab host. The DAPC analyses identified three genetic clusters. However, both haplotype networks and scatter plots supported connectivity of the host and the symbiotic barnacle throughout their distribution range, except for low subdivision of southern population. Isolation by distance were detected only for the symbiont O. angulata (R2 = 0.332, P = 0.05), while dbMEM supported spatial structure of both partners, but only at MEM-1 (Obs. 0.2686, P < 0.01 and Obs. 0.2096, P < 0.01, respectively).
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Affiliation(s)
- Binh Thuy Dang
- Institute for Biotechnology and Environment, Nha Trang University, Nha Trang, Khanh Hoa, Vietnam
| | - Oanh Thi Truong
- Institute for Biotechnology and Environment, Nha Trang University, Nha Trang, Khanh Hoa, Vietnam
| | - Sang Quang Tran
- Institute for Biotechnology and Environment, Nha Trang University, Nha Trang, Khanh Hoa, Vietnam
| | - Henrik Glenner
- Department of Biological Science, University of Bergen, Bergen, Norway
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Schmidt TL, Jasper M, Weeks AR, Hoffmann AA. Unbiased population heterozygosity estimates from genome‐wide sequence data. Methods Ecol Evol 2021. [DOI: 10.1111/2041-210x.13659] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Affiliation(s)
- Thomas L. Schmidt
- School of BioSciences Bio21 InstituteUniversity of Melbourne Parkville VIC Australia
| | - Moshe‐Elijah Jasper
- School of BioSciences Bio21 InstituteUniversity of Melbourne Parkville VIC Australia
| | - Andrew R Weeks
- School of BioSciences Bio21 InstituteUniversity of Melbourne Parkville VIC Australia
- cesar Pty Ltd Parkville VIC Australia
| | - Ary A Hoffmann
- School of BioSciences Bio21 InstituteUniversity of Melbourne Parkville VIC Australia
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How well do genetic markers inform about responses to intraspecific admixture? A comparative analysis of microsatellites and RADseq. BMC Genom Data 2021; 22:22. [PMID: 34182923 PMCID: PMC8237422 DOI: 10.1186/s12863-021-00974-3] [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: 02/17/2021] [Accepted: 05/20/2021] [Indexed: 11/21/2022] Open
Abstract
Background Fitness consequences of intraspecific genetic admixture can vary from positive to negative depending on the genetic composition of the populations and environmental conditions. Because admixture has potential to influence the success of management and conservation efforts, genetic similarity has been suggested to be used as a proxy to predict the outcome. Studies utilizing microsatellites (a neutral marker) to investigate associations between genetic distance and admixture effects show conflicting results. Marker types that yield information on genome-wide and/or adaptive variation might be more useful for predicting responses to inter-population hybridization. In this study we utilized published data for three populations of pike (Esox lucius) to investigate associations between offspring performance (hatching success) and parental genetic similarity in experimentally purebred and admixed families, based on neutral (microsatellites), genome-wide neutral (RADseq SNPs), and adaptive (SNPs under selection) markers. Results Estimated similarity varied among the markers, likely reflecting differences in their inherent properties, but was consistently higher in purebred than admixed families. A significant interaction between marker type and admixture treatment reflected that neutral SNPs yielded higher estimates than adaptive SNPs for admixed families whereas no difference was found for purebred families, which indicates that neutral similarity was not reflective of adaptive similarity. When all samples were pooled, no association between similarity and performance was found for any marker. For microsatellites, similarity was positively correlated with hatching success in purebred families, whereas no association was found in admixed families; however, the direction of the effect differed between the population combinations. Conclusions The results strengthen the notion that, as of today, there is no proxy that can reliably predicted the outcome of admixture. This emphasizes the need of further studies to advance knowledge that can shed light on how to safeguard against negative consequences of admixture, and thereby inform management and promote conservation of biological diversity. Supplementary Information The online version contains supplementary material available at 10.1186/s12863-021-00974-3.
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Volynkin V, Vasylyk I, Volodin V, Grigoreva E, Karzhaev D, Lushchay E, Ulianich P, Volkov V, Risovannaya V, Blinova S, Alekseev J, Gorislavets S, Likhovskoi V, Beatovic A, Potokina E. The Assessment of Agrobiological and Disease Resistance Traits of Grapevine Hybrid Populations ( Vitis vinifera L. × Muscadinia rotundifolia Michx.) in the Climatic Conditions of Crimea. PLANTS 2021; 10:plants10061215. [PMID: 34203712 PMCID: PMC8232157 DOI: 10.3390/plants10061215] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 06/06/2021] [Accepted: 06/11/2021] [Indexed: 11/24/2022]
Abstract
The Crimean autochthonous grape varieties are unique by their origin and serve as a valuable source for breeding new cultivars with increased salt and frost resistance, as well as high-quality berries. However, they suffer from fungal pathogens, as the dry and hot summer months contribute to the epiphytotic course of diseases. An increase in the resistance of Crimean grape varieties is currently achieved through interspecific hybridization. In this study, we describe the genetic and agrobiological diversity of three hybrid populations obtained using the Vitis interspecific hybrid ‘Magarach 31-77-10′ as a female parent and Muscadinia rotundifolia × Vitis vinifera BC5 hybrid plants as male parents. The hybrid nature of the populations was assessed using RADseq high-throughput genotyping. We discovered 12,734 SNPs, which were common to all three hybrid populations. We also proved with the SSR markers that the strong powdery and downy mildew resistance of the paternal genotypes is determined by the dominant Run1/Rpv1 locus inherited from M. rotundifolia. As a result, the disease development score (R, %) for both mildew diseases in the female parent ‘Magarach 31-77-10’ was three times higher than in male parents 2000-305-143 and 2000-305-163 over two years of phytopathological assessment. The highest values of yield-contributing traits (average bunch weight ~197 g and 1.3 kg as yield per plant) were detected in the population 4-11 (♀M. No. 31-77-10 × 2000-305-163). Despite the epiphytotic development of PM, the spread of oidium to the vegetative organs of hybrids 4-11 did not exceed 20%. Some hybrid genotypes with high productivity and resistance to pathogens were selected for further assessment as promising candidates for new varieties.
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Affiliation(s)
- Vladimir Volynkin
- All-Russian National Research Institute of Viticulture and Winemaking ‘Magarach’ RAS, 298600 Yalta, Russia; (V.V.); (I.V.); (V.V.); (E.G.); (D.K.); (E.L.); (P.U.); (V.V.); (V.R.); (J.A.); (S.G.); (V.L.)
| | - Irina Vasylyk
- All-Russian National Research Institute of Viticulture and Winemaking ‘Magarach’ RAS, 298600 Yalta, Russia; (V.V.); (I.V.); (V.V.); (E.G.); (D.K.); (E.L.); (P.U.); (V.V.); (V.R.); (J.A.); (S.G.); (V.L.)
| | - Vitalii Volodin
- All-Russian National Research Institute of Viticulture and Winemaking ‘Magarach’ RAS, 298600 Yalta, Russia; (V.V.); (I.V.); (V.V.); (E.G.); (D.K.); (E.L.); (P.U.); (V.V.); (V.R.); (J.A.); (S.G.); (V.L.)
| | - Elizaveta Grigoreva
- All-Russian National Research Institute of Viticulture and Winemaking ‘Magarach’ RAS, 298600 Yalta, Russia; (V.V.); (I.V.); (V.V.); (E.G.); (D.K.); (E.L.); (P.U.); (V.V.); (V.R.); (J.A.); (S.G.); (V.L.)
- Institute of Forest and Natural Resources Management, Saint Petersburg State Forest Technical University, 194021 St. Petersburg, Russia
- Information Technologies and Programming Faculty, ITMO University, 197101 St. Petersburg, Russia;
| | - Dmitry Karzhaev
- All-Russian National Research Institute of Viticulture and Winemaking ‘Magarach’ RAS, 298600 Yalta, Russia; (V.V.); (I.V.); (V.V.); (E.G.); (D.K.); (E.L.); (P.U.); (V.V.); (V.R.); (J.A.); (S.G.); (V.L.)
- Institute of Forest and Natural Resources Management, Saint Petersburg State Forest Technical University, 194021 St. Petersburg, Russia
| | - Ekaterina Lushchay
- All-Russian National Research Institute of Viticulture and Winemaking ‘Magarach’ RAS, 298600 Yalta, Russia; (V.V.); (I.V.); (V.V.); (E.G.); (D.K.); (E.L.); (P.U.); (V.V.); (V.R.); (J.A.); (S.G.); (V.L.)
| | - Pavel Ulianich
- All-Russian National Research Institute of Viticulture and Winemaking ‘Magarach’ RAS, 298600 Yalta, Russia; (V.V.); (I.V.); (V.V.); (E.G.); (D.K.); (E.L.); (P.U.); (V.V.); (V.R.); (J.A.); (S.G.); (V.L.)
- All-Russian Research Institute of Agricultural Microbiology, 196608 St. Petersburg, Russia
| | - Vladimir Volkov
- All-Russian National Research Institute of Viticulture and Winemaking ‘Magarach’ RAS, 298600 Yalta, Russia; (V.V.); (I.V.); (V.V.); (E.G.); (D.K.); (E.L.); (P.U.); (V.V.); (V.R.); (J.A.); (S.G.); (V.L.)
- Institute of Forest and Natural Resources Management, Saint Petersburg State Forest Technical University, 194021 St. Petersburg, Russia
| | - Valentina Risovannaya
- All-Russian National Research Institute of Viticulture and Winemaking ‘Magarach’ RAS, 298600 Yalta, Russia; (V.V.); (I.V.); (V.V.); (E.G.); (D.K.); (E.L.); (P.U.); (V.V.); (V.R.); (J.A.); (S.G.); (V.L.)
| | - Sofiya Blinova
- Syntol, 127434 Moscow, Russia;
- All-Russian Research Institute of Agricultural Biotechnology, 127434 Moscow, Russia
| | - Jakov Alekseev
- All-Russian National Research Institute of Viticulture and Winemaking ‘Magarach’ RAS, 298600 Yalta, Russia; (V.V.); (I.V.); (V.V.); (E.G.); (D.K.); (E.L.); (P.U.); (V.V.); (V.R.); (J.A.); (S.G.); (V.L.)
- Syntol, 127434 Moscow, Russia;
| | - Svetlana Gorislavets
- All-Russian National Research Institute of Viticulture and Winemaking ‘Magarach’ RAS, 298600 Yalta, Russia; (V.V.); (I.V.); (V.V.); (E.G.); (D.K.); (E.L.); (P.U.); (V.V.); (V.R.); (J.A.); (S.G.); (V.L.)
| | - Vladimir Likhovskoi
- All-Russian National Research Institute of Viticulture and Winemaking ‘Magarach’ RAS, 298600 Yalta, Russia; (V.V.); (I.V.); (V.V.); (E.G.); (D.K.); (E.L.); (P.U.); (V.V.); (V.R.); (J.A.); (S.G.); (V.L.)
| | - Aleksandar Beatovic
- Information Technologies and Programming Faculty, ITMO University, 197101 St. Petersburg, Russia;
| | - Elena Potokina
- All-Russian National Research Institute of Viticulture and Winemaking ‘Magarach’ RAS, 298600 Yalta, Russia; (V.V.); (I.V.); (V.V.); (E.G.); (D.K.); (E.L.); (P.U.); (V.V.); (V.R.); (J.A.); (S.G.); (V.L.)
- Institute of Forest and Natural Resources Management, Saint Petersburg State Forest Technical University, 194021 St. Petersburg, Russia
- Correspondence: ; Tel.: +7-911-084-1422
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