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Chaiphongpachara T, Laojun S, Changbunjong T, Wichit S, Villarroel PMS. Demographic inference from the mt-DNA COI gene and wing geometry of Culex gelidus (Diptera: Culicidae), an important vector of Japanese encephalitis in Thailand. Acta Trop 2024; 256:107276. [PMID: 38821146 DOI: 10.1016/j.actatropica.2024.107276] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2024] [Revised: 05/28/2024] [Accepted: 05/28/2024] [Indexed: 06/02/2024]
Abstract
Culex gelidus (Diptera: Culicidae), an important vector of the Japanese encephalitis virus (JEV), contributes to human viral encephalitis in many Asian countries, including Thailand. This study represents the first investigation of the demographic patterns of Cx. gelidus populations in Thailand using cytochrome c oxidase subunit I (COI) gene analysis and wing geometric morphometrics (GM). Mosquitoes were collected from 10 provinces across six regions of Thailand in 2022. Analysis of the COI sequences (n = 182) indicated high haplotype diversity (0.882) and low nucleotide diversity (0.006), with 72 haplotypes identified. The haplotype network demonstrated no profound splits among the geographic populations. Neutral tests, including Tajima's D and Fu's Fs, displayed negative values, with a significant result observed for Fu's Fs (-33.048, p < 0.05). The mismatch distribution analysis indicated that the population does not statistically deviate from a model of sudden population expansion (SSD = 0.010, p > 0.05; Rg = 0.022, p > 0.05). The estimations suggest that the Cx. gelidus population in Thailand began its expansion approximately between 459,243 and 707,011 years ago. The Mantel test showed no significant relationship between genetic and geographic distances (r = 0.048, p > 0.05). Significant phenotypic differences (based on wing shape) were observed among most populations. Additionally, in this study, we found no significant relationships between phenotypic and genetic distances (r = 0.250, p > 0.05). Understanding the genetic and morphological dynamics of Cx. gelidus is vital for developing targeted surveillance and vector control measures. This knowledge will also help to predict how future environmental changes might affect these populations, thereby informing long-term vector management strategies.
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Affiliation(s)
- Tanawat Chaiphongpachara
- Department of Public Health and Health Promotion, College of Allied Health Sciences, Suan Sunandha Rajabhat University, Samut Songkhram 75000, Thailand.
| | - Sedthapong Laojun
- Department of Public Health and Health Promotion, College of Allied Health Sciences, Suan Sunandha Rajabhat University, Samut Songkhram 75000, Thailand
| | - Tanasak Changbunjong
- Department of Pre-Clinic and Applied Animal Science, Faculty of Veterinary Science, Mahidol University, Nakhon Pathom 73170, Thailand; The Monitoring and Surveillance Center for Zoonotic Diseases in Wildlife and Exotic Animals (MoZWE), Faculty of Veterinary Science, Mahidol University, Nakhon Pathom 73170, Thailand
| | - Sineewanlaya Wichit
- Department of Clinical Microbiology and Applied Technology, Faculty of Medical Technology, Mahidol University, Nakhon Pathom 73170, Thailand; Viral Vector Joint Unit and Joint Laboratory, Mahidol University, Nakhon Pathom 73170, Thailand
| | - Paola Mariela Saba Villarroel
- Department of Clinical Microbiology and Applied Technology, Faculty of Medical Technology, Mahidol University, Nakhon Pathom 73170, Thailand; Viral Vector Joint Unit and Joint Laboratory, Mahidol University, Nakhon Pathom 73170, Thailand
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2
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Smeds L, Huson LSA, Ellegren H. Structural genomic variation in the inbred Scandinavian wolf population contributes to the realized genetic load but is positively affected by immigration. Evol Appl 2024; 17:e13652. [PMID: 38333557 PMCID: PMC10848878 DOI: 10.1111/eva.13652] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Revised: 01/08/2024] [Accepted: 01/16/2024] [Indexed: 02/10/2024] Open
Abstract
When populations decrease in size and may become isolated, genomic erosion by loss of diversity from genetic drift and accumulation of deleterious mutations is likely an inevitable consequence. In such cases, immigration (genetic rescue) is necessary to restore levels of genetic diversity and counteract inbreeding depression. Recent work in conservation genomics has studied these processes focusing on the genetic diversity of single nucleotide polymorphisms. In contrast, our knowledge about structural genomic variation (insertions, deletions, duplications and inversions) in endangered species is limited. We analysed whole-genome, short-read sequences from 212 wolves from the inbred Scandinavian population and from neighbouring populations in Finland and Russia, and detected >35,000 structural variants (SVs) after stringent quality and genotype frequency filtering; >26,000 high-confidence variants remained after manual curation. The majority of variants were shorter than 1 kb, with a distinct peak in the length distribution of deletions at 190 bp, corresponding to insertion events of SINE/tRNA-Lys elements. The site frequency spectrum of SVs in protein-coding regions was significantly shifted towards rare alleles compared to putatively neutral variants, consistent with purifying selection. The realized genetic load of SVs in protein-coding regions increased with inbreeding levels in the Scandinavian population, but immigration provided a genetic rescue effect by lowering the load and reintroducing ancestral alleles at loci fixed for derived SVs. Our study shows that structural variation comprises a common type of in part deleterious mutations in endangered species and that establishing gene flow is necessary to mitigate the negative consequences of loss of diversity.
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Affiliation(s)
- Linnéa Smeds
- Department of Ecology and Genetics, Evolutionary BiologyUppsala UniversityUppsalaSweden
| | - Lars S. A. Huson
- Department of Ecology and Genetics, Evolutionary BiologyUppsala UniversityUppsalaSweden
| | - Hans Ellegren
- Department of Ecology and Genetics, Evolutionary BiologyUppsala UniversityUppsalaSweden
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3
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French CM, Bertola LD, Carnaval AC, Economo EP, Kass JM, Lohman DJ, Marske KA, Meier R, Overcast I, Rominger AJ, Staniczenko PPA, Hickerson MJ. Global determinants of insect mitochondrial genetic diversity. Nat Commun 2023; 14:5276. [PMID: 37644003 PMCID: PMC10465557 DOI: 10.1038/s41467-023-40936-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Accepted: 08/15/2023] [Indexed: 08/31/2023] Open
Abstract
Understanding global patterns of genetic diversity is essential for describing, monitoring, and preserving life on Earth. To date, efforts to map macrogenetic patterns have been restricted to vertebrates, which comprise only a small fraction of Earth's biodiversity. Here, we construct a global map of predicted insect mitochondrial genetic diversity from cytochrome c oxidase subunit 1 sequences, derived from open data. We calculate the mitochondrial genetic diversity mean and genetic diversity evenness of insect assemblages across the globe, identify their environmental correlates, and make predictions of mitochondrial genetic diversity levels in unsampled areas based on environmental data. Using a large single-locus genetic dataset of over 2 million globally distributed and georeferenced mtDNA sequences, we find that mitochondrial genetic diversity evenness follows a quadratic latitudinal gradient peaking in the subtropics. Both mitochondrial genetic diversity mean and evenness positively correlate with seasonally hot temperatures, as well as climate stability since the last glacial maximum. Our models explain 27.9% and 24.0% of the observed variation in mitochondrial genetic diversity mean and evenness in insects, respectively, making an important step towards understanding global biodiversity patterns in the most diverse animal taxon.
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Affiliation(s)
- Connor M French
- Biology Department, City College of New York, New York, NY, USA.
- Biology Ph.D. Program, Graduate Center, City University of New York, New York, NY, USA.
| | - Laura D Bertola
- Biology Department, City College of New York, New York, NY, USA
- Section for Computational and RNA Biology, Department of Biology, University of Copenhagen, Copenhagen, N 2200, Denmark
| | - Ana C Carnaval
- Biology Department, City College of New York, New York, NY, USA
- Biology Ph.D. Program, Graduate Center, City University of New York, New York, NY, USA
| | - Evan P Economo
- Biodiversity and Biocomplexity Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, Japan
| | - Jamie M Kass
- Biodiversity and Biocomplexity Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, Japan
- Macroecology Laboratory, Graduate School of Life Sciences, Tohoku University, Sendai, Miyagi, Japan
| | - David J Lohman
- Biology Department, City College of New York, New York, NY, USA
- Biology Ph.D. Program, Graduate Center, City University of New York, New York, NY, USA
- Entomology Section, National Museum of Natural History, Manila, Philippines
| | | | - Rudolf Meier
- Institut für Biologie, Humboldt-Universität zu Berlin, Berlin, Germany
- Center for Integrative Biodiversity Discovery, Leibniz Institute for Evolution and Biodiversity Science, Museum für Naturkunde Berlin, Berlin, Germany
| | - Isaac Overcast
- Biology Ph.D. Program, Graduate Center, City University of New York, New York, NY, USA
- Institut de Biologie de l'Ecole Normale Superieure, Paris, France
- Department of Vertebrate Zoology, American Museum of Natural History, New York, NY, USA
| | - Andrew J Rominger
- School of Biology and Ecology, University of Maine, Orono, ME, USA
- Maine Center for Genetics in the Environment, University of Maine, Orono, ME, USA
| | | | - Michael J Hickerson
- Biology Department, City College of New York, New York, NY, USA
- Biology Ph.D. Program, Graduate Center, City University of New York, New York, NY, USA
- Division of Invertebrate Zoology, American Museum of Natural History, New York, NY, USA
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De Vivo M, Chen WY, Huang JP. Testing the efficacy of different molecular tools for parasite conservation genetics: a case study using horsehair worms (Phylum: Nematomorpha). Parasitology 2023; 150:842-851. [PMID: 37415562 PMCID: PMC10478060 DOI: 10.1017/s0031182023000641] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Revised: 06/26/2023] [Accepted: 06/27/2023] [Indexed: 07/08/2023]
Abstract
In recent years, parasite conservation has become a globally significant issue. Because of this, there is a need for standardized methods for inferring population status and possible cryptic diversity. However, given the lack of molecular data for some groups, it is challenging to establish procedures for genetic diversity estimation. Therefore, universal tools, such as double-digest restriction-site-associated DNA sequencing (ddRADseq), could be useful when conducting conservation genetic studies on rarely studied parasites. Here, we generated a ddRADseq dataset that includes all 3 described Taiwanese horsehair worms (Phylum: Nematomorpha), possibly one of the most understudied animal groups. Additionally, we produced data for a fragment of the cytochrome c oxidase subunit I (COXI) for the said species. We used the COXI dataset in combination with previously published sequences of the same locus for inferring the effective population size (Ne) trends and possible population genetic structure.We found that a larger and geographically broader sample size combined with more sequenced loci resulted in a better estimation of changes in Ne. We were able to detect demographic changes associated with Pleistocene events in all the species. Furthermore, the ddRADseq dataset for Chordodes formosanus did not reveal a genetic structure based on geography, implying a great dispersal ability, possibly due to its hosts. We showed that different molecular tools can be used to reveal genetic structure and demographic history at different historical times and geographical scales, which can help with conservation genetic studies in rarely studied parasites.
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Affiliation(s)
- Mattia De Vivo
- Department of Life Science, National Taiwan Normal University, Taipei, Taiwan
- Biodiversity Program, Taiwan International Graduate Program, Taipei, Taiwan
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Wei-Yun Chen
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Jen-Pan Huang
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
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5
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Atencio GWG, Zanini R, Deprá M, Romanowski HP. Preliminary population studies of the grassland swallowtail butterfly Euryades corethrus (Lepidoptera, Papilionidae). AN ACAD BRAS CIENC 2023; 95:e20210503. [PMID: 37341269 DOI: 10.1590/0001-3765202320210503] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Accepted: 06/10/2021] [Indexed: 06/22/2023] Open
Abstract
Euryades corethrus is a Troidini butterfly (Papilionidae, Papilioninae), endemic to grasslands in southern Brazil, Uruguay, Argentina and Paraguay. Formerly abundant, nowadays it is in the Red list of endangered species for those areas. During its larval stage, it feeds on Aristolochia spp, commonly found in southern grasslands. These native grassland areas are diminishing, being converted to crops and pastures, causing habitat loss for Aristolochia and E. corethrus. This study aimed to assess the genetic diversity, population structure and demographic history of E. corethrus. We sampled eight populations from Rio Grande do Sul, Brazil and based on Cytochrome Oxidase subunit I (COI) molecular marker, our results suggest a low genetic variability between populations, presence of gene flow and, consequently, lack of population structure. A single maternally inherited-genetic marker is insufficient for population-level decisions, but barcoding is a useful tool during early stages of population investigation, bringing out genomic diversity patterns within the target species. Those populations likely faced a bottleneck followed by a rapid expansion during the last glaciation and subsequent stabilization in effective population size. Habitat loss is a threat, which might cause isolation, loss of genetic variability and, ultimately, extinction of E. corethrus if no habitat conservation policy is adopted.
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Affiliation(s)
- Guilherme Wagner G Atencio
- Programa de Pós-Graduação em Biologia Animal, Universidade Federal do Rio Grande do Sul, Av. Bento Gonçalves, 9500, Bloco IV, Prédio 43433, Sala 214, Agronomia, 91501-970 Porto Alegre, RS, Brazil
- Universidade Federal do Rio Grande do Sul, Departamento de Zoologia, Laboratório de Ecologia de Insetos, Av. Bento Gonçalves, 9500, Bloco IV, Prédio 43435, Sala 218, Agronomia, 91501-970 Porto Alegre, RS, Brazil
- Universidade de Lisboa, Faculdade de Ciências, Centro de Ecologia, Evolução e Alterações Ambientais, Edifício C2, 5.º piso, Sala 2.5.46, Código Postal 1749-016, Campo Grande, Lisboa, Portugal
| | - Rebeca Zanini
- Universidade Federal do Rio Grande do Sul, Departamento de Genética, Laboratório de Drosophila, Av. Bento Gonçalves, 9500, Prédio 43323, Sala 210, Agronomia, 90650-001 Porto Alegre, RS, Brazil
- Universidade Nova de Lisboa, Faculdade de Ciências Médicas, Laboratório de Biomedicina Integrativa, Rua do Instituto Bacteriológico 5, Código Postal 1169-056, Lisboa, Portugal
| | - Maríndia Deprá
- Programa de Pós-Graduação em Biologia Animal, Universidade Federal do Rio Grande do Sul, Av. Bento Gonçalves, 9500, Bloco IV, Prédio 43433, Sala 214, Agronomia, 91501-970 Porto Alegre, RS, Brazil
- Universidade Federal do Rio Grande do Sul, Departamento de Genética, Laboratório de Drosophila, Av. Bento Gonçalves, 9500, Prédio 43323, Sala 210, Agronomia, 90650-001 Porto Alegre, RS, Brazil
- Programa de Pós-Graduação em Genética e Biologia Molecular, Universidade Federal do Rio Grande do Sul, Av. Bento Gonçalves, 9500, Prédio 43312 M, Caixa Postal 15053, Agronomia, 90650-001 Porto Alegre, RS, Brazil
| | - Helena P Romanowski
- Programa de Pós-Graduação em Biologia Animal, Universidade Federal do Rio Grande do Sul, Av. Bento Gonçalves, 9500, Bloco IV, Prédio 43433, Sala 214, Agronomia, 91501-970 Porto Alegre, RS, Brazil
- Universidade Federal do Rio Grande do Sul, Departamento de Zoologia, Laboratório de Ecologia de Insetos, Av. Bento Gonçalves, 9500, Bloco IV, Prédio 43435, Sala 218, Agronomia, 91501-970 Porto Alegre, RS, Brazil
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6
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Genetic Diversity and Insights about Distribution of Brown Howler Monkeys (Alouatta guariba Group) (Atelidae, Alouattinae). INT J PRIMATOL 2023. [DOI: 10.1007/s10764-023-00352-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/17/2023]
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7
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Schmidt C, Hoban S, Hunter M, Paz-Vinas I, Garroway CJ. Genetic diversity and IUCN Red List status. CONSERVATION BIOLOGY : THE JOURNAL OF THE SOCIETY FOR CONSERVATION BIOLOGY 2023:e14064. [PMID: 36751982 DOI: 10.1111/cobi.14064] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 01/11/2023] [Accepted: 01/18/2023] [Indexed: 06/18/2023]
Abstract
The International Union for Conservation of Nature (IUCN) Red List is an important and widely used tool for conservation assessment. The IUCN uses information about a species' range, population size, habitat quality and fragmentation levels, and trends in abundance to assess extinction risk. Genetic diversity is not considered, although it affects extinction risk. Declining populations are more strongly affected by genetic drift and higher rates of inbreeding, which can reduce the efficiency of selection, lead to fitness declines, and hinder species' capacities to adapt to environmental change. Given the importance of conserving genetic diversity, attempts have been made to find relationships between red-list status and genetic diversity. Yet, there is still no consensus on whether genetic diversity is captured by the current IUCN Red List categories in a way that is informative for conservation. To assess the predictive power of correlations between genetic diversity and IUCN Red List status in vertebrates, we synthesized previous work and reanalyzed data sets based on 3 types of genetic data: mitochondrial DNA, microsatellites, and whole genomes. Consistent with previous work, species with higher extinction risk status tended to have lower genetic diversity for all marker types, but these relationships were weak and varied across taxa. Regardless of marker type, genetic diversity did not accurately identify threatened species for any taxonomic group. Our results indicate that red-list status is not a useful metric for informing species-specific decisions about the protection of genetic diversity and that genetic data cannot be used to identify threat status in the absence of demographic data. Thus, there is a need to develop and assess metrics specifically designed to assess genetic diversity and inform conservation policy, including policies recently adopted by the UN's Convention on Biological Diversity Kunming-Montreal Global Biodiversity Framework.
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Affiliation(s)
- Chloé Schmidt
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut, USA
- Center for Biodiversity and Global Change, Yale University, New Haven, Connecticut, USA
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
| | - Sean Hoban
- The Center for Tree Science, The Morton Arboretum, Lisle, Illinois, USA
| | - Margaret Hunter
- Wetland and Aquatic Research Center, U.S. Geological Survey, Gainesville, Florida, USA
| | - Ivan Paz-Vinas
- Laboratoire Evolution et Diversité Biologique (EDB), UMR5174, Université Toulouse 3 Paul Sabatier, CNRS, IRD, Toulouse, France
| | - Colin J Garroway
- Department of Biological Sciences, University of Manitoba, Winnipeg, Manitoba, Canada
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Konopiński MK. Average weighted nucleotide diversity is more precise than pixy in estimating the true value of π from sequence sets containing missing data. Mol Ecol Resour 2023; 23:348-354. [PMID: 36031871 DOI: 10.1111/1755-0998.13707] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Revised: 06/03/2022] [Accepted: 07/27/2022] [Indexed: 01/04/2023]
Abstract
Nucleotide diversity remains an important statistic in population genetic/genomic studies. Although recent advances in massive sequencing make generating sequence data sets cheaper and faster, currently used technologies often introduce substantial amounts of missing nucleotides in their output. A novel method of estimating π from data sets containing missing data - pixy - has also recently been proposed. In this study, the pixy estimator, πpixy , was compared to average weighted nucleotide diversity, πW . The estimators were tested both on sequences simulated in fastsimcoal and real sequence sets. Both sets were modified by random insertion of missing nucleotides. Weighted nucleotide diversity performed better in all pairwise comparisons. It was characterized by a smaller error and a narrower distribution of the results. πpixy tends to overestimate the nucleotide diversity when both the proportion of missing data and the level of variation is low. Of the two estimators, only πW estimated the true nucleotide diversity in a part of the simulations. A simple formula for estimating πW allows for easy integration of the estimator in packages such as pixy, which would allow obtaining more precise estimates of nucleotide diversity either in a sliding window or for discrete genomic regions.
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Wootton E, Robert C, Taillon J, Côté SD, Shafer ABA. Genomic health is dependent on long-term population demographic history. Mol Ecol 2023; 32:1943-1954. [PMID: 36704858 DOI: 10.1111/mec.16863] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 01/08/2023] [Accepted: 01/13/2023] [Indexed: 01/28/2023]
Abstract
Current genetic methods of population assessment in conservation biology have been challenged by genome-scale analyses due to their quantitatively novel insights. These analyses include assessments of runs-of-homozygosity (ROH), genomic evolutionary rate profiling (GERP), and mutational load. Here, we aim to elucidate the relationships between these measures using three divergent ungulates: white-tailed deer, caribou, and mountain goat. The white-tailed deer is currently expanding, while caribou are in the midst of a significant decline. Mountain goats remain stable, having suffered a large historical bottleneck. We assessed genome-wide signatures of inbreeding using the inbreeding coefficient F and %ROH (FROH ) and identified evolutionarily constrained regions with GERP. Mutational load was estimated by identifying mutations in highly constrained elements (CEs) and sorting intolerant from tolerant (SIFT) mutations. Our results showed that F and FROH are higher in mountain goats than in caribou and white-tailed deer. Given the extended bottleneck and low Ne of the mountain goat, this supports the idea that the genome-wide effects of demographic change take time to accrue. Similarly, we found that mountain goats possess more highly constrained CEs and the lowest dN/dS values, both of which are indicative of greater purifying selection; this is also reflected by fewer mutations in CEs and deleterious mutations identified by SIFT. In contrast, white-tailed deer presented the highest mutational load with both metrics, in addition to dN/dS, while caribou were intermediate. Our results demonstrate that extended bottlenecks may lead to reduced diversity and increased FROH in ungulates, but not necessarily an increase in mutational load, probably due to the purging of deleterious alleles in small populations.
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Affiliation(s)
- Eric Wootton
- Biochemistry and Molecular Biology, Trent University, Peterborough, Ontario, Canada
| | - Claude Robert
- Département des Sciences Animales, Université Laval, Québec, Québec, Canada
| | - Joëlle Taillon
- Direction de l'Expertise sur la Faune Terrestre, l'Herpétofaune et l'Avifaune, Ministère des Forêts, de la Faune et des Parcs, Gouvernement du Québec, Québec, Québec, Canada
| | - Steeve D Côté
- Département de Biologie, Caribou Ungava and Centre d'Études Nordiques, Université Laval, Québec, Québec, Canada
| | - Aaron B A Shafer
- Environmental and Life Sciences Graduate Programme, Trent University, Peterborough, Ontario, Canada
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Phillips JD, Athey TB, McNicholas PD, Hanner RH. VLF: An R package for the analysis of very low frequency variants in DNA sequences. Biodivers Data J 2023; 11:e96480. [PMID: 38327328 PMCID: PMC10848336 DOI: 10.3897/bdj.11.e96480] [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: 10/18/2022] [Accepted: 11/30/2022] [Indexed: 01/27/2023] Open
Abstract
Here, we introduce VLF, an R package to determine the distribution of very low frequency variants (VLFs) in nucleotide and amino acid sequences for the analysis of errors in DNA sequence records. The package allows users to assess VLFs in aligned and trimmed protein-coding sequences by automatically calculating the frequency of nucleotides or amino acids in each sequence position and outputting those that occur under a user-specified frequency (default of p = 0.001). These results can then be used to explore fundamental population genetic and phylogeographic patterns, mechanisms and processes at the microevolutionary level, such as nucleotide and amino acid sequence conservation. Our package extends earlier work pertaining to an implementation of VLF analysis in Microsoft Excel, which was found to be both computationally slow and error prone. We compare those results to our own herein. Results between the two implementations are found to be highly consistent for a large DNA barcode dataset of bird species. Differences in results are readily explained by both manual human error and inadequate Linnean taxonomy (specifically, species synonymy). Here, VLF is also applied to a subset of avian barcodes to assess the extent of biological artifacts at the species level for Canada goose (Branta canadensis), as well as within a large dataset of DNA barcodes for fishes of forensic and regulatory importance. The novelty of VLF and its benefit over the previous implementation include its high level of automation, speed, scalability and ease-of-use, each desirable characteristics which will be extremely valuable as more sequence data are rapidly accumulated in popular reference databases, such as BOLD and GenBank.
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Affiliation(s)
- Jarrett D. Phillips
- School of Computer Science and Department of Integrative Biology, University of Guelph, Guelph, CanadaSchool of Computer Science and Department of Integrative Biology, University of GuelphGuelphCanada
| | - Taryn B.T. Athey
- Stollery Children's Hospital, Edmonton, CanadaStollery Children's HospitalEdmontonCanada
| | - Paul D. McNicholas
- Department of Mathematics and Statistics, McMaster University, Hamilton, CanadaDepartment of Mathematics and Statistics, McMaster UniversityHamiltonCanada
| | - Robert H. Hanner
- Biodiversity Institute of Ontario and Department of Integrative Biology, University of Guelph, Guelph, CanadaBiodiversity Institute of Ontario and Department of Integrative Biology, University of GuelphGuelphCanada
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11
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Pelletier TA, Parsons DJ, Decker SK, Crouch S, Franz E, Ohrstrom J, Carstens BC. phylogatR: Phylogeographic data aggregation and repurposing. Mol Ecol Resour 2022; 22:2830-2842. [PMID: 35748425 PMCID: PMC9796472 DOI: 10.1111/1755-0998.13673] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Revised: 03/10/2022] [Accepted: 06/07/2022] [Indexed: 01/01/2023]
Abstract
Patterns of genetic diversity within species contain information the history of that species, including how they have responded to historical climate change and how easily the organism is able to disperse across its habitat. More than 40,000 phylogeographic and population genetic investigations have been published to date, each collecting genetic data from hundreds of samples. Despite these millions of data points, meta-analyses are challenging because the synthesis of results across hundreds of studies, each using different methods and forms of analysis, is a daunting and time-consuming task. It is more efficient to proceed by repurposing existing data and using automated data analysis. To facilitate data repurposing, we created a database (phylogatR) that aggregates data from different sources and conducts automated multiple sequence alignments and data curation to provide users with nearly ready-to-analyse sets of data for thousands of species. Two types of scientific research will be made easier by phylogatR: large meta-analyses of thousands of species that can address classic questions in evolutionary biology and ecology, and student- or citizen- science based investigations that will introduce a broad range of people to the analysis of genetic data. phylogatR enhances the value of existing data via the creation of software and web-based tools that enable these data to be recycled and reanalysed and increase accessibility to big data for research laboratories and classroom instructors with limited computational expertise and resources.
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Affiliation(s)
| | - Danielle J. Parsons
- Department of Evolution, Ecology, and Organismal BiologyThe Ohio State UniversityColumbusOhioUSA,Museum of Biological DiversityThe Ohio State UniversityColumbusOhioUSA
| | - Sydney K. Decker
- Department of Evolution, Ecology, and Organismal BiologyThe Ohio State UniversityColumbusOhioUSA,Museum of Biological DiversityThe Ohio State UniversityColumbusOhioUSA
| | | | - Eric Franz
- Ohio Supercomputer CenterColumbusOhioUSA
| | | | - Bryan C. Carstens
- Department of Evolution, Ecology, and Organismal BiologyThe Ohio State UniversityColumbusOhioUSA,Museum of Biological DiversityThe Ohio State UniversityColumbusOhioUSA
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12
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Teles JN, França NFC, Mossolin EC, Mantelatto FL. Population structure and genetic connectivity of the freshwater shrimp Potimirim brasiliana Villalobos, 1959 inhabiting a continental island. J NAT HIST 2022. [DOI: 10.1080/00222933.2022.2119896] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
Affiliation(s)
- Jeniffer N. Teles
- Laboratory of Bioecology and Crustacean Systematics (LBSC), Department of Biology, Faculty of Philosophy, Science and Letters at Ribeirão Preto (FFCLRP), University of São Paulo (USP), Ribeirão Preto, Brazil
| | - Nielson F. C. França
- Laboratory of Bioecology and Crustacean Systematics (LBSC), Department of Biology, Faculty of Philosophy, Science and Letters at Ribeirão Preto (FFCLRP), University of São Paulo (USP), Ribeirão Preto, Brazil
| | - Emerson C. Mossolin
- Laboratory of Invertebrates (LABIN), Biological Science Department, Federal University of Catalão (UFCAT), Catalão, Brazil
| | - Fernando L. Mantelatto
- Laboratory of Bioecology and Crustacean Systematics (LBSC), Department of Biology, Faculty of Philosophy, Science and Letters at Ribeirão Preto (FFCLRP), University of São Paulo (USP), Ribeirão Preto, Brazil
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Kang JH, Yi DA, Kuprin AV, Han C, Bae YJ. Phylogeographic Investigation of an Endangered Longhorn Beetle, Callipogon relictus (Coleoptera: Cerambycidae), in Northeast Asia: Implications for Future Restoration in Korea. INSECTS 2021; 12:555. [PMID: 34203723 PMCID: PMC8232212 DOI: 10.3390/insects12060555] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Revised: 05/29/2021] [Accepted: 06/07/2021] [Indexed: 11/24/2022]
Abstract
The longhorn beetle, Callipogon (Eoxenus) relictus Semenov, is the only remnant species found in the Palearctic region, while all other Callipogon species are distributed mainly in Central America and partly in South America. This species has been placed in the first category (as 'critically endangered') of the Red Data Book in Russia and designated as one of the top-priority target species among all endangered invertebrate species for restoration in South Korea since 2006. Although its restricted distribution in Northeast Asia with a high conservational value has been highlighted, genetic features of C. relictus from different geographic regions remain unexplored. We first investigated the level of genetic diversity and phylogeographic patterns of C. relictus to evaluate the current conservational status and the feasibility of the implementation of a restoration program. The average genetic divergence of mitochondrial gene COI based on Kimura-2-parameter distance among the four regions in Russia, China, North Korea, and South Korea was 2.2%, which lies within the range of intraspecific levels. However, two separate clades with 3.8% divergence were identified, despite no geographical clustering of haplotypes. The linear pattern of the haplotype network with a high level of haplotype and nucleotide diversities suggests that the wide range of currently fragmented populations might be the remnant of genetically diverse populations in the past. This study will provide crucial information on the genetic characteristics and phylogeographic history of C. relictus, which will help to establish conservation strategies for this cherished insect species in Northeast Asia.
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Affiliation(s)
- Ji Hyoun Kang
- Korean Entomological Institute, Korea University, Seoul 02841, Korea;
| | - Dae-Am Yi
- Research Center of Natural Monument Insects, Yeongwol Insect Museum, Yeongwol 26210, Korea;
| | - Alexander V. Kuprin
- Federal Scientific Center of the East Asia Terrestrial Biodiversity, Far Eastern Branch of the Russian Academy of Sciences, 690022 Vladivostok, Russia;
| | - Changdo Han
- Wildlife Research Center, Korea University, Ogawa-chô, Kodaira City, Tokyo 187-0032, Japan;
| | - Yeon Jae Bae
- Division of Environmental Science and Ecological Engineering, Korea University, Seoul 02841, Korea
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