151
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Torres-Sánchez M. Variation under domestication in animal models: the case of the Mexican axolotl. BMC Genomics 2020; 21:827. [PMID: 33228551 PMCID: PMC7685626 DOI: 10.1186/s12864-020-07248-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Accepted: 11/18/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Species adaptation to laboratory conditions is a special case of domestication that has modified model organisms phenotypically and genetically. The characterisation of these changes is crucial to understand how this variation can affect the outcome of biological experiments. Yet despite the wide use of laboratory animals in biological research, knowledge of the genetic diversity within and between different strains and populations of some animal models is still scarce. This is particularly the case of the Mexican axolotl, which has been bred in captivity since 1864. RESULTS Using gene expression data from nine different projects, nucleotide sequence variants were characterised, and distinctive genetic background of the experimental specimens was uncovered. This study provides a catalogue of thousands of nucleotide variants along predicted protein-coding genes, while identifying genome-wide differences between pigment phenotypes in laboratory populations. CONCLUSIONS Awareness of the genetic variation could guide a better experimental design while helping to develop molecular tools for monitoring genetic diversity and studying gene functions in laboratory axolotls. Overall, this study highlights the cross-taxa utility that transcriptomic data might have to assess the genetic variation of the experimental specimens, which might help to shorten the journey towards reproducible research.
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Affiliation(s)
- María Torres-Sánchez
- Department of Neuroscience, Spinal Cord and Brain Injury Research Center & Ambystoma Genetic Stock Center, University of Kentucky, Lexington, KY, 40536, USA.
- Present address: Department of Biology, University of Florida, Gainesville, FL, 32611-8525, USA.
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152
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Ravagni S, Sanchez-Donoso I, Vilà C. Biased assessment of ongoing admixture using STRUCTURE in the absence of reference samples. Mol Ecol Resour 2020; 21:677-689. [PMID: 33085825 DOI: 10.1111/1755-0998.13286] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Revised: 10/05/2020] [Accepted: 10/09/2020] [Indexed: 11/30/2022]
Abstract
Detection of hybridization and introgression is important in ecological research as in conservation and evolutionary biology. STRUCTURE is one of the most popular software to study introgression and allows estimating what proportion of the genome of each individual belongs to each ancestral population, even in cases where no reference sample from the ancestral nonadmixed populations is previously identified. In spite of its frequent use, some studies have indicated that ancestry estimates may not always be reliable. We simulated population data under different conditions with regard to the genetic differentiation between ancestral populations, number of loci considered, number of alleles per marker and hybridization rate, and analysed data with STRUCTURE. When reference samples were not included, the comparison of the known degree of admixture for each simulated individual and the value estimated with STRUCTURE revealed a strong underestimation of the level of introgression, classifying many admixed individuals as nonadmixed. This derives from an inaccurate estimation of the ancestral allele frequencies. When samples from the nonadmixed ancestral population were included as reference in the analyses, the bias in the estimations was reduced. The most accurate estimates were obtained when potentially admixed samples were few in relation to reference samples. Thus, whenever possible, a very large proportion of nonadmixed reference samples should be included in admixture assessments and different approaches should be combined. The misestimate of the amount of introgression can impair our understanding of the evolutionary history of species and misguide conservation efforts.
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Affiliation(s)
- Sara Ravagni
- Conservation and Evolutionary Genetics Group, Doñana Biological Station (EBD-CSIC), Seville, Spain
| | - Ines Sanchez-Donoso
- Conservation and Evolutionary Genetics Group, Doñana Biological Station (EBD-CSIC), Seville, Spain
| | - Carles Vilà
- Conservation and Evolutionary Genetics Group, Doñana Biological Station (EBD-CSIC), Seville, Spain
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153
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Nolen ZJ, Yildirim B, Irisarri I, Liu S, Groot Crego C, Amby DB, Mayer F, Gilbert MTP, Pereira RJ. Historical isolation facilitates species radiation by sexual selection: Insights from
Chorthippus
grasshoppers. Mol Ecol 2020; 29:4985-5002. [DOI: 10.1111/mec.15695] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Revised: 09/29/2020] [Accepted: 10/05/2020] [Indexed: 01/01/2023]
Affiliation(s)
- Zachary J. Nolen
- Division of Evolutionary Biology Faculty of Biology II Ludwig‐ Maximilians‐Universität München München Germany
- Department of Biology Lund University Lund Sweden
| | - Burcin Yildirim
- Division of Evolutionary Biology Faculty of Biology II Ludwig‐ Maximilians‐Universität München München Germany
| | - Iker Irisarri
- Department of Biodiversity and Evolutionary Biology Museo Nacional de Ciencias Naturales (MNCN‐CSIC) Madrid Spain
- Department of Organismal Biology (Systematic Biology) Uppsala University Uppsala Sweden
- Department of Applied Bioinformatics, Institute for Microbiology and Genetics University of Goettingen, Campus Institute Data Science Goettingen Germany
| | - Shanlin Liu
- Natural History Museum of Denmark University of Copenhagen Copenhagen Denmark
- College of Plant Protection China Agricultural University Beijing China
| | - Clara Groot Crego
- Division of Evolutionary Biology Faculty of Biology II Ludwig‐ Maximilians‐Universität München München Germany
| | | | - Frieder Mayer
- Museum für Naturkunde – Leibniz Institute for Evolution and Biodiversity Science Berlin Germany
| | | | - Ricardo J. Pereira
- Division of Evolutionary Biology Faculty of Biology II Ludwig‐ Maximilians‐Universität München München Germany
- Natural History Museum of Denmark University of Copenhagen Copenhagen Denmark
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154
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Hinojosa JC, Koubínová D, Dincă V, Hernández-Roldán J, Munguira ML, García-Barros E, Vila M, Alvarez N, Mutanen M, Vila R. Rapid colour shift by reproductive character displacement in Cupido butterflies. Mol Ecol 2020; 29:4942-4955. [PMID: 33051915 DOI: 10.1111/mec.15682] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Revised: 09/25/2020] [Accepted: 10/05/2020] [Indexed: 12/27/2022]
Abstract
Reproductive character displacement occurs when competition for successful breeding imposes a divergent selection on the interacting species, causing a divergence of reproductive traits. Here, we show that a disputed butterfly taxon is actually a case of male wing colour shift, apparently produced by reproductive character displacement. Using double digest restriction-site associated DNA sequencing and mitochondrial DNA sequencing we studied four butterfly taxa of the subgenus Cupido (Lepidoptera: Lycaenidae): Cupido minimus and the taxon carswelli, both characterized by brown males and females, plus C. lorquinii and C. osiris, both with blue males and brown females. Unexpectedly, taxa carswelli and C. lorquinii were close to indistinguishable based on our genomic and mitochondrial data, despite displaying strikingly different male coloration. In addition, we report and analysed a brown male within the C. lorquinii range, which demonstrates that the brown morph occurs at very low frequency in C. lorquinii. Such evidence strongly suggests that carswelli is conspecific with C. lorquinii and represents populations with a fixed male brown colour morph. Considering that these brown populations occur in sympatry with or very close to the blue C. osiris, and that the blue C. lorquinii populations never do, we propose that the taxon carswelli could have lost the blue colour due to reproductive character displacement with C. osiris. Since male colour is important for conspecific recognition during courtship, we hypothesize that the observed colour shift may eventually trigger incipient speciation between blue and brown populations. Male colour seems to be an evolutionarily labile character in the Polyommatinae, and the mechanism described here might be at work in the wide diversification of this subfamily of butterflies.
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Affiliation(s)
| | | | - Vlad Dincă
- Ecology and Genetics Research Unit, University of Oulu, Oulu, Finland
| | - Juan Hernández-Roldán
- Departamento de Biología - Centro de Investigación en Biodiversidad y Cambio Global (CIBC-UAM), Universidad Autónoma de Madrid, Madrid, Spain
| | - Miguel L Munguira
- Departamento de Biología - Centro de Investigación en Biodiversidad y Cambio Global (CIBC-UAM), Universidad Autónoma de Madrid, Madrid, Spain
| | - Enrique García-Barros
- Departamento de Biología - Centro de Investigación en Biodiversidad y Cambio Global (CIBC-UAM), Universidad Autónoma de Madrid, Madrid, Spain
| | - Marta Vila
- GIBE Research Group, Universidade da Coruña, A Coruña, Spain
| | | | - Marko Mutanen
- Ecology and Genetics Research Unit, University of Oulu, Oulu, Finland
| | - Roger Vila
- Institut de Biologia Evolutiva (CSIC-UPF), Barcelona, Spain
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155
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Utsunomiya YT, Milanesi M, Barbato M, Utsunomiya ATH, Sölkner J, Ajmone‐Marsan P, Garcia JF. Unsupervised detection of ancestry tracks with the GHap
r
package. Methods Ecol Evol 2020. [DOI: 10.1111/2041-210x.13467] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Yuri Tani Utsunomiya
- Department of Support, Production and Animal Health School of Veterinary Medicine of Araçatuba São Paulo State University (Unesp) Araçatuba/SP Brazil
- International Atomic Energy Agency (IAEA) Collaborating Centre on Animal Genomics and Bioinformatics Araçatuba/SP Brazil
| | - Marco Milanesi
- Department of Support, Production and Animal Health School of Veterinary Medicine of Araçatuba São Paulo State University (Unesp) Araçatuba/SP Brazil
- International Atomic Energy Agency (IAEA) Collaborating Centre on Animal Genomics and Bioinformatics Araçatuba/SP Brazil
| | - Mario Barbato
- Department of Animal Science Food and Nutrition—DIANA and Nutrigenomics and Proteomics Research Center Università Cattolica del Sacro Cuore Piacenza Italy
| | - Adam Taiti Harth Utsunomiya
- Department of Support, Production and Animal Health School of Veterinary Medicine of Araçatuba São Paulo State University (Unesp) Araçatuba/SP Brazil
- International Atomic Energy Agency (IAEA) Collaborating Centre on Animal Genomics and Bioinformatics Araçatuba/SP Brazil
| | - Johann Sölkner
- Division of Livestook Sciences Department of Sustainable Agriculture System BOKU—University of Natural Resources and Life Sciences Vienna Austria
| | - Paolo Ajmone‐Marsan
- Department of Animal Science Food and Nutrition—DIANA and Nutrigenomics and Proteomics Research Center Università Cattolica del Sacro Cuore Piacenza Italy
| | - José Fernando Garcia
- Department of Support, Production and Animal Health School of Veterinary Medicine of Araçatuba São Paulo State University (Unesp) Araçatuba/SP Brazil
- International Atomic Energy Agency (IAEA) Collaborating Centre on Animal Genomics and Bioinformatics Araçatuba/SP Brazil
- Department of Preventive Veterinary Medicine and Animal Reproduction School of Agricultural and Veterinarian Sciences São Paulo State University (Unesp) Jaboticabal/SP Brazil
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156
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Nayfa MG, Jones DB, Benzie JAH, Jerry DR, Zenger KR. Comparing Genomic Signatures of Selection Between the Abbassa Strain and Eight Wild Populations of Nile Tilapia ( Oreochromis niloticus) in Egypt. Front Genet 2020; 11:567969. [PMID: 33193660 PMCID: PMC7593532 DOI: 10.3389/fgene.2020.567969] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Accepted: 08/31/2020] [Indexed: 11/16/2022] Open
Abstract
Domestication to captive rearing conditions, along with targeted selective breeding have genetic consequences that vary from those in wild environments. Nile tilapia (Oreochromis niloticus) is one of the most translocated and farmed aquaculture species globally, farmed throughout Asia, North and South America, and its African native range. In Egypt, a breeding program established the Abbassa Strain of Nile tilapia (AS) in 2002 based on local broodstock sourced from the Nile River. The AS has been intensively selected for growth and has gone through genetic bottlenecks which have likely shifted levels and composition of genetic diversity within the strain. Consequently, there are questions on the possible genetic impact AS escapees may have on endemic populations of Nile tilapia. However, to date there have been no genetic studies comparing genetic changes in the domesticated AS to local wild populations. This study used 9,827 genome-wide SNPs to investigate population genetic structure and signatures of selection in the AS (generations 9–11) and eight wild Nile tilapia populations from Egypt. SNP analyses identified two major genetic clusters (captive and wild populations), with wild populations showing evidence of isolation-by-distance among the Nile Delta and upstream riverine populations. Between genetic clusters, approximately 6.9% of SNPs were identified as outliers with outliers identified on all 22 O. niloticus chromosomes. A lack of localized outlier clustering on the genome suggests that no genes of major effect were presently detected. The AS has retained high levels of genetic diversity (Ho_All = 0.21 ± 0.01; He_All = 0.23 ± 0.01) when compared to wild populations (Ho_All = 0.18 ± 0.01; He_All = 0.17 ± 0.01) after 11 years of domestication and selective breeding. Additionally, 565 SNPs were unique within the AS line. While these private SNPs may be due to domestication signals or founder effects, it is suspected that introgression with blue tilapia (Oreochromis aureus) has occurred. This study highlights the importance of understanding the effects of domestication in addition to wild population structure to inform future management and dissemination decisions. Furthermore, by conducting a baseline genetic study of wild populations prior to the dissemination of a domestic line, the effects of aquaculture on these populations can be monitored over time.
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Affiliation(s)
- Maria G Nayfa
- Centre for Sustainable Tropical Fisheries and Aquaculture, College of Science and Engineering, James Cook University, Townsville, QLD, Australia.,Centre for Tropical Bioinformatics and Molecular Biology, College of Science and Engineering, James Cook University, Townsville, QLD, Australia
| | - David B Jones
- Centre for Sustainable Tropical Fisheries and Aquaculture, College of Science and Engineering, James Cook University, Townsville, QLD, Australia.,Centre for Tropical Bioinformatics and Molecular Biology, College of Science and Engineering, James Cook University, Townsville, QLD, Australia
| | - John A H Benzie
- WorldFish, Penang, Malaysia.,School of Biological, Earth and Environmental Sciences, University College Cork, Cork, Ireland
| | - Dean R Jerry
- Centre for Sustainable Tropical Fisheries and Aquaculture, College of Science and Engineering, James Cook University, Townsville, QLD, Australia.,Centre for Tropical Bioinformatics and Molecular Biology, College of Science and Engineering, James Cook University, Townsville, QLD, Australia.,Tropical Futures Institute, James Cook University, Singapore, Singapore
| | - Kyall R Zenger
- Centre for Sustainable Tropical Fisheries and Aquaculture, College of Science and Engineering, James Cook University, Townsville, QLD, Australia.,Centre for Tropical Bioinformatics and Molecular Biology, College of Science and Engineering, James Cook University, Townsville, QLD, Australia
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157
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Genome variation and population structure among 1142 mosquitoes of the African malaria vector species Anopheles gambiae and Anopheles coluzzii. Genome Res 2020; 30:1533-1546. [PMID: 32989001 PMCID: PMC7605271 DOI: 10.1101/gr.262790.120] [Citation(s) in RCA: 61] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Accepted: 08/27/2020] [Indexed: 01/03/2023]
Abstract
Mosquito control remains a central pillar of efforts to reduce malaria burden in sub-Saharan Africa. However, insecticide resistance is entrenched in malaria vector populations, and countries with a high malaria burden face a daunting challenge to sustain malaria control with a limited set of surveillance and intervention tools. Here we report on the second phase of a project to build an open resource of high-quality data on genome variation among natural populations of the major African malaria vector species Anopheles gambiae and Anopheles coluzzii We analyzed whole genomes of 1142 individual mosquitoes sampled from the wild in 13 African countries, as well as a further 234 individuals comprising parents and progeny of 11 laboratory crosses. The data resource includes high-confidence single-nucleotide polymorphism (SNP) calls at 57 million variable sites, genome-wide copy number variation (CNV) calls, and haplotypes phased at biallelic SNPs. We use these data to analyze genetic population structure and characterize genetic diversity within and between populations. We illustrate the utility of these data by investigating species differences in isolation by distance, genetic variation within proposed gene drive target sequences, and patterns of resistance to pyrethroid insecticides. This data resource provides a foundation for developing new operational systems for molecular surveillance and for accelerating research and development of new vector control tools. It also provides a unique resource for the study of population genomics and evolutionary biology in eukaryotic species with high levels of genetic diversity under strong anthropogenic evolutionary pressures.
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158
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Watson JA, Taylor AR, Ashley EA, Dondorp A, Buckee CO, White NJ, Holmes CC. A cautionary note on the use of unsupervised machine learning algorithms to characterise malaria parasite population structure from genetic distance matrices. PLoS Genet 2020; 16:e1009037. [PMID: 33035220 PMCID: PMC7577480 DOI: 10.1371/journal.pgen.1009037] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Revised: 10/21/2020] [Accepted: 08/08/2020] [Indexed: 11/20/2022] Open
Abstract
Genetic surveillance of malaria parasites supports malaria control programmes, treatment guidelines and elimination strategies. Surveillance studies often pose questions about malaria parasite ancestry (e.g. how antimalarial resistance has spread) and employ statistical methods that characterise parasite population structure. Many of the methods used to characterise structure are unsupervised machine learning algorithms which depend on a genetic distance matrix, notably principal coordinates analysis (PCoA) and hierarchical agglomerative clustering (HAC). PCoA and HAC are sensitive to both the definition of genetic distance and algorithmic specification. Importantly, neither algorithm infers malaria parasite ancestry. As such, PCoA and HAC can inform (e.g. via exploratory data visualisation and hypothesis generation), but not answer comprehensively, key questions about malaria parasite ancestry. We illustrate the sensitivity of PCoA and HAC using 393 Plasmodium falciparum whole genome sequences collected from Cambodia and neighbouring regions (where antimalarial resistance has emerged and spread recently) and we provide tentative guidance for the use and interpretation of PCoA and HAC in malaria parasite genetic epidemiology. This guidance includes a call for fully transparent and reproducible analysis pipelines that feature (i) a clearly outlined scientific question; (ii) a clear justification of analytical methods used to answer the scientific question along with discussion of any inferential limitations; (iii) publicly available genetic distance matrices when downstream analyses depend on them; and (iv) sensitivity analyses. To bridge the inferential disconnect between the output of non-inferential unsupervised learning algorithms and the scientific questions of interest, tailor-made statistical models are needed to infer malaria parasite ancestry. In the absence of such models speculative reasoning should feature only as discussion but not as results.
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Affiliation(s)
- James A. Watson
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Aimee R. Taylor
- Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard T. H. Chan School of Public Health, Boston, Massachusetts, USA
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Elizabeth A. Ashley
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
- Lao-Oxford-Mahosot Hospital Wellcome Trust Research Unit, Vientiane, Laos
| | - Arjen Dondorp
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Caroline O. Buckee
- Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard T. H. Chan School of Public Health, Boston, Massachusetts, USA
| | - Nicholas J. White
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Chris C. Holmes
- Department of Statistics, University of Oxford, Oxford, United Kingdom
- Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
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159
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The shaping of immunological responses through natural selection after the Roma Diaspora. Sci Rep 2020; 10:16134. [PMID: 32999407 PMCID: PMC7528012 DOI: 10.1038/s41598-020-73182-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Accepted: 09/02/2020] [Indexed: 01/20/2023] Open
Abstract
The Roma people are the largest transnational ethnic minority in Europe and can be considered the last human migration of South Asian origin into the continent. They left Northwest India approximately 1,000 years ago, reaching the Balkan Peninsula around the twelfth century and Romania in the fourteenth century. Here, we analyze whole-genome sequencing data of 40 Roma and 40 non-Roma individuals from Romania. We performed a genome-wide scan of selection comparing Roma, their local host population, and a Northwestern Indian population, to identify the selective pressures faced by the Roma mainly after they settled in Europe. We identify under recent selection several pathways implicated in immune responses, among them cellular metabolism pathways known to be rewired after immune stimulation. We validated the interaction between PIK3-mTOR-HIF-1α and cytokine response influenced by bacterial and fungal infections. Our results point to a significant role of these pathways for host defense against the most prevalent pathogens in Europe during the last millennium.
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160
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Corbett EC, Bravo GA, Schunck F, Naka LN, Silveira LF, Edwards SV. Evidence for the Pleistocene Arc Hypothesis from genome-wide SNPs in a Neotropical dry forest specialist, the Rufous-fronted Thornbird (Furnariidae: Phacellodomus rufifrons). Mol Ecol 2020; 29:4457-4472. [PMID: 32974981 DOI: 10.1111/mec.15640] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Revised: 08/15/2020] [Accepted: 08/27/2020] [Indexed: 11/29/2022]
Abstract
South American dry forests have a complex and poorly understood biogeographic history. Based on the fragmented distribution of many Neotropical dry forest species, it has been suggested that this biome was more widely distributed and contiguous under drier climate conditions in the Pleistocene. To test this scenario, known as the Pleistocene Arc Hypothesis, we studied the phylogeography of the Rufous-fronted Thornbird (Phacellodomus rufifrons), a widespread dry forest bird with a disjunct distribution closely matching that of the biome itself. We sequenced mtDNA and used ddRADseq to sample 7,167 genome-wide single-nucleotide polymorphisms from 74 P. rufifrons individuals across its range. We found low genetic differentiation over two prominent geographic breaks - particularly across a 1,000 km gap between populations in Bolivia and Northern Peru. Using demographic analyses of the joint site frequency spectrum, we found evidence of recent divergence without subsequent gene flow across those breaks. By contrast, parapatric morphologically distinct populations in northeastern Brazil show high genetic divergence with evidence of recent gene flow. These results, in combination with our paleoclimate species distribution modelling, support the idea that currently disjunct patches of dry forest were more connected in the recent past, probably during the Middle and Late Pleistocene. This notion fits the major predictions of the Pleistocene Arc Hypothesis and illustrates the importance of comprehensive genomic and geographic sampling for examining biogeographic and evolutionary questions in complex ecosystems like Neotropical dry forests.
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Affiliation(s)
- Eamon C Corbett
- Department of Organismic and Evolutionary Biology & Museum of Comparative Zoology, Harvard University, Cambridge, MA, USA.,Department of Biological Sciences & Museum of Natural Science, Louisiana State University, Baton Rouge, LA, USA
| | - Gustavo A Bravo
- Department of Organismic and Evolutionary Biology & Museum of Comparative Zoology, Harvard University, Cambridge, MA, USA
| | - Fabio Schunck
- Seção de Aves, Museu de Zoologia da Universidade de São Paulo, São Paulo, Brazil
| | - Luciano N Naka
- Department of Organismic and Evolutionary Biology & Museum of Comparative Zoology, Harvard University, Cambridge, MA, USA.,Departamento de Zoologia, Universidade Federal de Pernambuco, Recife, Brazil
| | - Luís F Silveira
- Seção de Aves, Museu de Zoologia da Universidade de São Paulo, São Paulo, Brazil
| | - Scott V Edwards
- Department of Organismic and Evolutionary Biology & Museum of Comparative Zoology, Harvard University, Cambridge, MA, USA
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161
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Camacho-Sanchez M, Velo-Antón G, Hanson JO, Veríssimo A, Martínez-Solano Í, Marques A, Moritz C, Carvalho SB. Comparative assessment of range-wide patterns of genetic diversity and structure with SNPs and microsatellites: A case study with Iberian amphibians. Ecol Evol 2020; 10:10353-10363. [PMID: 33072264 PMCID: PMC7548196 DOI: 10.1002/ece3.6670] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Accepted: 07/22/2020] [Indexed: 11/11/2022] Open
Abstract
Reduced representation genome sequencing has popularized the application of single nucleotide polymorphisms (SNPs) to address evolutionary and conservation questions in nonmodel organisms. Patterns of genetic structure and diversity based on SNPs often diverge from those obtained with microsatellites to different degrees, but few studies have explicitly compared their performance under similar sampling regimes in a shared analytical framework. We compared range‐wide patterns of genetic structure and diversity in two amphibians endemic to the Iberian Peninsula: Hyla molleri and Pelobates cultripes, based on microsatellite (18 and 14 loci) and SNP (15,412 and 33,140 loci) datasets of comparable sample size and spatial extent. Model‐based clustering analyses with STRUCTURE revealed minor differences in genetic structure between marker types, but inconsistent values of the optimal number of populations (K) inferred. SNPs yielded more repeatable and less admixed ancestries with increasing K compared to microsatellites. Genetic diversity was weakly correlated between marker types, with SNPs providing a better representation of southern refugia and of gradients of genetic diversity congruent with the demographic history of both species. Our results suggest that the larger number of loci in a SNP dataset can provide more reliable inferences of patterns of genetic structure and diversity than a typical microsatellite dataset, at least at the spatial and temporal scales investigated.
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Affiliation(s)
- Miguel Camacho-Sanchez
- CIBIO/InBIO Centro de Investigação em Biodiversidade e Recursos Genéticos da Universidade do Porto Vairão Portugal
| | - Guillermo Velo-Antón
- CIBIO/InBIO Centro de Investigação em Biodiversidade e Recursos Genéticos da Universidade do Porto Vairão Portugal
| | - Jeffrey O Hanson
- CIBIO/InBIO Centro de Investigação em Biodiversidade e Recursos Genéticos da Universidade do Porto Vairão Portugal
| | - Ana Veríssimo
- CIBIO/InBIO Centro de Investigação em Biodiversidade e Recursos Genéticos da Universidade do Porto Vairão Portugal
| | | | - Adam Marques
- CIBIO/InBIO Centro de Investigação em Biodiversidade e Recursos Genéticos da Universidade do Porto Vairão Portugal
| | - Craig Moritz
- Centre for Biodiversity Analysis and Research School of Biology The Australian National University Canberra ACT Australia
| | - Sílvia B Carvalho
- CIBIO/InBIO Centro de Investigação em Biodiversidade e Recursos Genéticos da Universidade do Porto Vairão Portugal
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162
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Schley RJ, Pennington RT, Pérez-Escobar OA, Helmstetter AJ, de la Estrella M, Larridon I, Sabino Kikuchi IAB, Barraclough TG, Forest F, Klitgård B. Introgression across evolutionary scales suggests reticulation contributes to Amazonian tree diversity. Mol Ecol 2020; 29:4170-4185. [PMID: 32881172 DOI: 10.1111/mec.15616] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Revised: 08/14/2020] [Accepted: 08/17/2020] [Indexed: 01/03/2023]
Abstract
Hybridization has the potential to generate or homogenize biodiversity and is a particularly common phenomenon in plants, with an estimated 25% of plant species undergoing interspecific gene flow. However, hybridization in Amazonia's megadiverse tree flora was assumed to be extremely rare despite extensive sympatry between closely related species, and its role in diversification remains enigmatic because it has not yet been examined empirically. Using members of a dominant Amazonian tree family (Brownea, Fabaceae) as a model to address this knowledge gap, our study recovered extensive evidence of hybridization among multiple lineages across phylogenetic scales. More specifically, using targeted sequence capture our results uncovered several historical introgression events between Brownea lineages and indicated that gene tree incongruence in Brownea is best explained by reticulation, rather than solely by incomplete lineage sorting. Furthermore, investigation of recent hybridization using ~19,000 ddRAD loci recovered a high degree of shared variation between two Brownea species that co-occur in the Ecuadorian Amazon. Our analyses also showed that these sympatric lineages exhibit homogeneous rates of introgression among loci relative to the genome-wide average, implying a lack of selection against hybrid genotypes and persistent hybridization. Our results demonstrate that gene flow between multiple Amazonian tree species has occurred across temporal scales, and contrasts with the prevailing view of hybridization's rarity in Amazonia. Overall, our results provide novel evidence that reticulate evolution influenced diversification in part of the Amazonian tree flora, which is the most diverse on Earth.
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Affiliation(s)
- Rowan J Schley
- Royal Botanic Gardens, Kew, Richmond, UK.,Department of Life Sciences, Imperial College London, Ascot, Berkshire, London, UK
| | - R Toby Pennington
- Geography, University of Exeter, Exeter, UK.,Royal Botanic Garden Edinburgh, Edinburgh, UK
| | | | - Andrew J Helmstetter
- Institut de Recherche pour le Développement (IRD), UMR-DIADE, Montpellier, France
| | - Manuel de la Estrella
- Departamento de Botánica, Ecología y Fisiología Vegetal, Facultad de Ciencias, Universidad de Córdoba, Córdoba, Spain
| | - Isabel Larridon
- Royal Botanic Gardens, Kew, Richmond, UK.,Systematic and Evolutionary Botany Lab, Department of Biology, Ghent University, K.L, Gent, Belgium
| | | | - Timothy G Barraclough
- Department of Life Sciences, Imperial College London, Ascot, Berkshire, London, UK.,Department of Zoology, University of Oxford, Oxford, UK
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163
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Carlson J, Harris K. Quantifying and contextualizing the impact of bioRxiv preprints through automated social media audience segmentation. PLoS Biol 2020; 18:e3000860. [PMID: 32960891 PMCID: PMC7508356 DOI: 10.1371/journal.pbio.3000860] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Accepted: 08/17/2020] [Indexed: 12/27/2022] Open
Abstract
Engagement with scientific manuscripts is frequently facilitated by Twitter and other social media platforms. As such, the demographics of a paper's social media audience provide a wealth of information about how scholarly research is transmitted, consumed, and interpreted by online communities. By paying attention to public perceptions of their publications, scientists can learn whether their research is stimulating positive scholarly and public thought. They can also become aware of potentially negative patterns of interest from groups that misinterpret their work in harmful ways, either willfully or unintentionally, and devise strategies for altering their messaging to mitigate these impacts. In this study, we collected 331,696 Twitter posts referencing 1,800 highly tweeted bioRxiv preprints and leveraged topic modeling to infer the characteristics of various communities engaging with each preprint on Twitter. We agnostically learned the characteristics of these audience sectors from keywords each user's followers provide in their Twitter biographies. We estimate that 96% of the preprints analyzed are dominated by academic audiences on Twitter, suggesting that social media attention does not always correspond to greater public exposure. We further demonstrate how our audience segmentation method can quantify the level of interest from nonspecialist audience sectors such as mental health advocates, dog lovers, video game developers, vegans, bitcoin investors, conspiracy theorists, journalists, religious groups, and political constituencies. Surprisingly, we also found that 10% of the preprints analyzed have sizable (>5%) audience sectors that are associated with right-wing white nationalist communities. Although none of these preprints appear to intentionally espouse any right-wing extremist messages, cases exist in which extremist appropriation comprises more than 50% of the tweets referencing a given preprint. These results present unique opportunities for improving and contextualizing the public discourse surrounding scientific research.
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Affiliation(s)
- Jedidiah Carlson
- Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
| | - Kelley Harris
- Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
- Computational Biology Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
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164
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Toyama KS, Crochet P, Leblois R. Sampling schemes and drift can bias admixture proportions inferred by
structure. Mol Ecol Resour 2020; 20:1769-1785. [DOI: 10.1111/1755-0998.13234] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Revised: 07/17/2020] [Accepted: 07/24/2020] [Indexed: 11/27/2022]
Affiliation(s)
- Ken S. Toyama
- Department of Ecology and Evolutionary Biology University of Toronto Toronto ON Canada
| | - Pierre‐André Crochet
- CEFE CNRS University of Montpellier Université Paul Valéry Montpellier 3 EPHE IRD Montpellier France
| | - Raphaël Leblois
- CBGP INRAE CIRAD IRD Montpellier SupAgro University of Montpellier Montpellier France
- Institut de Biologie Computationnelle University of Montpellier Montpellier France
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165
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O'Connell KA, Oaks JR, Hamidy A, Shaney KJ, Kurniawan N, Smith EN, Fujita MK. Impacts of the Toba eruption and montane forest expansion on diversification in Sumatran parachuting frogs (Rhacophorus). Mol Ecol 2020; 29:2994-3009. [PMID: 32633832 DOI: 10.1111/mec.15541] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Revised: 06/11/2020] [Accepted: 06/12/2020] [Indexed: 01/09/2023]
Abstract
Catastrophic events, such as volcanic eruptions, can have profound impacts on the demographic histories of resident taxa. Due to its presumed effect on biodiversity, the Pleistocene eruption of super-volcano Toba has received abundant attention. We test the effects of the Toba eruption on the diversification, genetic diversity, and demography of three co-distributed species of parachuting frogs (Genus Rhacophorus) on Sumatra. We generate target-capture data (~950 loci and ~440,000 bp) for three species of parachuting frogs and use these data paired with previously generated double digest restriction-site associated DNA (ddRADseq) data to estimate population structure and genetic diversity, to test for population size changes using demographic modelling, and to estimate the temporal clustering of size change events using a full-likelihood Bayesian method. We find that populations around Toba exhibit reduced genetic diversity compared with southern populations, and that northern populations exhibit a shift in effective population size around the time of the eruption (~80 kya). However, we infer a stronger signal of expansion in southern populations around ~400 kya, and at least two of the northern populations may have also expanded at this time. Taken together, these findings suggest that the Toba eruption precipitated population declines in northern populations, but that the demographic history of these three species was also strongly impacted by mid-Pleistocene forest expansion during glacial periods. We propose local rather than regional effects of the Toba eruption, and emphasize the dynamic nature of diversification on the Sunda Shelf.
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Affiliation(s)
- Kyle A O'Connell
- Global Genome Initiative, National Museum of Natural History, Smithsonian Institute, Washington, DC, USA.,Division of Amphibians and Reptiles, Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institute, Washington, DC, USA.,Department of Biology and Amphibian and Reptile Diversity Research Center, The University of Texas at Arlington, Arlington, TX, USA.,Department of Biological Sciences, The George Washington University, Washington, DC, USA
| | - Jamie R Oaks
- Department of Biological Sciences and Museum of Natural History, Auburn University, Auburn, Alabama, USA
| | - Amir Hamidy
- Zoology Division, Museum Zoologicum Bogoriense, Research Center for Biology, Indonesian Institute of Sciences. Gd, Bogor, West Java, Indonesia
| | - Kyle J Shaney
- Institute of Ecology, National Autonomous University of Mexico, Mexico City, Mexico
| | - Nia Kurniawan
- Department of Biology, Universitas Brawijaya, Malang, East Java, Indonesia
| | - Eric N Smith
- Department of Biology and Amphibian and Reptile Diversity Research Center, The University of Texas at Arlington, Arlington, TX, USA
| | - Matthew K Fujita
- Department of Biology and Amphibian and Reptile Diversity Research Center, The University of Texas at Arlington, Arlington, TX, USA
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166
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Ito T, Kanthaswamy S, Bunlungsup S, Oldt RF, Houghton P, Hamada Y, Malaivijitnond S. Secondary contact and genomic admixture between rhesus and long-tailed macaques in the Indochina Peninsula. J Evol Biol 2020; 33:1164-1179. [PMID: 33448526 DOI: 10.1111/jeb.13681] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2020] [Revised: 06/11/2020] [Accepted: 07/08/2020] [Indexed: 01/07/2023]
Abstract
Understanding the process and consequences of hybridization is one of the major challenges in evolutionary biology. A growing body of literature has reported evidence of ancient hybridization events or natural hybrid zones in primates, including humans; however, we still have relatively limited knowledge about the pattern and history of admixture because there have been little studies that simultaneously achieved genome-scale analysis and a geographically wide sampling of wild populations. Our study applied double-digest restriction site-associated DNA sequencing to samples from the six localities in and around the provisional hybrid zone of rhesus and long-tailed macaques and evaluated population structure, phylogenetic relationships, demographic history, and geographic clines of morphology and allele frequencies. A latitudinal gradient of genetic components was observed, highlighting the transition from rhesus (north) to long-tailed macaque distribution (south) as well as the presence of one northern population of long-tailed macaques exhibiting unique genetic structure. Interspecific gene flow was estimated to have recently occurred after an isolation period, and the migration rate from rhesus to long-tailed macaques was slightly greater than in the opposite direction. Although some rhesus macaque-biased alleles have widely introgressed into long-tailed macaque populations, the inflection points of allele frequencies have been observed as concentrated around the traditionally recognized interspecific boundary where morphology discontinuously changed; this pattern was more pronounced in the X chromosome than in autosomes. Thus, due to geographic separation before secondary contact, reproductive isolation could have evolved, contributing to the maintenance of an interspecific boundary and species-specific morphological characteristics.
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Affiliation(s)
- Tsuyoshi Ito
- Department of Evolution and Phylogeny, Primate Research Institute, Kyoto University, Aichi, Japan
| | - Sreetharan Kanthaswamy
- School of Mathematical and Natural Sciences, New College of Interdisciplinary Arts and Sciences, Arizona State University West Campus, Glendale, AZ, USA
| | - Srichan Bunlungsup
- Department of Biology, Faculty of Science, Chulalongkorn University, Bangkok, Thailand.,National Primate Research Center of Thailand-Chulalongkorn University, Saraburi, Thailand
| | - Robert F Oldt
- School of Mathematical and Natural Sciences, New College of Interdisciplinary Arts and Sciences, Arizona State University West Campus, Glendale, AZ, USA
| | | | - Yuzuru Hamada
- Department of Evolution and Phylogeny, Primate Research Institute, Kyoto University, Aichi, Japan
| | - Suchinda Malaivijitnond
- Department of Biology, Faculty of Science, Chulalongkorn University, Bangkok, Thailand.,National Primate Research Center of Thailand-Chulalongkorn University, Saraburi, Thailand
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167
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Eydivandi S, Sahana G, Momen M, Moradi MH, Schönherz AA. Genetic diversity in Iranian indigenous sheep vis-à-vis selected exogenous sheep breeds and wild mouflon. Anim Genet 2020; 51:772-787. [PMID: 32729152 DOI: 10.1111/age.12985] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Revised: 06/09/2020] [Accepted: 06/22/2020] [Indexed: 11/29/2022]
Abstract
The heterogeneity of climate and different agro-ecological conditions in Iran have resulted in development of 27 indigenous sheep breeds. Wild Asiatic mouflon (Ovis orientalis) is believed to be the ancestor of Iranian sheep. Evaluation of genetic diversity and population structure within and among domestic breeds has important implications for animal breeding programs and genetic resources management. Based on 50K SNP genotype data, we studied the genetic diversity of five indigenous Iranian sheep breeds: Afshari (n = 37), Moghani (n = 34), Qezel (n = 35), Zel (n = 46) and Lori-Bakhtiari (n = 46), and Asiatic mouflon (n = 8) sampled from Iran. Furthermore, genetic diversity and the breed admixture of Iranian sheep were assessed on a larger geographic scale using a reference panel comprising: three indigenous Afghan breeds - Arabi (n = 15), Balouchi (n = 15) and Gadik (n = 15); three indigenous breeds from Turkey and Cyprus - Cyprus Fat Tail (n = 30), Karakas (n = 18) and Norduz (n = 20); and three commercial European breeds - Suffolk (n = 19), Comisana (n = 24) and Engadine Red Sheep (n = 24). The results revealed that the investigated breeds are divided into five genetically distinct clusters according to their geographic origin. Afshari was closest to the local mouflon population and showed signs of mouflon admixture. Qezel was identified as a hybrid sheep breed. Much evidence supported the Afghan breeds being identical. Inbreeding values, which were estimated based on ROHs, were highest for Suffolk (FROH = 0.0544) and lowest for Balouchi (FROH = 0.0078). In conclusion, analysis of selected breeds from neighboring countries along with Asiatic mouflon gave a deeper insight into the evolutionary history and origin of Iranian sheep with important implications for future breed management.
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Affiliation(s)
- S Eydivandi
- Department of Animal Science, Behbahan Branch, Islamic Azad University, Behbahan, 63617-13198, Iran.,Faculty of Technical Sciences, Center for Quantitative Genetics and Genomics, Aarhus University, Tjele, 8830, Denmark
| | - G Sahana
- Faculty of Technical Sciences, Center for Quantitative Genetics and Genomics, Aarhus University, Tjele, 8830, Denmark
| | - M Momen
- Department of Surgical Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - M H Moradi
- Department of Animal Science, Faculty of Agriculture and Natural Resources, Arak University, Arak, Iran
| | - A A Schönherz
- Faculty of Technical Sciences, Center for Quantitative Genetics and Genomics, Aarhus University, Tjele, 8830, Denmark
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168
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Mountford HS, Villanueva P, Fernández MA, Jara L, De Barbieri Z, Carvajal-Carmona LG, Cazier JB, Newbury DF. The Genetic Population Structure of Robinson Crusoe Island, Chile. Front Genet 2020; 11:669. [PMID: 32676101 PMCID: PMC7333314 DOI: 10.3389/fgene.2020.00669] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Accepted: 06/02/2020] [Indexed: 11/30/2022] Open
Abstract
Studies examining genetic conditions common in Latin America are highly underrepresented in the scientific literature. Understanding of the population structure is limited, particularly Chile, in part due to the lack of available population specific data. An important first-step in elucidating disease mechanisms in Latin America countries is to understand the genetic structure of isolated populations. Robinson Crusoe Island (RCI) is a small land mass off the coast of Chile. The current population of over 900 inhabitants are primarily descended from a small number of founders who colonized the island in the late 1800s. Extensive genealogical records can trace the ancestry of almost the entire population. We perform a comprehensive genetic analysis to investigate the ancestry of the island population, examining ancestral mitochondrial and Y chromosome haplogroups, as well as autosomal admixture. Mitochondrial and Y chromosome haplogroups indicated a substantial European genetic contribution to the current RCI population. Analysis of the mitochondrial haplogroups found in the present-day population revealed that 79.1% of islanders carried European haplogroups, compared to 60.0% of the mainland Chilean controls from Santiago. Both groups showed a substantially lower contribution of indigenous haplogroups than expected. Analysis of the Y chromosome haplogroups also showed predominantly European haplogroups detected in 92.3% of male islanders and 86.7% of mainland Chilean controls. Using the near-complete genealogical data collected from the RCI population, we successfully inferred the ancestral haplogroups of 16/23 founder individuals, revealing genetic ancestry from Northern and Southern Europe. As mitochondrial and Y investigations only provide information for direct maternal and paternal lineages, we expanded this to investigate genetic admixture using the autosomes. Admixture analysis identified substantial indigenous genetic admixture in the RCI population (46.9%), higher than that found in the Santiago mainland Chilean controls (43.4%), but lower than a more representative Chilean population (Chile_GRU) (49.1%). Our study revealed the Robinson Crusoe Island population show a substantial genetic contribution for indigenous Chileans, similar to the level reported in mainland Chileans. However, direct maternal and paternal haplogroup analysis revealed strong European genetic contributions consistent with the history of the Island.
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Affiliation(s)
- Hayley S Mountford
- Department of Biological and Medical Sciences, Faculty of Health and Life Sciences, Oxford Brookes University, Oxford, United Kingdom
| | - Pía Villanueva
- Department of Speech Language and Hearing Sciences, Faculty of Medicine, University of Chile, Santiago, Chile.,Human Genetics Division, Faculty of Medicine, Institute of Biomedical Sciences, University of Chile, Santiago, Chile
| | - María Angélica Fernández
- Department of Speech Language and Hearing Sciences, Faculty of Medicine, University of Chile, Santiago, Chile
| | - Lilian Jara
- Human Genetics Division, Faculty of Medicine, Institute of Biomedical Sciences, University of Chile, Santiago, Chile
| | - Zulema De Barbieri
- Directorate of Academic Development, Academic Vice-Rectory, Research and Postgraduate, Saint Thomas University, Santiago, Chile
| | - Luis G Carvajal-Carmona
- Department of Biochemistry and Molecular Medicine, School of Medicine Genome Center, University of California, Davis, Davis, CA, United States
| | - Jean-Baptiste Cazier
- Centre for Computational Biology, University of Birmingham, Birmingham, United Kingdom.,Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Dianne F Newbury
- Department of Biological and Medical Sciences, Faculty of Health and Life Sciences, Oxford Brookes University, Oxford, United Kingdom
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169
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Scheper C, Bohlouli M, Brügemann K, Weimann C, Vanvanhossou SFU, König S, Dossa LH. The role of agro-ecological factors and transboundary transhumance in shaping the genetic diversity in four indigenous cattle populations of Benin. J Anim Breed Genet 2020; 137:622-640. [PMID: 32672901 DOI: 10.1111/jbg.12495] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Revised: 05/29/2020] [Accepted: 06/17/2020] [Indexed: 01/03/2023]
Abstract
The indigenous cattle population of Benin is a diverse mix of taurine and hybrid breeds shaped by diverse ecological and climatic conditions with eight agro-ecological zones (AEZ). Presumably, the taurine breeds face current endangerment due to ongoing indicine introgression following climate change and transboundary transhumance. The aim of the study was to investigate the genetic diversity and population structure of the indigenous breeds Lagune, Somba, Pabli and Borgou considering spatial agro-ecological and socio-economic factors (transhumance) based on 50k SNP and microsatellite data. Among the four sampled breeds, six genetic clusters were identified using model-free (discriminant analysis of principal components) and model-based (TESS and ADMIXTURE) methods separating taurine from hybrid breeds. Results based on an extension with publicly available historic SNP data sets from taurine and indicine West African cattle and additional outgroups provided additional insight into changes of genetic structure in the sampled breeds over time. Both taurine breeds, Somba and Lagune, showed a stable foundation but also spatially limited partial indicine introgression associated with transhumance leading to high genetic diversity. In addition, we found evidence for spatial diversity and changes in genetic structure over time in the Borgou breed in comparison of our samples with the historic samples which could be explained by potential continuous indicine introgression into the Borgou breed in two sample regions. Results for the Pabli breed do not conclusively point to full absorbance by the Borgou in comparison with all available Borgou samples. Further research is needed in this regard.
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Affiliation(s)
- Carsten Scheper
- Institute of Animal Breeding and Genetics, Justus-Liebig-University of Gießen, Gießen, Germany
| | - Mehdi Bohlouli
- Institute of Animal Breeding and Genetics, Justus-Liebig-University of Gießen, Gießen, Germany
| | - Kerstin Brügemann
- Institute of Animal Breeding and Genetics, Justus-Liebig-University of Gießen, Gießen, Germany
| | - Christina Weimann
- Institute of Animal Breeding and Genetics, Justus-Liebig-University of Gießen, Gießen, Germany
| | | | - Sven König
- Institute of Animal Breeding and Genetics, Justus-Liebig-University of Gießen, Gießen, Germany
| | - Luc Hippolyte Dossa
- Ecole des Sciences et Techniques de Production Animale, Faculté des Sciences Agronomiques, Université d'Abomey-Calavi, Cotonou, Bénin
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170
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Ioannidis AG, Blanco-Portillo J, Sandoval K, Hagelberg E, Miquel-Poblete JF, Moreno-Mayar JV, Rodríguez-Rodríguez JE, Quinto-Cortés CD, Auckland K, Parks T, Robson K, Hill AVS, Avila-Arcos MC, Sockell A, Homburger JR, Wojcik GL, Barnes KC, Herrera L, Berríos S, Acuña M, Llop E, Eng C, Huntsman S, Burchard EG, Gignoux CR, Cifuentes L, Verdugo RA, Moraga M, Mentzer AJ, Bustamante CD, Moreno-Estrada A. Native American gene flow into Polynesia predating Easter Island settlement. Nature 2020; 583:572-577. [PMID: 32641827 PMCID: PMC8939867 DOI: 10.1038/s41586-020-2487-2] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2019] [Accepted: 05/22/2020] [Indexed: 11/08/2022]
Abstract
The possibility of voyaging contact between prehistoric Polynesian and Native American populations has long intrigued researchers. Proponents have pointed to the existence of New World crops, such as the sweet potato and bottle gourd, in the Polynesian archaeological record, but nowhere else outside the pre-Columbian Americas1-6, while critics have argued that these botanical dispersals need not have been human mediated7. The Norwegian explorer Thor Heyerdahl controversially suggested that prehistoric South American populations had an important role in the settlement of east Polynesia and particularly of Easter Island (Rapa Nui)2. Several limited molecular genetic studies have reached opposing conclusions, and the possibility continues to be as hotly contested today as it was when first suggested8-12. Here we analyse genome-wide variation in individuals from islands across Polynesia for signs of Native American admixture, analysing 807 individuals from 17 island populations and 15 Pacific coast Native American groups. We find conclusive evidence for prehistoric contact of Polynesian individuals with Native American individuals (around AD 1200) contemporaneous with the settlement of remote Oceania13-15. Our analyses suggest strongly that a single contact event occurred in eastern Polynesia, before the settlement of Rapa Nui, between Polynesian individuals and a Native American group most closely related to the indigenous inhabitants of present-day Colombia.
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Affiliation(s)
- Alexander G Ioannidis
- Institute for Computational and Mathematical Engineering, Stanford University, Stanford, CA, USA.
- National Laboratory of Genomics for Biodiversity (LANGEBIO), Unit of Advanced Genomics, CINVESTAV, Irapuato, Mexico.
| | - Javier Blanco-Portillo
- National Laboratory of Genomics for Biodiversity (LANGEBIO), Unit of Advanced Genomics, CINVESTAV, Irapuato, Mexico
| | - Karla Sandoval
- National Laboratory of Genomics for Biodiversity (LANGEBIO), Unit of Advanced Genomics, CINVESTAV, Irapuato, Mexico
| | - Erika Hagelberg
- Department of Biosciences, University of Oslo, Blindern, Oslo, Norway
| | | | | | | | - Consuelo D Quinto-Cortés
- National Laboratory of Genomics for Biodiversity (LANGEBIO), Unit of Advanced Genomics, CINVESTAV, Irapuato, Mexico
| | - Kathryn Auckland
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Tom Parks
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Kathryn Robson
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Adrian V S Hill
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
- The Jenner Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - María C Avila-Arcos
- International Laboratory for Human Genome Research (LIIGH), UNAM Juriquilla, Queretaro, Mexico
| | - Alexandra Sockell
- Center for Computational, Evolutionary and Human Genomics (CEHG), Stanford University, Stanford, CA, USA
| | - Julian R Homburger
- Center for Computational, Evolutionary and Human Genomics (CEHG), Stanford University, Stanford, CA, USA
| | - Genevieve L Wojcik
- Center for Computational, Evolutionary and Human Genomics (CEHG), Stanford University, Stanford, CA, USA
| | - Kathleen C Barnes
- Division of Biomedical Informatics and Personalized Medicine, University of Colorado, Denver, CO, USA
| | - Luisa Herrera
- Human Genetics Program, Institute of Biomedical Sciences, Faculty of Medicine, University of Chile, Santiago, Chile
| | - Soledad Berríos
- Human Genetics Program, Institute of Biomedical Sciences, Faculty of Medicine, University of Chile, Santiago, Chile
| | - Mónica Acuña
- Human Genetics Program, Institute of Biomedical Sciences, Faculty of Medicine, University of Chile, Santiago, Chile
| | - Elena Llop
- Human Genetics Program, Institute of Biomedical Sciences, Faculty of Medicine, University of Chile, Santiago, Chile
| | - Celeste Eng
- Program in Pharmaceutical Sciences and Pharmacogenomics, Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Scott Huntsman
- Program in Pharmaceutical Sciences and Pharmacogenomics, Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Esteban G Burchard
- Program in Pharmaceutical Sciences and Pharmacogenomics, Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Christopher R Gignoux
- Division of Biomedical Informatics and Personalized Medicine, University of Colorado, Denver, CO, USA
| | - Lucía Cifuentes
- Human Genetics Program, Institute of Biomedical Sciences, Faculty of Medicine, University of Chile, Santiago, Chile
| | - Ricardo A Verdugo
- Human Genetics Program, Institute of Biomedical Sciences, Faculty of Medicine, University of Chile, Santiago, Chile
- Basic-Applied Oncology Department, Faculty of Medicine, University of Chile, Santiago, Chile
| | - Mauricio Moraga
- Human Genetics Program, Institute of Biomedical Sciences, Faculty of Medicine, University of Chile, Santiago, Chile
- Department of Anthropology, Faculty of Social Sciences, University of Chile, Santiago, Chile
| | - Alexander J Mentzer
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford, UK
| | - Carlos D Bustamante
- Center for Computational, Evolutionary and Human Genomics (CEHG), Stanford University, Stanford, CA, USA
- Department of Biomedical Data Science, Stanford University, Stanford, CA, USA
| | - Andrés Moreno-Estrada
- National Laboratory of Genomics for Biodiversity (LANGEBIO), Unit of Advanced Genomics, CINVESTAV, Irapuato, Mexico.
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171
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Quigley KM, Bay LK, van Oppen MJH. Genome-wide SNP analysis reveals an increase in adaptive genetic variation through selective breeding of coral. Mol Ecol 2020; 29:2176-2188. [PMID: 32453867 DOI: 10.1111/mec.15482] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2020] [Accepted: 05/13/2020] [Indexed: 12/18/2022]
Abstract
Marine heat waves are increasing in magnitude, duration, and frequency as a result of climate change and are the principal global driver of mortality in reef-building corals. Resilience-based genetic management may increase coral heat tolerance, but it is unclear how temperature responses are regulated at the genome level and thus how corals may adapt to warming naturally or through selective breeding. Here we combine phenotypic, pedigree, and genomic marker data from colonies sourced from a warm reef on the Great Barrier Reef reproductively crossed with conspecific colonies from a cooler reef to produce combinations of warm purebreds and warm-cool hybrid larvae and juveniles. Interpopulation breeding created significantly greater genetic diversity across the coral genome compared to breeding between populations and maintained diversity in key regions associated with heat tolerance and fitness. High-density genome-wide scans of single nucleotide polymorphisms (SNPs) identified alleles significantly associated with larval families reared at 27.5°C (87-2,224 loci), including loci putatively associated with proteins involved in responses to heat stress (cell membrane formation, metabolism, and immune responses). Underlying genetics of these families explained 43% of PCoA multilocus variation in survival, growth, and bleaching responses at 27.5°C and 31°C at the juvenile stage. Genetic marker contribution to total variation in fitness traits (narrow-sense heritability) was high for survival but not for growth and bleaching in juveniles, with heritability of these traits being higher at 31°C relative to 27.5°C. While based on only a limited number of crosses, the mechanistic understanding presented here demonstrates that allele frequencies are affected by one generation of selective breeding, key information for the assessments of genetic intervention feasibility and modelling of reef futures.
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Affiliation(s)
- Kate M Quigley
- Australian Institute of Marine Science, Townsville, Qld, Australia
| | - Line K Bay
- Australian Institute of Marine Science, Townsville, Qld, Australia
| | - Madeleine J H van Oppen
- Australian Institute of Marine Science, Townsville, Qld, Australia.,School of BioSciences, The University of Melbourne, Parkville, Vic, Australia
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172
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Wang Y, Wu XL, Li Z, Bao Z, Tait RG, Bauck S, Rosa GJM. Estimation of Genomic Breed Composition for Purebred and Crossbred Animals Using Sparsely Regularized Admixture Models. Front Genet 2020; 11:576. [PMID: 32595700 PMCID: PMC7300184 DOI: 10.3389/fgene.2020.00576] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2019] [Accepted: 05/11/2020] [Indexed: 12/26/2022] Open
Abstract
A variety of statistical methods, such as admixture models, have been used to estimate genomic breed composition (GBC). These methods, however, tend to produce non-zero components to reference breeds that shared some genomic similarity with a test animal. These non-essential GBC components, in turn, offset the estimated GBC for the breed to which it belongs. As a result, not all purebred animals have 100% GBC of their respective breeds, which statistically indicates an elevated false-negative rate in the identification of purebred animals with 100% GBC as the cutoff. Otherwise, a lower cutoff of estimated GBC will have to be used, which is arbitrary, and the results are less interpretable. In the present study, three admixture models with regularization were proposed, which produced sparse solutions through suppressing the noise in the estimated GBC due to genomic similarities. The regularization or penalty forms included the L1 norm penalty, minimax concave penalty (MCP), and smooth clipped absolute deviation (SCAD). The performances of these regularized admixture models on the estimation of GBC were examined in purebred and composite animals, respectively, and compared to that of the non-regularized admixture model as the baseline model. The results showed that, given optimal values for λ, the three sparsely regularized admixture models had higher power and thus reduced the false-negative rate for the breed identification of purebred animals than the non-regularized admixture model. Of the three regularized admixture models, the two with a non-convex penalty outperformed the one with L1 norm penalty. In the Brangus, a composite cattle breed, estimated GBC were roughly comparable among the four admixture models, but all the four models underestimated the GBC for these composite animals when non-ancestral breeds were included as the reference. In conclusion, the admixture models with sparse regularization gave more parsimonious, consistent and interpretable results of estimated GBC for purebred animals than the non-regularized admixture model. Nevertheless, the utility of regularized admixture models for estimating GBC in crossbred or composite animals needs to be taken with caution.
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Affiliation(s)
- Yangfan Wang
- Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Science, Ocean University of China, Qingdao, China.,Department of Animal Sciences, University of Wisconsin, Madison, WI, United States
| | - Xiao-Lin Wu
- Department of Animal Sciences, University of Wisconsin, Madison, WI, United States.,Biostatistics and Bioinformatics, Neogen GeneSeek, Lincoln, NE, United States
| | - Zhi Li
- Biostatistics and Bioinformatics, Neogen GeneSeek, Lincoln, NE, United States.,Department of Animal Science, University of Wyoming, Laramie, WY, United States
| | - Zhenmin Bao
- Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Science, Ocean University of China, Qingdao, China.,Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Richard G Tait
- Biostatistics and Bioinformatics, Neogen GeneSeek, Lincoln, NE, United States
| | - Stewart Bauck
- Biostatistics and Bioinformatics, Neogen GeneSeek, Lincoln, NE, United States
| | - Guilherme J M Rosa
- Department of Animal Sciences, University of Wisconsin, Madison, WI, United States
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173
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Tonzo V, Papadopoulou A, Ortego J. Genomic footprints of an old affair: Single nucleotide polymorphism data reveal historical hybridization and the subsequent evolution of reproductive barriers in two recently diverged grasshoppers with partly overlapping distributions. Mol Ecol 2020; 29:2254-2268. [DOI: 10.1111/mec.15475] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Revised: 05/10/2020] [Accepted: 05/11/2020] [Indexed: 12/17/2022]
Affiliation(s)
- Vanina Tonzo
- Department of Integrative Ecology Estación Biológica de Doñana (EBD‐CSIC) Seville Spain
| | - Anna Papadopoulou
- Department of Biological Sciences University of Cyprus Nicosia Cyprus
| | - Joaquín Ortego
- Department of Integrative Ecology Estación Biológica de Doñana (EBD‐CSIC) Seville Spain
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174
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Recent introgression between Taiga Bean Goose and Tundra Bean Goose results in a largely homogeneous landscape of genetic differentiation. Heredity (Edinb) 2020; 125:73-84. [PMID: 32451423 PMCID: PMC7413267 DOI: 10.1038/s41437-020-0322-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Revised: 05/11/2020] [Accepted: 05/12/2020] [Indexed: 02/06/2023] Open
Abstract
Several studies have uncovered a highly heterogeneous landscape of genetic differentiation across the genomes of closely related species. Specifically, genetic differentiation is often concentrated in particular genomic regions (“islands of differentiation”) that might contain barrier loci contributing to reproductive isolation, whereas the rest of the genome is homogenized by introgression. Alternatively, linked selection can produce differentiation islands in allopatry without introgression. We explored the influence of introgression on the landscape of genetic differentiation in two hybridizing goose taxa: the Taiga Bean Goose (Anser fabalis) and the Tundra Bean Goose (A. serrirostris). We re-sequenced the whole genomes of 18 individuals (9 of each taxon) and, using a combination of population genomic summary statistics and demographic modeling, we reconstructed the evolutionary history of these birds. Next, we quantified the impact of introgression on the build-up and maintenance of genetic differentiation. We found evidence for a scenario of allopatric divergence (about 2.5 million years ago) followed by recent secondary contact (about 60,000 years ago). Subsequent introgression events led to high levels of gene flow, mainly from the Tundra Bean Goose into the Taiga Bean Goose. This scenario resulted in a largely undifferentiated genomic landscape (genome-wide FST = 0.033) with a few notable differentiation peaks that were scattered across chromosomes. The summary statistics indicated that some peaks might contain barrier loci while others arose in allopatry through linked selection. Finally, based on the low genetic differentiation, considerable morphological variation and incomplete reproductive isolation, we argue that the Taiga and the Tundra Bean Goose should be treated as subspecies.
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175
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Garcia-Erill G, Albrechtsen A. Evaluation of model fit of inferred admixture proportions. Mol Ecol Resour 2020; 20:936-949. [PMID: 32323416 DOI: 10.1111/1755-0998.13171] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Revised: 03/11/2020] [Accepted: 04/15/2020] [Indexed: 12/12/2022]
Abstract
Model based methods for genetic clustering of individuals, such as those implemented in structure or ADMIXTURE, allow the user to infer individual ancestries and study population structure. The underlying model makes several assumptions about the demographic history that shaped the analysed genetic data. One assumption is that all individuals are a result of K homogeneous ancestral populations that are all well represented in the data, while another assumption is that no drift happened after the admixture event. The histories of many real world populations do not conform to that model, and in that case taking the inferred admixture proportions at face value might be misleading. We propose a method to evaluate the fit of admixture models based on estimating the correlation of the residual difference between the true genotypes and the genotypes predicted by the model. When the model assumptions are not violated, the residuals from a pair of individuals are not correlated. In the case of a bad fitting admixture model, individuals with similar demographic histories have a positive correlation of their residuals. Using simulated and real data, we show how the method is able to detect a bad fit of inferred admixture proportions due to using an insufficient number of clusters K or to demographic histories that deviate significantly from the admixture model assumptions, such as admixture from ghost populations, drift after admixture events and nondiscrete ancestral populations. We have implemented the method as an open source software that can be applied to both unphased genotypes and low depth sequencing data.
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Affiliation(s)
- Genís Garcia-Erill
- Section for Computational and RNA Biology, Department of Biology, University of Copenhagen, Copenhagen N, Denmark
| | - Anders Albrechtsen
- Section for Computational and RNA Biology, Department of Biology, University of Copenhagen, Copenhagen N, Denmark
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176
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The Genomic History of the Bronze Age Southern Levant. Cell 2020; 181:1146-1157.e11. [DOI: 10.1016/j.cell.2020.04.024] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Revised: 02/10/2020] [Accepted: 04/15/2020] [Indexed: 01/27/2023]
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177
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Racimo F, Woodbridge J, Fyfe RM, Sikora M, Sjögren KG, Kristiansen K, Vander Linden M. The spatiotemporal spread of human migrations during the European Holocene. Proc Natl Acad Sci U S A 2020; 117:8989-9000. [PMID: 32238559 PMCID: PMC7183159 DOI: 10.1073/pnas.1920051117] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
The European continent was subject to two major migrations of peoples during the Holocene: the northwestward movement of Anatolian farmer populations during the Neolithic and the westward movement of Yamnaya steppe peoples during the Bronze Age. These movements changed the genetic composition of the continent's inhabitants. The Holocene was also characterized by major changes in vegetation composition, which altered the environment occupied by the original hunter-gatherer populations. We aim to test to what extent vegetation change through time is associated with changes in population composition as a consequence of these migrations, or with changes in climate. Using ancient DNA in combination with geostatistical techniques, we produce detailed maps of ancient population movements, which allow us to visualize how these migrations unfolded through time and space. We find that the spread of Neolithic farmer ancestry had a two-pronged wavefront, in agreement with similar findings on the cultural spread of farming from radiocarbon-dated archaeological sites. This movement, however, did not have a strong association with changes in the vegetational landscape. In contrast, the Yamnaya migration speed was at least twice as fast and coincided with a reduction in the amount of broad-leaf forest and an increase in the amount of pasture and natural grasslands in the continent. We demonstrate the utility of integrating ancient genomes with archaeometric datasets in a spatiotemporal statistical framework, which we foresee will enable future studies of ancient populations' movements, and their putative effects on local fauna and flora.
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Affiliation(s)
- Fernando Racimo
- Lundbeck GeoGenetics Centre, The Globe Institute, University of Copenhagen, 1350 Copenhagen, Denmark;
| | - Jessie Woodbridge
- School of Geography, Earth, and Environmental Sciences, University of Plymouth, Plymouth PL4 8AA, United Kingdom
| | - Ralph M Fyfe
- School of Geography, Earth, and Environmental Sciences, University of Plymouth, Plymouth PL4 8AA, United Kingdom
| | - Martin Sikora
- Lundbeck GeoGenetics Centre, The Globe Institute, University of Copenhagen, 1350 Copenhagen, Denmark
| | - Karl-Göran Sjögren
- Department of Historical Studies, University of Gothenburg, 405 30 Gothenburg, Sweden
| | - Kristian Kristiansen
- Department of Historical Studies, University of Gothenburg, 405 30 Gothenburg, Sweden
| | - Marc Vander Linden
- Department of Archaeology, University of Cambridge, Cambridge CB2 1TN, United Kingdom
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178
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Yamasaki YY, Takeshima H, Kano Y, Oseko N, Suzuki T, Nishida M, Watanabe K. Ecosystem size predicts the probability of speciation in migratory freshwater fish. Mol Ecol 2020; 29:3071-3084. [DOI: 10.1111/mec.15415] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Revised: 02/13/2020] [Accepted: 03/05/2020] [Indexed: 12/01/2022]
Affiliation(s)
- Yo Y. Yamasaki
- Graduate School of Science Kyoto University Sakyo Kyoto Japan
- Ecological Genetics Laboratory Department of Genomics and Evolutionary Biology National Institute of Genetics Mishima Shizuoka Japan
| | - Hirohiko Takeshima
- Research Institute for Humanity and Nature Kita Kyoto Japan
- Department of Marine Biology Tokai University Shimizu Shizuoka Japan
| | - Yuichi Kano
- Graduate Education and Research Training Programme in Decision Science for a Sustainable Society Kyushu University Fukuoka Japan
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179
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Barbato M, Reichel MP, Passamonti M, Low WY, Colli L, Tearle R, Williams JL, Ajmone Marsan P. A genetically unique Chinese cattle population shows evidence of common ancestry with wild species when analysed with a reduced ascertainment bias SNP panel. PLoS One 2020; 15:e0231162. [PMID: 32271816 PMCID: PMC7145104 DOI: 10.1371/journal.pone.0231162] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2019] [Accepted: 03/17/2020] [Indexed: 02/07/2023] Open
Abstract
In Hong Kong, there is a cattle population of ~1,200 individuals of uncertain origin and genetic diversity. This population shows heterogeneous morphology, both in body type and pigmentation. Once used as draught animals by the local farmers, they were abandoned around the 1970s due to changes in the economy, and since then have lived as feral populations. To explore the origins of these cattle, we analysed ~50k genotype data of 21 Hong Kong feral cattle, along with data from 703 individuals of 36 cattle populations of European, African taurine, and Asian origin, the wild x domestic hybrid gayal, plus two wild bovine species, gaur and banteng. To reduce the effect of ascertainment bias ~4k loci that are polymorphic in the two wild species were selected for further analysis. The stringent SNP selection we applied resulted in increased heterozygosity across all populations studies, compared with the full panel of SNP, thus reducing the impact of ascertainment bias and facilitating the comparison of divergent breeds of cattle. Our results showed that Hong Kong feral cattle have relatively high levels of genetic distinctiveness, possibly due to the low level of artificial selection, and a likely common ancestry with wild species. We found signs of a putative taurine introgression, probably dating to the import of north European breeds during the British colonialism of Hong Kong. We showed that Hong Kong feral cattle, are distinct from Bos taurus and Bos indicus breeds. Our results highlight the distinctiveness of Hong Kong feral cattle and stress the conservation value of this indigenous breed that is likely to harbour adaptive genetic variation, which is a fundamental livestock resource in the face of climate change and diversifying market demands.
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Affiliation(s)
- Mario Barbato
- Department of Animal Science, Food and Technology–DIANA, and Nutrigenomics and Proteomics Research Center–PRONUTRIGEN, Università Cattolica del Sacro Cuore, Piacenza, Italy
- * E-mail: (MB); (PAM)
| | - Michael P. Reichel
- Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Kowloon, Hong Kong
| | - Matilde Passamonti
- Department of Animal Science, Food and Technology–DIANA, and Nutrigenomics and Proteomics Research Center–PRONUTRIGEN, Università Cattolica del Sacro Cuore, Piacenza, Italy
| | - Wai Yee Low
- School of Animal and Veterinary Sciences, Davies Research Centre, University of Adelaide, Roseworthy, Australia
| | - Licia Colli
- Department of Animal Science, Food and Technology–DIANA, and Nutrigenomics and Proteomics Research Center–PRONUTRIGEN, Università Cattolica del Sacro Cuore, Piacenza, Italy
- Research Center on Biodiversity and Ancient DNA–BioDNA, Università Cattolica del Sacro Cuore, Piacenza, Italy
| | - Rick Tearle
- School of Animal and Veterinary Sciences, Davies Research Centre, University of Adelaide, Roseworthy, Australia
| | - John L. Williams
- School of Animal and Veterinary Sciences, Davies Research Centre, University of Adelaide, Roseworthy, Australia
| | - Paolo Ajmone Marsan
- Department of Animal Science, Food and Technology–DIANA, and Nutrigenomics and Proteomics Research Center–PRONUTRIGEN, Università Cattolica del Sacro Cuore, Piacenza, Italy
- Research Center on Biodiversity and Ancient DNA–BioDNA, Università Cattolica del Sacro Cuore, Piacenza, Italy
- * E-mail: (MB); (PAM)
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180
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Lim HC, Shakya SB, Harvey MG, Moyle RG, Fleischer RC, Braun MJ, Sheldon FH. Opening the door to greater phylogeographic inference in Southeast Asia: Comparative genomic study of five codistributed rainforest bird species using target capture and historical DNA. Ecol Evol 2020; 10:3222-3247. [PMID: 32273983 PMCID: PMC7141000 DOI: 10.1002/ece3.5964] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Revised: 12/02/2019] [Accepted: 12/06/2019] [Indexed: 12/30/2022] Open
Abstract
Indochina and Sundaland are biologically diverse, interconnected regions of Southeast Asia with complex geographic histories. Few studies have examined phylogeography of bird species that span the two regions because of inadequate population sampling. To determine how geographic barriers/events and disparate dispersal potential have influenced the population structure, gene flow, and demographics of species that occupy the entire area, we studied five largely codistributed rainforest bird species: Arachnothera longirostra, Irena puella, Brachypodius atriceps, Niltava grandis, and Stachyris nigriceps. We accomplished relatively thorough sampling and data collection by sequencing ultraconserved elements (UCEs) using DNA extracted from modern and older (historical) specimens. We obtained a genome-wide set of 753-4,501 variable loci and 3,919-18,472 single nucleotide polymorphisms. The formation of major within-species lineages occurred within a similar span of time (0.5-1.5 mya). Major patterns in population genetic structure are largely consistent with the dispersal potential and habitat requirements of the study species. A population break across the Isthmus of Kra was shared only by the two hill/submontane insectivores (N. grandis and S. nigriceps). Across Sundaland, there is little structure in B. atriceps, which is a eurytopic and partially frugivorous species that often utilizes forest edges. Two other eurytopic species, A. longirostra and I. puella, possess highly divergent populations in peripheral Sunda Islands (Java and/or Palawan) and India. These species probably possess intermediate dispersal abilities that allowed them to colonize new areas, and then remained largely isolated subsequently. We also observed an east-west break in Indochina that was shared by B. atriceps and S. nigriceps, species with very different habitat requirements and dispersal potential. By analyzing high-throughput DNA data, our study provides an unprecedented comparative perspective on the process of avian population divergence across Southeast Asia, a process that is determined by geography, species characteristics, and the stochastic nature of dispersal and vicariance events.
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Affiliation(s)
- Haw Chuan Lim
- Department of BiologyGeorge Mason UniversityFairfaxVirginia
- Department of Vertebrate ZoologyNational Museum of Natural HistorySmithsonian InstitutionWashingtonDistrict of Columbia
- Center for Conservation GenomicsSmithsonian Conservation Biology InstituteWashingtonDistrict of Columbia
| | - Subir B. Shakya
- Museum of Natural Science and Department of Biological SciencesLouisiana State UniversityBaton RougeLouisiana
| | - Michael G. Harvey
- Department of Ecology and Evolutionary BiologyUniversity of TennesseeKnoxvilleTennessee
| | - Robert G. Moyle
- Biodiversity Institute and Department of Ecology and Evolutionary BiologyUniversity of KansasLawrenceKansas
| | - Robert C. Fleischer
- Center for Conservation GenomicsSmithsonian Conservation Biology InstituteWashingtonDistrict of Columbia
| | - Michael J. Braun
- Department of Vertebrate ZoologyNational Museum of Natural HistorySmithsonian InstitutionWashingtonDistrict of Columbia
| | - Frederick H. Sheldon
- Museum of Natural Science and Department of Biological SciencesLouisiana State UniversityBaton RougeLouisiana
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181
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Mas-Sandoval A, Arauna LR, Gouveia MH, Barreto ML, Horta BL, Lima-Costa MF, Pereira AC, Salzano FM, Hünemeier T, Tarazona-Santos E, Bortolini MC, Comas D. Reconstructed Lost Native American Populations from Eastern Brazil Are Shaped by Differential Jê/Tupi Ancestry. Genome Biol Evol 2020; 11:2593-2604. [PMID: 31328768 PMCID: PMC6756188 DOI: 10.1093/gbe/evz161] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/17/2019] [Indexed: 01/19/2023] Open
Abstract
After the colonization of the Americas by Europeans and the consequent Trans-Atlantic Slave Trade, most Native American populations in eastern Brazil disappeared or went through an admixture process that configured a population composed of three main genetic components: the European, the sub-Saharan African, and the Native American. The study of the Native American genetic history is challenged by the lack of availability of genome-wide samples from Native American populations, the technical difficulties to develop ancient DNA studies, and the low proportions of the Native American component in the admixed Brazilian populations (on average 7%). We analyzed genome-wide data of 5,825 individuals from three locations of eastern Brazil: Salvador (North-East), Bambui (South-East), and Pelotas (South) and we reconstructed populations that emulate the Native American groups that were living in the 16th century around the sampling locations. This genetic reconstruction was performed after local ancestry analysis of the admixed Brazilian populations, through the rearrangement of the Native American haplotypes into reconstructed individuals with full Native American ancestry (51 reconstructed individuals in Salvador, 45 in Bambui, and 197 in Pelotas). We compared the reconstructed populations with nonadmixed Native American populations from other regions of Brazil through haplotype-based methods. Our results reveal a population structure shaped by the dichotomy of Tupi-/Jê-speaking ancestry related groups. We also show evidence of a decrease of the diversity of nonadmixed Native American groups after the European contact, in contrast with the reconstructed populations, suggesting a reservoir of the Native American genetic diversity within the admixed Brazilian population.
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Affiliation(s)
- Alex Mas-Sandoval
- Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil.,Departament de Ciències Experimentals i de la Salut, Institute of Evolutionary Biology (CSIC-UPF), Universitat Pompeu Fabra, Barcelona, Spain
| | - Lara R Arauna
- Departament de Ciències Experimentals i de la Salut, Institute of Evolutionary Biology (CSIC-UPF), Universitat Pompeu Fabra, Barcelona, Spain
| | - Mateus H Gouveia
- Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil.,Center for Research on Genomics and Global Health, National Institutes of Health, Bethesda, Maryland
| | - Mauricio L Barreto
- Instituto de Saúde Coletiva, Universidade Federal da Bahia, Salvador, Bahia, Brazil.,Center for Data and Knowledge Integration for Health, Institute Gonçalo Muniz, Fundação Oswaldo Cruz, Salvador, Bahia, Brazil
| | - Bernardo L Horta
- Programa de Pós-Graduação em Epidemiologia, Universidade Federal de Pelotas, Rio Grande do Sul, Brazil
| | | | | | - Francisco M Salzano
- Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil
| | - Tábita Hünemeier
- Department of Genetics and Evolutionary Biology, Biosciences Institute, University of São Paulo, São Paulo, Brazil
| | - Eduardo Tarazona-Santos
- Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Maria Cátira Bortolini
- Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil
| | - David Comas
- Departament de Ciències Experimentals i de la Salut, Institute of Evolutionary Biology (CSIC-UPF), Universitat Pompeu Fabra, Barcelona, Spain
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182
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Knudson A, González-Casabianca F, Feged-Rivadeneira A, Pedreros MF, Aponte S, Olaya A, Castillo CF, Mancilla E, Piamba-Dorado A, Sanchez-Pedraza R, Salazar-Terreros MJ, Lucchi N, Udhayakumar V, Jacob C, Pance A, Carrasquilla M, Apráez G, Angel JA, Rayner JC, Corredor V. Spatio-temporal dynamics of Plasmodium falciparum transmission within a spatial unit on the Colombian Pacific Coast. Sci Rep 2020; 10:3756. [PMID: 32111872 PMCID: PMC7048816 DOI: 10.1038/s41598-020-60676-1] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Accepted: 01/29/2020] [Indexed: 02/07/2023] Open
Abstract
As malaria control programmes concentrate their efforts towards malaria elimination a better understanding of malaria transmission patterns at fine spatial resolution units becomes necessary. Defining spatial units that consider transmission heterogeneity, human movement and migration will help to set up achievable malaria elimination milestones and guide the creation of efficient operational administrative control units. Using a combination of genetic and epidemiological data we defined a malaria transmission unit as the area contributing 95% of malaria cases diagnosed at the catchment facility located in the town of Guapi in the South Pacific Coast of Colombia. We provide data showing that P. falciparum malaria transmission is heterogeneous in time and space and analysed, using topological data analysis, the spatial connectivity, at the micro epidemiological level, between parasite populations circulating within the unit. To illustrate the necessity to evaluate the efficacy of malaria control measures within the transmission unit in order to increase the efficiency of the malaria control effort, we provide information on the size of the asymptomatic reservoir, the nature of parasite genotypes associated with drug resistance as well as the frequency of the Pfhrp2/3 deletion associated with false negatives when using Rapid Diagnostic Tests.
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Affiliation(s)
- Angélica Knudson
- Departamento de Microbiología, Facultad de Medicina, Universidad Nacional de Colombia, Bogotá, Colombia
| | - Felipe González-Casabianca
- Departamento de Matemáticas, Facultad de Ciencias, Universidad de Los Andes, Bogotá, Colombia.,Gestión y desarrollo urbanos, Facultad de Ciencia Política, Universidad del Rosario, Bogotá, Colombia
| | | | - Maria Fernanda Pedreros
- Departamento de Salud Pública, Facultad de Medicina, Universidad Nacional de Colombia, Bogotá, Colombia
| | - Samanda Aponte
- Departamento de Salud Pública, Facultad de Medicina, Universidad Nacional de Colombia, Bogotá, Colombia
| | - Adriana Olaya
- Secretaría Departamental de Salud del Cauca, Popayán, Colombia
| | | | - Elvira Mancilla
- Secretaría Departamental de Salud del Cauca, Popayán, Colombia
| | | | - Ricardo Sanchez-Pedraza
- Departamento de Psiquiatria, Facultad de Medicina, Universidad Nacional de Colombia, Bogotá, Colombia
| | - Myriam Janeth Salazar-Terreros
- Post-doctoral fellow, Centro de Hematologia e Hemoterapia (HEMOCENTRO), Universidade Estadual de Campinas (UNICAMP), Campinas, Brazil
| | - Naomi Lucchi
- Malaria Branch, Division of Parasitic Diseases and Malaria, Centers for Global Health, Centers for Disease Control and Prevention, Atlanta, 30030, GA, United States of America
| | - Venkatachalam Udhayakumar
- Malaria Branch, Division of Parasitic Diseases and Malaria, Centers for Global Health, Centers for Disease Control and Prevention, Atlanta, 30030, GA, United States of America
| | - Chris Jacob
- Malaria Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, CB10 1SA, United Kingdom
| | - Alena Pance
- Malaria Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, CB10 1SA, United Kingdom
| | - Manuela Carrasquilla
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, 02115, USA
| | - Giovanni Apráez
- Departamento de Salud Pública, Facultad de Medicina, Universidad Nacional de Colombia, Bogotá, Colombia.,Secretaría Departamental de Salud del Cauca, Popayán, Colombia
| | - Jairo Andrés Angel
- Departamento de Matemáticas, Facultad de Ciencias, Universidad de Los Andes, Bogotá, Colombia.,Department of Mathematics and Statistics, Universidad del Norte, Barranquilla, Colombia
| | - Julian C Rayner
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, CB2 0XY, United Kingdom.
| | - Vladimir Corredor
- Departamento de Salud Pública, Facultad de Medicina, Universidad Nacional de Colombia, Bogotá, Colombia.
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183
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Cullingham CI, Miller JM, Peery RM, Dupuis JR, Malenfant RM, Gorrell JC, Janes JK. Confidently identifying the correctKvalue using the ΔKmethod: When doesK = 2? Mol Ecol 2020; 29:862-869. [DOI: 10.1111/mec.15374] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Revised: 01/29/2020] [Accepted: 02/05/2020] [Indexed: 01/20/2023]
Affiliation(s)
| | - Joshua M. Miller
- Department of Biological Sciences University of Alberta Edmonton AB Canada
| | - Rhiannon M. Peery
- Department of Biological Sciences University of Alberta Edmonton AB Canada
| | - Julian R. Dupuis
- Department of Entomology University of Kentucky Lexington KY USA
| | - René M. Malenfant
- Department of Biology University of New Brunswick Fredericton NB Canada
| | | | - Jasmine K. Janes
- Biology Department Vancouver Island University Nanaimo BC Canada
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184
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Serendipitous In Situ Conservation of Faba Bean Landraces in Tunisia: A Case Study. Genes (Basel) 2020; 11:genes11020236. [PMID: 32102450 PMCID: PMC7074078 DOI: 10.3390/genes11020236] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Revised: 02/13/2020] [Accepted: 02/16/2020] [Indexed: 12/19/2022] Open
Abstract
Cultivation of faba bean (Vicia faba L.) in Tunisia is largely based on improved varieties of the crop. However, a few farmers continue to produce local cultivars or landraces. The National Gene Bank of Tunisia (NGBT) recently launched a collection project for faba bean landraces, with special focus on the regions of the North West, traditionally devoted to cultivating grain legumes, and where around 80% of the total national faba bean cultivation area is located. The seed phenotypic features of the collected samples were studied, and the genetic diversity and population structure analyzed using simple sequence repeat markers. The genetic constitution of the present samples was compared to that of faba bean samples collected by teams of the International Center for Agricultural Research in the Dry Areas (ICARDA) in the 1970s in the same region, and stored at the ICARDA gene bank. The results of the diversity analysis demonstrate that the recently collected samples and those stored at ICARDA largely overlap, thus demonstrating that over the past 50 years, little genetic change has occurred to the local faba bean populations examined. These findings suggest that farmers serendipitously applied international best practices for in situ conservation of agricultural crops.
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185
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The genetic history of France. Eur J Hum Genet 2020; 28:853-865. [PMID: 32042083 DOI: 10.1038/s41431-020-0584-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Revised: 11/25/2019] [Accepted: 01/28/2020] [Indexed: 12/15/2022] Open
Abstract
The study of the genetic structure of different countries within Europe has provided significant insights into their demographic history and population structure. Although France occupies a particular location at the western part of Europe and at the crossroads of migration routes, few population genetic studies have been conducted so far with genome-wide data. In this study, we analyzed SNP-chip genetic data from 2184 individuals born in France who were enrolled in two independent population cohorts. Using FineSTRUCTURE, six different genetic clusters of individuals were found that were very consistent between the two cohorts. These clusters correspond closely to geographic, historical, and linguistic divisions of France, and contain different proportions of ancestry from Stone and Bronze Age populations. By modeling the relationship between genetics and geography using EEMS, we were able to detect gene flow barriers that are similar across the two cohorts and correspond to major rivers and mountain ranges. Estimations of effective population sizes also revealed very similar patterns in both cohorts with a rapid increase of effective population sizes over the last 150 generations similar to other European countries. A marked bottleneck is also consistently seen in the two datasets starting in the 14th century when the Black Death raged in Europe. In conclusion, by performing the first exhaustive study of the genetic structure of France, we fill a gap in genetic studies of Europe that will be useful to medical geneticists, historians, and archeologists.
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186
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Bergey CM, Lukindu M, Wiltshire RM, Fontaine MC, Kayondo JK, Besansky NJ. Assessing connectivity despite high diversity in island populations of a malaria mosquito. Evol Appl 2020; 13:417-431. [PMID: 31993086 PMCID: PMC6976967 DOI: 10.1111/eva.12878] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Revised: 08/28/2019] [Accepted: 09/27/2019] [Indexed: 12/14/2022] Open
Abstract
Documenting isolation is notoriously difficult for species with vast polymorphic populations. High proportions of shared variation impede estimation of connectivity, even despite leveraging information from many genetic markers. We overcome these impediments by combining classical analysis of neutral variation with assays of the structure of selected variation, demonstrated using populations of the principal African malaria vector Anopheles gambiae. Accurate estimation of mosquito migration is crucial for efforts to combat malaria. Modeling and cage experiments suggest that mosquito gene drive systems will enable malaria eradication, but establishing safety and efficacy requires identification of isolated populations in which to conduct field testing. We assess Lake Victoria islands as candidate sites, finding one island 30 km offshore is as differentiated from mainland samples as populations from across the continent. Collectively, our results suggest sufficient contemporary isolation of these islands to warrant consideration as field-testing locations and illustrate shared adaptive variation as a useful proxy for connectivity in highly polymorphic species.
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Affiliation(s)
- Christina M. Bergey
- Department of Biological SciencesUniversity of Notre DameNotre DameINUSA
- Eck Institute for Global HealthUniversity of Notre DameNotre DameINUSA
- Department of GeneticsRutgers UniversityPiscatawayNJUSA
- Departments of Anthropology and BiologyPennsylvania State UniversityUniversity ParkPAUSA
| | - Martin Lukindu
- Department of Biological SciencesUniversity of Notre DameNotre DameINUSA
- Eck Institute for Global HealthUniversity of Notre DameNotre DameINUSA
| | - Rachel M. Wiltshire
- Department of Biological SciencesUniversity of Notre DameNotre DameINUSA
- Eck Institute for Global HealthUniversity of Notre DameNotre DameINUSA
| | - Michael C. Fontaine
- Groningen Institute for Evolutionary Life Sciences (GELIFES)University of GroningenGroningenThe Netherlands
- MIVEGECIRDCNRSUniversity of MontpellierMontpellierFrance
| | | | - Nora J. Besansky
- Department of Biological SciencesUniversity of Notre DameNotre DameINUSA
- Eck Institute for Global HealthUniversity of Notre DameNotre DameINUSA
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187
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Battey CJ. Evidence of linked selection on the Z chromosome of hybridizing hummingbirds. Evolution 2020; 74:725-739. [PMID: 31859363 DOI: 10.1111/evo.13888] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Revised: 10/01/2019] [Accepted: 11/12/2019] [Indexed: 12/25/2022]
Abstract
Levels of genetic differentiation vary widely along the genomes of recently diverged species. What processes cause this variation? Here, I analyze geographic population structure and genome-wide patterns of variation in the Rufous, Allen's, and Calliope Hummingbirds (Selasphorus rufus/Selasphorus sasin/Selasphorus calliope) and assess evidence that linked selection on the Z chromosome drives patterns of genetic differentiation in a pair of hybridizing species. Demographic models, introgression tests, and genotype clustering analyses support a reticulate evolutionary history consistent with divergence during the late Pleistocene followed by gene flow across migrant Rufous and Allen's Hummingbirds during the Holocene. Relative genetic differentiation ( F s t ) is elevated, and within-population diversity (π) is depressed on the Z chromosome in all interspecific comparisons. The ratio of Z to autosomal within-population diversity is much lower than that expected from population size effects alone, and Tajima's D is depressed on the Z chromosome in S. rufus and S. calliope. These results suggest that conserved structural features of the genome play a prominent role in shaping genetic differentiation through the early stages of speciation in northern Selasphorus hummingbirds, and that the Z chromosome is a likely site of genes underlying behavioral and morphological variation in the group.
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Affiliation(s)
- Christopher J Battey
- Department of Biology, University of Washington, Seattle, Washington, 97403-1201.,Current Address: Institute of Ecology and Evolution, University of Oregon, Eugene, OR, 97403
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188
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West FL, Algee-Hewitt BF. Cadaveric blood cards: Assessing DNA quality and quantity and the utility of STRs for the individual estimation of trihybrid ancestry and admixture proportions. Forensic Sci Int Synerg 2020; 2:114-122. [PMID: 32412010 PMCID: PMC7219121 DOI: 10.1016/j.fsisyn.2020.03.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Revised: 03/04/2020] [Accepted: 03/06/2020] [Indexed: 02/04/2023]
Abstract
As part a body donation program, blood samples were collected and stored on untreated (non-FTA) blood cards. The blood cards were evaluated in terms of DNA preservation and STR typing success with resulting profiles assessed with special consideration given to profile matching for positive identification and biogeographic ancestry estimation. While STR profiles were successfully generated for all samples, results indicate that the time interval between date of death and sample collection have an impact on DNA quantity and quality. There is a statistically significant decrease in relative fluorescent unit (RFU) values with increasing time interval between date of death and sample collection, indicating degradation in the blood card samples related to the post-mortem interval prior to sample collection. The STR profiles were used to estimate ancestry and admixture using the program STRUCTURE, demonstrating utility of these markers beyond individual identification purposes, with caveats for application based on population history.
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Affiliation(s)
- Frankie L. West
- Forensic Science Program, Western Carolina University, USA
- Corresponding author.
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189
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Lawson DJ, Davies NM, Haworth S, Ashraf B, Howe L, Crawford A, Hemani G, Davey Smith G, Timpson NJ. Is population structure in the genetic biobank era irrelevant, a challenge, or an opportunity? Hum Genet 2020; 139:23-41. [PMID: 31030318 PMCID: PMC6942007 DOI: 10.1007/s00439-019-02014-8] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2018] [Accepted: 04/12/2019] [Indexed: 12/11/2022]
Abstract
Replicable genetic association signals have consistently been found through genome-wide association studies in recent years. The recent dramatic expansion of study sizes improves power of estimation of effect sizes, genomic prediction, causal inference, and polygenic selection, but it simultaneously increases susceptibility of these methods to bias due to subtle population structure. Standard methods using genetic principal components to correct for structure might not always be appropriate and we use a simulation study to illustrate when correction might be ineffective for avoiding biases. New methods such as trans-ethnic modeling and chromosome painting allow for a richer understanding of the relationship between traits and population structure. We illustrate the arguments using real examples (stroke and educational attainment) and provide a more nuanced understanding of population structure, which is set to be revisited as a critical aspect of future analyses in genetic epidemiology. We also make simple recommendations for how problems can be avoided in the future. Our results have particular importance for the implementation of GWAS meta-analysis, for prediction of traits, and for causal inference.
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Affiliation(s)
- Daniel John Lawson
- MRC Integrative Epidemiology Unit, Population Health Sciences, Bristol Medical School, University of Bristol, Oakfield House, Oakfield Grove, Bristol, BS8 2BN, UK.
| | - Neil Martin Davies
- MRC Integrative Epidemiology Unit, Population Health Sciences, Bristol Medical School, University of Bristol, Oakfield House, Oakfield Grove, Bristol, BS8 2BN, UK
| | - Simon Haworth
- MRC Integrative Epidemiology Unit, Population Health Sciences, Bristol Medical School, University of Bristol, Oakfield House, Oakfield Grove, Bristol, BS8 2BN, UK
| | - Bilal Ashraf
- MRC Integrative Epidemiology Unit, Population Health Sciences, Bristol Medical School, University of Bristol, Oakfield House, Oakfield Grove, Bristol, BS8 2BN, UK
| | - Laurence Howe
- Institute of Cardiovascular Science, Faculty of Population Health Sciences, University College London, Gower Street, London, WC1E 6BT, UK
| | - Andrew Crawford
- MRC Integrative Epidemiology Unit, Population Health Sciences, Bristol Medical School, University of Bristol, Oakfield House, Oakfield Grove, Bristol, BS8 2BN, UK
| | - Gibran Hemani
- MRC Integrative Epidemiology Unit, Population Health Sciences, Bristol Medical School, University of Bristol, Oakfield House, Oakfield Grove, Bristol, BS8 2BN, UK
| | - George Davey Smith
- MRC Integrative Epidemiology Unit, Population Health Sciences, Bristol Medical School, University of Bristol, Oakfield House, Oakfield Grove, Bristol, BS8 2BN, UK
| | - Nicholas John Timpson
- MRC Integrative Epidemiology Unit, Population Health Sciences, Bristol Medical School, University of Bristol, Oakfield House, Oakfield Grove, Bristol, BS8 2BN, UK
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190
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Han B, Ma X, Cui D, Wang Y, Geng L, Cao G, Zhang H, Koh H, Han L. Analysis of evolutionary relationships provides new clues to the origins of weedy rice. Ecol Evol 2020; 10:891-900. [PMID: 32015852 PMCID: PMC6988545 DOI: 10.1002/ece3.5948] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2019] [Revised: 11/27/2019] [Accepted: 11/28/2019] [Indexed: 11/18/2022] Open
Abstract
Weedy rice (WR) (Oryza sativa f. spontanea) is considered to be a pest in modern rice production systems because it competes for resources, has poor yield characteristics, and subsequently has a negative effect on rice grain yield. The evolutionary relationships among WR, landrace rice (LR), improved rice (IR) cultivars, and wild rice are largely unknown. In this study, we conducted a population genetic analysis based on neutral markers and gene haplotypes in 524 rice accessions and a comparative transcriptomic analysis using 15 representative samples. The results showed that WR populations have the highest level of genetic diversity (H e = 0.8386) and can be divided into two groups (japonica-type and indica-type). The japonica-type WR accessions from Heilongjiang province (HLJ), Jilin province (JL), Liaoning province (LN), and NX provinces clustered with the landraces grown in these same provinces. The indica-types from Jiangsu province (JS) also clustered with the indica-type landraces from JS province. Comparative transcriptome analysis of WR' IR and LR from HLJ, JL, and LN provinces showed that the WR still clustered with the LR, and that the IR lines comprise a single population. Thirty-two differentially expressed genes were shared by the IR and LR groups as well as between the IR and WR groups. Using Gene ontology (GO) analysis, we identified 19 shared GO terms in the IR and LR groups as well as between the IR and WR groups. Our results suggest that WR populations in China have diverse origins, and comparative transcriptome analysis of different types of rice from HLJ, JL, and LN provinces suggests that IR populations have become a end point in the evolution of WR, which provides a new perspective for the study of WR origins and lays a solid foundation for rice breeding.
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Affiliation(s)
- Bing Han
- Institute of Crop SciencesChinese Academy of Agricultural SciencesBeijingChina
| | - Xiaoding Ma
- Institute of Crop SciencesChinese Academy of Agricultural SciencesBeijingChina
| | - Di Cui
- Institute of Crop SciencesChinese Academy of Agricultural SciencesBeijingChina
| | - Yanjie Wang
- Institute of Crop SciencesChinese Academy of Agricultural SciencesBeijingChina
| | - Leiyue Geng
- Institute of Crop SciencesChinese Academy of Agricultural SciencesBeijingChina
| | - Guilan Cao
- Institute of Crop SciencesChinese Academy of Agricultural SciencesBeijingChina
| | - Hui Zhang
- Institute of Crop SciencesChinese Academy of Agricultural SciencesBeijingChina
| | - Hee‐Jong Koh
- Department of Plant Science, Plant Genomics and Breeding Institute of Agriculture and Life ScienceSeoul National UniversitySeoulKorea
| | - Longzhi Han
- Institute of Crop SciencesChinese Academy of Agricultural SciencesBeijingChina
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191
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Gautason E, Schönherz AA, Sahana G, Guldbrandtsen B. Relationship of Icelandic cattle with Northern and Western European cattle breeds, admixture and population structure. ACTA AGR SCAND A-AN 2019. [DOI: 10.1080/09064702.2019.1699951] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Egill Gautason
- Center for Quantitative Genetics and Genomics, Department of Molecular Biology and Genetics, Aarhus University, Tjele, Denmark
| | - Anna A. Schönherz
- Center for Quantitative Genetics and Genomics, Department of Molecular Biology and Genetics, Aarhus University, Tjele, Denmark
| | - Goutam Sahana
- Center for Quantitative Genetics and Genomics, Department of Molecular Biology and Genetics, Aarhus University, Tjele, Denmark
| | - Bernt Guldbrandtsen
- Center for Quantitative Genetics and Genomics, Department of Molecular Biology and Genetics, Aarhus University, Tjele, Denmark
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192
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Cao L, Gao Y, Gong Y, Chen J, Chen M, Hoffmann A, Wei S. Population analysis reveals genetic structure of an invasive agricultural thrips pest related to invasion of greenhouses and suitable climatic space. Evol Appl 2019; 12:1868-1880. [PMID: 31700532 PMCID: PMC6824073 DOI: 10.1111/eva.12847] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Revised: 07/07/2019] [Accepted: 07/11/2019] [Indexed: 01/09/2023] Open
Abstract
Biological invasions of pests into climatically unsuitable areas can be facilitated by human-regulated environments, in which case there may be an impact on genetic structure through population processes and/or adaptation. Here, we investigated the population genetic structure of an invasive agricultural pest, Thrips palmi, in China, which has expanded its distribution range through using greenhouses. Early invaded populations showed a relatively higher level of genetic diversity than recently expanded greenhouse populations. Strong population genetic structure corresponded to a pattern of isolation by distance, with no recent gene flow and low historical gene flow among populations, reflecting limited ongoing dispersal. A genetic signature of population expansion was detected in early invaded populations and three northern populations from greenhouses, suggesting that the greenhouse environments facilitated expansion of this species. Redundancy analysis showed that the independent effects of environment and geography could explain 51.68% and 32.06% of the genetic variance, respectively. These findings point to climate- and greenhouse-related spatial expansion, with the potential for adaptation by T. palmi. They emphasize the contribution of human-regulated environments on the successes of this invasive species, a situation likely to apply to other invasive species that use greenhouse environments.
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Affiliation(s)
- Li‐Jun Cao
- Institute of Plant and Environmental ProtectionBeijing Academy of Agriculture and Forestry SciencesBeijingChina
| | - Yong‐Fu Gao
- Institute of Plant and Environmental ProtectionBeijing Academy of Agriculture and Forestry SciencesBeijingChina
- Beijing Key Laboratory for Forest Pest Control, College of ForestryBeijing Forestry UniversityBeijingChina
| | - Ya‐Jun Gong
- Institute of Plant and Environmental ProtectionBeijing Academy of Agriculture and Forestry SciencesBeijingChina
| | - Jin‐Cui Chen
- Institute of Plant and Environmental ProtectionBeijing Academy of Agriculture and Forestry SciencesBeijingChina
| | - Min Chen
- Beijing Key Laboratory for Forest Pest Control, College of ForestryBeijing Forestry UniversityBeijingChina
| | - Ary Hoffmann
- School of BioSciences, Bio21 InstituteThe University of MelbourneParkvilleVICAustralia
| | - Shu‐Jun Wei
- Institute of Plant and Environmental ProtectionBeijing Academy of Agriculture and Forestry SciencesBeijingChina
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193
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Abstract
Interspecific hybridization is the process where closely related species mate and produce offspring with admixed genomes. The genomic revolution has shown that hybridization is common, and that it may represent an important source of novel variation. Although most interspecific hybrids are sterile or less fit than their parents, some may survive and reproduce, enabling the transfer of adaptive variants across the species boundary, and even result in the formation of novel evolutionary lineages. There are two main variants of hybrid species genomes: allopolyploid, which have one full chromosome set from each parent species, and homoploid, which are a mosaic of the parent species genomes with no increase in chromosome number. The establishment of hybrid species requires the development of reproductive isolation against parental species. Allopolyploid species often have strong intrinsic reproductive barriers due to differences in chromosome number, and homoploid hybrids can become reproductively isolated from the parent species through assortment of genetic incompatibilities. However, both types of hybrids can become further reproductively isolated, gaining extrinsic isolation barriers, by exploiting novel ecological niches, relative to their parents. Hybrids represent the merging of divergent genomes and thus face problems arising from incompatible combinations of genes. Thus hybrid genomes are highly dynamic and undergo rapid evolutionary change, including genome stabilization in which selection against incompatible combinations results in fixation of compatible ancestry block combinations within the hybrid species. The potential for rapid adaptation or speciation makes hybrid genomes a particularly exciting subject of in evolutionary biology. Here we summarize how introgressed alleles or hybrid species can establish and how the resulting hybrid genomes evolve.
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Affiliation(s)
- Anna Runemark
- Department of Biology, Lund University, Lund, Sweden
- * E-mail:
| | - Mario Vallejo-Marin
- Biological and Environmental Sciences, University of Stirling, Stirling, Scotland, United Kingdom
| | - Joana I. Meier
- St John's College, Cambridge, Cambridge, United Kingdom
- Department of Zoology, University of Cambridge, Cambridge, United Kingdom
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194
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Kuismin M, Saatoglu D, Niskanen AK, Jensen H, Sillanpää MJ. Genetic assignment of individuals to source populations using network estimation tools. Methods Ecol Evol 2019. [DOI: 10.1111/2041-210x.13323] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Markku Kuismin
- Research Unit of Mathematical Sciences University of Oulu Oulu Finland
- Biocenter Oulu University of Oulu Oulu Finland
| | - Dilan Saatoglu
- Centre for Biodiversity Dynamics Department of Biology Norwegian University of Science and Technology Trondheim Norway
| | - Alina K. Niskanen
- Centre for Biodiversity Dynamics Department of Biology Norwegian University of Science and Technology Trondheim Norway
- Ecology and Genetics Research Unit University of Oulu Oulu Finland
| | - Henrik Jensen
- Centre for Biodiversity Dynamics Department of Biology Norwegian University of Science and Technology Trondheim Norway
| | - Mikko J. Sillanpää
- Research Unit of Mathematical Sciences University of Oulu Oulu Finland
- Biocenter Oulu University of Oulu Oulu Finland
- Infotech Oulu University of Oulu Oulu Finland
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195
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Bakovic V, Schuler H, Schebeck M, Feder JL, Stauffer C, Ragland GJ. Host plant-related genomic differentiation in the European cherry fruit fly, Rhagoletis cerasi. Mol Ecol 2019; 28:4648-4666. [PMID: 31495015 PMCID: PMC6899720 DOI: 10.1111/mec.15239] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Revised: 08/29/2019] [Accepted: 08/30/2019] [Indexed: 12/13/2022]
Abstract
Elucidating the mechanisms and conditions facilitating the formation of biodiversity are central topics in evolutionary biology. A growing number of studies imply that divergent ecological selection may often play a critical role in speciation by counteracting the homogenising effects of gene flow. Several examples involve phytophagous insects, where divergent selection pressures associated with host plant shifts may generate reproductive isolation, promoting speciation. Here, we use ddRADseq to assess the population structure and to test for host‐related genomic differentiation in the European cherry fruit fly, Rhagoletis cerasi (L., 1758) (Diptera: Tephritidae). This tephritid is distributed throughout Europe and western Asia, and has adapted to two different genera of host plants, Prunus spp. (cherries) and Lonicera spp. (honeysuckle). Our data imply that geographic distance and geomorphic barriers serve as the primary factors shaping genetic population structure across the species range. Locally, however, flies genetically cluster according to host plant, with consistent allele frequency differences displayed by a subset of loci between Prunus and Lonicera flies across four sites surveyed in Germany and Norway. These 17 loci display significantly higher FST values between host plants than others. They also showed high levels of linkage disequilibrium within and between Prunus and Lonicera flies, supporting host‐related selection and reduced gene flow. Our findings support the existence of sympatric host races in R. cerasi embedded within broader patterns of geographic variation in the fly, similar to the related apple maggot, Rhagoletis pomonella, in North America.
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Affiliation(s)
- Vid Bakovic
- Department of Forest and Soil Sciences, BOKU, University of Natural Resources and Life Sciences Vienna, Vienna, Austria.,Department of Biology, IFM, University of Linköping, Linköping, Sweden
| | - Hannes Schuler
- Faculty of Science and Technology, Free University of Bozen-Bolzano, Bolzano, Italy
| | - Martin Schebeck
- Department of Forest and Soil Sciences, BOKU, University of Natural Resources and Life Sciences Vienna, Vienna, Austria
| | - Jeffrey L Feder
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, USA
| | - Christian Stauffer
- Department of Forest and Soil Sciences, BOKU, University of Natural Resources and Life Sciences Vienna, Vienna, Austria
| | - Gregory J Ragland
- Department of Integrative Biology, University of Colorado-Denver, Denver, CO, USA
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196
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Kastally C, Trasoletti M, Mardulyn P. Limited gene exchange between two sister species of leaf beetles within a hybrid zone in the Alps. J Evol Biol 2019; 32:1406-1417. [DOI: 10.1111/jeb.13538] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Revised: 08/02/2019] [Accepted: 08/30/2019] [Indexed: 12/24/2022]
Affiliation(s)
- Chedly Kastally
- Evolutionary Biology and Ecology Université Libre de Bruxelles Brussels Belgium
| | - Marta Trasoletti
- Evolutionary Biology and Ecology Université Libre de Bruxelles Brussels Belgium
| | - Patrick Mardulyn
- Evolutionary Biology and Ecology Université Libre de Bruxelles Brussels Belgium
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197
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Driscoe AL, Nice CC, Busbee RW, Hood GR, Egan SP, Ott JR. Host plant associations and geography interact to shape diversification in a specialist insect herbivore. Mol Ecol 2019; 28:4197-4211. [DOI: 10.1111/mec.15220] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Revised: 07/26/2019] [Accepted: 08/07/2019] [Indexed: 12/21/2022]
Affiliation(s)
- Amanda L. Driscoe
- Population and Conservation Biology Program Department of Biology Texas State University San Marcos Texas
| | - Chris C. Nice
- Population and Conservation Biology Program Department of Biology Texas State University San Marcos Texas
| | - Robert W. Busbee
- Population and Conservation Biology Program Department of Biology Texas State University San Marcos Texas
| | - Glen R. Hood
- Department of Biological Sciences Wayne State University Detroit Michigan
| | - Scott P. Egan
- Department of Biosciences Rice University Houston Texas
| | - James R. Ott
- Population and Conservation Biology Program Department of Biology Texas State University San Marcos Texas
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198
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Martin SL, Parent JS, Laforest M, Page E, Kreiner JM, James T. Population Genomic Approaches for Weed Science. PLANTS (BASEL, SWITZERLAND) 2019; 8:E354. [PMID: 31546893 PMCID: PMC6783936 DOI: 10.3390/plants8090354] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Revised: 09/12/2019] [Accepted: 09/14/2019] [Indexed: 12/16/2022]
Abstract
Genomic approaches are opening avenues for understanding all aspects of biological life, especially as they begin to be applied to multiple individuals and populations. However, these approaches typically depend on the availability of a sequenced genome for the species of interest. While the number of genomes being sequenced is exploding, one group that has lagged behind are weeds. Although the power of genomic approaches for weed science has been recognized, what is needed to implement these approaches is unfamiliar to many weed scientists. In this review we attempt to address this problem by providing a primer on genome sequencing and provide examples of how genomics can help answer key questions in weed science such as: (1) Where do agricultural weeds come from; (2) what genes underlie herbicide resistance; and, more speculatively, (3) can we alter weed populations to make them easier to control? This review is intended as an introduction to orient weed scientists who are thinking about initiating genome sequencing projects to better understand weed populations, to highlight recent publications that illustrate the potential for these methods, and to provide direction to key tools and literature that will facilitate the development and execution of weed genomic projects.
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Affiliation(s)
- Sara L Martin
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON K1A 0C6, Canada.
| | - Jean-Sebastien Parent
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON K1A 0C6, Canada.
| | - Martin Laforest
- Saint-Jean-sur-Richelieu Research and Development Centre, Agriculture and Agri-Food Canada, Saint-Jean-sur-Richelieu, QC J3B 3E6, Canada.
| | - Eric Page
- Harrow Research and Development Centre, Agriculture and Agri-Food Canada, Harrow, ON N0R 1G0, Canada.
| | - Julia M Kreiner
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON M5S 3B2, Canada.
| | - Tracey James
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON K1A 0C6, Canada.
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199
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Pavan S, Bardaro N, Fanelli V, Marcotrigiano AR, Mangini G, Taranto F, Catalano D, Montemurro C, De Giovanni C, Lotti C, Ricciardi L. Genotyping by Sequencing of Cultivated Lentil ( Lens culinaris Medik.) Highlights Population Structure in the Mediterranean Gene Pool Associated With Geographic Patterns and Phenotypic Variables. Front Genet 2019; 10:872. [PMID: 31620173 PMCID: PMC6759463 DOI: 10.3389/fgene.2019.00872] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Accepted: 08/20/2019] [Indexed: 11/13/2022] Open
Abstract
Cultivated lentil (Lens culinaris Medik.) is one of the oldest domesticated crops and one of the most important grain legumes worldwide. The Mediterranean Basin holds large part of lentil biodiversity; however, no genetic structure was defined within the Mediterranean gene pool. In this study, we used high-throughput genotyping by sequencing to resolve the genetic structure of the Mediterranean ex situ lentil collection held at the Italian National Research Council. Sequencing of a 188-plex genotyping-by-sequencing library and bioinformatics treatment of data yielded 6,693 single nucleotide polymorphisms. Analysis of nonredundant genotypes with nonparametric and parametric methods highlighted the occurrence of five highly differentiated genetic clusters. Clustering could be related to geographic patterns and phenotypic traits, indicating that post-domestication routes introducing cultivation in Mediterranean countries and selection were major forces shaping lentil population structure. The estimation of the fixation index FST at individual single nucleotide polymorphism loci allowed the identification of distinctive alleles across clusters, suggesting the possibility to set up molecular keys for the assignment of lentil germplasm to specific genetic groups. Finally, significant associations between markers and phenotypic data were identified. Overall, the results of this study are of major importance for lentil conservation genetics and breeding and provide insights on the lentil evolutionary history.
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Affiliation(s)
- Stefano Pavan
- Department of Soil, Plant and Food Science, Section of Genetics and Plant Breeding, University of Bari Aldo Moro, Bari, Italy.,Institute of Biomedical Technologies, National Research Council (CNR), Bari, Italy
| | - Nicoletta Bardaro
- Department of Soil, Plant and Food Science, Section of Genetics and Plant Breeding, University of Bari Aldo Moro, Bari, Italy
| | - Valentina Fanelli
- Department of Soil, Plant and Food Science, Section of Genetics and Plant Breeding, University of Bari Aldo Moro, Bari, Italy
| | - Angelo Raffaele Marcotrigiano
- Department of Soil, Plant and Food Science, Section of Genetics and Plant Breeding, University of Bari Aldo Moro, Bari, Italy
| | - Giacomo Mangini
- Department of Soil, Plant and Food Science, Section of Genetics and Plant Breeding, University of Bari Aldo Moro, Bari, Italy
| | - Francesca Taranto
- Department of Soil, Plant and Food Science, Section of Genetics and Plant Breeding, University of Bari Aldo Moro, Bari, Italy.,CREA Research Centre for Cereal and Industrial Crops (CREA-CI), Foggia, Italy
| | - Domenico Catalano
- Institute of Biomedical Technologies, National Research Council (CNR), Bari, Italy
| | - Cinzia Montemurro
- Department of Soil, Plant and Food Science, Section of Genetics and Plant Breeding, University of Bari Aldo Moro, Bari, Italy
| | - Claudio De Giovanni
- Department of Soil, Plant and Food Science, Section of Genetics and Plant Breeding, University of Bari Aldo Moro, Bari, Italy
| | - Concetta Lotti
- Department of Agricultural, Food and Environmental Sciences, University of Foggia, Foggia, Italy
| | - Luigi Ricciardi
- Department of Soil, Plant and Food Science, Section of Genetics and Plant Breeding, University of Bari Aldo Moro, Bari, Italy
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200
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When West Meets East: The Origins and Spread of Weedy Rice Between Continental and Island Southeast Asia. G3-GENES GENOMES GENETICS 2019; 9:2941-2950. [PMID: 31292156 PMCID: PMC6723143 DOI: 10.1534/g3.119.400021] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Weedy crop relatives are among the world’s most problematic agricultural weeds, and their ability to rapidly evolve can be enhanced by gene flow from both domesticated crop varieties and wild crop progenitor species. In this study, we examined the role of modern commercial crop cultivars, traditional landraces, and wild relatives in the recent emergence and proliferation of weedy rice in East Malaysia on the island of Borneo. This region of Malaysia is separated from the Asian continent by the South China Sea, and weedy rice has become a major problem there more recently than on the Malaysian peninsular mainland. Using 24 polymorphic SSR loci and genotype data from the awn-length domestication gene An-1, we assessed the genetic diversity, population structure and potential origins of East Malaysian weeds; 564 weedy, cultivated and wild rice accessions were analyzed from samples collected in East Malaysia, Peninsular Malaysia and neighboring countries. While there is considerable evidence for contributions of Peninsular Malaysian weed ecotypes to East Malaysian populations, we find that local crop cultivars and/or landraces from neighboring countries are also likely contributors to the weedy rice infestations. These findings highlight the implications of genetic admixture from different cultivar source populations in the spread of weedy crop relatives and the urgent need for preventive measurements to maintain sustainable crop yields.
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