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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] [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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Kipp EJ, Lindsey LL, Khoo B, Faulk C, Oliver JD, Larsen PA. Metagenomic surveillance for bacterial tick-borne pathogens using nanopore adaptive sampling. Sci Rep 2023; 13:10991. [PMID: 37419899 PMCID: PMC10328957 DOI: 10.1038/s41598-023-37134-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Accepted: 06/16/2023] [Indexed: 07/09/2023] Open
Abstract
Technological and computational advancements in the fields of genomics and bioinformatics are providing exciting new opportunities for pathogen discovery and genomic surveillance. In particular, single-molecule nucleotide sequence data originating from Oxford Nanopore Technologies (ONT) sequencing platforms can be bioinformatically leveraged, in real-time, for enhanced biosurveillance of a vast array of zoonoses. The recently released nanopore adaptive sampling (NAS) strategy facilitates immediate mapping of individual nucleotide molecules to a given reference as each molecule is being sequenced. User-defined thresholds then allow for the retention or rejection of specific molecules, informed by the real-time reference mapping results, as they are physically passing through a given sequencing nanopore. Here, we show how NAS can be used to selectively sequence DNA of multiple bacterial tick-borne pathogens circulating in wild populations of the blacklegged tick vector, Ixodes scapularis.
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Affiliation(s)
- Evan J Kipp
- Department of Veterinary and Biomedical Sciences, College of Veterinary Medicine, University of Minnesota-Twin Cities, St. Paul, MN, USA.
| | - Laramie L Lindsey
- Department of Veterinary and Biomedical Sciences, College of Veterinary Medicine, University of Minnesota-Twin Cities, St. Paul, MN, USA
| | - Benedict Khoo
- Division of Environmental Health Sciences, School of Public Health, University of Minnesota-Twin Cities, Minneapolis, MN, USA
| | - Christopher Faulk
- Department of Animal Science, College of Food, Agricultural and Natural Resource Sciences, University of Minnesota-Twin Cities, St. Paul, MN, USA
| | - Jonathan D Oliver
- Division of Environmental Health Sciences, School of Public Health, University of Minnesota-Twin Cities, Minneapolis, MN, USA
| | - Peter A Larsen
- Department of Veterinary and Biomedical Sciences, College of Veterinary Medicine, University of Minnesota-Twin Cities, St. Paul, MN, USA
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Feng S, Wan W, Li Y, Wang D, Ren G, Ma T, Ru D. Transcriptome-based analyses of adaptive divergence between two closely related spruce species on the Qinghai-Tibet plateau and adjacent regions. Mol Ecol 2023; 32:476-491. [PMID: 36320185 DOI: 10.1111/mec.16758] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Revised: 10/07/2022] [Accepted: 10/17/2022] [Indexed: 11/17/2022]
Abstract
Speciation among populations connected by gene flow is driven by adaptation to different environments, but underlying gene-environment associations remain largely unknown. Here, 162 individuals from 32 populations were sampled to obtain 191,648 independent single nucleotide polymorphisms (SNPs) across the genomes of two closely related spruce species, Picea asperata and Picea crassifolia, which occur on the Qinghai-Tibet Plateau and in surrounding regions. Using the SNP data set, genotype-environment associations and demographic modelling were used to examine local adaptation and genetic divergence between these two species. While morphologically similar, the two Picea species were genetically differentiated in multiple analyses. These species diverged despite continuous gene flow, and their initial divergence was dated back to the late Quaternary. The effective population sizes of both species have expanded since their divergence, as confirmed by niche distribution simulations. A total of 6365 genes were associated with the tested environmental variables; of these, 41 were positively selected in P. asperata and were mainly associated with temperature, while 83 were positively selected in P. crassifolia and were primarily associated with precipitation. These results deepen our understanding of the adaptive divergence and demographic histories of these two spruce species and highlight the importance of genomic data in deciphering the environmental selection underlying Quaternary interspecific divergence.
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Affiliation(s)
- Shuo Feng
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, China
| | - Wei Wan
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, China
| | - Yang Li
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, China
| | - DongLei Wang
- Key Laboratory for Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Guangpeng Ren
- State Key Laboratory of Grassland Agro-Ecosystems, College of Ecology, Lanzhou University, Lanzhou, China
| | - Tao Ma
- Key Laboratory for Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Dafu Ru
- State Key Laboratory of Grassland Agro-Ecosystems, College of Ecology, Lanzhou University, Lanzhou, China
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Forcina G, Camacho-Sanchez M, Cornellas A, Leonard JA. Complete mitogenomes reveal limited genetic variability in the garden dormouse Eliomys quercinus of the Iberian Peninsula. ANIMAL BIODIVERSITY AND CONSERVATION 2022. [DOI: 10.32800/abc.2022.45.0107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The garden dormouse Eliomys quercinus is a poorly known Western Palearctic species experiencing a global decline. Even though the availability of genetic information is key to assess the driversunderlying demographic changes in wild populations and plan adequate management, data on E. quercinus are still scant. In this study, we reconstructed the complete mitogenomes of four E. quercinus individuals from southern Spain using in–solution enriched libraries, and found evidence of limited genetic variability. We then compared their cytochrome b sequences to those of conspecifics from other countries and supported the divergent but genetically depauperate position of this evolutionarily significant unit (ESU). The information produced will assist future conservation studies on this little–studied rodent.
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Affiliation(s)
- G. Forcina
- Conservation and Evolutionary Genetics Group, Estación Biológica de Doñana, Sevilla, Spain
| | - M. Camacho-Sanchez
- Conservation and Evolutionary Genetics Group, Estación Biológica de Doñana, Sevilla, Spain
| | - A. Cornellas
- Conservation and Evolutionary Genetics Group, Estación Biológica de Doñana, Sevilla, Spain
| | - J. A. Leonard
- Conservation and Evolutionary Genetics Group, Estación Biológica de Doñana, Sevilla, Spain
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Byer NW, Holding ML, Crowell MM, Pierson TW, Dilts TE, Larrucea ES, Shoemaker KT, Matocq MD. Adaptive divergence despite low effective population size in a peripherally isolated population of the pygmy rabbit, Brachylagus idahoensis. Mol Ecol 2021; 30:4173-4188. [PMID: 34166550 DOI: 10.1111/mec.16040] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2020] [Revised: 06/01/2021] [Accepted: 06/18/2021] [Indexed: 11/30/2022]
Abstract
Local adaptation can occur when spatially separated populations are subjected to contrasting environmental conditions. Historically, understanding the genetic basis of adaptation has been difficult, but increased availability of genome-wide markers facilitates studies of local adaptation in non-model organisms of conservation concern. The pygmy rabbit (Brachylagus idahoensis) is an imperiled lagomorph that relies on sagebrush for forage and cover. This reliance has led to widespread population declines following reductions in the distribution of sagebrush, leading to geographic separation between populations. In this study, we used >20,000 single nucleotide polymorphisms, genotype-environment association methods, and demographic modeling to examine neutral genetic variation and local adaptation in the pygmy rabbit in Nevada and California. We identified 308 loci as outliers, many of which had functional annotations related to metabolism of plant secondary compounds. Likewise, patterns of spatial variation in outlier loci were correlated with landscape and climatic variables including proximity to streams, sagebrush cover, and precipitation. We found that populations in the Mono Basin of California probably diverged from other Great Basin populations during late Pleistocene climate oscillations, and that this region is adaptively differentiated from other regions in the southern Great Basin despite limited gene flow and low effective population size. Our results demonstrate that peripherally isolated populations can maintain adaptive divergence.
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Affiliation(s)
- Nathan W Byer
- Department of Natural Resources and Environmental Science, University of Nevada-Reno, Reno, Nevada, USA
| | - Matthew L Holding
- Department of Natural Resources and Environmental Science, University of Nevada-Reno, Reno, Nevada, USA
| | - Miranda M Crowell
- Department of Natural Resources and Environmental Science, University of Nevada-Reno, Reno, Nevada, USA
| | - Todd W Pierson
- Department of Ecology, Evolution, and Organismal Biology, Kennesaw State University, Kennesaw, Georgia, USA
| | - Thomas E Dilts
- Department of Natural Resources and Environmental Science, University of Nevada-Reno, Reno, Nevada, USA
| | | | - Kevin T Shoemaker
- Department of Natural Resources and Environmental Science, University of Nevada-Reno, Reno, Nevada, USA
| | - Marjorie D Matocq
- Department of Natural Resources and Environmental Science, University of Nevada-Reno, Reno, Nevada, USA
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Peel E, Frankenberg S, Hogg CJ, Pask A, Belov K. Annotation of immune genes in the extinct thylacine (Thylacinus cynocephalus). Immunogenetics 2021; 73:263-275. [PMID: 33544183 DOI: 10.1007/s00251-020-01197-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Accepted: 11/24/2020] [Indexed: 11/28/2022]
Abstract
Advances in genome sequencing technology have enabled genomes of extinct species to be sequenced. However, given the fragmented nature of these genome assemblies, it is not clear whether it is possible to comprehensively annotate highly variable and repetitive genes such as those involved in immunity. As such, immune genes have only been investigated in a handful of extinct genomes, mainly in human lineages. In 2018 the genome of the thylacine (Thylacinus cynocephalus), a carnivorous marsupial from Tasmania that went extinct in 1936, was sequenced. Here we attempt to characterise the immune repertoire of the thylacine and determine similarity to its closest relative with a genome available, the Tasmanian devil (Sarcophilus harrisii), as well as other marsupials. Members from all major immune gene families were identified. However, variable regions could not be characterised, and complex families such as the major histocompatibility complex (MHC) were highly fragmented and located across multiple small scaffolds. As such, at a gene level we were unable to reconstruct full-length coding sequences for the majority of thylacine immune genes. Despite this, we identified genes encoding functionally important receptors and immune effector molecules, which suggests the functional capacity of the thylacine immune system was similar to other mammals. However, the high number of partial immune gene sequences identified limits our ability to reconstruct an accurate picture of the thylacine immune repertoire.
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Affiliation(s)
- Emma Peel
- School of Life and Environmental Sciences, Faculty of Science, The University of Sydney, Sydney, NSW, Australia
| | | | - Carolyn J Hogg
- School of Life and Environmental Sciences, Faculty of Science, The University of Sydney, Sydney, NSW, Australia
| | - Andrew Pask
- School of BioSciences, The University of Melbourne, Vic, Australia
| | - Katherine Belov
- School of Life and Environmental Sciences, Faculty of Science, The University of Sydney, Sydney, NSW, Australia.
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Abstract
Background and aims Wildlife conservation has focused primarily on species for the last decades. Recently, popular perception and laws have begun to recognize the central importance of genetic diversity in the conservation of biodiversity. How to incorporate genetic diversity in ongoing monitoring and management of wildlife is still an open question. Methods We tested a panel of multiplexed, high-throughput sequenced introns in the small mammal communities of two UNESCO World Heritage Sites on different continents to assess their viability for large-scale monitoring of genetic variability in a spectrum of diverse species. To enhance applicability across other systems, the bioinformatic pipeline for primer design was outlined. Results The number of loci amplified and amplification evenness decreased as phylogenetic distance increased from the reference taxa, yet several loci were still variable across multiple mammal orders. Conclusions Genetic variability found is informative for population genetic analyses and for addressing phylogeographic and phylogenetic questions, illustrated by small mammal examples here.
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Brandies P, Peel E, Hogg CJ, Belov K. The Value of Reference Genomes in the Conservation of Threatened Species. Genes (Basel) 2019; 10:E846. [PMID: 31717707 PMCID: PMC6895880 DOI: 10.3390/genes10110846] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Revised: 10/18/2019] [Accepted: 10/23/2019] [Indexed: 12/17/2022] Open
Abstract
Conservation initiatives are now more crucial than ever-over a million plant and animal species are at risk of extinction over the coming decades. The genetic management of threatened species held in insurance programs is recommended; however, few are taking advantage of the full range of genomic technologies available today. Less than 1% of the 13505 species currently listed as threated by the International Union for Conservation of Nature (IUCN) have a published genome. While there has been much discussion in the literature about the importance of genomics for conservation, there are limited examples of how having a reference genome has changed conservation management practice. The Tasmanian devil (Sarcophilus harrisii), is an endangered Australian marsupial, threatened by an infectious clonal cancer devil facial tumor disease (DFTD). Populations have declined by 80% since the disease was first recorded in 1996. A reference genome for this species was published in 2012 and has been crucial for understanding DFTD and the management of the species in the wild. Here we use the Tasmanian devil as an example of how a reference genome has influenced management actions in the conservation of a species.
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Affiliation(s)
| | | | | | - Katherine Belov
- School of Life & Environmental Sciences, The University of Sydney, Sydney 2006, Australia; (P.B.); (E.P.); (C.J.H.)
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Baird AB, Robinson MJ, Bickham JW. The role of the American Society of Mammalogists in mammalian conservation: from politics to conservation genetics. J Mammal 2019. [DOI: 10.1093/jmammal/gyz028] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Affiliation(s)
- Amy B Baird
- Department of Natural Sciences, University of Houston - Downtown, Houston, TX, USA
| | | | - John W Bickham
- Department of Wildlife and Fisheries Sciences, Texas A&M University, College Station, TX, USA
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