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Garrett MJ, Nerkowski SA, Kieran S, Campbell NR, Barbosa S, Conway CJ, Hohenlohe PA, Waits LP. Development and validation of a GT-seq panel for genetic monitoring in a threatened species using minimally invasive sampling. Ecol Evol 2024; 14:e11321. [PMID: 38770122 PMCID: PMC11103765 DOI: 10.1002/ece3.11321] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2024] [Revised: 04/03/2024] [Accepted: 04/05/2024] [Indexed: 05/22/2024] Open
Abstract
Minimally invasive samples are often the best option for collecting genetic material from species of conservation concern, but they perform poorly in many genomic sequencing methods due to their tendency to yield low DNA quality and quantity. Genotyping-in-thousands by sequencing (GT-seq) is a powerful amplicon sequencing method that can genotype large numbers of variable-quality samples at a standardized set of single nucleotide polymorphism (SNP) loci. Here, we develop, optimize, and validate a GT-seq panel for the federally threatened northern Idaho ground squirrel (Urocitellus brunneus) to provide a standardized approach for future genetic monitoring and assessment of recovery goals using minimally invasive samples. The optimized panel consists of 224 neutral and 81 putatively adaptive SNPs. DNA collected from buccal swabs from 2016 to 2020 had 73% genotyping success, while samples collected from hair from 2002 to 2006 had little to no DNA remaining and did not genotype successfully. We evaluated our GT-seq panel by measuring genotype discordance rates compared to RADseq and whole-genome sequencing. GT-seq and other sequencing methods had similar population diversity and F ST estimates, but GT-seq consistently called more heterozygotes than expected, resulting in negative F IS values at the population level. Genetic ancestry assignment was consistent when estimated with different sequencing methods and numbers of loci. Our GT-seq panel is an effective and efficient genotyping tool that will aid in the monitoring and recovery of this threatened species, and our results provide insights for applying GT-seq for minimally invasive DNA sampling techniques in other rare animals.
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Affiliation(s)
- Molly J. Garrett
- Department of Fish and Wildlife Sciences, College of Natural ResourcesUniversity of IdahoMoscowIdahoUSA
| | - Stacey A. Nerkowski
- Department of Fish and Wildlife Sciences, College of Natural ResourcesUniversity of IdahoMoscowIdahoUSA
| | - Shannon Kieran
- Department of Fish and Wildlife Sciences, College of Natural ResourcesUniversity of IdahoMoscowIdahoUSA
| | | | - Soraia Barbosa
- Department of Fish and Wildlife Sciences, College of Natural ResourcesUniversity of IdahoMoscowIdahoUSA
| | - Courtney J. Conway
- U.S. Geological Survey, Idaho Cooperative Fish & Wildlife Research UnitUniversity of IdahoMoscowIdahoUSA
| | - Paul A. Hohenlohe
- Department of Biological Sciences, College of ScienceUniversity of IdahoMoscowIdahoUSA
| | - Lisette P. Waits
- Department of Fish and Wildlife Sciences, College of Natural ResourcesUniversity of IdahoMoscowIdahoUSA
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2
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Gu T, Hu J, Yu L. Evolution and conservation genetics of pangolins. Integr Zool 2024; 19:426-441. [PMID: 38146613 DOI: 10.1111/1749-4877.12796] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2023]
Abstract
Pangolins (Pholidota, Manidae) are classified as an evolutionarily distinct and globally endangered mammal due to their unique morphology (nail-like scales and a myrmecophagous diet) and being the victim of heavy poaching and worldwide trafficking. As such, pangolins serve as a textbook example for studying the special phenotypic evolutionary adaptations and conservation genetics of an endangered species. Recent years have demonstrated significant advancements in the fields of molecular genetics and genomics, which have translated to a series of important research achievements and breakthroughs concerning the evolution and conservation genetics of pangolins. This review comprehensively presents the hitherto advances in phylogeny, adaptive evolution, conservation genetics, and conservation genomics that are related to pangolins, which will provide an ample understanding of their diversity, molecular adaptation mechanisms, and evolutionary potentials. In addition, we highlight the priority of investigating species/population diversity among pangolins and suggest several avenues of research that are highly relevant for future pangolin conservation.
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Affiliation(s)
- Tongtong Gu
- State Key Laboratory for Conservation and Utilization of Bio-Resource in Yunnan, School of Life Sciences, Yunnan University, Kunming, China
| | - Jingyang Hu
- State Key Laboratory for Conservation and Utilization of Bio-Resource in Yunnan, School of Life Sciences, Yunnan University, Kunming, China
| | - Li Yu
- State Key Laboratory for Conservation and Utilization of Bio-Resource in Yunnan, School of Life Sciences, Yunnan University, Kunming, China
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3
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Gargiulo R, Decroocq V, González‐Martínez SC, Paz‐Vinas I, Aury J, Lesur Kupin I, Plomion C, Schmitt S, Scotti I, Heuertz M. Estimation of contemporary effective population size in plant populations: Limitations of genomic datasets. Evol Appl 2024; 17:e13691. [PMID: 38707994 PMCID: PMC11069024 DOI: 10.1111/eva.13691] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Revised: 03/22/2024] [Accepted: 04/03/2024] [Indexed: 05/07/2024] Open
Abstract
Effective population size (N e) is a pivotal evolutionary parameter with crucial implications in conservation practice and policy. Genetic methods to estimate N e have been preferred over demographic methods because they rely on genetic data rather than time-consuming ecological monitoring. Methods based on linkage disequilibrium (LD), in particular, have become popular in conservation as they require a single sampling and provide estimates that refer to recent generations. A software program based on the LD method, GONE, looks particularly promising to estimate contemporary and recent-historical N e (up to 200 generations in the past). Genomic datasets from non-model species, especially plants, may present some constraints to the use of GONE, as linkage maps and reference genomes are seldom available, and SNP genotyping is usually based on reduced-representation methods. In this study, we use empirical datasets from four plant species to explore the limitations of plant genomic datasets when estimating N e using the algorithm implemented in GONE, in addition to exploring some typical biological limitations that may affect N e estimation using the LD method, such as the occurrence of population structure. We show how accuracy and precision of N e estimates potentially change with the following factors: occurrence of missing data, limited number of SNPs/individuals sampled, and lack of information about the location of SNPs on chromosomes, with the latter producing a significant bias, previously unexplored with empirical data. We finally compare the N e estimates obtained with GONE for the last generations with the contemporary N e estimates obtained with the programs currentNe and NeEstimator.
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Affiliation(s)
| | | | | | - Ivan Paz‐Vinas
- Department of BiologyColorado State UniversityFort CollinsColoradoUSA
- CNRS, ENTPE, UMR5023 LEHNAUniversité Claude Bernard Lyon 1VilleurbanneFrance
| | - Jean‐Marc Aury
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ EvryUniversité Paris‐SaclayEvryFrance
| | | | | | - Sylvain Schmitt
- AMAPUniv. Montpellier, CIRAD, CNRS, INRAE, IRDMontpellierFrance
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4
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Liu X, Lin L, Sinding MHS, Bertola LD, Hanghøj K, Quinn L, Garcia-Erill G, Rasmussen MS, Schubert M, Pečnerová P, Balboa RF, Li Z, Heaton MP, Smith TPL, Pinto RR, Wang X, Kuja J, Brüniche-Olsen A, Meisner J, Santander CG, Ogutu JO, Masembe C, da Fonseca RR, Muwanika V, Siegismund HR, Albrechtsen A, Moltke I, Heller R. Introgression and disruption of migration routes have shaped the genetic integrity of wildebeest populations. Nat Commun 2024; 15:2921. [PMID: 38609362 PMCID: PMC11014984 DOI: 10.1038/s41467-024-47015-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Accepted: 03/11/2024] [Indexed: 04/14/2024] Open
Abstract
The blue wildebeest (Connochaetes taurinus) is a keystone species in savanna ecosystems from southern to eastern Africa, and is well known for its spectacular migrations and locally extreme abundance. In contrast, the black wildebeest (C. gnou) is endemic to southern Africa, barely escaped extinction in the 1900s and is feared to be in danger of genetic swamping from the blue wildebeest. Despite the ecological importance of the wildebeest, there is a lack of understanding of how its unique migratory ecology has affected its gene flow, genetic structure and phylogeography. Here, we analyze whole genomes from 121 blue and 22 black wildebeest across the genus' range. We find discrete genetic structure consistent with the morphologically defined subspecies. Unexpectedly, our analyses reveal no signs of recent interspecific admixture, but rather a late Pleistocene introgression of black wildebeest into the southern blue wildebeest populations. Finally, we find that migratory blue wildebeest populations exhibit a combination of long-range panmixia, higher genetic diversity and lower inbreeding levels compared to neighboring populations whose migration has recently been disrupted. These findings provide crucial insights into the evolutionary history of the wildebeest, and tangible genetic evidence for the negative effects of anthropogenic activities on highly migratory ungulates.
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Affiliation(s)
- Xiaodong Liu
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Long Lin
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | | | - Laura D Bertola
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Kristian Hanghøj
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Liam Quinn
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | | | | | - Mikkel Schubert
- Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, Denmark
| | | | - Renzo F Balboa
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Zilong Li
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Michael P Heaton
- USDA, ARS, U.S. Meat Animal Research Center (USMARC), Clay Center, NE, USA
| | - Timothy P L Smith
- USDA, ARS, U.S. Meat Animal Research Center (USMARC), Clay Center, NE, USA
| | - Rui Resende Pinto
- CIIMAR-Interdisciplinary Centre of Marine and Environmental Research-University of Porto, Porto, Portugal
- Section for Biodiversity, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Xi Wang
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Josiah Kuja
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | | | - Jonas Meisner
- Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, Denmark
- Copenhagen Research Centre for Mental Health, Copenhagen University Hospital, Copenhagen, Denmark
| | - Cindy G Santander
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Joseph O Ogutu
- Biostatistics Unit, Institute of Crop Science, University of Hohenheim, Stuttgart, Germany
| | - Charles Masembe
- Department of Zoology, Entomology and Fisheries Sciences, Makerere University, P. O. Box 7062, Kampala, Uganda
| | - Rute R da Fonseca
- CIIMAR-Interdisciplinary Centre of Marine and Environmental Research-University of Porto, Porto, Portugal
- Section for Biodiversity, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Vincent Muwanika
- Department of Environmental Management, Makerere University, PO Box 7062, Kampala, Uganda
| | - Hans R Siegismund
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | | | - Ida Moltke
- Department of Biology, University of Copenhagen, Copenhagen, Denmark.
| | - Rasmus Heller
- Department of Biology, University of Copenhagen, Copenhagen, Denmark.
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5
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Xiang KL, Wu SD, Lian L, He WC, Peng D, Peng HW, Zhang XN, Li HL, Xue JY, Shan HY, Xu GX, Liu Y, Wu ZQ, Wang W. Genomic data and ecological niche modeling reveal an unusually slow rate of molecular evolution in the Cretaceous Eupteleaceae. Sci China Life Sci 2024; 67:803-816. [PMID: 38087029 DOI: 10.1007/s11427-023-2448-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2023] [Accepted: 09/11/2023] [Indexed: 04/06/2024]
Abstract
Living fossils are evidence of long-term sustained ecological success. However, whether living fossils have little molecular changes remains poorly known, particularly in plants. Here, we have introduced a novel method that integrates phylogenomic, comparative genomic, and ecological niche modeling analyses to investigate the rate of molecular evolution of Eupteleaceae, a Cretaceous relict angiosperm family endemic to East Asia. We assembled a high-quality chromosome-level nuclear genome, and the chloroplast and mitochondrial genomes of a member of Eupteleaceae (Euptelea pleiosperma). Our results show that Eupteleaceae is most basal in Ranunculales, the earliest-diverging order in eudicots, and shares an ancient whole-genome duplication event with the other Ranunculales. We document that Eupteleaceae has the slowest rate of molecular changes in the observed angiosperms. The unusually low rate of molecular evolution of Eupteleaceae across all three independent inherited genomes and genes within each of the three genomes is in association with its conserved genome architecture, ancestral woody habit, and conserved niche requirements. Our findings reveal the evolution and adaptation of living fossil plants through large-scale environmental change and also provide new insights into early eudicot diversification.
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Affiliation(s)
- Kun-Li Xiang
- State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
- China National Botanical Garden, Beijing, 100093, China
| | - Sheng-Dan Wu
- State Key Laboratory of Grassland Agro-Ecosystems and College of Ecology, Lanzhou University, Lanzhou, 730000, China
| | - Lian Lian
- State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- China National Botanical Garden, Beijing, 100093, China
| | - Wen-Chuang He
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
| | - Dan Peng
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
| | - Huan-Wen Peng
- State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- China National Botanical Garden, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xiao-Ni Zhang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
| | - Hong-Lei Li
- College of Landscape Architecture and Life Science/Institute of Special Plants, Chongqing University of Arts and Sciences, Chongqing, 402160, China
| | - Jia-Yu Xue
- College of Horticulture, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing, 210095, China
| | - Hong-Yan Shan
- State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- China National Botanical Garden, Beijing, 100093, China
| | - Gui-Xia Xu
- State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- China National Botanical Garden, Beijing, 100093, China
| | - Yang Liu
- Fairylake Botanical Garden, Shenzhen & Chinese Academy of Sciences, Shenzhen, 518004, China
| | - Zhi-Qiang Wu
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China.
| | - Wei Wang
- State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China.
- China National Botanical Garden, Beijing, 100093, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
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6
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Jeffery NW, Vercaemer B, Stanley RRE, Kess T, Dufresne F, Noisette F, O'Connor MI, Wong MC. Variation in genomic vulnerability to climate change across temperate populations of eelgrass ( Zostera marina). Evol Appl 2024; 17:e13671. [PMID: 38650965 PMCID: PMC11033490 DOI: 10.1111/eva.13671] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 02/05/2024] [Accepted: 02/07/2024] [Indexed: 04/25/2024] Open
Abstract
A global decline in seagrass populations has led to renewed calls for their conservation as important providers of biogenic and foraging habitat, shoreline stabilization and carbon storage. Eelgrass (Zostera marina) occupies the largest geographic range among seagrass species spanning a commensurately broad spectrum of environmental conditions. In Canada, eelgrass is managed as a single phylogroup despite occurring across three oceans and a range of ocean temperatures and salinity gradients. Previous research has focused on applying relatively few markers to reveal population structure of eelgrass, whereas a whole-genome approach is warranted to investigate cryptic structure among populations inhabiting different ocean basins and localized environmental conditions. We used a pooled whole-genome re-sequencing approach to characterize population structure, gene flow and environmental associations of 23 eelgrass populations ranging from the Northeast United States to Atlantic, subarctic and Pacific Canada. We identified over 500,000 SNPs, which when mapped to a chromosome-level genome assembly revealed six broad clades of eelgrass across the study area, with pairwise F ST ranging from 0 among neighbouring populations to 0.54 between Pacific and Atlantic coasts. Genetic diversity was highest in the Pacific and lowest in the subarctic, consistent with colonization of the Arctic and Atlantic oceans from the Pacific less than 300 kya. Using redundancy analyses and two climate change projection scenarios, we found that subarctic populations are predicted to be potentially more vulnerable to climate change through genomic offset predictions. Conservation planning in Canada should thus ensure that representative populations from each identified clade are included within a national network so that latent genetic diversity is protected, and gene flow is maintained. Northern populations, in particular, may require additional mitigation measures given their potential susceptibility to a rapidly changing climate.
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Affiliation(s)
- Nicholas W. Jeffery
- Fisheries and Oceans CanadaBedford Institute of OceanographyDartmouthNova ScotiaCanada
| | - Benedikte Vercaemer
- Fisheries and Oceans CanadaBedford Institute of OceanographyDartmouthNova ScotiaCanada
| | - Ryan R. E. Stanley
- Fisheries and Oceans CanadaBedford Institute of OceanographyDartmouthNova ScotiaCanada
| | - Tony Kess
- Fisheries and Oceans Canada, Northwest Atlantic Fisheries CentreSt. John'sNewfoundland and LabradorCanada
| | - France Dufresne
- Département de BiologieUniversité du Québec à RimouskiRimouskiQuebecCanada
| | - Fanny Noisette
- Institut des Sciences de la mer, Université du Québec à RimouskiRimouskiQuebecCanada
| | - Mary I. O'Connor
- Department of Zoology and Biodiversity Research CentreUniversity of British ColumbiaVancouverBritish ColumbiaCanada
| | - Melisa C. Wong
- Fisheries and Oceans CanadaBedford Institute of OceanographyDartmouthNova ScotiaCanada
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7
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Guan DL, Chen YZ, Qin YC, Li XD, Deng WA. Chromosomal-Level Reference Genome for the Chinese Endemic Pygmy Grasshopper, Zhengitettix transpicula, Sheds Light on Tetrigidae Evolution and Advancing Conservation Efforts. Insects 2024; 15:223. [PMID: 38667352 PMCID: PMC11049975 DOI: 10.3390/insects15040223] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2024] [Revised: 03/15/2024] [Accepted: 03/16/2024] [Indexed: 04/28/2024]
Abstract
The pygmy grasshopper, Zhengitettix transpicula, is a Chinese endemic species with an exceedingly limited distribution and fragile population structure, rendering it vulnerable to extinction. We present a high-continuity, chromosome-scale reference genome assembly to elucidate this species' distinctive biology and inform conservation. Employing an integrated sequencing approach, we achieved a 970.40 Mb assembly with 96.32% coverage across seven pseudo-chromosomes and impressive continuity (N50 > 220 Mb). Genome annotation achieves identification with 99.2% BUSCO completeness, supporting quality. Comparative analyses with 14 genomes from Orthoptera-facilitated phylogenomics and revealed 549 significantly expanded gene families in Z. transpicula associated with metabolism, stress response, and development. However, genomic analysis exposed remarkably low heterozygosity (0.02%), implying a severe genetic bottleneck from small, fragmented populations, characteristic of species vulnerable to extinction from environmental disruptions. Elucidating the genetic basis of population dynamics and specialization provides an imperative guideline for habitat conservation and restoration of this rare organism. Moreover, divergent evolution analysis of the CYP305m2 gene regulating locust aggregation highlighted potential structural and hence functional variations between Acrididae and Tetrigidae. Our chromosomal genomic characterization of Z. transpicula advances Orthopteran resources, establishing a framework for evolutionary developmental explorations and applied conservation genomics, reversing the trajectory of this unique grasshopper lineage towards oblivion.
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Affiliation(s)
- De-Long Guan
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection, Guangxi Normal University, Ministry of Education, Guilin 541006, China; (D.-L.G.); (Y.-C.Q.)
- Guangxi Key Laboratory of Sericulture Ecology and Applied Intelligent Technology, School of Chemistry and Bioengineering, Hechi University, Hechi 546300, China;
| | - Ya-Zhen Chen
- Guangxi Key Laboratory of Sericulture Ecology and Applied Intelligent Technology, School of Chemistry and Bioengineering, Hechi University, Hechi 546300, China;
| | - Ying-Can Qin
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection, Guangxi Normal University, Ministry of Education, Guilin 541006, China; (D.-L.G.); (Y.-C.Q.)
- Guangxi Key Laboratory of Sericulture Ecology and Applied Intelligent Technology, School of Chemistry and Bioengineering, Hechi University, Hechi 546300, China;
| | - Xiao-Dong Li
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection, Guangxi Normal University, Ministry of Education, Guilin 541006, China; (D.-L.G.); (Y.-C.Q.)
- Guangxi Key Laboratory of Sericulture Ecology and Applied Intelligent Technology, School of Chemistry and Bioengineering, Hechi University, Hechi 546300, China;
| | - Wei-An Deng
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection, Guangxi Normal University, Ministry of Education, Guilin 541006, China; (D.-L.G.); (Y.-C.Q.)
- Guangxi Key Laboratory of Sericulture Ecology and Applied Intelligent Technology, School of Chemistry and Bioengineering, Hechi University, Hechi 546300, China;
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8
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Kellner FL, Le Moullec M, Ellegaard MR, Rosvold J, Peeters B, Burnett HA, Pedersen ÅØ, Brealey JC, Dussex N, Bieker VC, Hansen BB, Martin MD. A palaeogenomic investigation of overharvest implications in an endemic wild reindeer subspecies. Mol Ecol 2024; 33:e17274. [PMID: 38279681 DOI: 10.1111/mec.17274] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 12/11/2023] [Accepted: 01/09/2024] [Indexed: 01/28/2024]
Abstract
Overharvest can severely reduce the abundance and distribution of a species and thereby impact its genetic diversity and threaten its future viability. Overharvest remains an ongoing issue for Arctic mammals, which due to climate change now also confront one of the fastest changing environments on Earth. The high-arctic Svalbard reindeer (Rangifer tarandus platyrhynchus), endemic to Svalbard, experienced a harvest-induced demographic bottleneck that occurred during the 17-20th centuries. Here, we investigate changes in genetic diversity, population structure, and gene-specific differentiation during and after this overharvesting event. Using whole-genome shotgun sequencing, we generated the first ancient and historical nuclear (n = 11) and mitochondrial (n = 18) genomes from Svalbard reindeer (up to 4000 BP) and integrated these data with a large collection of modern genome sequences (n = 90) to infer temporal changes. We show that hunting resulted in major genetic changes and restructuring in reindeer populations. Near-extirpation followed by pronounced genetic drift has altered the allele frequencies of important genes contributing to diverse biological functions. Median heterozygosity was reduced by 26%, while the mitochondrial genetic diversity was reduced only to a limited extent, likely due to already low pre-harvest diversity and a complex post-harvest recolonization process. Such genomic erosion and genetic isolation of populations due to past anthropogenic disturbance will likely play a major role in metapopulation dynamics (i.e., extirpation, recolonization) under further climate change. Our results from a high-arctic case study therefore emphasize the need to understand the long-term interplay of past, current, and future stressors in wildlife conservation.
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Affiliation(s)
- Fabian L Kellner
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
- Centre for Biodiversity Dynamics, Department of Biology, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Mathilde Le Moullec
- Centre for Biodiversity Dynamics, Department of Biology, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
- Department of Mammals and Birds, Greenland Institute of Natural Resources (GINR), Nuuk, Greenland
| | - Martin R Ellegaard
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Jørgen Rosvold
- Department of Terrestrial Biodiversity, Norwegian Institute for Nature Research (NINA), Trondheim, Norway
| | - Bart Peeters
- Centre for Biodiversity Dynamics, Department of Biology, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Hamish A Burnett
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
- Centre for Biodiversity Dynamics, Department of Biology, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | | | - Jaelle C Brealey
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Nicolas Dussex
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Vanessa C Bieker
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Brage B Hansen
- Centre for Biodiversity Dynamics, Department of Biology, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
- Department of Terrestrial Ecology, Norwegian Institute for Nature Research (NINA), Trondheim, Norway
| | - Michael D Martin
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
- Centre for Biodiversity Dynamics, Department of Biology, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
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9
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Payne N, Erwin JA, Morrison JL, Dwyer JF, Culver M. Genomic insights into isolation of the threatened Florida crested caracara (Caracara plancus). J Hered 2024; 115:45-56. [PMID: 37837958 DOI: 10.1093/jhered/esad057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Revised: 09/18/2023] [Accepted: 09/24/2023] [Indexed: 10/16/2023] Open
Abstract
We conducted a population genomic study of the crested caracara (Caracara plancus) using samples (n = 290) collected from individuals in Florida, Texas, and Arizona, United States. Crested caracaras are non-migratory raptors ranging from the southern tip of South America to the southern United States, including a federally protected relict population in Florida long thought to have been isolated since the last ice age. Our objectives were to evaluate genetic diversity and population structure of Florida's apparently isolated population and to evaluate taxonomic relationships of crested caracaras at the northern edge of their range. Using DNA purified from blood samples, we conducted double-digest restriction site associated DNA sequencing and sequenced the mitochondrial ND2 gene. Analyses of population structure using over 9,000 SNPs suggest that two major clusters are best supported, one cluster including only Florida individuals and the other cluster including Arizona and Texas individuals. Both SNPs and mitochondrial haplotypes reveal the Florida population to be highly differentiated genetically from Arizona and Texas populations, whereas, Arizona and Texas populations are moderately differentiated from each other. The Florida population's mitochondrial haplotypes form a separate monophyletic group, while Arizona and Texas populations share mitochondrial haplotypes. Results of this study provide substantial genetic evidence that Florida's crested caracaras have experienced long-term isolation from caracaras in Arizona and Texas and thus, represent a distinct evolutionary lineage possibly warranting distinction as an Evolutionarily Significant Unit (ESU) or subspecies. This study will inform conservation strategies focused on long-term survival of Florida's distinct, panmictic population.
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Affiliation(s)
- Natalie Payne
- Genetics Graduate Interdisciplinary Program, University of Arizona, Tucson, AZ 85719, United States
| | - John A Erwin
- Florida International University College of Law, Miami, FL 33199, United States
| | - Joan L Morrison
- Department of Biology, Trinity College, 300 Summit Street, Hartford, CT 06106, United States
| | - James F Dwyer
- EDM International, Inc., Fort Collins, CO 80525, United States
| | - Melanie Culver
- Genetics Graduate Interdisciplinary Program, University of Arizona, Tucson, AZ 85719, United States
- U.S. Geological Survey, Arizona Cooperative Fish and Wildlife Research Unit, University of Arizona, Tucson, AZ 85721, United States
- School of Natural Resources and the Environment, University of Arizona, Tucson, AZ 85721, United States
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10
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Sang H, Li Y, Tan S, Gao P, Wang B, Guo S, Luo S, Sun C. Conservation genomics analysis reveals recent population decline and possible causes in bumblebee Bombus opulentus. Insect Sci 2024. [PMID: 38297451 DOI: 10.1111/1744-7917.13324] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Revised: 11/29/2023] [Accepted: 12/07/2023] [Indexed: 02/02/2024]
Abstract
Bumblebees are a genus of pollinators (Bombus) that play important roles in natural ecosystem and agricultural production. Several bumblebee species have been recorded as under population decline, and the proportion of species experiencing population decline within subgenus Thoracobombus is higher than average. Bombus opulentus is 1 species in Thoracobombus, but little is known about its recent population dynamics. Here, we employed conservation genomics methods to investigate the population dynamics of B. opulentus during the recent past and identify the likely environmental factors that may cause population decline. Firstly, we placed the scaffold-level of B. opulentus reference genome sequence onto chromosome-level using Hi-C technique. Then, based on this reference genome and whole-genome resequencing data for 51 B. opulentus samples, we reconstructed the population structure and effective population size (Ne ) trajectories of B. opulentus and identified genes that were under positive selection. Our results revealed that the collected B. opulentus samples could be divided into 2 populations, and 1 of them experienced a recent population decline; the declining population also exhibited lower genetic diversity and higher inbreeding levels. Genes related to high-temperature tolerance, immune response, and detoxication showed signals of positive selection in the declining population, suggesting that climate warming and pathogen/pesticide exposures may contribute to the decline of this B. opulentus population. Taken together, our study provided insights into the demography of B. opulentus populations and highlighted that populations of the same bumblebee species could have contrasting Ne trajectories and population decline could be caused by a combination of various stressors.
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Affiliation(s)
- Huiling Sang
- College of Life Sciences, Capital Normal University, Beijing, China
- State Key Laboratory of Resource Insects, Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yancan Li
- State Key Laboratory of Resource Insects, Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, Beijing, China
- Western Research Institute, Chinese Academy of Agricultural Sciences, Changji, Xinjiang, China
| | - Shuxin Tan
- College of Life Sciences, Capital Normal University, Beijing, China
| | - Pu Gao
- College of Life Sciences, Capital Normal University, Beijing, China
| | - Bei Wang
- Yan'an Beekeeping Experimental Station, Yan'an, Shannxi, China
| | - Shengnan Guo
- Hengshui center for Disease Prevention and Control, Hengshui, Hebei, China
| | - Shudong Luo
- State Key Laboratory of Resource Insects, Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, Beijing, China
- Western Research Institute, Chinese Academy of Agricultural Sciences, Changji, Xinjiang, China
| | - Cheng Sun
- College of Life Sciences, Capital Normal University, Beijing, China
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11
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Fleck SJ, Tomlin C, da Silva Coelho FA, Richter M, Danielson ES, Backenstose N, Krabbenhoft T, Lindqvist C, Albert VA. High quality genomes produced from single MinION flow cells clarify polyploid and demographic histories of critically endangered Fraxinus (ash) species. Commun Biol 2024; 7:54. [PMID: 38184717 PMCID: PMC10771460 DOI: 10.1038/s42003-023-05748-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Accepted: 12/27/2023] [Indexed: 01/08/2024] Open
Abstract
With populations of threatened and endangered species declining worldwide, efforts are being made to generate high quality genomic records of these species before they are lost forever. Here, we demonstrate that data from single Oxford Nanopore Technologies (ONT) MinION flow cells can, even in the absence of highly accurate short DNA-read polishing, produce high quality de novo plant genome assemblies adequate for downstream analyses, such as synteny and ploidy evaluations, paleodemographic analyses, and phylogenomics. This study focuses on three North American ash tree species in the genus Fraxinus (Oleaceae) that were recently added to the International Union for Conservation of Nature (IUCN) Red List as critically endangered. Our results support a hexaploidy event at the base of the Oleaceae as well as a subsequent whole genome duplication shared by Syringa, Osmanthus, Olea, and Fraxinus. Finally, we demonstrate the use of ONT long-read sequencing data to reveal patterns in demographic history.
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Affiliation(s)
- Steven J Fleck
- Department of Biological Sciences, University at Buffalo, Buffalo, NY, 14260, USA.
| | - Crystal Tomlin
- Department of Biological Sciences, University at Buffalo, Buffalo, NY, 14260, USA
| | | | - Michaela Richter
- Department of Biological Sciences, University at Buffalo, Buffalo, NY, 14260, USA
| | | | - Nathan Backenstose
- Department of Biological Sciences, University at Buffalo, Buffalo, NY, 14260, USA
| | - Trevor Krabbenhoft
- Department of Biological Sciences, University at Buffalo, Buffalo, NY, 14260, USA
| | - Charlotte Lindqvist
- Department of Biological Sciences, University at Buffalo, Buffalo, NY, 14260, USA
| | - Victor A Albert
- Department of Biological Sciences, University at Buffalo, Buffalo, NY, 14260, USA.
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12
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Mirchandani CD, Shultz AJ, Thomas GWC, Smith SJ, Baylis M, Arnold B, Corbett-Detig R, Enbody E, Sackton TB. A Fast, Reproducible, High-throughput Variant Calling Workflow for Population Genomics. Mol Biol Evol 2024; 41:msad270. [PMID: 38069903 PMCID: PMC10764099 DOI: 10.1093/molbev/msad270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Revised: 10/27/2023] [Accepted: 11/22/2023] [Indexed: 01/05/2024] Open
Abstract
The increasing availability of genomic resequencing data sets and high-quality reference genomes across the tree of life present exciting opportunities for comparative population genomic studies. However, substantial challenges prevent the simple reuse of data across different studies and species, arising from variability in variant calling pipelines, data quality, and the need for computationally intensive reanalysis. Here, we present snpArcher, a flexible and highly efficient workflow designed for the analysis of genomic resequencing data in nonmodel organisms. snpArcher provides a standardized variant calling pipeline and includes modules for variant quality control, data visualization, variant filtering, and other downstream analyses. Implemented in Snakemake, snpArcher is user-friendly, reproducible, and designed to be compatible with high-performance computing clusters and cloud environments. To demonstrate the flexibility of this pipeline, we applied snpArcher to 26 public resequencing data sets from nonmammalian vertebrates. These variant data sets are hosted publicly to enable future comparative population genomic analyses. With its extensibility and the availability of public data sets, snpArcher will contribute to a broader understanding of genetic variation across species by facilitating the rapid use and reuse of large genomic data sets.
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Affiliation(s)
- Cade D Mirchandani
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA 95064, USA
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Allison J Shultz
- Ornithology Department, Natural History Museum of Los Angeles County, Los Angeles, CA 90007, USA
| | | | - Sara J Smith
- Informatics Group, Harvard University, Cambridge, MA, USA
- Biology, Mount Royal University, Calgary, AB T3E 6K6, Canada
| | - Mara Baylis
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA 95064, USA
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Brian Arnold
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, USA
- Center for Statistics and Machine Learning, Princeton University, Princeton, NJ, USA
| | - Russ Corbett-Detig
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA 95064, USA
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Erik Enbody
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA 95064, USA
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13
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Benham PM, Walsh J, Bowie RCK. Spatial variation in population genomic responses to over a century of anthropogenic change within a tidal marsh songbird. Glob Chang Biol 2024; 30:e17126. [PMID: 38273486 DOI: 10.1111/gcb.17126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Revised: 11/22/2023] [Accepted: 12/13/2023] [Indexed: 01/27/2024]
Abstract
Combating the current biodiversity crisis requires the accurate documentation of population responses to human-induced ecological change. However, our ability to pinpoint population responses to human activities is often limited to the analysis of populations studied well after the fact. Museum collections preserve a record of population responses to anthropogenic change that can provide critical baseline data on patterns of genetic diversity, connectivity, and population structure prior to the onset of human perturbation. Here, we leverage a spatially replicated time series of specimens to document population genomic responses to the destruction of nearly 90% of coastal habitats occupied by the Savannah sparrow (Passerculus sandwichensis) in California. We sequenced 219 sparrows collected from 1889 to 2017 across the state of California using an exome capture approach. Spatial-temporal analyses of genetic diversity found that the amount of habitat lost was not predictive of genetic diversity loss. Sparrow populations from southern California historically exhibited lower levels of genetic diversity and experienced the most significant temporal declines in genetic diversity. Despite experiencing the greatest levels of habitat loss, we found that genetic diversity in the San Francisco Bay area remained relatively high. This was potentially related to an observed increase in gene flow into the Bay Area from other populations. While gene flow may have minimized genetic diversity declines, we also found that immigration from inland freshwater-adapted populations into tidal marsh populations led to the erosion of divergence at loci associated with tidal marsh adaptation. Shifting patterns of gene flow through time in response to habitat loss may thus contribute to negative fitness consequences and outbreeding depression. Together, our results underscore the importance of tracing the genomic trajectories of multiple populations over time to address issues of fundamental conservation concern.
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Affiliation(s)
- Phred M Benham
- Museum of Vertebrate Zoology, University of California, Berkeley, Berkeley, California, USA
- Department of Integrative Biology, University of California, Berkeley, Berkeley, California, USA
| | - Jennifer Walsh
- Fuller Evolutionary Biology Program, Cornell Lab of Ornithology, Cornell University, Ithaca, New York, USA
| | - Rauri C K Bowie
- Museum of Vertebrate Zoology, University of California, Berkeley, Berkeley, California, USA
- Department of Integrative Biology, University of California, Berkeley, Berkeley, California, USA
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14
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Feng Y, Comes HP, Chen J, Zhu S, Lu R, Zhang X, Li P, Qiu J, Olsen KM, Qiu Y. Genome sequences and population genomics provide insights into the demographic history, inbreeding, and mutation load of two 'living fossil' tree species of Dipteronia. Plant J 2024; 117:177-192. [PMID: 37797086 DOI: 10.1111/tpj.16486] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Revised: 08/29/2023] [Accepted: 09/20/2023] [Indexed: 10/07/2023]
Abstract
'Living fossils', that is, ancient lineages of low taxonomic diversity, represent an exceptional evolutionary heritage, yet we know little about how demographic history and deleterious mutation load have affected their long-term survival and extinction risk. We performed whole-genome sequencing and population genomic analyses on Dipteronia sinensis and D. dyeriana, two East Asian Tertiary relict trees. We found large-scale genome reorganizations and identified species-specific genes under positive selection that are likely involved in adaptation. Our demographic analyses suggest that the wider-ranged D. sinensis repeatedly recovered from population bottlenecks over late Tertiary/Quaternary periods of adverse climate conditions, while the population size of the narrow-ranged D. dyeriana steadily decreased since the late Miocene, especially after the Last Glacial Maximum (LGM). We conclude that the efficient purging of deleterious mutations in D. sinensis facilitated its survival and repeated demographic recovery. By contrast, in D. dyeriana, increased genetic drift and reduced selection efficacy, due to recent severe population bottlenecks and a likely preponderance of vegetative propagation, resulted in fixation of strongly deleterious mutations, reduced fitness, and continuous population decline, with likely detrimental consequences for the species' future viability and adaptive potential. Overall, our findings highlight the significant impact of demographic history on levels of accumulation and purging of putatively deleterious mutations that likely determine the long-term survival and extinction risk of Tertiary relict trees.
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Affiliation(s)
- Yu Feng
- Systematic & Evolutionary Botany and Biodiversity group, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China
- Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei, 430074, China
| | - Hans Peter Comes
- Department of Environment & Biodiversity, Salzburg University, Salzburg, Austria
| | - Jun Chen
- Systematic & Evolutionary Botany and Biodiversity group, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China
| | - Shanshan Zhu
- Systematic & Evolutionary Botany and Biodiversity group, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Ningbo University, Ningbo, Zhejiang, 315211, China
| | - Ruisen Lu
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, 210014, China
| | - Xinyi Zhang
- Systematic & Evolutionary Botany and Biodiversity group, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China
- Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei, 430074, China
| | - Pan Li
- Systematic & Evolutionary Botany and Biodiversity group, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China
| | - Jie Qiu
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, 200234, China
| | - Kenneth M Olsen
- Department of Biology, Washington University in St Louis, St Louis, Missouri, 63130, USA
| | - Yingxiong Qiu
- Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei, 430074, China
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15
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Minich JJ, Moore ML, Allsing NA, Aylward A, Murray ER, Tran L, Michael TP. Generating high-quality plant and fish reference genomes from field-collected specimens by optimizing preservation. Commun Biol 2023; 6:1246. [PMID: 38071270 PMCID: PMC10710401 DOI: 10.1038/s42003-023-05615-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Accepted: 11/20/2023] [Indexed: 12/18/2023] Open
Abstract
Sample preservation often impedes efforts to generate high-quality reference genomes or pangenomes for Earth's more than 2 million plant and animal species due to nucleotide degradation. Here we compare the impacts of storage methods including solution type, temperature, and time on DNA quality and Oxford Nanopore long-read sequencing quality in 9 fish and 4 plant species. We show 95% ethanol largely protects against degradation for fish blood (22 °C, ≤6 weeks) and plant tissue (4 °C, ≤3 weeks). From this furthest storage timepoint, we assemble high-quality reference genomes of 3 fish and 2 plant species with contiguity (contig N50) and completeness (BUSCO) that achieve the Vertebrate Genome Project benchmarking standards. For epigenetic applications, we also report methylation frequency compared to liquid nitrogen control. The results presented here remove the necessity for cryogenic storage in many long read applications and provide a framework for future studies focused on sampling in remote locations, which may represent a large portion of the future sequencing of novel organisms.
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Affiliation(s)
- Jeremiah J Minich
- The Plant Molecular and Cellular Biology Laboratory, Salk Institute for Biological Studies, 10010 N. Torrey Pines Rd., La Jolla, CA, 92037, USA
| | - Malia L Moore
- The Plant Molecular and Cellular Biology Laboratory, Salk Institute for Biological Studies, 10010 N. Torrey Pines Rd., La Jolla, CA, 92037, USA
- Scripps Institution of Oceanography, University of California San Diego, 8622 Kennel Way, La Jolla, CA, 92093, USA
| | - Nicholas A Allsing
- The Plant Molecular and Cellular Biology Laboratory, Salk Institute for Biological Studies, 10010 N. Torrey Pines Rd., La Jolla, CA, 92037, USA
| | - Anthony Aylward
- The Plant Molecular and Cellular Biology Laboratory, Salk Institute for Biological Studies, 10010 N. Torrey Pines Rd., La Jolla, CA, 92037, USA
| | - Emily R Murray
- The Plant Molecular and Cellular Biology Laboratory, Salk Institute for Biological Studies, 10010 N. Torrey Pines Rd., La Jolla, CA, 92037, USA
| | - Loi Tran
- The Plant Molecular and Cellular Biology Laboratory, Salk Institute for Biological Studies, 10010 N. Torrey Pines Rd., La Jolla, CA, 92037, USA
| | - Todd P Michael
- The Plant Molecular and Cellular Biology Laboratory, Salk Institute for Biological Studies, 10010 N. Torrey Pines Rd., La Jolla, CA, 92037, USA.
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16
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Marino A, Reboud EL, Chevalier E, Tilak MK, Contreras-Garduño J, Nabholz B, Condamine FL. Genomics of the relict species Baronia brevicornis sheds light on its demographic history and genome size evolution across swallowtail butterflies. G3 (Bethesda) 2023; 13:jkad239. [PMID: 37847748 DOI: 10.1093/g3journal/jkad239] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Revised: 05/22/2023] [Accepted: 10/09/2023] [Indexed: 10/19/2023]
Abstract
Relict species, like coelacanth, gingko, tuatara, are the remnants of formerly more ecologically and taxonomically diverse lineages. It raises the questions of why they are currently species-poor, have restrained ecology, and are often vulnerable to extinction. Estimating heterozygosity level and demographic history can guide our understanding of the evolutionary history and conservation status of relict species. However, few studies have focused on relict invertebrates compared to vertebrates. We sequenced the genome of Baronia brevicornis (Lepidoptera: Papilionidae), which is an endangered species, the sister species of all swallowtail butterflies, and is the oldest lineage of all extant butterflies. From a dried specimen, we were able to generate both long-read and short-read data and assembled a genome of 406 Mb for Baronia. We found a fairly high level of heterozygosity (0.58%) compared to other swallowtail butterflies, which contrasts with its endangered and relict status. Taking into account the high ratio of recombination over mutation, demographic analyses indicated a sharp decline of the effective population size initiated in the last million years. Moreover, the Baronia genome was used to study genome size variation in Papilionidae. Genome sizes are mostly explained by transposable elements activities, suggesting that large genomes appear to be a derived feature in swallowtail butterflies as transposable elements activity is recent and involves different transposable elements classes among species. This first Baronia genome provides a resource for assisting conservation in a flagship and relict insect species as well as for understanding swallowtail genome evolution.
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Affiliation(s)
- Alba Marino
- Institut des Sciences de l'Evolution de Montpellier (Université de Montpellier | CNRS | IRD | EPHE), Place Eugène Bataillon, 34095 Montpellier, France
| | - Eliette L Reboud
- Institut des Sciences de l'Evolution de Montpellier (Université de Montpellier | CNRS | IRD | EPHE), Place Eugène Bataillon, 34095 Montpellier, France
| | - Emmanuelle Chevalier
- Institut des Sciences de l'Evolution de Montpellier (Université de Montpellier | CNRS | IRD | EPHE), Place Eugène Bataillon, 34095 Montpellier, France
| | - Marie-Ka Tilak
- Institut des Sciences de l'Evolution de Montpellier (Université de Montpellier | CNRS | IRD | EPHE), Place Eugène Bataillon, 34095 Montpellier, France
| | - Jorge Contreras-Garduño
- Universidad Nacional Autónoma de México, Escuela Nacional de Estudios Superiores, campus Morelia, Antigua Carretera a Pátzcuaro #8701, Col. Ex-Hacienda San José de la Huerta, 58190 Morelia, Michoacán, Mexico
| | - Benoit Nabholz
- Institut des Sciences de l'Evolution de Montpellier (Université de Montpellier | CNRS | IRD | EPHE), Place Eugène Bataillon, 34095 Montpellier, France
- Institut Universitaire de France (IUF), Paris, France
| | - Fabien L Condamine
- Institut des Sciences de l'Evolution de Montpellier (Université de Montpellier | CNRS | IRD | EPHE), Place Eugène Bataillon, 34095 Montpellier, France
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17
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Black JG, van Rooyen ARJ, Heinze D, Gaffney R, Hoffmann AA, Schmidt TL, Weeks AR. Heterogeneous patterns of heterozygosity loss in isolated populations of the threatened eastern barred bandicoot (Perameles gunnii). Mol Ecol 2023. [PMID: 38013623 DOI: 10.1111/mec.17224] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Revised: 11/06/2023] [Accepted: 11/14/2023] [Indexed: 11/29/2023]
Abstract
Identifying and analysing isolated populations is critical for conservation. Isolation can make populations vulnerable to local extinction due to increased genetic drift and inbreeding, both of which should leave imprints of decreased genome-wide heterozygosity. While decreases in heterozygosity among populations are frequently investigated, fewer studies have analysed how heterozygosity varies among individuals, including whether heterozygosity varies geographically along lines of discrete population structure or with continuous patterns analogous to isolation by distance. Here we explore geographical patterns of differentiation and individual heterozygosity in the threatened eastern barred bandicoot (Perameles gunnii) in Tasmania, Australia, using genomic data from 85 samples collected between 2008 and 2011. Our analyses identified two isolated demes undergoing significant genetic drift, and several areas of fine-scale differentiation across Tasmania. We observed discrete genetic structures across geographical barriers and continuous patterns of isolation by distance, with little evidence of recent or historical migration. Using a recently developed analytical pipeline for estimating autosomal heterozygosity, we found individual heterozygosities varied within demes by up to a factor of two, and demes with low-heterozygosity individuals also still contained those with high heterozygosity. Spatial interpolation of heterozygosity scores clarified these patterns and identified the isolated Tasman Peninsula as a location where low-heterozygosity individuals were more common than elsewhere. Our results provide novel insights into the relationship between isolation-driven genetic structure and local heterozygosity patterns. These may help improve translocation efforts, by identifying populations in need of assistance, and by providing an individualised metric for identifying source animals for translocation.
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Affiliation(s)
- John G Black
- School of Biosciences, The University of Melbourne, Melbourne, Victoria, Australia
| | | | - Dean Heinze
- Research Centre of Applied Alpine Ecology, La Trobe University, Melbourne, Victoria, Australia
| | - Robbie Gaffney
- Department of Natural Resources and Environment, Hobart, Tasmania, Australia
| | - Ary A Hoffmann
- School of Biosciences, The University of Melbourne, Melbourne, Victoria, Australia
| | - Thomas L Schmidt
- School of Biosciences, The University of Melbourne, Melbourne, Victoria, Australia
| | - Andrew R Weeks
- School of Biosciences, The University of Melbourne, Melbourne, Victoria, Australia
- Cesar Australia, Brunswick, Victoria, Australia
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18
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Humble E, Hosegood J, Carvalho G, de Bruyn M, Creer S, Stevens GMW, Armstrong A, Bonfil R, Deakos M, Fernando D, Froman N, Peel LR, Pollett S, Ponzo A, Stewart JD, Wintner S, Ogden R. Comparative population genomics of manta rays has global implications for management. Mol Ecol 2023. [PMID: 37994168 DOI: 10.1111/mec.17220] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 11/06/2023] [Accepted: 11/14/2023] [Indexed: 11/24/2023]
Abstract
Understanding population connectivity and genetic diversity is of fundamental importance to conservation. However, in globally threatened marine megafauna, challenges remain due to their elusive nature and wide-ranging distributions. As overexploitation continues to threaten biodiversity across the globe, such knowledge gaps compromise both the suitability and effectiveness of management actions. Here, we use a comparative framework to investigate genetic differentiation and diversity of manta rays, one of the most iconic yet vulnerable groups of elasmobranchs on the planet. Despite their recent divergence, we show how oceanic manta rays (Mobula birostris) display significantly higher heterozygosity than reef manta rays (Mobula alfredi) and that M. birostris populations display higher connectivity worldwide. Through inferring modes of colonization, we reveal how both contemporary and historical forces have likely influenced these patterns, with important implications for population management. Our findings highlight the potential for fisheries to disrupt population dynamics at both local and global scales and therefore have direct relevance for international conservation of marine species.
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Affiliation(s)
- Emily Humble
- Royal (Dick) School of Veterinary Studies and the Roslin Institute, University of Edinburgh, Edinburgh, UK
- The Manta Trust, Catemwood House, Dorset, UK
| | - Jane Hosegood
- The Manta Trust, Catemwood House, Dorset, UK
- Molecular Ecology and Evolution Group, Bangor University, Bangor, UK
| | - Gary Carvalho
- Molecular Ecology and Evolution Group, Bangor University, Bangor, UK
| | - Mark de Bruyn
- Molecular Ecology and Evolution Group, Bangor University, Bangor, UK
- Australian Research Centre for Human Evolution, Griffith University, Nathan, Queensland, Australia
| | - Simon Creer
- Molecular Ecology and Evolution Group, Bangor University, Bangor, UK
| | | | - Amelia Armstrong
- School of Biomedical Sciences, The University of Queensland, St. Lucia, Queensland, Australia
| | - Ramon Bonfil
- Océanos Vivientes AC, Mexico City, Mexico
- Consejo Nacional de Humanidades Ciencia y Tecnología (CONAHCyT), Mexico City, Mexico
- El Colegio de la Frontera Sur, Unidad Chetumal, Chetumal, Mexico
| | - Mark Deakos
- Hawai'i Association for Marine Education and Research, Lahaina, USA
| | - Daniel Fernando
- The Manta Trust, Catemwood House, Dorset, UK
- Blue Resources Trust, Colombo, Sri Lanka
| | - Niv Froman
- The Manta Trust, Catemwood House, Dorset, UK
| | - Lauren R Peel
- The Manta Trust, Catemwood House, Dorset, UK
- Save Our Seas Foundation - D'Arros Research Centre, Geneva, Switzerland
- School of Biological Sciences, Oceans Institute and Oceans Graduate School, The University of Western Australia, Crawley, Western Australia, Australia
| | | | - Alessandro Ponzo
- Large Marine Vertebrates Research Institute Philippines, Jagna, Philippines
| | - Joshua D Stewart
- The Manta Trust, Catemwood House, Dorset, UK
- Ocean Ecology Lab, Marine Mammal Institute, Department of Fisheries, Wildlife & Conservation Sciences, Oregon State University, Newport, Oregon, USA
| | - Sabine Wintner
- KwaZulu-Natal Sharks Board, Umhlanga Rocks, South Africa
- School of Life Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Rob Ogden
- Royal (Dick) School of Veterinary Studies and the Roslin Institute, University of Edinburgh, Edinburgh, UK
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19
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Clark MS, Hoffman JI, Peck LS, Bargelloni L, Gande D, Havermans C, Meyer B, Patarnello T, Phillips T, Stoof-Leichsenring KR, Vendrami DLJ, Beck A, Collins G, Friedrich MW, Halanych KM, Masello JF, Nagel R, Norén K, Printzen C, Ruiz MB, Wohlrab S, Becker B, Dumack K, Ghaderiardakani F, Glaser K, Heesch S, Held C, John U, Karsten U, Kempf S, Lucassen M, Paijmans A, Schimani K, Wallberg A, Wunder LC, Mock T. Multi-omics for studying and understanding polar life. Nat Commun 2023; 14:7451. [PMID: 37978186 PMCID: PMC10656552 DOI: 10.1038/s41467-023-43209-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Accepted: 11/02/2023] [Indexed: 11/19/2023] Open
Abstract
Polar ecosystems are experiencing amongst the most rapid rates of regional warming on Earth. Here, we discuss 'omics' approaches to investigate polar biodiversity, including the current state of the art, future perspectives and recommendations. We propose a community road map to generate and more fully exploit multi-omics data from polar organisms. These data are needed for the comprehensive evaluation of polar biodiversity and to reveal how life evolved and adapted to permanently cold environments with extreme seasonality. We argue that concerted action is required to mitigate the impact of warming on polar ecosystems via conservation efforts, to sustainably manage these unique habitats and their ecosystem services, and for the sustainable bioprospecting of novel genes and compounds for societal gain.
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Affiliation(s)
- M S Clark
- British Antarctic Survey, UKRI-NERC, High Cross, Madingley Road, Cambridge, CB3 0ET, UK.
| | - J I Hoffman
- British Antarctic Survey, UKRI-NERC, High Cross, Madingley Road, Cambridge, CB3 0ET, UK.
- Universität Bielefeld, VHF, Konsequenz 45, 33615, Bielefeld, Germany.
| | - L S Peck
- British Antarctic Survey, UKRI-NERC, High Cross, Madingley Road, Cambridge, CB3 0ET, UK.
| | - L Bargelloni
- Department of Comparative Biomedicine and Food Science, Università degli Studi di Padova, Viale dell'Università 16, I-35020, Legnaro, Italy
| | - D Gande
- Microbial Ecophysiology Group, Faculty of Biology/Chemistry & MARUM, University of Bremen, Leobener Straße 3, 28359, Bremen, Germany
| | - C Havermans
- Alfred-Wegener-Institut Helmholtz-Zentrum für Polar- und Meeresforschung, Am Handelshafen 12, 27570, Bremerhaven, Germany
| | - B Meyer
- Alfred-Wegener-Institut Helmholtz-Zentrum für Polar- und Meeresforschung, Am Handelshafen 12, 27570, Bremerhaven, Germany
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany
- Helmholtz Institute for Functional Marine Biodiversity at the University of Oldenburg (HIFMB), 23129, Oldenburg, Germany
| | - T Patarnello
- Department of Comparative Biomedicine and Food Science, Università degli Studi di Padova, Viale dell'Università 16, I-35020, Legnaro, Italy
| | - T Phillips
- British Antarctic Survey, UKRI-NERC, High Cross, Madingley Road, Cambridge, CB3 0ET, UK
| | - K R Stoof-Leichsenring
- Alfred-Wegener-Institute Helmholtz Centre for Polar and Marine Research, 14473, Potsdam, Germany
| | - D L J Vendrami
- Universität Bielefeld, VHF, Konsequenz 45, 33615, Bielefeld, Germany
| | - A Beck
- Staatliche Naturwissenschaftliche Sammlungen Bayerns, Botanische Staatssammlung München (SNSB-BSM), Menzinger Str. 67, 80638, München, Germany
| | - G Collins
- Senckenberg Biodiversity and Climate Research Centre & Loewe-Centre for Translational Biodiversity Genomics, Senckenberganlage 25, 60325, Frankfurt am Main, Germany
- Manaaki Whenua-Landcare Research, 231 Morrin Road St Johns, Auckland, 1072, New Zealand
| | - M W Friedrich
- Microbial Ecophysiology Group, Faculty of Biology/Chemistry & MARUM, University of Bremen, Leobener Straße 3, 28359, Bremen, Germany
| | - K M Halanych
- Center for Marine Science, University of North Carolina, 5600 Marvin K. Moss Lane, Wilmington, NC, 28409, USA
| | - J F Masello
- Universität Bielefeld, VHF, Konsequenz 45, 33615, Bielefeld, Germany
- Justus-Liebig-Universität Gießen, Giessen, Germany
| | - R Nagel
- Universität Bielefeld, VHF, Konsequenz 45, 33615, Bielefeld, Germany
- School of Biology, University of St Andrews, St Andrews, Fife, KY16 9TH, UK
| | - K Norén
- Department of Zoology, Stockholm University, 106 91, Stockholm, Sweden
| | - C Printzen
- Senckenberg Biodiversity and Climate Research Centre & Loewe-Centre for Translational Biodiversity Genomics, Senckenberganlage 25, 60325, Frankfurt am Main, Germany
- Natural History Museum Frankfurt, Senckenberganlage 25, 60325, Frankfurt am Main, Germany
| | - M B Ruiz
- Alfred-Wegener-Institut Helmholtz-Zentrum für Polar- und Meeresforschung, Am Handelshafen 12, 27570, Bremerhaven, Germany
- Universität Duisburg-Essen, Universitätstrasse 5, 45151, Essen, Germany
| | - S Wohlrab
- Alfred-Wegener-Institut Helmholtz-Zentrum für Polar- und Meeresforschung, Am Handelshafen 12, 27570, Bremerhaven, Germany
- Helmholtz Institute for Functional Marine Biodiversity at the University of Oldenburg (HIFMB), 23129, Oldenburg, Germany
| | - B Becker
- Universität zu Köln, Institut für Pflanzenwissenschaften, Zülpicher Str. 47b, 60674, Köln, Germany
| | - K Dumack
- Universität zu Köln, Terrestrische Ökologie, Zülpicher Str. 47b, 60674, Köln, Germany
| | - F Ghaderiardakani
- Institute for Inorganic and Analytical Chemistry, Friedrich Schiller University Jena, Lessingstraße 8, 07743, Jena, Germany
| | - K Glaser
- Institute of Biological Sciences, Applied Ecology and Phycology, University of Rostock, Albert-Einstein-Straße 3, 18059, Rostock, Germany
| | - S Heesch
- Institute of Biological Sciences, Applied Ecology and Phycology, University of Rostock, Albert-Einstein-Straße 3, 18059, Rostock, Germany
| | - C Held
- Alfred-Wegener-Institut Helmholtz-Zentrum für Polar- und Meeresforschung, Am Handelshafen 12, 27570, Bremerhaven, Germany
| | - U John
- Alfred-Wegener-Institut Helmholtz-Zentrum für Polar- und Meeresforschung, Am Handelshafen 12, 27570, Bremerhaven, Germany
| | - U Karsten
- Institute of Biological Sciences, Applied Ecology and Phycology, University of Rostock, Albert-Einstein-Straße 3, 18059, Rostock, Germany
| | - S Kempf
- Alfred-Wegener-Institut Helmholtz-Zentrum für Polar- und Meeresforschung, Am Handelshafen 12, 27570, Bremerhaven, Germany
| | - M Lucassen
- Alfred-Wegener-Institut Helmholtz-Zentrum für Polar- und Meeresforschung, Am Handelshafen 12, 27570, Bremerhaven, Germany
| | - A Paijmans
- Universität Bielefeld, VHF, Konsequenz 45, 33615, Bielefeld, Germany
| | - K Schimani
- Botanischer Garten und Botanisches Museum Berlin, Freie Universität Berlin, Königin-Luise-Straße 6-8, 14195, Berlin, Germany
| | - A Wallberg
- Department of Medical Biochemistry and Microbiology, Uppsala University, Husargatan 3, 751 23, Uppsala, Sweden
| | - L C Wunder
- Microbial Ecophysiology Group, Faculty of Biology/Chemistry & MARUM, University of Bremen, Leobener Straße 3, 28359, Bremen, Germany
| | - T Mock
- School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK.
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20
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Mathur S, Mason AJ, Bradburd GS, Gibbs HL. Functional genomic diversity is correlated with neutral genomic diversity in populations of an endangered rattlesnake. Proc Natl Acad Sci U S A 2023; 120:e2303043120. [PMID: 37844221 PMCID: PMC10614936 DOI: 10.1073/pnas.2303043120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Accepted: 09/19/2023] [Indexed: 10/18/2023] Open
Abstract
Theory predicts that genetic erosion in small, isolated populations of endangered species can be assessed using estimates of neutral genetic variation, yet this widely used approach has recently been questioned in the genomics era. Here, we leverage a chromosome-level genome assembly of an endangered rattlesnake (Sistrurus catenatus) combined with whole genome resequencing data (N = 110 individuals) to evaluate the relationship between levels of genome-wide neutral and functional diversity over historical and future timescales. As predicted, we found positive correlations between genome-wide estimates of neutral genetic diversity (π) and inferred levels of adaptive variation and an estimate of inbreeding mutation load, and a negative relationship between neutral diversity and an estimate of drift mutation load. However, these correlations were half as strong for projected future levels of neutral diversity based on contemporary effective population sizes. Broadly, our results confirm that estimates of neutral genetic diversity provide an accurate measure of genetic erosion in populations of a threatened vertebrate. They also provide nuance to the neutral-functional diversity controversy by suggesting that while these correlations exist, anthropogenetic impacts may have weakened these associations in the recent past and into the future.
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Affiliation(s)
- Samarth Mathur
- Department of Evolution, Ecology, and Organismal Biology, The Ohio State University, Columbus, OH48824
- Ohio Biodiversity Conservation Partnership, The Ohio State University, Columbus, OH43210
| | - Andrew J. Mason
- Department of Evolution, Ecology, and Organismal Biology, The Ohio State University, Columbus, OH48824
- Ohio Biodiversity Conservation Partnership, The Ohio State University, Columbus, OH43210
| | - Gideon S. Bradburd
- Evolution and Behavior Program, Department of Integrative Biology, Ecology, Michigan State University, East Lansing, MI48824
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI48109
| | - H. Lisle Gibbs
- Department of Evolution, Ecology, and Organismal Biology, The Ohio State University, Columbus, OH48824
- Ohio Biodiversity Conservation Partnership, The Ohio State University, Columbus, OH43210
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21
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Rasmussen L, Fontsere C, Soto-Calderón ID, Guillen R, Savage A, Hansen AJ, Hvilsom C, Gilbert MTP. Assessing the genetic composition of cotton-top tamarins (Saguinus oedipus) before sweeping anthropogenic impact. Mol Ecol 2023; 32:5514-5527. [PMID: 37702122 DOI: 10.1111/mec.17130] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Revised: 08/14/2023] [Accepted: 08/30/2023] [Indexed: 09/14/2023]
Abstract
During the last century, the critically endangered cotton-top tamarin (Saguinus oedipus) has been threatened by multiple anthropogenic factors that drastically affected their habitat and population size. As the genetic impact of these pressures is largely unknown, this study aimed to establish a genetic baseline with the use of temporal sampling to determine the genetic makeup before detrimental anthropogenic impact. Genomes were resequenced from a combination of historical museum samples and modern wild samples at low-medium coverage, to unravel how the cotton-top tamarin population structure and genomic diversity may have changed during this period. Our data suggest two populations can be differentiated, probably separated historically by the mountain ranges of the Paramillo Massif in Colombia. Although this population structure persists in the current populations, modern samples exhibit genomic signals consistent with recent inbreeding, such as long runs of homozygosity and a reduction in genome-wide heterozygosity especially in the greater northeast population. This loss is likely the consequence of the population reduction following the mass exportation of cotton-top tamarins for biomedical research in the 1960s, coupled with the habitat loss this species continues to experience. However, current populations have not experienced an increase in genetic load. We propose that the historical genetic baseline established in this study can be used to provide insight into alteration in the modern population influenced by a drastic reduction in population size as well as providing background information to be used for future conservation decision-making for the species.
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Affiliation(s)
- Linett Rasmussen
- Center for Evolutionary Hologenomics, The Globe Institute, University of Copenhagen, Copenhagen, Denmark
- Research and Conservation, Copenhagen Zoo, Frederiksberg, Denmark
| | - Claudia Fontsere
- Center for Evolutionary Hologenomics, The Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Iván D Soto-Calderón
- Laboratorio de Genética Animal. Grupo Agrociencias, Biodiversidad y Territorio, Instituto de Biología, Facultad de Ciencias Exactas y Naturales, Universidad de Antioquia, Medellín, Medellín, Colombia
| | | | | | - Anders Johannes Hansen
- Center for Evolutionary Hologenomics, The Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | | | - M Thomas P Gilbert
- Center for Evolutionary Hologenomics, The Globe Institute, University of Copenhagen, Copenhagen, Denmark
- University Museum, NTNU, Trondheim, Norway
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22
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Martchenko D, Shafer ABA. Contrasting whole-genome and reduced representation sequencing for population demographic and adaptive inference: an alpine mammal case study. Heredity (Edinb) 2023; 131:273-281. [PMID: 37532838 PMCID: PMC10539292 DOI: 10.1038/s41437-023-00643-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2022] [Revised: 07/22/2023] [Accepted: 07/22/2023] [Indexed: 08/04/2023] Open
Abstract
Genomes capture the adaptive and demographic history of a species, but the choice of sequencing strategy and sample size can impact such inferences. We compared whole genome and reduced representation sequencing approaches to study the population demographic and adaptive signals of the North American mountain goat (Oreamnos americanus). We applied the restriction site-associated DNA sequencing (RADseq) approach to 254 individuals and whole genome resequencing (WGS) approach to 35 individuals across the species range at mid-level coverage (9X) and to 5 individuals at high coverage (30X). We used ANGSD to estimate the genotype likelihoods and estimated the effective population size (Ne), population structure, and explicitly modelled the demographic history with δaδi and MSMC2. The data sets were overall concordant in supporting a glacial induced vicariance and extremely low Ne in mountain goats. We evaluated a set of climatic variables and geographic location as predictors of genetic diversity using redundancy analysis. A moderate proportion of total variance (36% for WGS and 21% for RADseq data sets) was explained by geography and climate variables; both data sets support a large impact of drift and some degree of local adaptation. The empirical similarities of WGS and RADseq presented herein reassuringly suggest that both approaches will recover large demographic and adaptive signals in a population; however, WGS offers several advantages over RADseq, such as inferring adaptive processes and calculating runs-of-homozygosity estimates. Considering the predicted climate-induced changes in alpine environments and the genetically depauperate mountain goat, the long-term adaptive capabilities of this enigmatic species are questionable.
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Affiliation(s)
- Daria Martchenko
- Environmental and Life Sciences Graduate Program, Trent University, 2140 East Bank Drive, Peterborough, ON, K9J 7B8, Canada.
| | - Aaron B A Shafer
- Environmental and Life Sciences Graduate Program, Trent University, 2140 East Bank Drive, Peterborough, ON, K9J 7B8, Canada
- Department of Forensics & Environmental and Life Sciences Graduate Program, Trent University, 2140 East Bank Drive, Peterborough, ON, K9J 7B8, Canada
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23
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Skorupski J, Brandes F, Seebass C, Festl W, Śmietana P, Balacco J, Jain N, Tilley T, Abueg L, Wood J, Sims Y, Formenti G, Fedrigo O, Jarvis ED. Prioritizing Endangered Species in Genome Sequencing: Conservation Genomics in Action with the First Platinum-Standard Reference-Quality Genome of the Critically Endangered European Mink Mustela lutreola L., 1761. Int J Mol Sci 2023; 24:14816. [PMID: 37834264 PMCID: PMC10573602 DOI: 10.3390/ijms241914816] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Revised: 09/23/2023] [Accepted: 09/26/2023] [Indexed: 10/15/2023] Open
Abstract
The European mink Mustela lutreola (Mustelidae) ranks among the most endangered mammalian species globally, experiencing a rapid and severe decline in population size, density, and distribution. Given the critical need for effective conservation strategies, understanding its genomic characteristics becomes paramount. To address this challenge, the platinum-quality, chromosome-level reference genome assembly for the European mink was successfully generated under the project of the European Mink Centre consortium. Leveraging PacBio HiFi long reads, we obtained a 2586.3 Mbp genome comprising 25 scaffolds, with an N50 length of 154.1 Mbp. Through Hi-C data, we clustered and ordered the majority of the assembly (>99.9%) into 20 chromosomal pseudomolecules, including heterosomes, ranging from 6.8 to 290.1 Mbp. The newly sequenced genome displays a GC base content of 41.9%. Additionally, we successfully assembled the complete mitochondrial genome, spanning 16.6 kbp in length. The assembly achieved a BUSCO (Benchmarking Universal Single-Copy Orthologs) completeness score of 98.2%. This high-quality reference genome serves as a valuable genomic resource for future population genomics studies concerning the European mink and related taxa. Furthermore, the newly assembled genome holds significant potential in addressing key conservation challenges faced by M. lutreola. Its applications encompass potential revision of management units, assessment of captive breeding impacts, resolution of phylogeographic questions, and facilitation of monitoring and evaluating the efficiency and effectiveness of dedicated conservation strategies for the European mink. This species serves as an example that highlights the paramount importance of prioritizing endangered species in genome sequencing projects due to the race against time, which necessitates the comprehensive exploration and characterization of their genomic resources before their populations face extinction.
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Affiliation(s)
- Jakub Skorupski
- Institute of Marine and Environmental Sciences, University of Szczecin, Wąska 13 St., 71-415 Szczecin, Poland
- Polish Society for Conservation Genetics LUTREOLA, Maciejkowa 21 St., 71-784 Szczecin, Poland
| | - Florian Brandes
- Wildtier- und Artenschutzstation e.V., Hohe Warte 1, 31553 Sachsenhagen, Germany
| | | | - Wolfgang Festl
- EuroNerz e.V., Kleine Gildewart 3, 49074 Osnabrück, Germany
| | - Przemysław Śmietana
- Institute of Marine and Environmental Sciences, University of Szczecin, Wąska 13 St., 71-415 Szczecin, Poland
- Polish Society for Conservation Genetics LUTREOLA, Maciejkowa 21 St., 71-784 Szczecin, Poland
| | - Jennifer Balacco
- Vertebrate Genome Laboratory, The Rockefeller University, 1230 York Avenue, Box 366, New York, NY 10065, USA
| | - Nivesh Jain
- Vertebrate Genome Laboratory, The Rockefeller University, 1230 York Avenue, Box 366, New York, NY 10065, USA
| | - Tatiana Tilley
- Vertebrate Genome Laboratory, The Rockefeller University, 1230 York Avenue, Box 366, New York, NY 10065, USA
| | - Linelle Abueg
- Vertebrate Genome Laboratory, The Rockefeller University, 1230 York Avenue, Box 366, New York, NY 10065, USA
| | - Jonathan Wood
- Vertebrate Genome Laboratory, The Rockefeller University, 1230 York Avenue, Box 366, New York, NY 10065, USA
| | - Ying Sims
- Vertebrate Genome Laboratory, The Rockefeller University, 1230 York Avenue, Box 366, New York, NY 10065, USA
| | - Giulio Formenti
- Vertebrate Genome Laboratory, The Rockefeller University, 1230 York Avenue, Box 366, New York, NY 10065, USA
| | - Olivier Fedrigo
- Vertebrate Genome Laboratory, The Rockefeller University, 1230 York Avenue, Box 366, New York, NY 10065, USA
| | - Erich D. Jarvis
- Vertebrate Genome Laboratory, The Rockefeller University, 1230 York Avenue, Box 366, New York, NY 10065, USA
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24
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DeSaix MG, Anderson EC, Bossu CM, Rayne CE, Schweizer TM, Bayly NJ, Narang DS, Hagelin JC, Gibbs HL, Saracco JF, Sherry TW, Webster MS, Smith TB, Marra PP, Ruegg KC. Low-coverage whole genome sequencing for highly accurate population assignment: Mapping migratory connectivity in the American Redstart (Setophaga ruticilla). Mol Ecol 2023; 32:5528-5540. [PMID: 37706673 DOI: 10.1111/mec.17137] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 08/26/2023] [Accepted: 09/04/2023] [Indexed: 09/15/2023]
Abstract
Understanding the geographic linkages among populations across the annual cycle is an essential component for understanding the ecology and evolution of migratory species and for facilitating their effective conservation. While genetic markers have been widely applied to describe migratory connections, the rapid development of new sequencing methods, such as low-coverage whole genome sequencing (lcWGS), provides new opportunities for improved estimates of migratory connectivity. Here, we use lcWGS to identify fine-scale population structure in a widespread songbird, the American Redstart (Setophaga ruticilla), and accurately assign individuals to genetically distinct breeding populations. Assignment of individuals from the nonbreeding range reveals population-specific patterns of varying migratory connectivity. By combining migratory connectivity results with demographic analysis of population abundance and trends, we consider full annual cycle conservation strategies for preserving numbers of individuals and genetic diversity. Notably, we highlight the importance of the Northern Temperate-Greater Antilles migratory population as containing the largest proportion of individuals in the species. Finally, we highlight valuable considerations for other population assignment studies aimed at using lcWGS. Our results have broad implications for improving our understanding of the ecology and evolution of migratory species through conservation genomics approaches.
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Affiliation(s)
- Matthew G DeSaix
- Department of Biology, Colorado State University, Fort Collins, Colorado, USA
| | - Eric C Anderson
- Department of Biology, Colorado State University, Fort Collins, Colorado, USA
- Fisheries Ecology Division, Southwest Fisheries Science Center, National Marine Fisheries Service, NOAA, Santa Cruz, California, USA
- Department of Fisheries, Wildlife, and Conservation Biology, Colorado State University, Fort Collins, Colorado, USA
| | - Christen M Bossu
- Department of Biology, Colorado State University, Fort Collins, Colorado, USA
| | - Christine E Rayne
- Department of Biology, Colorado State University, Fort Collins, Colorado, USA
| | - Teia M Schweizer
- Department of Fisheries, Wildlife, and Conservation Biology, Colorado State University, Fort Collins, Colorado, USA
| | - Nicholas J Bayly
- SELVA Investigación para la conservación en el Neotropico, DG42A #20-37, Bogotá, Colombia
| | - Darshan S Narang
- Trinidad and Tobago Field Naturalists' Club, Port of Spain, Trinidad and Tobago
| | - Julie C Hagelin
- Threatened, Endangered and Diversity Program, Alaska Department of Fish and Game, Fairbanks, Alaska, USA
| | - H Lisle Gibbs
- Department of Evolution, Ecology, and Organismal Biology, The Ohio State University, Columbus, Ohio, USA
- Ohio Biodiversity Conservation Partnership, The Ohio State University, Columbus, Ohio, USA
| | - James F Saracco
- The Institute for Bird Populations, Petaluma, California, USA
| | - Thomas W Sherry
- Department of Ecology and Evolutionary Biology, Tulane University, New Orleans, Louisiana, USA
- Department of Biological Sciences, Dartmouth College, Hanover, New Hampshire, USA
| | - Michael S Webster
- Cornell Lab of Ornithology, Ithaca, New York, USA
- Department of Neurobiology and Behavior, Cornell University, Ithaca, New York, USA
| | - Thomas B Smith
- Center for Tropical Research, Institute of the Environment & Sustainability, University of California Los Angeles, Los Angeles, California, USA
- Department of Ecology and Evolutionary Biology, University of California Los Angeles, Los Angeles, California, USA
| | - Peter P Marra
- Department of Biology, Georgetown University, Washington, District of Columbia, USA
- McCourt School of Public Policy, Georgetown University, Washington, District of Columbia, USA
| | - Kristen C Ruegg
- Department of Biology, Colorado State University, Fort Collins, Colorado, USA
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25
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Alexandre NM, Cameron AC, Tian D, Chatla K, Kolora SRR, Whiteman NK, Turner TF, Reinthal PN. Chromosome-level reference genomes of two imperiled desert fishes: spikedace (Meda fulgida) and loach minnow (Tiaroga cobitis). G3 (Bethesda) 2023; 13:jkad157. [PMID: 37466215 PMCID: PMC10542311 DOI: 10.1093/g3journal/jkad157] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Revised: 06/21/2023] [Accepted: 06/28/2023] [Indexed: 07/20/2023]
Abstract
North American minnows (Cypriniformes: Leuciscidae) comprise a diverse taxonomic group, but many members, particularly those inhabiting deserts, face elevated extinction risks. Despite conservation concerns, leuciscids remain under sampled for reference assemblies relative to other groups of freshwater fishes. Here, we present 2 chromosome-scale reference genome assemblies spikedace (Meda fulgida) and loach minnow (Tiaroga cobitis) using PacBio, Illumina and Omni-C technologies. The complete assembly for spikedace was 882.1 Mb in total length comprised of 83 scaffolds with N50 = 34.8 Mb, L50 = 11, N75 = 32.3 Mb, and L75 = 18. The complete assembly for loach minnow was 1.3 Gb in total length comprised of 550 scaffolds with N50 = 48.6 Mb, L50 = 13, N75 = 42.3 Mb, and L75 = 20. Completeness assessed via Benchmarking Universal Single-Copy Orthologues (BUSCO) metrics using the Actinopterygii BUSCO database showed ∼97% for spikedace and ∼98% for loach minnow of complete BUSCO proportions. Annotation revealed approximately 32.58 and 29.04% of spikedace and loach minnow total genome lengths to be comprised of protein-coding genes, respectively. Comparative genomic analyses of these endangered and co-distributed fishes revealed widespread structural variants, gene family expansions, and evidence of positive selection in both genomes.
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Affiliation(s)
- Nicolas M Alexandre
- Department of Integrative Biology, University of California, Berkeley, CA 94720, USA
- Museum of Vertebrate Zoology, Berkeley, CA 94720, USA
| | - Alexander C Cameron
- Museum of Southwestern Biology and Department of Biology, University of New Mexico, Albuquerque, NM 87131, USA
| | - David Tian
- Department of Integrative Biology, University of California, Berkeley, CA 94720, USA
- Museum of Vertebrate Zoology, Berkeley, CA 94720, USA
| | - Kamalakar Chatla
- Department of Integrative Biology, University of California, Berkeley, CA 94720, USA
- Museum of Vertebrate Zoology, Berkeley, CA 94720, USA
| | - Sree R R Kolora
- Department of Integrative Biology, University of California, Berkeley, CA 94720, USA
- Museum of Vertebrate Zoology, Berkeley, CA 94720, USA
| | - Noah K Whiteman
- Department of Integrative Biology, University of California, Berkeley, CA 94720, USA
- Museum of Vertebrate Zoology, Berkeley, CA 94720, USA
| | - Thomas F Turner
- Museum of Southwestern Biology and Department of Biology, University of New Mexico, Albuquerque, NM 87131, USA
| | - Peter N Reinthal
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721, USA
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San MH, Kawamura Y, Kimura K, Witharana EP, Shimogiri T, Aye SS, Min TT, Aung C, Khaing MM, Nagano Y. Characterization and organelle genome sequencing of Pyropia species from Myanmar. Sci Rep 2023; 13:15677. [PMID: 37735516 PMCID: PMC10514050 DOI: 10.1038/s41598-023-42262-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Accepted: 09/07/2023] [Indexed: 09/23/2023] Open
Abstract
Pyropia is a genus comprising red algae of the Bangiaceae family that is commonly found in intertidal zones worldwide. However, understanding of Pyropia species that are prone to tropical regions remains limited despite recent breakthroughs in genomic research. Within the realm of Pyropia species thriving in tropical regions, P. vietnamensis stands out as a widely recognized species. In this study, we aimed to investigate Pyropia species in the southwest coast of Myanmar using physiological and molecular approaches, culture-based analyses, chloroplast rbcL and nuclear SSU gene sequencing, and whole chloroplast and mitochondrial genome sequencing. Physiological analysis showed that the Myanmar samples were more heat-tolerant than their Japanese counterparts, including those of subtropical origin. Additionally, molecular characterization revealed that the Myanmar samples were closely related to P. vietnamensis from India. This study is the first to sequence the chloroplast and mitochondrial genomes of Pyropia species from tropical regions. A unique deletion event was observed within a ribosomal RNA gene cluster in the chloroplast genome of the studied Pyropia species, which is a deviation from the usual characteristics of most Pyropia species. This study improves current understanding of the physiological and molecular characteristics of this comparatively understudied Pyropia species that grows in tropical regions.
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Affiliation(s)
- Myat Htoo San
- The United Graduate School of Agricultural Sciences, Kagoshima University, Kagoshima, Japan.
- Analytical Research Center for Experimental Sciences, Saga University, Saga, Japan.
| | | | - Kei Kimura
- The United Graduate School of Agricultural Sciences, Kagoshima University, Kagoshima, Japan
- Faculty of Agriculture, Saga University, Saga, Japan
| | | | - Takeshi Shimogiri
- The United Graduate School of Agricultural Sciences, Kagoshima University, Kagoshima, Japan
- Faculty of Agriculture, Kagoshima University, Kagoshima, Japan
| | | | - Thu Thu Min
- Marine Science Department, Pathein University, Pathein, Myanmar
| | - Cherry Aung
- Marine Science Department, Myeik University, Myeik, Myanmar
| | | | - Yukio Nagano
- The United Graduate School of Agricultural Sciences, Kagoshima University, Kagoshima, Japan.
- Analytical Research Center for Experimental Sciences, Saga University, Saga, Japan.
- Graduate School of Advanced Health Science, Saga University, Saga, Japan.
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27
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López A, Carreras C, Pascual M, Pegueroles C. Evaluating restriction enzyme selection for reduced representation sequencing in conservation genomics. Mol Ecol Resour 2023. [PMID: 37706675 DOI: 10.1111/1755-0998.13865] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2022] [Revised: 07/28/2023] [Accepted: 08/09/2023] [Indexed: 09/15/2023]
Abstract
Conservation genomic studies in non-model organisms generally rely on reduced representation sequencing techniques based on restriction enzymes to identify population structure as well as candidate loci for local adaptation. While the expectation is that the reduced representation of the genome is randomly distributed, the proportion of the genome sampled might depend on the GC content of the recognition site of the restriction enzyme used. Here, we evaluated the distribution and functional composition of loci obtained after a reduced representation approach using Genotyping-by-Sequencing (GBS). To do so, we compared experimental data from two endemic fish species (Symphodus ocellatus and Symphodus tinca, EcoT22I enzyme) and two ecosystem engineer sea urchins (Paracentrotus lividus and Arbacia lixula, ApeKI enzyme). In brief, we mapped the sequenced loci to the phylogenetically closest reference genome available (Labrus bergylta in the fish and Strongylocentrotus purpuratus in the sea urchin datasets), classified them as exonic, intronic and intergenic, and studied their function by using Gene Ontology (GO) terms. We also simulated the effect of using both enzymes in the two reference genomes. In both simulated and experimental data, we detected an enrichment towards exonic or intergenic regions depending on the restriction enzyme used and failed to detect differences between total loci and candidate loci for adaptation in the empirical dataset. Most of the functions assigned to the mapped loci were shared between the four species and involved a myriad of general functions. Our results highlight the importance of restriction enzyme selection and the need for high-quality annotated genomes in conservation genomic studies.
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Affiliation(s)
- Ainhoa López
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia, Universitat de Barcelona (UB), Barcelona, Spain
- Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona (UB), Barcelona, Spain
| | - Carlos Carreras
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia, Universitat de Barcelona (UB), Barcelona, Spain
- Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona (UB), Barcelona, Spain
| | - Marta Pascual
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia, Universitat de Barcelona (UB), Barcelona, Spain
- Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona (UB), Barcelona, Spain
| | - Cinta Pegueroles
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia, Universitat de Barcelona (UB), Barcelona, Spain
- Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona (UB), Barcelona, Spain
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28
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Nigenda-Morales SF, Lin M, Nuñez-Valencia PG, Kyriazis CC, Beichman AC, Robinson JA, Ragsdale AP, Urbán R J, Archer FI, Viloria-Gómora L, Pérez-Álvarez MJ, Poulin E, Lohmueller KE, Moreno-Estrada A, Wayne RK. The genomic footprint of whaling and isolation in fin whale populations. Nat Commun 2023; 14:5465. [PMID: 37699896 PMCID: PMC10497599 DOI: 10.1038/s41467-023-40052-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Accepted: 07/10/2023] [Indexed: 09/14/2023] Open
Abstract
Twentieth century industrial whaling pushed several species to the brink of extinction, with fin whales being the most impacted. However, a small, resident population in the Gulf of California was not targeted by whaling. Here, we analyzed 50 whole-genomes from the Eastern North Pacific (ENP) and Gulf of California (GOC) fin whale populations to investigate their demographic history and the genomic effects of natural and human-induced bottlenecks. We show that the two populations diverged ~16,000 years ago, after which the ENP population expanded and then suffered a 99% reduction in effective size during the whaling period. In contrast, the GOC population remained small and isolated, receiving less than one migrant per generation. However, this low level of migration has been crucial for maintaining its viability. Our study exposes the severity of whaling, emphasizes the importance of migration, and demonstrates the use of genome-based analyses and simulations to inform conservation strategies.
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Affiliation(s)
- Sergio F Nigenda-Morales
- Advanced Genomics Unit, National Laboratory of Genomics for Biodiversity (Langebio), Center for Research and Advanced Studies (Cinvestav), Irapuato, Guanajuato, 36824, Mexico.
- Department of Biological Sciences, California State University San Marcos, San Marcos, CA, 92096, USA.
| | - Meixi Lin
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, CA, 90095, USA.
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA, 94305, USA.
| | - Paulina G Nuñez-Valencia
- Advanced Genomics Unit, National Laboratory of Genomics for Biodiversity (Langebio), Center for Research and Advanced Studies (Cinvestav), Irapuato, Guanajuato, 36824, Mexico
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México (UNAM), Cuernavaca, Morelos, México
| | - Christopher C Kyriazis
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - Annabel C Beichman
- Department of Genome Sciences, University of Washington, Seattle, WA, 98195, USA
| | - Jacqueline A Robinson
- Institute for Human Genetics, University of California, San Francisco (UCSF), San Francisco, CA, 94143, USA
| | - Aaron P Ragsdale
- Advanced Genomics Unit, National Laboratory of Genomics for Biodiversity (Langebio), Center for Research and Advanced Studies (Cinvestav), Irapuato, Guanajuato, 36824, Mexico
- Department of Integrative Biology, University of Wisconsin, Madison, WI, 53706, USA
| | - Jorge Urbán R
- Departamento de Ciencias Marinas y Costeras, Universidad Autónoma de Baja California Sur (UABCS), La Paz, Baja California Sur, Mexico
| | - Frederick I Archer
- Marine Mammal and Turtle Division, Southwest Fisheries Science Center, La Jolla, CA, 92037, USA
| | - Lorena Viloria-Gómora
- Departamento de Ciencias Marinas y Costeras, Universidad Autónoma de Baja California Sur (UABCS), La Paz, Baja California Sur, Mexico
| | - María José Pérez-Álvarez
- Escuela de Medicina Veterinaria, Facultad de Medicina y Ciencias de la Salud, Universidad Mayor, Santiago, Chile
- Millennium Institute Biodiversity of Antarctic and Subantarctic Ecosystems (BASE), Universidad de Chile, Santiago, Chile
| | - Elie Poulin
- Millennium Institute Biodiversity of Antarctic and Subantarctic Ecosystems (BASE), Universidad de Chile, Santiago, Chile
| | - Kirk E Lohmueller
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, CA, 90095, USA.
- Interdepartmental Program in Bioinformatics, University of California, Los Angeles, CA, 90095, USA.
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, CA, USA.
| | - Andrés Moreno-Estrada
- Advanced Genomics Unit, National Laboratory of Genomics for Biodiversity (Langebio), Center for Research and Advanced Studies (Cinvestav), Irapuato, Guanajuato, 36824, Mexico.
| | - Robert K Wayne
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, CA, 90095, USA
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Swift DG, O'Leary SJ, Grubbs RD, Frazier BS, Fields AT, Gardiner JM, Drymon JM, Bethea DM, Wiley TR, Portnoy DS. Philopatry influences the genetic population structure of the blacktip shark (Carcharhinus limbatus) at multiple spatial scales. Mol Ecol 2023; 32:4953-4970. [PMID: 37566208 DOI: 10.1111/mec.17096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Revised: 07/22/2023] [Accepted: 07/28/2023] [Indexed: 08/12/2023]
Abstract
Understanding how interactions among microevolutionary forces generate genetic population structure of exploited species is vital to the implementation of management policies that facilitate persistence. Philopatry displayed by many coastal shark species can impact gene flow and facilitate selection, and has direct implications for the spatial scales of management. Here, genetic structure of the blacktip shark (Carcharhinus limbatus) was examined using a mixed-marker approach employing mitochondrial control region sequences and 4339 SNP-containing loci generated using ddRAD-Seq. Genetic variation was assessed among young-of-the-year sampled in 11 sites in waters of the United States in the western North Atlantic Ocean, including the Gulf of Mexico. Spatial and environmental analyses detected 68 nuclear loci putatively under selection, enabling separate assessments of neutral and adaptive genetic structure. Both mitochondrial and neutral SNP data indicated three genetically distinct units-the Atlantic, eastern Gulf, and western Gulf-that align with regional stocks and suggest regional philopatry by males and females. Heterogeneity at loci putatively under selection, associated with temperature and salinity, was observed among sites within Gulf units, suggesting local adaptation. Furthermore, five pairs of siblings were identified in the same site across timescales corresponding with female reproductive cycles. This indicates that females re-used a site for parturition, which has the potential to facilitate the sorting of adaptive variation among neighbouring sites. The results demonstrate differential impacts of microevolutionary forces at varying spatial scales and highlight the importance of conserving essential habitats to maintain sources of adaptive variation that may buffer species against environmental change.
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Affiliation(s)
- Dominic G Swift
- Marine Genomics Laboratory, Department of Life Sciences, Texas A&M University-Corpus Christi, Corpus Christi, Texas, USA
| | - Shannon J O'Leary
- Marine Genomics Laboratory, Department of Life Sciences, Texas A&M University-Corpus Christi, Corpus Christi, Texas, USA
- Department of Biology, Saint Anselm College, Manchester, New Hampshire, USA
| | - R Dean Grubbs
- Florida State University Coastal and Marine Laboratory, St. Teresa, Florida, USA
| | - Bryan S Frazier
- South Carolina Department of Natural Resources, Marine Resources Research Institute, Charleston, South Carolina, USA
| | - Andrew T Fields
- Marine Genomics Laboratory, Department of Life Sciences, Texas A&M University-Corpus Christi, Corpus Christi, Texas, USA
| | - Jayne M Gardiner
- Division of Natural Sciences, New College of Florida, Sarasota, Florida, USA
| | - J Marcus Drymon
- Coastal Research and Extension Center, Mississippi State University, Biloxi, Mississippi, USA
- Mississippi-Alabama Sea Grant Consortium, Ocean Springs, Mississippi, USA
| | - Dana M Bethea
- NOAA Fisheries, U.S. Department of Commerce, Southeast Regional Office, Interagency Cooperation Branch, Protected Resources Division, St. Petersburg, Florida, USA
| | - Tonya R Wiley
- Havenworth Coastal Conservation, Palmetto, Florida, USA
| | - David S Portnoy
- Marine Genomics Laboratory, Department of Life Sciences, Texas A&M University-Corpus Christi, Corpus Christi, Texas, USA
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30
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Zhu X, Zou R, Qin H, Chai S, Tang J, Li Y, Wei X. Genome-wide diversity evaluation and core germplasm extraction in ex situ conservation: A case of golden Camellia tunghinensis. Evol Appl 2023; 16:1519-1530. [PMID: 37752963 PMCID: PMC10519411 DOI: 10.1111/eva.13584] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 07/17/2023] [Accepted: 07/26/2023] [Indexed: 09/28/2023] Open
Abstract
Whether ex situ populations constructed in the limited nursery resources of botanical gardens can preserve enough genetic diversity of endangered plants in the wild remains uncertain. Here, a case study was conducted with Camellia tunghinensis, which is one of the species with the lowest natural distribution area in the sect. Chrysantha (golden camellia) of the family Theaceae. We investigated the genetic diversity and population structure of 229 samples from wild and ex situ populations using genotyping by sequencing (GBS). Core germplasm was constructed from these samples. The results showed that wild C. tunghinensis exhibited high genetic diversity, with observed heterozygosity of 0.257-0.293 and expected heterozygosity of 0.247-0.262. Compared with wild populations, the genetic diversity of ex situ populations established by transplanting wild seedlings was close to or even higher. However, the genetic diversity of those established by seed or cuttings of a few superior trees was lower. The Admixture analysis revealed that the structure of the ex situ populations derived from seeds and cuttings was relatively simple compared with the ex situ populations derived from transplanted wild seedlings and wild populations. These results suggested that direct transplanting of wild seedlings was more conducive to preserving the genetic diversity of endangered plants in the wild. In addition, wild populations demonstrated a small differentiation (mean F ST = 0.044) among themselves, possibly due to long-term and frequent gene flow between the wild populations. In contrast, moderate differentiation (mean F ST > 0.05) was detected among ex situ populations and between ex situ and wild populations. This may be the combined result of the absence of gene flow pathways and strong selection pressure in various ex situ environments. Finally, 77 core germplasms were extracted from 229, likely representing the genetic diversity of C. tunghinensis. This study provides future strategies for the ex situ conservation and management of the golden camellia species and other rare and endangered plants.
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Affiliation(s)
- Xianliang Zhu
- Guangxi Key Laboratory of Plant Functional Phytochemicals and Sustainable UtilizationGuangxi Institute of Botany, Guangxi Zhuang Autonomous Region and Chinese Academy of SciencesGuilinChina
| | - Rong Zou
- Guangxi Key Laboratory of Plant Functional Phytochemicals and Sustainable UtilizationGuangxi Institute of Botany, Guangxi Zhuang Autonomous Region and Chinese Academy of SciencesGuilinChina
| | - Huizhen Qin
- Guangxi Key Laboratory of Plant Functional Phytochemicals and Sustainable UtilizationGuangxi Institute of Botany, Guangxi Zhuang Autonomous Region and Chinese Academy of SciencesGuilinChina
| | - Shengfeng Chai
- Guangxi Key Laboratory of Plant Functional Phytochemicals and Sustainable UtilizationGuangxi Institute of Botany, Guangxi Zhuang Autonomous Region and Chinese Academy of SciencesGuilinChina
| | - Jianmin Tang
- Guangxi Key Laboratory of Plant Functional Phytochemicals and Sustainable UtilizationGuangxi Institute of Botany, Guangxi Zhuang Autonomous Region and Chinese Academy of SciencesGuilinChina
| | - Yingying Li
- Institute of Forestry Economic Science, Guangdong Academy of ForestryGuangzhouChina
| | - Xiao Wei
- Guangxi Key Laboratory of Plant Functional Phytochemicals and Sustainable UtilizationGuangxi Institute of Botany, Guangxi Zhuang Autonomous Region and Chinese Academy of SciencesGuilinChina
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31
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Hirschfeld M, Barnett A, Sheaves M, Dudgeon C. What Darwin could not see: island formation and historical sea levels shape genetic divergence and island biogeography in a coastal marine species. Heredity (Edinb) 2023; 131:189-200. [PMID: 37400518 PMCID: PMC10462691 DOI: 10.1038/s41437-023-00635-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2022] [Revised: 06/12/2023] [Accepted: 06/13/2023] [Indexed: 07/05/2023] Open
Abstract
Oceanic islands play a central role in the study of evolution and island biogeography. The Galapagos Islands are one of the most studied oceanic archipelagos but research has almost exclusively focused on terrestrial organisms compared to marine species. Here we used the Galapagos bullhead shark (Heterodontus quoyi) and single nucleotide polymorphisms (SNPs) to examine evolutionary processes and their consequences for genetic divergence and island biogeography in a shallow-water marine species without larval dispersal. The sequential separation of individual islands from a central island cluster gradually established different ocean depths between islands that pose barriers to dispersal in H. quoyi. Isolation by resistance analysis suggested that ocean bathymetry and historical sea level fluctuations modified genetic connectivity. These processes resulted in at least three genetic clusters that exhibit low genetic diversity and effective population sizes that scale with island size and the level of geographic isolation. Our results exemplify that island formation and climatic cycles shape genetic divergence and biogeography of coastal marine organisms with limited dispersal comparable to terrestrial taxa. Because similar scenarios exist in oceanic islands around the globe our research provides a new perspective on marine evolution and biogeography with implications for the conservation of island biodiversity.
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Affiliation(s)
- Maximilian Hirschfeld
- College of Science and Engineering, James Cook University, Townsville, Queensland, Australia.
- Galápagos Science Center, Universidad San Francisco de Quito, Isla San Cristóbal, Galápagos, Ecuador.
| | - Adam Barnett
- College of Science and Engineering, James Cook University, Townsville, Queensland, Australia
- Marine Data Technology Hub, James Cook University, Townsville, Queensland, Australia
- Biopixel Oceans Foundation, Cairns, Queensland, Australia
| | - Marcus Sheaves
- College of Science and Engineering, James Cook University, Townsville, Queensland, Australia
- Marine Data Technology Hub, James Cook University, Townsville, Queensland, Australia
| | - Christine Dudgeon
- Biopixel Oceans Foundation, Cairns, Queensland, Australia
- School of Biomedical Sciences, The University of Queensland, Saint Lucia, Queensland, Australia
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32
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Sánchez-Barreiro F, De Cahsan B, Westbury MV, Sun X, Margaryan A, Fontsere C, Bruford MW, Russo IRM, Kalthoff DC, Sicheritz-Pontén T, Petersen B, Dalén L, Zhang G, Marquès-Bonet T, Gilbert MTP, Moodley Y. Historic Sampling of a Vanishing Beast: Population Structure and Diversity in the Black Rhinoceros. Mol Biol Evol 2023; 40:msad180. [PMID: 37561011 PMCID: PMC10500089 DOI: 10.1093/molbev/msad180] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Revised: 08/01/2023] [Accepted: 08/08/2023] [Indexed: 08/11/2023] Open
Abstract
The black rhinoceros (Diceros bicornis L.) is a critically endangered species historically distributed across sub-Saharan Africa. Hunting and habitat disturbance have diminished both its numbers and distribution since the 19th century, but a poaching crisis in the late 20th century drove them to the brink of extinction. Genetic and genomic assessments can greatly increase our knowledge of the species and inform management strategies. However, when a species has been severely reduced, with the extirpation and artificial admixture of several populations, it is extremely challenging to obtain an accurate understanding of historic population structure and evolutionary history from extant samples. Therefore, we generated and analyzed whole genomes from 63 black rhinoceros museum specimens collected between 1775 and 1981. Results showed that the black rhinoceros could be genetically structured into six major historic populations (Central Africa, East Africa, Northwestern Africa, Northeastern Africa, Ruvuma, and Southern Africa) within which were nested four further subpopulations (Maasailand, southwestern, eastern rift, and northern rift), largely mirroring geography, with a punctuated north-south cline. However, we detected varying degrees of admixture among groups and found that several geographical barriers, most prominently the Zambezi River, drove population discontinuities. Genomic diversity was high in the middle of the range and decayed toward the periphery. This comprehensive historic portrait also allowed us to ascertain the ancestry of 20 resequenced genomes from extant populations. Lastly, using insights gained from this unique temporal data set, we suggest management strategies, some of which require urgent implementation, for the conservation of the remaining black rhinoceros diversity.
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Affiliation(s)
| | - Binia De Cahsan
- Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | | | - Xin Sun
- Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Ashot Margaryan
- Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Claudia Fontsere
- Globe Institute, University of Copenhagen, Copenhagen, Denmark
- Institut de Biologia Evolutiva (Consejo Superior de Investigaciones Científicas–Universitat Pompeu Fabra), Barcelona Biomedical Research Park, Barcelona, Catalonia, Spain
| | | | | | - Daniela C Kalthoff
- Department of Zoology, Swedish Museum of Natural History, Stockholm, Sweden
| | - Thomas Sicheritz-Pontén
- Globe Institute, University of Copenhagen, Copenhagen, Denmark
- Centre of Excellence for Omics-Driven Computational Biodiscovery (COMBio), Faculty of Applied Sciences, AIMST University, Kedah, Malaysia
| | - Bent Petersen
- Globe Institute, University of Copenhagen, Copenhagen, Denmark
- Centre of Excellence for Omics-Driven Computational Biodiscovery (COMBio), Faculty of Applied Sciences, AIMST University, Kedah, Malaysia
| | - Love Dalén
- Department of Zoology, Centre for Palaeogenetics, Stockholm University, Stockholm, Sweden
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden
| | - Guojie Zhang
- Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Copenhagen, Denmark
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, People's Republic of China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, People's Republic of China
- BGI Research, BGI-Shenzhen, Shenzhen, People's Republic of China
| | - Tomás Marquès-Bonet
- Institut de Biologia Evolutiva (Consejo Superior de Investigaciones Científicas–Universitat Pompeu Fabra), Barcelona Biomedical Research Park, Barcelona, Catalonia, Spain
- National Centre for Genomic Analysis–Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona, Spain
- Life & Medical Sciences, Institucio Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Catalonia, Spain
| | - M Thomas P Gilbert
- Globe Institute, University of Copenhagen, Copenhagen, Denmark
- Department of Natural History, NTNU University Museum, Trondheim, Norway
| | - Yoshan Moodley
- Department of Biological Sciences, University of Venda, Thohoyandou, Republic of South Africa
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33
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Mamoozadeh NR, Whiteley AR, Letcher BH, Kazyak DC, Tarsa C, Meek MH. A new genomic resource to enable standardized surveys of SNPs across the native range of brook trout (Salvelinus fontinalis). Mol Ecol Resour 2023. [PMID: 37584304 DOI: 10.1111/1755-0998.13853] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Revised: 07/10/2023] [Accepted: 07/31/2023] [Indexed: 08/17/2023]
Abstract
Understanding how genetic diversity is distributed across spatiotemporal scales in species of conservation or management concern is critical for identifying large-scale mechanisms affecting local conservation status and implementing large-scale biodiversity monitoring programmes. However, cross-scale surveys of genetic diversity are often impractical within single studies, and combining datasets to increase spatiotemporal coverage is frequently impeded by using different sets of molecular markers. Recently developed molecular tools make surveys based on standardized single-nucleotide polymorphism (SNP) panels more feasible than ever, but require existing genomic information. Here, we conduct the first survey of genome-wide SNPs across the native range of brook trout (Salvelinus fontinalis), a cold-adapted species that has been the focus of considerable conservation and management effort across eastern North America. Our dataset can be leveraged to easily design SNP panels that allow datasets to be combined for large-scale analyses. We performed restriction site-associated DNA sequencing for wild brook trout from 82 locations spanning much of the native range and domestic brook trout from 24 hatchery strains used in stocking efforts. We identified over 24,000 SNPs distributed throughout the brook trout genome. We explored the ability of these SNPs to resolve relationships across spatial scales, including population structure and hatchery admixture. Our dataset captures a wide spectrum of genetic diversity in native brook trout, offering a valuable resource for developing SNP panels. We highlight potential applications of this resource with the goal of increasing the integration of genomic information into decision-making for brook trout and other species of conservation or management concern.
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Affiliation(s)
- Nadya R Mamoozadeh
- Department of Integrative Biology, Program in Ecology, Evolution, and Behavior, Michigan State University, Michigan, East Lansing, USA
| | - Andrew R Whiteley
- W.A. Franke College of Forestry and Conservation, Wildlife Biology Program, University of Montana, Missoula, Montana, USA
| | - Benjamin H Letcher
- U.S. Geological Survey, Eastern Ecological Science Center, Turners Falls, Massachusetts, USA
| | - David C Kazyak
- U.S. Geological Survey, Eastern Ecological Science Center, Kearneysville, West Virginia, USA
| | - Charlene Tarsa
- Department of Integrative Biology, Program in Ecology, Evolution, and Behavior, Michigan State University, Michigan, East Lansing, USA
| | - Mariah H Meek
- Department of Integrative Biology, Program in Ecology, Evolution, and Behavior, Michigan State University, Michigan, East Lansing, USA
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34
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Narváez-Barandica JC, Quintero-Galvis JF, Aguirre-Pabón JC, Castro LR, Betancur R, Acero Pizarro A. A Comparative Phylogeography of Three Marine Species with Different PLD Modes Reveals Two Genetic Breaks across the Southern Caribbean Sea. Animals (Basel) 2023; 13:2528. [PMID: 37570336 PMCID: PMC10417521 DOI: 10.3390/ani13152528] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 07/02/2023] [Accepted: 07/19/2023] [Indexed: 08/13/2023] Open
Abstract
The comparative phylogeography of marine species with contrasting dispersal potential across the southern Caribbean Sea was evaluated by the presence of two putative barriers: the Magdalena River plume (MRP) and the combination of the absence of a rocky bottom and the almost permanent upwelling in the La Guajira Peninsula (ARB + PUG). Three species with varying biological and ecological characteristics (i.e., dispersal potentials) that inhabit shallow rocky bottoms were selected: Cittarium pica (PLD < 6 days), Acanthemblemaria rivasi (PLD < 22 days), and Nerita tessellata (PLD > 60 days). We generated a set of SNPs for the three species using the ddRad-seq technique. Samples of each species were collected in five locations from Capurganá to La Guajira. For the first time, evidence of a phylogeographic break caused by the MRP is provided, mainly for A. rivasi (AMOVA: ΦCT = 0.420). The ARB + PUG barrier causes another break for A. rivasi (ΦCT = 0.406) and C. pica (ΦCT = 0.224). Three populations (K = 3) were identified for A. rivasi and C. pica, while N. tessellata presented one population (K = 1). The Mantel correlogram indicated that A. rivasi and C. pica fit the hierarchical population model, and only the A. rivasi and C. pica comparisons showed phylogeographic congruence. Our results demonstrate how the biological traits of these three species and the biogeographic barriers have influenced their phylogeographic structure.
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Affiliation(s)
- Juan Carlos Narváez-Barandica
- Centro de Genética y Biología Molecular, Universidad del Magdalena, Carrera 32 No 22–08, Santa Marta 470004, Colombia; (J.C.A.-P.); (L.R.C.)
| | - Julián F. Quintero-Galvis
- Instituto de Ciencias Ambientales y Evolutivas, Facultad de Ciencias, Universidad Austral de Chile, Valdivia 5110566, Chile;
| | - Juan Carlos Aguirre-Pabón
- Centro de Genética y Biología Molecular, Universidad del Magdalena, Carrera 32 No 22–08, Santa Marta 470004, Colombia; (J.C.A.-P.); (L.R.C.)
| | - Lyda R. Castro
- Centro de Genética y Biología Molecular, Universidad del Magdalena, Carrera 32 No 22–08, Santa Marta 470004, Colombia; (J.C.A.-P.); (L.R.C.)
| | - Ricardo Betancur
- Biology Department, University of Oklahoma, Norman, OK 73019, USA;
| | - Arturo Acero Pizarro
- Instituto de Estudios en Ciencias del Mar (CECIMAR), Universidad Nacional de Colombia sede Caribe, Santa Marta 470006, Colombia;
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Gallego-García N, Vargas-Ramírez M, Shaffer HB. The importance of cryptic diversity in the conservation of wide-ranging species: The red-footed tortoise Chelonoidis carbonarius in Colombia. Mol Ecol 2023; 32:4531-4545. [PMID: 37340598 DOI: 10.1111/mec.17052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Revised: 05/23/2023] [Accepted: 06/07/2023] [Indexed: 06/22/2023]
Abstract
Wide-ranging species are seldom considered conservation priorities, yet they have the potential to harbour genetically deeply differentiated units across environments or ecological barriers, including some that warrant taxonomic recognition. Documenting such cryptic genetic diversity is especially important for wide-ranging species that are in decline, as they may comprise a set of even more endangered lineages or species with small distributions. However, studies of wide-ranging species, particularly when they cross political borders, are extremely challenging. One approach to overcoming these challenges is to conduct detailed local analyses in combination with less detailed, range-wide studies. We used this approach with the red-footed tortoise (Chelonoidis carbonarius), a threatened species likely to contain cryptic diversity given its vast range and the distinctive ecoregions that it inhabits. Previous single-gene molecular studies indicated the presence of at least five lineages, two of which occur in different ecoregions separated by the Andes within Colombia. We used a comprehensive genomic analysis to test the hypothesis of cryptic diversity within the single jurisdiction of Colombia. We used a combination of restriction-site-associated DNA sequencing and environmental niche modelling to provide three independent lines of evidence that support the presence of important cryptic diversity that may deserve taxonomic recognition: allopatric reproductive isolation, local adaptation and ecological divergence. We also provide a fine-scale genetic map with the distribution of conservation units in Colombia. As we complete ongoing range-wide analyses and make taxonomic adjustments, we recommend that the two lineages in Colombia be treated as separate units for conservation purposes.
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Affiliation(s)
- Natalia Gallego-García
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, California, USA
| | - Mario Vargas-Ramírez
- Biodiversidad y Conservación Genética, Instituto de Genética, Universidad Nacional de Colombia, Bogotá, Colombia
| | - H Bradley Shaffer
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, California, USA
- La Kretz Center for California Conservation Science, Institute of the Environment and Sustainability, University of California, Los Angeles, Los Angeles, California, USA
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Ramsay MS, Sgarlata GM, Barratt CD, Salmona J, Andriatsitohaina B, Kiene F, Manzi S, Ramilison ML, Rakotondravony R, Chikhi L, Lehman SM, Radespiel U. Effects of Forest Fragmentation on Connectivity and Genetic Diversity in an Endemic and an Invasive Rodent in Northwestern Madagascar. Genes (Basel) 2023; 14:1451. [PMID: 37510355 PMCID: PMC10378931 DOI: 10.3390/genes14071451] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Revised: 07/07/2023] [Accepted: 07/13/2023] [Indexed: 07/30/2023] Open
Abstract
Habitat loss and fragmentation are of concern to conservation biologists worldwide. However, not all organisms are affected equally by these processes; thus, it is important to study the effects of living in fragmented habitats on species that differ in lifestyle and habitat requirements. In this study, we examined the dispersal and connectivity patterns of rodents, one endemic (Eliurus myoxinus) and one invasive (Rattus rattus), in two landscapes containing forest fragments and adjacent continuous forest patches in northwestern Madagascar. We generated genetic (RADseq) data for 66 E. myoxinus and 81 R. rattus individuals to evaluate differences in genetic diversity as well as inbreeding and connectivity in two landscapes. We found higher levels of inbreeding and lower levels of genetic diversity in E. myoxinus compared with R. rattus. We observed related dyads both within and between habitat patches and positive spatial autocorrelation at lower distance classes for both species, with a stronger pattern of spatial autocorrelation in R. rattus. Across each site, we identified contrasting migration rates for each species, but these did not correspond to habitat-matrix dichotomies. The relatively low genetic diversity in the endemic E. myoxinus suggests ecological constraints that require further investigation.
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Affiliation(s)
- Malcolm S Ramsay
- Department of Anthropology, University of Toronto, Toronto, ON M5S 2S2, Canada
- Institute of Zoology, University of Veterinary Medicine Hannover, Foundation, 30559 Hannover, Germany
| | | | - Christopher D Barratt
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, 04103 Leipzig, Germany
| | - Jordi Salmona
- CNRS-UPS-IRD, UMR5174, Laboratoire Évolution & Diversité Biologique, Université Paul Sabatier, 31062 Toulouse, France
| | - Bertrand Andriatsitohaina
- Planet Madagascar, Antananarivo 101, Madagascar
- Faculté des Sciences, de Technologies et de l'Environnement, Université de Mahajanga, Mahajanga 401, Madagascar
| | - Frederik Kiene
- Institute of Zoology, University of Veterinary Medicine Hannover, Foundation, 30559 Hannover, Germany
| | - Sophie Manzi
- CNRS-UPS-IRD, UMR5174, Laboratoire Évolution & Diversité Biologique, Université Paul Sabatier, 31062 Toulouse, France
| | - Miarisoa L Ramilison
- Faculté des Sciences, de Technologies et de l'Environnement, Université de Mahajanga, Mahajanga 401, Madagascar
- Department of Primate Behavior and Ecology, Central Washington University, Ellensburg, WA 98926, USA
| | - Romule Rakotondravony
- Faculté des Sciences, de Technologies et de l'Environnement, Université de Mahajanga, Mahajanga 401, Madagascar
| | - Lounès Chikhi
- Instituto Gulbenkian de Ciência, 2780-156 Oeiras, Portugal
- CNRS-UPS-IRD, UMR5174, Laboratoire Évolution & Diversité Biologique, Université Paul Sabatier, 31062 Toulouse, France
| | - Shawn M Lehman
- Department of Anthropology, University of Toronto, Toronto, ON M5S 2S2, Canada
| | - Ute Radespiel
- Institute of Zoology, University of Veterinary Medicine Hannover, Foundation, 30559 Hannover, Germany
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Huynh S, Cloutier A, Chen G, Chan DTC, Lam DK, Huyvaert KP, Sato F, Edwards SV, Sin SYW. Whole-genome analyses reveal past population fluctuations and low genetic diversities of the North Pacific albatrosses. Mol Biol Evol 2023:msad155. [PMID: 37402641 PMCID: PMC10348050 DOI: 10.1093/molbev/msad155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Revised: 06/06/2023] [Accepted: 07/02/2023] [Indexed: 07/06/2023] Open
Abstract
Throughout the Plio-Pleistocene, climate change has impacted tropical marine ecosystems substantially, with even more severe impacts predicted in the Anthropocene. Although many studies have clarified demographic histories of seabirds in polar regions, the history of keystone seabirds of the tropics is unclear, despite the prominence of albatrosses (Diomedeidae, Procellariiformes) as the largest and most threatened group of oceanic seabirds. To understand the impact of climate change on tropical albatrosses, we investigated the evolutionary and demographic histories of all four North Pacific albatrosses and their prey using whole-genome analyses. We report a striking concordance in demographic histories among the four species, with a notable dip in effective population size at the beginning of the Pleistocene and a population expansion in the Last Glacial Period when sea levels were low, which resulted in increased potential coastal breeding sites. Abundance of the black-footed albatross dropped again during the Last Glacial Maximum, potentially linked to climate-driven loss of breeding sites and concordant genome-derived decreases in its major prey. We find very low genome-wide (π < 0.001) and adaptative genetic diversities across the albatrosses, with genes of the major histocompatibility complex close to monomorphic. We also identify recent selective sweeps at genes associated with hyperosmotic adaptation, longevity, and cognition and memory. Our study has shed light on the evolutionary and demographic histories of the largest tropical oceanic seabirds and provides evidence for their large population fluctuations and alarmingly low genetic diversities.
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Affiliation(s)
- Stella Huynh
- School of Biological Sciences, The University of Hong Kong, Pok Fu Lam Road, Hong Kong, China
| | - Alison Cloutier
- School of Biological Sciences, The University of Hong Kong, Pok Fu Lam Road, Hong Kong, China
- Department of Organismic and Evolutionary Biology, Museum of Comparative Zoology, Harvard University, 26 Oxford Street, Cambridge, MA 02138, USA
| | - Guoling Chen
- School of Biological Sciences, The University of Hong Kong, Pok Fu Lam Road, Hong Kong, China
| | - David Tsz Chung Chan
- School of Biological Sciences, The University of Hong Kong, Pok Fu Lam Road, Hong Kong, China
| | - Derek Kong Lam
- School of Biological Sciences, The University of Hong Kong, Pok Fu Lam Road, Hong Kong, China
| | - Kathryn P Huyvaert
- Department of Fish, Wildlife and Conservation Biology, Colorado State University, Fort Collins, Colorado, USA
- Department of Veterinary Microbiology and Pathology, Washington State University, Pullman, WA 99164, USA
| | - Fumio Sato
- Yamashina Institute for Ornithology, Abiko, Japan
| | - Scott V Edwards
- Department of Organismic and Evolutionary Biology, Museum of Comparative Zoology, Harvard University, 26 Oxford Street, Cambridge, MA 02138, USA
| | - Simon Yung Wa Sin
- School of Biological Sciences, The University of Hong Kong, Pok Fu Lam Road, Hong Kong, China
- Department of Organismic and Evolutionary Biology, Museum of Comparative Zoology, Harvard University, 26 Oxford Street, Cambridge, MA 02138, USA
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Solmundson K, Bowman J, Manseau M, Taylor RS, Keobouasone S, Wilson PJ. Genomic population structure and inbreeding history of Lake Superior caribou. Ecol Evol 2023; 13:e10278. [PMID: 37424935 PMCID: PMC10326607 DOI: 10.1002/ece3.10278] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 06/19/2023] [Accepted: 06/23/2023] [Indexed: 07/11/2023] Open
Abstract
Caribou (Rangifer tarandus) have experienced dramatic declines in both range and population size across Canada over the past century. Boreal caribou (R. t. caribou), 1 of the 12 Designatable Units, has lost approximately half of its historic range in the last 150 years, particularly along the southern edge of its distribution. Despite this overall northward contraction, some populations have persisted at the trailing range edge, over 150 km south of the continuous boreal caribou range in Ontario, along the coast and nearshore islands of Lake Superior. The population history of caribou along Lake Superior remains unclear. It appears that these caribou likely represent a remnant distribution at the trailing edge of the receding population of boreal caribou, but they may also exhibit local adaptation to the coastal environment. A better understanding of the population structure and history of caribou along Lake Superior is important for their conservation and management. Here, we use high-coverage whole genomes (N = 20) from boreal, eastern migratory, and barren-ground caribou sampled in Manitoba, Ontario, and Quebec to investigate population structure and inbreeding histories. We discovered that caribou from the Lake Superior range form a distinct group but also found some evidence of gene flow with the continuous boreal caribou range. Notably, caribou along Lake Superior demonstrated relatively high levels of inbreeding (measured as runs of homozygosity; ROH) and genetic drift, which may contribute to the differentiation observed between ranges. Despite inbreeding, caribou along Lake Superior retained high heterozygosity, particularly in genomic regions without ROH. These results suggest that they present distinct genomic characteristics but also some level of gene flow with the continuous range. Our study provides key insights into the genomics of the southernmost range of caribou in Ontario, beginning to unravel the evolutionary history of these small, isolated caribou populations.
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Affiliation(s)
- Kirsten Solmundson
- Environmental & Life Sciences Graduate ProgramTrent UniversityPeterboroughOntarioCanada
| | - Jeff Bowman
- Environmental & Life Sciences Graduate ProgramTrent UniversityPeterboroughOntarioCanada
- Wildlife Research and Monitoring Section, Ontario Ministry of Natural Resources and ForestryTrent UniversityPeterboroughOntarioCanada
| | - Micheline Manseau
- Environmental & Life Sciences Graduate ProgramTrent UniversityPeterboroughOntarioCanada
- Landscape Science and Technology DivisionEnvironment and Climate Change CanadaOttawaOntarioCanada
| | - Rebecca S. Taylor
- Landscape Science and Technology DivisionEnvironment and Climate Change CanadaOttawaOntarioCanada
| | - Sonesinh Keobouasone
- Landscape Science and Technology DivisionEnvironment and Climate Change CanadaOttawaOntarioCanada
| | - Paul J. Wilson
- Biology DepartmentTrent UniversityPeterboroughOntarioCanada
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Aguirre-Liguori JA, Morales-Cruz A, Gaut BS, Ramírez-Barahona S. Sampling effect in predicting the evolutionary response of populations to climate change. Mol Ecol Resour 2023. [PMID: 37392001 DOI: 10.1111/1755-0998.13828] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Revised: 06/01/2023] [Accepted: 06/19/2023] [Indexed: 07/02/2023]
Abstract
Genomic data and machine learning approaches have gained interest due to their potential to identify adaptive genetic variation across populations and to assess species vulnerability to climate change. By identifying gene-environment associations for putatively adaptive loci, these approaches project changes to adaptive genetic composition as a function of future climate change (genetic offsets), which are interpreted as measuring the future maladaptation of populations due to climate change. In principle, higher genetic offsets relate to increased population vulnerability and therefore can be used to set priorities for conservation and management. However, it is not clear how sensitive these metrics are to the intensity of population and individual sampling. Here, we use five genomic datasets with varying numbers of SNPs (NSNPs = 7006-1,398,773), sampled populations (Npop = 23-47) and individuals (Nind = 185-595) to evaluate the estimation sensitivity of genetic offsets to varying degrees of sampling intensity. We found that genetic offsets are sensitive to the number of populations being sampled, especially with less than 10 populations and when genetic structure is high. We also found that the number of individuals sampled per population had small effects on the estimation of genetic offsets, with more robust results when five or more individuals are sampled. Finally, uncertainty associated with the use of different future climate scenarios slightly increased estimation uncertainty in the genetic offsets. Our results suggest that sampling efforts should focus on increasing the number of populations, rather than the number of individuals per populations, and that multiple future climate scenarios should be evaluated to ascertain estimation sensitivity.
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Affiliation(s)
- Jonás A Aguirre-Liguori
- Departamento de Botánica, Instituto de Biología, Universidad Nacional Autónoma de México (UNAM), Ciudad de México, Mexico
- Departamento de Ecología Tropical, Campus de Ciencias Biológicas y Agropecuarias, Universidad Autónoma de Yucatán, Mérida, Mexico
| | - Abraham Morales-Cruz
- Department of Ecology and Evolutionary Biology, University of California, Irvine, Irvine, California, USA
| | - Brandon S Gaut
- Department of Ecology and Evolutionary Biology, University of California, Irvine, Irvine, California, USA
| | - Santiago Ramírez-Barahona
- Departamento de Botánica, Instituto de Biología, Universidad Nacional Autónoma de México (UNAM), Ciudad de México, Mexico
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40
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Forester BR, Day CC, Ruegg K, Landguth EL. Evolutionary potential mitigates extinction risk under climate change in the endangered southwestern willow flycatcher. J Hered 2023; 114:341-353. [PMID: 36738446 PMCID: PMC10287148 DOI: 10.1093/jhered/esac067] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Accepted: 12/09/2022] [Indexed: 02/05/2023] Open
Abstract
The complexity of global anthropogenic change makes forecasting species responses and planning effective conservation actions challenging. Additionally, important components of a species' adaptive capacity, such as evolutionary potential, are often not included in quantitative risk assessments due to lack of data. While genomic proxies for evolutionary potential in at-risk species are increasingly available, they have not yet been included in extinction risk assessments at a species-wide scale. In this study, we used an individual-based, spatially explicit, dynamic eco-evolutionary simulation model to evaluate the extinction risk of an endangered desert songbird, the southwestern willow flycatcher (Empidonax traillii extimus), in response to climate change. Using data from long-term demographic and habitat studies in conjunction with genome-wide ecological genomics research, we parameterized simulations that include 418 sites across the breeding range, genomic data from 225 individuals, and climate change forecasts spanning 3 generalized circulation models and 3 emissions scenarios. We evaluated how evolutionary potential, and the lack of it, impacted population trajectories in response to climate change. We then investigated the compounding impact of drought and warming temperatures on extinction risk through the mechanism of increased nest failure. Finally, we evaluated how rapid action to reverse greenhouse gas emissions would influence population responses and species extinction risk. Our results illustrate the value of incorporating evolutionary, demographic, and dispersal processes in a spatially explicit framework to more comprehensively evaluate the extinction risk of threatened and endangered species and conservation actions to promote their recovery.
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Affiliation(s)
- Brenna R Forester
- Department of Biology, Colorado State University, Fort Collins, CO, United States
| | - Casey C Day
- Computational Ecology Lab, School of Public and Community Health Sciences, University of Montana, Missoula, MT, United States
| | - Kristen Ruegg
- Department of Biology, Colorado State University, Fort Collins, CO, United States
| | - Erin L Landguth
- Computational Ecology Lab, School of Public and Community Health Sciences, University of Montana, Missoula, MT, United States
- Center for Population Health Research, School of Public and Community Health Sciences, University of Montana, Missoula, MT, United States
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Bailey S, Guhlin J, Senanayake DS, Scherer P, Brekke P, Ewen JG, Santure AW, Whibley A. Assembly of female and male hihi genomes (stitchbird; Notiomystis cincta) enables characterization of the W chromosome and resources for conservation genomics. Mol Ecol Resour 2023. [PMID: 37332137 DOI: 10.1111/1755-0998.13823] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 05/18/2023] [Accepted: 05/25/2023] [Indexed: 06/20/2023]
Abstract
A high-quality reference genome can be a valuable resource for threatened species by providing a foundation to assess their evolutionary potential to adapt to future pressures such as environmental change. We assembled the genome of a female hihi (Notiomysits cincta), a threatened passerine bird endemic to Aotearoa New Zealand. The assembled genome is 1.06 Gb, and is of high quality and highly contiguous, with a contig N50 of 7.0 Mb, estimated QV of 44 and a BUSCO completeness of 96.8%. A male assembly of comparable quality was generated in parallel. A population linkage map was used to scaffold the autosomal contigs into chromosomes. Female and male sequence coverage and comparative genomics analyses were used to identify Z-, and W-linked contigs. In total, 94.6% of the assembly length was assigned to putative nuclear chromosome scaffolds. Native DNA methylation was highly correlated between sexes, with the W chromosome contigs more highly methylated than autosomal chromosomes and Z contigs. 43 differentially methylated regions were identified, and these may represent interesting candidates for the establishment or maintenance of sex differences. By generating a high-quality reference assembly of the heterogametic sex, we have created a resource that enables characterization of genome-wide diversity and facilitates the investigation of female-specific evolutionary processes. The reference genomes will form the basis for fine-scale assessment of the impacts of low genetic diversity and inbreeding on the adaptive potential of the species and will therefore enable tailored and informed conservation management of this threatened taonga (treasured) species.
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Affiliation(s)
- Sarah Bailey
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
- Centre for Biodiversity and Biosecurity, School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Joseph Guhlin
- Biochemistry Department, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand
| | - Dinindu S Senanayake
- New Zealand eScience Infrastructure (NeSI), University of Auckland, Auckland, New Zealand
| | - Phoebe Scherer
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Patricia Brekke
- Institute of Zoology, Zoological Society of London, London, UK
| | - John G Ewen
- Institute of Zoology, Zoological Society of London, London, UK
| | - Anna W Santure
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
- Centre for Biodiversity and Biosecurity, School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Annabel Whibley
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
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Forde S, von der Heyden S, Le Moan A, Nielsen ES, Durholtz D, Kainge P, Kathena JN, Lipinski MR, Ndjaula HON, Matthee CA, Henriques R. Management and conservation implications of cryptic population substructure for two commercially exploited fishes (Merluccius spp.) in southern Africa. Mol Ecol Resour 2023. [PMID: 37291747 DOI: 10.1111/1755-0998.13820] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 05/16/2023] [Accepted: 05/24/2023] [Indexed: 06/10/2023]
Abstract
Genomic information can aid in the establishment of sustainable management plans for commercially exploited marine fishes, aiding in the long-term conservation of these resources. The southern African hakes (Merluccius capensis and M. paradoxus) are commercially valuable demersal fishes with similar distribution ranges but exhibiting contrasting life histories. Using a comparative framework based on Pool-Seq genome-wide SNP data, we investigated whether the evolutionary processes that shaped extant patterns of diversity and divergence are shared among these two congeneric fishes, or unique to each one. Our findings revealed that M. capensis and M. paradoxus show similar levels of genome-wide diversity, despite different census sizes and life-history features. In addition, M. capensis shows three highly structured geographic populations across the Benguela Current region (one in the northern Benguela and two in the southern Benguela), with no consistent genome-environment associations detected. In contrast, although population structure and outlier analyses suggested panmixia for M. paradoxus, reconstruction of its demographic history suggested the presence of an Atlantic-Indian Ocean subtle substructuring pattern. Therefore, it appears that M. paradoxus might be composed by two highly connected populations, one in the Atlantic and one in the southwest Indian Ocean. The reported similar low levels of genomic diversity, as well as newly discovered genetically distinct populations in both hake species can thus assist in informing and improving conservation and management plans for the commercially important southern African Merluccius.
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Affiliation(s)
- Sarah Forde
- Marine Genomics Group, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Hatfield, South Africa
| | - Sophie von der Heyden
- Evolutionary Genomics Group, Department of Botany and Zoology, Stellenbosch University, Stellenbosch, South Africa
| | - Alan Le Moan
- CNRS-Sorbonne Université, Station Biologique de Roscoff, Place Georges Tessier, Roscoff, France
| | | | - Deon Durholtz
- Department of Forestry, Fisheries and Environment, Cape Town, South Africa
| | - Paulus Kainge
- National Marine Information and Research Centre, Ministry of Fisheries and Marine Resources, Swakopmund, Namibia
| | - Johannes N Kathena
- National Marine Information and Research Centre, Ministry of Fisheries and Marine Resources, Swakopmund, Namibia
| | - Marek R Lipinski
- Department of Ichthyology and Fisheries Science, Rhodes University, Makhanda, South Africa
| | - Hilkka O N Ndjaula
- Sam Nujoma Marine and Coastal Resources Research Centre, University of Namibia, Henties Bay, Namibia
| | - Conrad A Matthee
- Evolutionary Genomics Group, Department of Botany and Zoology, Stellenbosch University, Stellenbosch, South Africa
| | - Romina Henriques
- Marine Genomics Group, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Hatfield, South Africa
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Winter S, Meißner R, Greve C, Ben Hamadou A, Horin P, Prost S, Burger PA. A chromosome-scale high-contiguity genome assembly of the cheetah (Acinonyx jubatus). J Hered 2023; 114:271-278. [PMID: 36869783 PMCID: PMC10212127 DOI: 10.1093/jhered/esad015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Accepted: 02/28/2023] [Indexed: 03/05/2023] Open
Abstract
The cheetah (Acinonyx jubatus, SCHREBER 1775) is a large felid and is considered the fastest land animal. Historically, it inhabited open grassland across Africa, the Arabian Peninsula, and southwestern Asia; however, only small and fragmented populations remain today. Here, we present a de novo genome assembly of the cheetah based on PacBio continuous long reads and Hi-C proximity ligation data. The final assembly (VMU_Ajub_asm_v1.0) has a total length of 2.38 Gb, of which 99.7% are anchored into the expected 19 chromosome-scale scaffolds. The contig and scaffold N50 values of 96.8 Mb and 144.4 Mb, respectively, a BUSCO completeness of 95.4% and a k-mer completeness of 98.4%, emphasize the high quality of the assembly. Furthermore, annotation of the assembly identified 23,622 genes and a repeat content of 40.4%. This new highly contiguous and chromosome-scale assembly will greatly benefit conservation and evolutionary genomic analyses and will be a valuable resource, e.g., to gain a detailed understanding of the function and diversity of immune response genes in felids.
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Affiliation(s)
- Sven Winter
- Research Institute of Wildlife Ecology, University of Veterinary Medicine Vienna, Vienna, Austria
| | - René Meißner
- Research Institute of Wildlife Ecology, University of Veterinary Medicine Vienna, Vienna, Austria
| | - Carola Greve
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Frankfurt am Main, Germany
| | - Alexander Ben Hamadou
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Frankfurt am Main, Germany
| | - Petr Horin
- Department of Animal Genetics, University of Veterinary Sciences, Brno, Czech Republic
- Central European Institute of Technology, University of Veterinary Sciences Brno (CEITEC Vetuni), Brno, Czech Republic
| | - Stefan Prost
- Ecology and Genetics Research Unit, University of Oulu, Oulu, Finland
- Konrad Lorenz Institute of Ethology, University of Veterinary Medicine Vienna, Vienna, Austria
- Natural History Museum Vienna, Central Research Laboratories, Vienna, Austria
- South African National Biodiversity Institute, National Zoological Garden, Pretoria, South Africa
| | - Pamela A Burger
- Research Institute of Wildlife Ecology, University of Veterinary Medicine Vienna, Vienna, Austria
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44
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Adams NE, Edmands S. Genomic recovery lags behind demographic recovery in bottlenecked populations of the Channel Island fox, Urocyon littoralis. Mol Ecol 2023. [PMID: 37212171 DOI: 10.1111/mec.17025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Revised: 04/26/2023] [Accepted: 05/05/2023] [Indexed: 05/23/2023]
Abstract
With continued global change, recovery of species listed under the Endangered Species Act is increasingly challenging. One rare success was the recovery and delisting of the Channel Island fox (Urocyon littoralis) after 90%-99% population declines in the 1990s. While their demographic recovery was marked, less is known about their genetic recovery. To address genetic changes, we conducted the first multi-individual and population-level direct genetic comparison of samples collected before and after the recent bottlenecks. Using whole-exome sequencing, we found that already genetically depauperate populations were further degraded by the 1990s declines and remain low, particularly on San Miguel and Santa Rosa Islands, which underwent the most severe bottlenecks. The two other islands that experienced recent bottlenecks (Santa Cruz, and Santa Catalina islands) showed mixed results based on multiple metrics of genetic diversity. Previous island fox genomics studies showed low genetic diversity before the declines and no change after the demographic recovery, thus this is the first study to show a decrease in genetic diversity over time in U. littoralis. Additionally, we found that divergence between populations consistently increased over time, complicating prospects for using inter-island translocation as a conservation tool. The Santa Catalina subspecies is now federally listed as threatened, yet other de-listed subspecies are still recovering genetic variation which may limit their ability to adapt to changing environmental conditions. This study further demonstrates that species conservation is more complex than population size and that some island fox populations are not yet 'out of the woods'.
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Affiliation(s)
- Nicole E Adams
- Department of Biological Sciences, University of Southern California, Los Angeles, California, USA
| | - Suzanne Edmands
- Department of Biological Sciences, University of Southern California, Los Angeles, California, USA
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45
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Wang X, Peischl S, Heckel G. Demographic history and genomic consequences of 10,000 generations of isolation in a wild mammal. Curr Biol 2023; 33:2051-2062.e4. [PMID: 37178689 DOI: 10.1016/j.cub.2023.04.042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Revised: 12/20/2022] [Accepted: 04/17/2023] [Indexed: 05/15/2023]
Abstract
Increased human activities caused the isolation of populations in many species-often associated with genetic depletion and negative fitness effects. The effects of isolation are predicted by theory, but long-term data from natural populations are scarce. We show, with full genome sequences, that common voles (Microtus arvalis) in the Orkney archipelago have remained genetically isolated from conspecifics in continental Europe since their introduction by humans over 5,000 years ago. Modern Orkney vole populations are genetically highly differentiated from continental conspecifics as a result of genetic drift processes. Colonization likely started on the biggest Orkney island and vole populations on smaller islands were gradually split off, without signs of secondary admixture. Despite having large modern population sizes, Orkney voles are genetically depauperate and successive introductions to smaller islands resulted in further reduction of genetic diversity. We detected high levels of fixation of predicted deleterious variation compared with continental populations, particularly on smaller islands, yet the fitness effects realized in nature are unknown. Simulations showed that predominantly mildly deleterious mutations were fixed in populations, while highly deleterious mutations were purged early in the history of the Orkney population. Relaxation of selection overall due to benign environmental conditions on the islands and the effects of soft selection may have contributed to the repeated, successful establishment of Orkney voles despite potential fitness loss. Furthermore, the specific life history of these small mammals, resulting in relatively large population sizes, has probably been important for their long-term persistence in full isolation.
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Affiliation(s)
- Xuejing Wang
- Institute of Ecology and Evolution, University of Bern, Baltzerstrasse 6, 3012 Bern, Switzerland
| | - Stephan Peischl
- Interfaculty Bioinformatics Unit, University of Bern, Baltzerstrasse 6, 3012 Bern, Switzerland; Swiss Institute of Bioinformatics, Amphipôle, Quartier UNIL-Sorge, 1015 Lausanne, Switzerland
| | - Gerald Heckel
- Institute of Ecology and Evolution, University of Bern, Baltzerstrasse 6, 3012 Bern, Switzerland; Swiss Institute of Bioinformatics, Amphipôle, Quartier UNIL-Sorge, 1015 Lausanne, Switzerland.
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46
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Tyagi A, Godbole M, Vanak AT, Ramakrishnan U. Citizen science facilitates first ever genetic detection of wolf-dog hybridization in Indian savannahs. Ecol Evol 2023; 13:e10100. [PMID: 37214618 PMCID: PMC10191802 DOI: 10.1002/ece3.10100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Revised: 05/03/2023] [Accepted: 05/04/2023] [Indexed: 05/24/2023] Open
Abstract
Human demographic expansion has confined wildlife to fragmented habitats, often in proximity to human-modified landscapes. Such interfaces facilitate increased interactions between feral or domesticated animals and wildlife, posing a high risk to wild species. This is especially relevant for free-ranging dogs (Canis lupus familiaris) and wild canids like gray wolves (Canis lupus) and golden jackals (Canis aureus). Wolf-dog hybridization may lead to a significant reduction of specific adaptations in wolves that could result in the decline of wolf populations. Detection and genetic discrimination of hybrids between dogs and wolves are challenging because of their complex demographic history and close ancestry. Citizen scientists identified two phenotypically different-looking individuals and subsequently collected non-invasive samples that were used by geneticists to test wolf-dog hybridization. Genomic data from shed hair samples of suspected hybrid individuals using double-digest restriction-site-associated DNA (ddRAD) sequencing resulted in 698 single nucleotide polymorphism (SNP) markers. We investigated the genetic origin of these two individuals analyzed with genetically known dogs, wolves, and other canid species including jackals and dholes (Cuon alpinus). Our results provide the first genetic evidence of one F2 hybrid and the other individual could be a complex hybrid between dogs and wolves. Our results re-iterate the power of next-generation sequencing (NGS) for non-invasive samples as an efficient tool for detecting hybrids. Our results suggest the need for more robust monitoring of wolf populations and highlight the tremendous potential for collaborative approaches between citizens and conservation scientists to detect and monitor threats to biodiversity.
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Affiliation(s)
- Abhinav Tyagi
- National Centre for Biological SciencesTata Institute of Fundamental ResearchBengaluruKarnatakaIndia
- SASTRA Deemed to be UniversityThanjavurTamilnaduIndia
| | | | - Abi Tamim Vanak
- Ashoka Trust for Research in Ecology and the EnvironmentBengaluruKarnatakaIndia
- School of Life SciencesUniversity of KwaZulu‐NatalDurbanSouth Africa
| | - Uma Ramakrishnan
- National Centre for Biological SciencesTata Institute of Fundamental ResearchBengaluruKarnatakaIndia
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Kieran Blair SR, Schreier A, Escalona M, Finger AJ, Joslin SEK, Sahasrabudhe R, Marimuthu MPA, Nguyen O, Chumchim N, Morris ER, Mangelson H, Hull J. A draft reference genome of the Vernal Pool Fairy Shrimp, Branchinecta lynchi. J Hered 2023; 114:81-87. [PMID: 36222891 PMCID: PMC10019022 DOI: 10.1093/jhered/esac056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Accepted: 10/10/2022] [Indexed: 11/12/2022] Open
Abstract
We present the reference genome of the Vernal Pool Fairy Shrimp Branchinecta lynchi. This branchiopod crustacean is endemic to California's freshwater ephemeral ponds. It faces enormous habitat loss and fragmentation as urbanization and agriculture have fundamentally changed the vernal pool landscape over the past 3 centuries. The assembled genome consists of 22 chromosome-length scaffolds that account for 96.85% of the total sequence. One hundred and ninety-five unscaffolded contigs comprise the rest of the genome's 575.6 Mb length. The genome is substantially complete with a BUSCO score of 90.0%. There is no immediately identifiable sex chromosome, typical for this class of organism. This new resource will permit researchers to better understand the adaptive capacity of this imperiled species, as well as answer lingering questions about anostracan physiology, sex determination, and development.
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Affiliation(s)
| | - Andrea Schreier
- Genomic Variation Laboratory, Department of Animal Science, University of California, Davis, Davis, CA, United States
| | - Merly Escalona
- Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, CA, United States
| | - Amanda J Finger
- Genomic Variation Laboratory, Department of Animal Science, University of California, Davis, Davis, CA, United States
| | - Shannon E K Joslin
- U.S. National Park Service, Yosemite National Park, El Portal, CA, United States
| | - Ruta Sahasrabudhe
- DNA Technologies and Expression Analysis Cores, UC Davis Genome Center, University of California, Davis, Davis, CA, United States
| | - Mohan P A Marimuthu
- DNA Technologies and Expression Analysis Cores, UC Davis Genome Center, University of California, Davis, Davis, CA, United States
| | - Oanh Nguyen
- DNA Technologies and Expression Analysis Cores, UC Davis Genome Center, University of California, Davis, Davis, CA, United States
| | - Noravit Chumchim
- DNA Technologies and Expression Analysis Cores, UC Davis Genome Center, University of California, Davis, Davis, CA, United States
| | | | | | - Joshua Hull
- U.S. Fish and Wildlife Service, Sacramento Fish and Wildlife Office, Sacramento, CA, United States
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48
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Wold JR, Guhlin JG, Dearden PK, Santure AW, Steeves TE. The promise and challenges of characterizing genome-wide structural variants: A case study in a critically endangered parrot. Mol Ecol Resour 2023. [PMID: 36916824 DOI: 10.1111/1755-0998.13783] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 02/24/2023] [Accepted: 03/09/2023] [Indexed: 03/15/2023]
Abstract
There is growing interest in the role of structural variants (SVs) as drivers of local adaptation and speciation. From a biodiversity genomics perspective, the characterization of genome-wide SVs provides an exciting opportunity to complement single nucleotide polymorphisms (SNPs). However, little is known about the impacts of SV discovery and genotyping strategies on the characterization of genome-wide SV diversity within and among populations. Here, we explore a near whole-species resequence data set, and long-read sequence data for a subset of highly represented individuals in the critically endangered kākāpō (Strigops habroptilus). We demonstrate that even when using a highly contiguous reference genome, different discovery and genotyping strategies can significantly impact the type, size and location of SVs characterized genome-wide. Further, we found that the mean number of SVs in each of two kākāpō lineages differed both within and across generations. These combined results suggest that genome-wide characterization of SVs remains challenging at the population-scale. We are optimistic that increased accessibility to long-read sequencing and advancements in bioinformatic approaches including multireference approaches like genome graphs will alleviate at least some of the challenges associated with resolving SV characteristics below the species level. In the meantime, we address caveats, highlight considerations, and provide recommendations for the characterization of genome-wide SVs in biodiversity genomic research.
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Affiliation(s)
- Jana R Wold
- University of Canterbury, Christchurch, New Zealand
| | - Joseph G Guhlin
- Genomics Aotearoa and Biochemistry Department, University of Otago, Dunedin, New Zealand
| | - Peter K Dearden
- Genomics Aotearoa and Biochemistry Department, University of Otago, Dunedin, New Zealand
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Zuccolo A, Mfarrej S, Celii M, Mussurova S, Rivera LF, Llaca V, Mohammed N, Pain A, Alrefaei AF, Alrefaei AF, Wing RA. The gyrfalcon (Falco rusticolus) genome. G3 (Bethesda) 2023; 13:6972330. [PMID: 36611193 PMCID: PMC9997569 DOI: 10.1093/g3journal/jkad001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 12/22/2022] [Accepted: 12/26/2022] [Indexed: 01/09/2023]
Abstract
High-quality genome assemblies are characterized by high-sequence contiguity, completeness, and a low error rate, thus providing the basis for a wide array of studies focusing on natural species ecology, conservation, evolution, and population genomics. To provide this valuable resource for conservation projects and comparative genomics studies on gyrfalcon (Falco rusticolus), we sequenced and assembled the genome of this species using third-generation sequencing strategies and optical maps. Here, we describe a highly contiguous and complete genome assembly comprising 20 scaffolds and 13 contigs with a total size of 1.193 Gbp, including 8,064 complete Benchmarking Universal Single-Copy Orthologs (BUSCOs) of the total 8,338 BUSCO groups present in the library aves_odb10. Of these BUSCO genes, 96.7% were complete, 96.1% were present as a single copy, and 0.6% were duplicated. Furthermore, 0.8% of BUSCO genes were fragmented and 2.5% (210) were missing. A de novo search for transposable elements (TEs) identified 5,716 TEs that masked 7.61% of the F. rusticolus genome assembly when combined with publicly available TE collections. Long interspersed nuclear elements, in particular, the element Chicken-repeat 1 (CR1), were the most abundant TEs in the F. rusticolus genome. A de novo first-pass gene annotation was performed using 293,349 PacBio Iso-Seq transcripts and 496,195 transcripts derived from the assembly of 42,429,525 Illumina PE RNA-seq reads. In all, 19,602 putative genes, of which 59.31% were functionally characterized and associated with Gene Ontology terms, were annotated. A comparison of the gyrfalcon genome assembly with the publicly available assemblies of the domestic chicken (Gallus gallus), zebra finch (Taeniopygia guttata), and hummingbird (Calypte anna) revealed several genome rearrangements. In particular, nine putative chromosome fusions were identified in the gyrfalcon genome assembly compared with those in the G. gallus genome assembly. This genome assembly, its annotation for TEs and genes, and the comparative analyses presented, complement and strength the base of high-quality genome assemblies and associated resources available for comparative studies focusing on the evolution, ecology, and conservation of Aves.
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Affiliation(s)
- Andrea Zuccolo
- Center for Desert Agriculture (CDA), Biological and Environmental Sciences & Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia.,Crop Science Research Center, Sant'Anna School of Advanced Studies, Piazza Martiri della Libertà 33, 56127 Pisa, Italy
| | - Sara Mfarrej
- King Abdullah University of Science and Technology (KAUST), Pathogen Genomics Laboratory, Biological and Environmental Science and Engineering (BESE), Thuwal-Jeddah 23955-6900, Saudi Arabia
| | - Mirko Celii
- Center for Desert Agriculture (CDA), Biological and Environmental Sciences & Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - Saule Mussurova
- Center for Desert Agriculture (CDA), Biological and Environmental Sciences & Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - Luis F Rivera
- Center for Desert Agriculture (CDA), Biological and Environmental Sciences & Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - Victor Llaca
- Research and Development, Corteva Agriscience, Johnston, IA 50131, USA
| | - Nahed Mohammed
- Center for Desert Agriculture (CDA), Biological and Environmental Sciences & Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - Arnab Pain
- King Abdullah University of Science and Technology (KAUST), Pathogen Genomics Laboratory, Biological and Environmental Science and Engineering (BESE), Thuwal-Jeddah 23955-6900, Saudi Arabia
| | | | - Abdulwahed Fahad Alrefaei
- Department of Zoology, College of Science, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia
| | - Rod A Wing
- Center for Desert Agriculture (CDA), Biological and Environmental Sciences & Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia.,School of Plant Sciences, Arizona Genomics Institute, University of Arizona, 24 Tucson, Arizona 85721, USA
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50
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Abstract
Insects constitute vital components of ecosystems. There is alarming evidence for global declines in insect species diversity, abundance, and biomass caused by anthropogenic drivers such as habitat degradation or loss, agricultural practices, climate change, and environmental pollution. This raises important concerns about human food security and ecosystem functionality and calls for more research to assess insect population trends and identify threatened species and the causes of declines to inform conservation strategies. Analysis of genetic diversity is a powerful tool to address these goals, but so far animal conservation genetics research has focused strongly on endangered vertebrates, devoting less attention to invertebrates, such as insects, that constitute most biodiversity. Insects' shorter generation times and larger population sizes likely necessitate different analytical methods and management strategies. The availability of high-quality reference genome assemblies enables population genomics to address several key issues. These include precise inference of past demographic fluctuations and recent declines, measurement of genetic load levels, delineation of evolutionarily significant units and cryptic species, and analysis of genetic adaptation to stressors. This enables identification of populations that are particularly vulnerable to future threats, considering their potential to adapt and evolve. We review the application of population genomics to insect conservation and the outlook for averting insect declines.
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Affiliation(s)
- Matthew T Webster
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden;
| | - Alexis Beaurepaire
- Institute of Bee Health, Vetsuisse Faculty, University of Bern, Bern, Switzerland.,Agroscope, Swiss Bee Research Centre, Bern, Switzerland
| | - Peter Neumann
- Institute of Bee Health, Vetsuisse Faculty, University of Bern, Bern, Switzerland.,Agroscope, Swiss Bee Research Centre, Bern, Switzerland
| | - Eckart Stolle
- Leibniz Institute for the Analysis of Biodiversity Change, Museum Koenig, Bonn, Germany
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