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Peralta-Serrano M, Hernández JC, Guet R, González-Delgado S, Pérez-Sorribes L, Lopes EP, Pérez-Portela R. Population genomic structure of the sea urchin Diadema africanum, a relevant species in the rocky reef systems across the Macaronesian archipelagos. Sci Rep 2024; 14:22494. [PMID: 39341905 PMCID: PMC11439068 DOI: 10.1038/s41598-024-73354-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2024] [Accepted: 09/17/2024] [Indexed: 10/01/2024] Open
Abstract
The sea urchin Diadema africanum is a macro-herbivore found in the rocky reef systems of the West African region and Macaronesian archipelagos. Over several decades, high densities of this species have generated marine barrens in certain areas at the Canary Islands. In contrast, more recently, during the last few years, the species has suffered mass mortality events that continue to the present day. In this study, we used 9,109 Single Nucleotide Polymorphisms (SNPs) and a fragment of a mitochondrial gene to evaluate the species' population structure, effects of mass mortalities on its diversity, and potential local adaptation across the Canary Islands and Cabo Verde. Our research provides compelling evidence of low genomic diversity and homogeneity across the studied area for neutral markers, along with recent demographic fluctuations. The high connectivity among distant areas likely allows a rapid recovering of the populations from local mortality events. Interestingly, we also observed genomic sub-structure from 405 SNPs identified as candidate loci under selection for seawater temperature. The lack of divergence among distant sites and the low diversity found can be attributed to the species' divergence from a small ancestral genomic pool, followed by a contemporary demographic expansion, and ongoinggene flow.
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Affiliation(s)
- Marc Peralta-Serrano
- Departament de Biologia Evolutiva, Ecologia i Ciències Ambientals, Facultat de Biologia, Universitat de Barcelona (UB), Av. Diagonal 643, 08028, Barcelona, Spain
| | - José Carlos Hernández
- Marine Comunity Ecology and Conservation, Departamento de Biología Animal, Edafología y Geología, Faculty of Science (Biology), University of La Laguna, San Cristóbal de La Laguna, Tenerife, Canary Islands, Spain
| | - Romain Guet
- Departament de Biologia Evolutiva, Ecologia i Ciències Ambientals, Facultat de Biologia, Universitat de Barcelona (UB), Av. Diagonal 643, 08028, Barcelona, Spain
- Marine Comunity Ecology and Conservation, Departamento de Biología Animal, Edafología y Geología, Faculty of Science (Biology), University of La Laguna, San Cristóbal de La Laguna, Tenerife, Canary Islands, Spain
| | - Sara González-Delgado
- Departament de Biologia Evolutiva, Ecologia i Ciències Ambientals, Facultat de Biologia, Universitat de Barcelona (UB), Av. Diagonal 643, 08028, Barcelona, Spain
| | - Laia Pérez-Sorribes
- Departament de Biologia Evolutiva, Ecologia i Ciències Ambientals, Facultat de Biologia, Universitat de Barcelona (UB), Av. Diagonal 643, 08028, Barcelona, Spain
- Department of Ecology and Evolution, Estación Biológica de Doñana (CSIC), Seville, Spain
| | - Evandro P Lopes
- Instituto de Engenharias e Ciências do Mar, Universidade Técnica do Atlântico, C.P. 163, Mindelo, Republic of Cabo Verde
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, BIOPOLIS Program in Genomics, Biodiversity and Land Planning, Campus de Vairão, Universidade do Porto, 4485-661, Vairão, Portugal
| | - Rocio Pérez-Portela
- Departament de Biologia Evolutiva, Ecologia i Ciències Ambientals, Facultat de Biologia, Universitat de Barcelona (UB), Av. Diagonal 643, 08028, Barcelona, Spain.
- Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Barcelona, Spain.
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Spencer HG, Walter CB. Polymorphism and the Red Queen: the selective maintenance of allelic variation in a deteriorating environment. G3 (BETHESDA, MD.) 2024; 14:jkae107. [PMID: 38770661 PMCID: PMC11228834 DOI: 10.1093/g3journal/jkae107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2024] [Revised: 02/21/2024] [Accepted: 05/12/2024] [Indexed: 05/22/2024]
Abstract
Although allelic variation is ubiquitous in natural populations, our theoretical models are poor at predicting the existence and properties of these observed polymorphisms. In this study, inspired by Van Valen's Red Queen hypothesis, we modeled the effect of viability selection in a deteriorating environment on the properties of allelic variation in populations subject to recurrent mutation. In Monte Carlo simulations, we found that levels of polymorphism consistently built up over time. We censused the simulated populations after 10,000 generations of mutation and selection, revealing that, compared with models assuming a constant environment, the mean number of alleles was greater, as was the range of allele numbers. These results were qualitatively robust to the addition of genetic drift and to the relaxation of the assumption that the viabilities of phenogenotypes containing a new mutation are independent of each other (i.e. incorporating a model of generalized dominance). The broad range of allele numbers realized in the simulated populations-from monomorphisms to highly polymorphic populations-more closely corresponds to the observed range from numerous surveys of natural populations than previously found in theoretical studies. This match suggests that, contrary to the views of some writers, selection may actively maintain genetic variation in natural populations, particularly if the selective environment is gradually becoming harsher. Our simulations also generated many populations with heterozygote advantage, a mismatch with real data that implies that this selective property must arise extremely rarely in natural populations.
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Affiliation(s)
- Hamish G Spencer
- Department of Zoology, University of Otago, Dunedin 9054, New Zealand
| | - Callum B Walter
- Department of Zoology, University of Otago, Dunedin 9054, New Zealand
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Taylor CS, Lawson DJ. Heritability of complex traits in sub-populations experiencing bottlenecks and growth. J Hum Genet 2024; 69:329-335. [PMID: 38589509 PMCID: PMC11199143 DOI: 10.1038/s10038-024-01249-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2023] [Revised: 03/20/2024] [Accepted: 03/23/2024] [Indexed: 04/10/2024]
Abstract
Populations that have experienced a bottleneck are regularly used in Genome Wide Association Studies (GWAS) to investigate variants associated with complex traits. It is generally understood that these isolated sub-populations may experience high frequency of otherwise rare variants with large effect size, and therefore provide a unique opportunity to study said trait. However, the demographic history of the population under investigation affects all SNPs that determine the complex trait genome-wide, changing its heritability and genetic architecture. We use a simulation based approach to identify the impact of the demographic processes of drift, expansion, and migration on the heritability of complex trait. We show that demography has considerable impact on complex traits. We then investigate the power to resolve heritability of complex traits in GWAS studies subjected to demographic effects. We find that demography is an important component for interpreting inference of complex traits and has a nuanced impact on the power of GWAS. We conclude that demographic histories need to be explicitly modelled to properly quantify the history of selection on a complex trait.
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Affiliation(s)
| | - Daniel J Lawson
- School of Mathematics, University of Bristol, Bristol, UK.
- MRC Integrative Epidemiology Unit, Bristol Medical School, University of Bristol, Bristol, UK.
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Elidottir H, Bjarnadottir SR, Baldursson O, Jonsdottir B. Cystic fibrosis in Iceland and the high prevalence of the N1303K variant. Pediatr Pulmonol 2024; 59:1944-1951. [PMID: 38629430 DOI: 10.1002/ppul.27019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Revised: 03/22/2024] [Accepted: 04/08/2024] [Indexed: 07/22/2024]
Abstract
BACKGROUND Cystic fibrosis (CF) is most common in populations of Northern European ancestry where the F508del variant predominates. In 2020, Iceland became a member of the European Cystic Fibrosis Society Patient Registry, and we launched an epidemiological study of CF in Iceland. The study aimed to determine the prevalence and the genetic variants present in the country. Furthermore, we aimed to describe the previous and the current situation regarding lung function, infections, complications, treatment, and follow-up to understand the strengths and weaknesses of CF care in Iceland. METHODS This retrospective study included all individuals in Iceland with a confirmed CF diagnosis between 1955 and 2021. We conducted a medical records search for CF diagnosis codes and found 30 people with CF who were included in the study. Two hundred sixteen clinical variables were registered. A descriptive analysis of these was performed. RESULTS The prevalence of CF in Iceland is 0.372:10,000 inhabitants. The F508del is the most common CF transmembrane conductance regulator (CFTR) variant (46.4%), closely followed by N1303K (44.6%). Staphylococcus aureus was the most common airway pathogen, followed by Pseudomonas aeruginosa. Nasal polyps and CF-related diabetes were the most common complications. Modern CF medications, including the recent CFTR modulators, are available. CONCLUSION Even though Iceland has a relatively low prevalence of CF, it holds the highest known prevalence of the N1303K variant in Europe. Access to necessary treatment is satisfactory, but improvements are advisable for some aspects of the routine assessments by best practice guidelines.
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Affiliation(s)
- Helga Elidottir
- Children's Hospital, Landspitali-The National University Hospital of Iceland, Reykjavík, Iceland
- Department of Pediatrics, Institution of Clinical Sciences, Lund University, Lund, Sweden
- Department of Respiratory Medicine, Landspitali-The National University Hospital of Iceland, Reykjavik, Iceland
- Faculty of Medicine, The University of Iceland, Reykjavik, Iceland
| | | | - Olafur Baldursson
- Department of Respiratory Medicine, Landspitali-The National University Hospital of Iceland, Reykjavik, Iceland
- Faculty of Medicine, The University of Iceland, Reykjavik, Iceland
| | - Brynja Jonsdottir
- Department of Respiratory Medicine, Landspitali-The National University Hospital of Iceland, Reykjavik, Iceland
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Barkdull M, Moreau CS. Worker Reproduction and Caste Polymorphism Impact Genome Evolution and Social Genes Across the Ants. Genome Biol Evol 2023; 15:evad095. [PMID: 37243539 PMCID: PMC10287540 DOI: 10.1093/gbe/evad095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 05/16/2023] [Accepted: 05/23/2023] [Indexed: 05/29/2023] Open
Abstract
Eusocial insects are characterized by several traits, including reproductive division of labor and caste polymorphisms, which likely modulate genome evolution. Concomitantly, evolution may act on specific genes and pathways underlying these novel, sociality-associated phenotypes. Reproductive division of labor should increase the magnitude of genetic drift and reduce the efficacy of selection by reducing effective population size. Caste polymorphism has been associated with relaxed selection and may facilitate directional selection on caste-specific genes. Here, we use comparative analyses of 22 ant genomes to test how reproductive division of labor and worker polymorphism influence positive selection and selection intensity across the genome. Our results demonstrate that worker reproductive capacity is associated with a reduction in the degree of relaxed selection but is not associated with any significant change to positive selection. We find decreases in positive selection in species with polymorphic workers, but no increase in the degree of relaxed selection. Finally, we explore evolutionary patterns in specific candidate genes associated with our focal traits in eusocial insects. Two oocyte patterning genes previously implicated in worker sterility evolve under intensified selection in species with reproductive workers. Behavioral caste genes generally experience relaxed selection associated with worker polymorphism, whereas vestigial and spalt, both associated with soldier development in Pheidole ants, experience intensified selection in worker polymorphic species. These findings expand our understanding of the genetic mechanisms underlying elaborations of sociality. The impacts of reproductive division of labor and caste polymorphisms on specific genes illuminate those genes' roles in generating complex eusocial phenotypes.
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Affiliation(s)
- Megan Barkdull
- Department of Ecology & Evolutionary Biology, Cornell University
| | - Corrie S Moreau
- Department of Ecology & Evolutionary Biology, Cornell University
- Department of Entomology, Cornell University
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dos Santos ALC, Sullasi HSL, Gokcumen O, Lindo J, DeGiorgio M. Spatiotemporal fluctuations of population structure in the Americas revealed by a meta-analysis of the first decade of archaeogenomes. AMERICAN JOURNAL OF BIOLOGICAL ANTHROPOLOGY 2023; 180:703-714. [PMID: 39081397 PMCID: PMC11288623 DOI: 10.1002/ajpa.24673] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Accepted: 11/15/2022] [Indexed: 08/02/2024]
Abstract
Objectives Since 2010, genome-wide data from hundreds of ancient Native Americans have contributed to the understanding of Americas' prehistory. However, these samples have never been studied as a single dataset, and distinct relationships among themselves and with present-day populations may have never come to light. Here, we reassess genomic diversity and population structure of 223 ancient Native Americans published between 2010 and 2019. Materials and Methods The genomic data from ancient Americas was merged with a worldwide reference panel of 278 present-day genomes from the Simons Genome Diversity Project and then analyzed through ADMIXTURE, D-statistics, PCA, t-SNE, and UMAP. Results We find largely similar population structures in ancient and present-day Americas. However, the population structure of contemporary Native Americans, traced here to at least 10,000 years before present, is noticeably less diverse than their ancient counterparts, a possible outcome of the European contact. Additionally, in the past there were greater levels of population structure in North than in South America, except for ancient Brazil, which harbors comparatively high degrees of structure. Moreover, we find a component of genetic ancestry in the ancient dataset that is closely related to that of present-day Oceanic populations but does not correspond to the previously reported Australasian signal. Lastly, we report an expansion of the Ancient Beringian ancestry, previously reported for only one sample. Discussion Overall, our findings support a complex scenario for the settlement of the Americas, accommodating the occurrence of founder effects and the emergence of ancestral mixing events at the regional level.
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Affiliation(s)
- Andre Luiz Campelo dos Santos
- Department of Electrical Engineering and Computer Science, Florida Atlantic University, Boca Raton, Florida, USA
- Department of Archaeology, Federal University of Pernambuco, Recife, Pernambuco, Brazil
| | | | - Omer Gokcumen
- Department of Biological Sciences, University at Buffalo, Buffalo, New York, USA
| | - John Lindo
- Department of Anthropology, Emory University, Atlanta, Georgia, USA
| | - Michael DeGiorgio
- Department of Electrical Engineering and Computer Science, Florida Atlantic University, Boca Raton, Florida, USA
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Margawati ET, Putra WPB, Rizki M, Soetrisno E, Raadsma HW. Detection of carrier Booroola (Fec B) allele in BMPR1B gene of MEGA (Merino × Garut) sheep and its association with growth traits. J Genet Eng Biotechnol 2023; 21:19. [PMID: 36790660 PMCID: PMC9931984 DOI: 10.1186/s43141-023-00475-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Accepted: 01/27/2023] [Indexed: 02/16/2023]
Abstract
BACKGROUND Bone morphogenetic protein receptor 1B (BMPR1B) gene is one of candidate genes for reproductive and growth traits in sheep. The present study was aimed to detect the Booroola (FecB) allele in BMPR1B gene and its association with growth traits in MEGA (Merino × Garut) sheep. A total of 82DNA samples collected from individual lamb (mixed-sex) blood were genotyped for allelic polymorphism using a PCR-RFLP method. RESULTS The PCR analysis in BMPR1B gene resulted the amplicons with size of140 bp. The RFLP analysis with AvaII restriction enzymeresultedtwo allelic types of wildtype (A/Fec+) and mutant or Booroola (G/FecB) with frequency of 0.89 and 0.11, respectively. However, the genetic diversity in BMPR1B/AvaII gene of animal studies was categorized tolow category (PIC = 0.18)and under in a genetic equilibrium (χ2 = 1.25). CONCLUSIONS Itshowed us that carrying FecB allele in the heterozygous sheep were not associated with growth traits in MEGA sheep.
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Affiliation(s)
- Endang Tri Margawati
- Research Center for Applied Zoology, National Research and Innovation Agency (BRIN), Bogor, 16911, Indonesia.
| | - Widya Pintaka Bayu Putra
- Research Center for Applied Zoology, National Research and Innovation Agency (BRIN), Bogor, 16911 Indonesia
| | - Muhammad Rizki
- grid.443165.10000 0001 0096 1344Department of Animal Science, Faculty of Agriculture, University of Bengkulu, Bengkulu, 38371 Indonesia
| | - Edi Soetrisno
- grid.443165.10000 0001 0096 1344Department of Animal Science, Faculty of Agriculture, University of Bengkulu, Bengkulu, 38371 Indonesia
| | - Herman Willem Raadsma
- grid.1013.30000 0004 1936 834XCenter for Advanced Technologies for Animal Genetics and Reproduction, Faculty of Veterinary Science, University of Sydney, Camden, NSW 2006 Australia
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Männer L, Mundinger C, Haase M. Stay in shape: Assessing the adaptive potential of shell morphology and its sensitivity to temperature in the invasive New Zealand mud snail Potamopyrgus antipodarum through phenotypic plasticity and natural selection in Europe. Ecol Evol 2022; 12:e9314. [PMID: 36203624 PMCID: PMC9526036 DOI: 10.1002/ece3.9314] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Revised: 08/09/2022] [Accepted: 08/19/2022] [Indexed: 11/16/2022] Open
Abstract
Climate change may force organisms to adapt genetically or plastically to new environmental conditions. Invasive species show remarkable potential for rapid adaptation. The ovoviviparous New Zealand mud snail (NZMS), Potamopyrgus antipodarum, has successfully established across Europe with two clonally reproducing mitochondrial lineages since its arrival in the first half of the 19th century. Its remarkable variation in shell morphology was shown to be fitness relevant. We investigated the effects of temperature on shell morphology across 11 populations from Germany and the Iberian Peninsula in a common garden across three temperatures. We analyzed size and shape using geometric morphometrics. For both, we compared reaction norms and estimated heritabilities. For size, the interaction of temperature and haplotype explained about 50% of the total variance. We also observed more genotype by environment interactions indicating a higher degree of population differentiation than in shape. Across the three temperatures, size followed the expectations of the temperature-size rule, with individuals growing larger in cold environments. Changes in shape may have compensated for changes in size affecting space for brooding embryos. Heritability estimates were relatively high. As indicated by the very low coefficients of variation for clonal repeatability (CV A ), they can probably not be compared in absolute terms. However, they showed some sensitivity to temperature, in haplotype t more so than in z, which was only found in Portugal. The low CV A values indicate that genetic variation among European populations is still restricted with a low potential to react to selection. A considerable fraction of the genetic variation was due to differences between the clonal lineages. The NZMS has apparently not been long enough in Europe to accumulate significant genetic variation relevant for morphological adaptation. As temperature is obviously not the sole factor influencing shell morphology, their interaction will probably not be a factor limiting population persistence under a warming climate in Europe.
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Affiliation(s)
- Lisa Männer
- AG Vogelwarte, Zoological Institute and MuseumUniversity of GreifswaldGreifswaldGermany
| | - Carolin Mundinger
- AG Applied Zoology and Nature Conservation, Zoological Institute and MuseumUniversity of GreifswaldGreifswaldGermany
| | - Martin Haase
- AG Vogelwarte, Zoological Institute and MuseumUniversity of GreifswaldGreifswaldGermany
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Mansour H, Alsamadany H, Al-Hasawi ZM. Molecular Assessment of Genetic Diversity and Genetic Structure of Rhanterium epapposum Oliv. in Scarce Populations in Some Regions of Western Saudi Arabia. PLANTS 2022; 11:plants11121560. [PMID: 35736710 PMCID: PMC9230628 DOI: 10.3390/plants11121560] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Revised: 06/06/2022] [Accepted: 06/07/2022] [Indexed: 11/16/2022]
Abstract
Rhanterium epapposum Oliv. is a perennial medicinal shrub growing mainly in desert habitats in the Arabian Peninsula. In western Saudi Arabia, the remaining few populations of this species are exposed to many threats, including overcutting, overgrazing, and recently, increasing human activities. These threats are predicted to be exacerbated by the advancement of aridification caused by climate change. The conservation and recovering of the diminished populations of R. epapposum necessitate measurement of their genetic diversity and genetic differentiation. To accomplish this objective, we tested 150 simple sequence repeat (SSR) primer pairs, with which 40 polymorphic loci were identified. These polymorphic loci were used to determine the population genetics of 540 plant accessions sampled from a total of 45 populations of R. epapposum located in 8 sites in western Saudi Arabia: Wadi Khurieba, Wadi Al Khamas, Gebel Al Twaal, Al Asaafer, Wadi ALHamda, Wadi Al Nassayeif, Wadi Qaraba, Wadi Kuliayah, and Wadi Dahban. Low levels of genetic diversity were found in all populations (the values of the PPL ranged between 52.5 and 15) along with a declined value of HT (0.123) and a considerable inbreeding value (F = 0.942), which confirmed a noticeable shortage of heterozygotes. High genetic differentiation among the populations and a low value of gene flow are indicative of high isolation among the R. epapposum populations, which has caused a severe deficiency in gene migration. The data obtained herein inspire several recommendations for conservation and retrieval of the existing populations, including seed banks, restoration of diminished populations, and monitoring and prevention of cutting and grazing activities at threatened sites. All of these measures are urgently required to avoid imminent extinction.
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Affiliation(s)
- Hassan Mansour
- Department of Biological Sciences, College of Science & Arts, King Abdulaziz University, Rabigh 21911, Saudi Arabia;
- Department of Botany, Faculty of Science, Suez Canal University, Ismailia 41522, Egypt
- Correspondence: ; Tel.: +96-65-0674-1048
| | - Hameed Alsamadany
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia;
| | - Zaki M. Al-Hasawi
- Department of Biological Sciences, College of Science & Arts, King Abdulaziz University, Rabigh 21911, Saudi Arabia;
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia;
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Li F, Rane RV, Luria V, Xiong Z, Chen J, Li Z, Catullo RA, Griffin PC, Schiffer M, Pearce S, Lee SF, McElroy K, Stocker A, Shirriffs J, Cockerell F, Coppin C, Sgrò CM, Karger A, Cain JW, Weber JA, Santpere G, Kirschner MW, Hoffmann AA, Oakeshott JG, Zhang G. Phylogenomic analyses of the genus Drosophila reveals genomic signals of climate adaptation. Mol Ecol Resour 2022; 22:1559-1581. [PMID: 34839580 PMCID: PMC9299920 DOI: 10.1111/1755-0998.13561] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Accepted: 11/10/2021] [Indexed: 01/13/2023]
Abstract
Many Drosophila species differ widely in their distributions and climate niches, making them excellent subjects for evolutionary genomic studies. Here, we have developed a database of high-quality assemblies for 46 Drosophila species and one closely related Zaprionus. Fifteen of the genomes were newly sequenced, and 20 were improved with additional sequencing. New or improved annotations were generated for all 47 species, assisted by new transcriptomes for 19. Phylogenomic analyses of these data resolved several previously ambiguous relationships, especially in the melanogaster species group. However, it also revealed significant phylogenetic incongruence among genes, mainly in the form of incomplete lineage sorting in the subgenus Sophophora but also including asymmetric introgression in the subgenus Drosophila. Using the phylogeny as a framework and taking into account these incongruences, we then screened the data for genome-wide signals of adaptation to different climatic niches. First, phylostratigraphy revealed relatively high rates of recent novel gene gain in three temperate pseudoobscura and five desert-adapted cactophilic mulleri subgroup species. Second, we found differing ratios of nonsynonymous to synonymous substitutions in several hundred orthologues between climate generalists and specialists, with trends for significantly higher ratios for those in tropical and lower ratios for those in temperate-continental specialists respectively than those in the climate generalists. Finally, resequencing natural populations of 13 species revealed tropics-restricted species generally had smaller population sizes, lower genome diversity and more deleterious mutations than the more widespread species. We conclude that adaptation to different climates in the genus Drosophila has been associated with large-scale and multifaceted genomic changes.
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Affiliation(s)
- Fang Li
- BGI‐ShenzhenShenzhenChina
- Section for Ecology and EvolutionDepartment of BiologyUniversity of CopenhagenCopenhagenDenmark
| | - Rahul V. Rane
- Commonwealth Scientific and Industrial Research OrganisationActonACTAustralia
- Bio21 InstituteSchool of BioSciencesUniversity of MelbourneParkvilleVic.Australia
| | - Victor Luria
- Department of Systems BiologyHarvard Medical SchoolBostonMassachusettsUSA
| | - Zijun Xiong
- BGI‐ShenzhenShenzhenChina
- State Key Laboratory of Genetic Resources and EvolutionKunming Institute of ZoologyChinese Academy of Sciences (CAS)KunmingYunnanChina
- College of Life SciencesUniversity of Chinese Academy of SciencesBeijingChina
| | | | | | - Renee A. Catullo
- Commonwealth Scientific and Industrial Research OrganisationActonACTAustralia
- Division of Ecology and EvolutionCentre for Biodiversity AnalysisThe Australian National UniversityActonACTAustralia
| | - Philippa C. Griffin
- Bio21 InstituteSchool of BioSciencesUniversity of MelbourneParkvilleVic.Australia
| | - Michele Schiffer
- Bio21 InstituteSchool of BioSciencesUniversity of MelbourneParkvilleVic.Australia
- Daintree Rainforest ObservatoryJames Cook UniversityCape TribulationQldAustralia
| | - Stephen Pearce
- Commonwealth Scientific and Industrial Research OrganisationActonACTAustralia
| | - Siu Fai Lee
- Commonwealth Scientific and Industrial Research OrganisationActonACTAustralia
- Applied BioSciencesMacquarie UniversityNorth RydeNSWAustralia
| | - Kerensa McElroy
- Commonwealth Scientific and Industrial Research OrganisationActonACTAustralia
| | - Ann Stocker
- Bio21 InstituteSchool of BioSciencesUniversity of MelbourneParkvilleVic.Australia
| | - Jennifer Shirriffs
- Bio21 InstituteSchool of BioSciencesUniversity of MelbourneParkvilleVic.Australia
| | - Fiona Cockerell
- School of Biological SciencesMonash UniversityClaytonVic.Australia
| | - Chris Coppin
- Commonwealth Scientific and Industrial Research OrganisationActonACTAustralia
| | - Carla M. Sgrò
- School of Biological SciencesMonash UniversityClaytonVic.Australia
| | - Amir Karger
- IT ‐ Research ComputingHarvard Medical SchoolBostonMassachusettsUSA
| | - John W. Cain
- Department of MathematicsHarvard UniversityCambridgeMassachusettsUSA
| | - Jessica A. Weber
- Department of GeneticsHarvard Medical SchoolBostonMassachusettsUSA
| | - Gabriel Santpere
- Neurogenomics Group, Research Programme on Biomedical Informatics (GRIB)Department of Experimental and Health Sciences (DCEXS)Hospital del Mar Medical Research Institute (IMIM)Universitat Pompeu FabraBarcelonaCataloniaSpain
| | - Marc W. Kirschner
- Department of Systems BiologyHarvard Medical SchoolBostonMassachusettsUSA
| | - Ary A. Hoffmann
- Bio21 InstituteSchool of BioSciencesUniversity of MelbourneParkvilleVic.Australia
| | - John G. Oakeshott
- Commonwealth Scientific and Industrial Research OrganisationActonACTAustralia
- Applied BioSciencesMacquarie UniversityNorth RydeNSWAustralia
| | - Guojie Zhang
- BGI‐ShenzhenShenzhenChina
- Section for Ecology and EvolutionDepartment of BiologyUniversity of CopenhagenCopenhagenDenmark
- State Key Laboratory of Genetic Resources and EvolutionKunming Institute of ZoologyChinese Academy of Sciences (CAS)KunmingYunnanChina
- Center for Excellence in Animal Evolution and GeneticsChinese Academy of SciencesKunmingChina
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11
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Sabatino SJ, Pereira P, Carneiro M, Dilytė J, Archer JP, Munoz A, Nonnis-Marzano F, Murias A. The genetics of adaptation in freshwater Eurasian shad ( Alosa). Ecol Evol 2022; 12:e8908. [PMID: 35646309 PMCID: PMC9130566 DOI: 10.1002/ece3.8908] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Accepted: 04/19/2022] [Indexed: 11/10/2022] Open
Abstract
Studying the genetics of phenotypic convergence can yield important insights into adaptive evolution. Here, we conducted a comparative genomic study of four lineages (species and subspecies) of anadromous shad (Alosa) that have independently evolved life cycles entirely completed in freshwater. Three naturally diverged (A. fallax lacustris, A. f. killarnensis, and A. macedonica), and the fourth (A. alosa) was artificially landlocked during the last century. To conduct this analysis, we assembled and annotated a draft of the A. alosa genome and generated whole‐genome sequencing for 16 anadromous and freshwater populations of shad. Widespread evidence for parallel genetic changes in freshwater populations within lineages was found. In freshwater A. alosa, which have only been diverging for tens of generations, this shows that parallel adaptive evolution can rapidly occur. However, parallel genetic changes across lineages were comparatively rare. The degree of genetic parallelism was not strongly related to the number of shared polymorphisms between lineages, thus suggesting that other factors such as divergence among ancestral populations or environmental variation may influence genetic parallelism across these lineages. These overall patterns were exemplified by genetic differentiation involving a paralog of ATPase‐α1 that appears to be under selection in just two of the more distantly related lineages studied, A. f. lacustris and A. alosa. Our findings provide insights into the genetic architecture of adaptation and parallel evolution along a continuum of population divergence.
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Affiliation(s)
- Stephen J Sabatino
- CIBIO - Centro de Investigação em Biodiversidade e Recursos Genéticos Universidade do Porto Vairão Portugal.,BIOPOLIS - Program in Genomics, Biodiversity and Land Planning CIBIO Vairão Portugal.,Departamento de Biologia Faculdade de Ciências Universidade do Porto Porto Portugal
| | - Paulo Pereira
- CIBIO - Centro de Investigação em Biodiversidade e Recursos Genéticos Universidade do Porto Vairão Portugal.,BIOPOLIS - Program in Genomics, Biodiversity and Land Planning CIBIO Vairão Portugal.,Departamento de Biologia Faculdade de Ciências Universidade do Porto Porto Portugal
| | - Miguel Carneiro
- CIBIO - Centro de Investigação em Biodiversidade e Recursos Genéticos Universidade do Porto Vairão Portugal.,BIOPOLIS - Program in Genomics, Biodiversity and Land Planning CIBIO Vairão Portugal.,Departamento de Biologia Faculdade de Ciências Universidade do Porto Porto Portugal
| | - Jolita Dilytė
- CIBIO - Centro de Investigação em Biodiversidade e Recursos Genéticos Universidade do Porto Vairão Portugal.,BIOPOLIS - Program in Genomics, Biodiversity and Land Planning CIBIO Vairão Portugal
| | - John Patrick Archer
- CIBIO - Centro de Investigação em Biodiversidade e Recursos Genéticos Universidade do Porto Vairão Portugal.,BIOPOLIS - Program in Genomics, Biodiversity and Land Planning CIBIO Vairão Portugal
| | - Antonio Munoz
- CIBIO - Centro de Investigação em Biodiversidade e Recursos Genéticos Universidade do Porto Vairão Portugal.,BIOPOLIS - Program in Genomics, Biodiversity and Land Planning CIBIO Vairão Portugal
| | - Francesco Nonnis-Marzano
- Departamento de Biologia Faculdade de Ciências Universidade do Porto Porto Portugal.,Department of Chemistry, Life Sciences and Environmental Sustainability Università di Parma Parma Italy
| | - Antonio Murias
- CIBIO - Centro de Investigação em Biodiversidade e Recursos Genéticos Universidade do Porto Vairão Portugal.,BIOPOLIS - Program in Genomics, Biodiversity and Land Planning CIBIO Vairão Portugal.,Departamento de Biologia Faculdade de Ciências Universidade do Porto Porto Portugal
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12
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O'Leary SJ, Hollenbeck CM, Vega RR, Portnoy DS. Disentangling complex genomic signals to understand population structure of an exploited, estuarine-dependent flatfish. Ecol Evol 2021; 11:13415-13429. [PMID: 34646479 PMCID: PMC8495835 DOI: 10.1002/ece3.8064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2021] [Revised: 07/19/2021] [Accepted: 08/09/2021] [Indexed: 11/17/2022] Open
Abstract
Interpreting contemporary patterns of population structure requires an understanding of the interactions among microevolutionary forces and past demographic events. Here, 4,122 SNP-containing loci were used to assess structure in southern flounder (Paralichthys lethostigma) sampled across its range in the US Atlantic Ocean (Atlantic) and Gulf of Mexico (Gulf) and relationships among components of genomic variation and spatial and environmental variables were assessed across estuarine population samples in the Gulf. While hierarchical amova revealed significant heterogeneity within and between the Atlantic and Gulf, pairwise comparisons between samples within ocean basins demonstrated that all significant heterogeneity occurred within the Gulf. The distribution of Tajima's D estimated at a genome-wide scale differed significantly from equilibrium in all estuaries, with more negative values occurring in the Gulf. Components of genomic variation were significantly associated with environmental variables describing individual estuaries, and environment explained a larger component of variation than spatial proximity. Overall, results suggest that there is genetic spatial autocorrelation caused by shared larval sources for proximal nurseries (migration/drift), but that it is modified by environmentally driven differentiation (selection). This leads to conflicting signals in different parts of the genome and creates patterns of divergence that do not correspond to paradigms of strong local directional selection.
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Affiliation(s)
| | - Christopher M. Hollenbeck
- Marine Genomics LaboratoryDepartment of Life SciencesTexas A&M University Corpus ChristiCorpus ChristiTexasUSA
| | - Robert R. Vega
- CCA Marine Development CenterTexas Parks and Wildlife DepartmentCorpus ChristiTexasUSA
| | - David S. Portnoy
- Marine Genomics LaboratoryDepartment of Life SciencesTexas A&M University Corpus ChristiCorpus ChristiTexasUSA
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13
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Jiménez-Ramírez A, Grivet D, Robledo-Arnuncio JJ. Measuring recent effective gene flow among large populations in Pinus sylvestris: Local pollen shedding does not preclude substantial long-distance pollen immigration. PLoS One 2021; 16:e0255776. [PMID: 34388195 PMCID: PMC8362938 DOI: 10.1371/journal.pone.0255776] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Accepted: 07/26/2021] [Indexed: 11/18/2022] Open
Abstract
The estimation of recent gene flow rates among vast and often weakly genetically differentiated tree populations remains a great challenge. Yet, empirical information would help understanding the interaction between gene flow and local adaptation in present-day non-equilibrium forests. We investigate here recent gene flow rates between two large native Scots pine (Pinus sylvestris L.) populations in central Iberian Peninsula (Spain), which grow on contrasting edaphic conditions six kilometers apart from each other and show substantial quantitative trait divergence in common garden experiments. Using a sample of 1,200 adult and offspring chloroplast-microsatellite haplotypes and a Bayesian inference model, we estimated substantial male gametic gene flow rates (8 and 21%) between the two natural populations, and even greater estimated immigration rates (42 and 64%) from nearby plantations into the two natural populations. Our results suggest that local pollen shedding within large tree populations does not preclude long-distance pollen immigration from large external sources, supporting the role of gene flow as a homogenizing evolutionary force contributing to low molecular genetic differentiation among populations of widely distributed wind-pollinated species. Our results also indicate the high potential for reproductive connectivity in large fragmented populations of wind-pollinated trees, and draw attention to a potential scenario of adaptive genetic divergence in quantitative traits under high gene flow.
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Affiliation(s)
- Azucena Jiménez-Ramírez
- Department of Forest Ecology & Genetics, Forest Research Center (INIA, CSIC), Madrid, Spain
- Department of Genetics, Faculty of Biological Sciences, Complutense University of Madrid, Madrid, Spain
- * E-mail: (JJRA); (AJR)
| | - Delphine Grivet
- Department of Forest Ecology & Genetics, Forest Research Center (INIA, CSIC), Madrid, Spain
| | - Juan José Robledo-Arnuncio
- Department of Forest Ecology & Genetics, Forest Research Center (INIA, CSIC), Madrid, Spain
- * E-mail: (JJRA); (AJR)
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14
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Ye H, Wang Z, Hou H, Wu J, Gao Y, Han W, Ru W, Sun G, Wang Y. Localized environmental heterogeneity drives the population differentiation of two endangered and endemic Opisthopappus Shih species. BMC Ecol Evol 2021; 21:56. [PMID: 33858342 PMCID: PMC8050911 DOI: 10.1186/s12862-021-01790-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Accepted: 04/08/2021] [Indexed: 12/03/2022] Open
Abstract
BACKGROUND Climate heterogeneity not only indirectly shapes the genetic structures of plant populations, but also drives adaptive divergence by impacting demographic dynamics. The variable localized climates and topographic complexity of the Taihang Mountains make them a major natural boundary in Northern China that influences the divergence of organisms distributed across this region. Opisthopappus is an endemic genus of the Taihang Mountains that includes only two spatially partitioned species Opisthopappus longilobus and Opisthopappus taihangensis. For this study, the mechanisms behind the genetic variations in Opisthopappus populations were investigated. RESULTS Using SNP and InDel data coupled with geographic and climatic information, significant genetic differentiation was found to exist either between Opisthopappus populations or two species. All studied populations were divided into two genetic groups with the differentiation of haplotypes between the groups. At approximately 17.44 Ma of the early Miocene, O. taihangensis differentiated from O. longilobus under differing precipitation regimes due to the intensification of the Asian monsoon. Subsequently, intraspecific divergence might be induced by the dramatic climatic transformation from the mid- to late Miocene. During the Pleistocene period, the rapid uplift of the Taihang Mountains coupled with violent climatic oscillations would further promote the diversity of the two species. Following the development of the Taihang Mountains, its complex topography created geographical and ecological heterogeneity, which could lead to spatiotemporal isolation between the Opisthopappus populations. Thus the adaptive divergence might occur within these intraspecific populations in the localized heterogeneous environment of the Taihang Mountains. CONCLUSIONS The localized environmental events through the integration of small-scale spatial effects impacted the demographic history and differentiation mechanism of Opisthopappus species in the Taihang Mountains. The results provide useful information for us to understand the ecology and evolution of organisms in the mountainous environment from population and species perspective.
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Affiliation(s)
- Hang Ye
- College of Life Science, Shanxi Normal University, Linfen, China
| | - Zhi Wang
- College of Life Science, Shanxi Normal University, Linfen, China
| | - Huimin Hou
- College of Life Science, Shanxi Normal University, Linfen, China
| | - Jiahui Wu
- College of Life Science, Shanxi Normal University, Linfen, China
- Changzhi University, Changzhi, China
| | - Yue Gao
- College of Life Science, Shanxi Normal University, Linfen, China
| | - Wei Han
- College of Life Science, Shanxi Normal University, Linfen, China
| | | | - Genlou Sun
- Saint Mary's University, Halifax, Canada
| | - Yiling Wang
- College of Life Science, Shanxi Normal University, Linfen, China.
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15
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Muñoz-Pajares AJ, Abdelaziz M, Picó FX. Temporal migration rates affect the genetic structure of populations in the biennial Erysimum mediohispanicum with reproductive asynchrony. AOB PLANTS 2020; 12:plaa037. [PMID: 32904355 PMCID: PMC7454028 DOI: 10.1093/aobpla/plaa037] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Accepted: 07/20/2020] [Indexed: 05/06/2023]
Abstract
Migration is a process with important implications for the genetic structure of populations. However, there is an aspect of migration seldom investigated in plants: migration between temporally isolated groups of individuals within the same geographic population. The genetic implications of temporal migration can be particularly relevant for semelparous organisms, which are those that reproduce only once in a lifetime after a certain period of growth. In this case, reproductive asynchrony in individuals of the same population generates demes of individuals differing in their developmental stage (non-reproductive and reproductive). These demes are connected by temporal migrants, that is, individuals that become annually asynchronous with respect to the rest of individuals of their same deme. Here, we investigated the extent of temporal migration and its effects on temporal genetic structure in the biennial plant Erysimum mediohispanicum. To this end, we conducted two independent complementary approaches. First, we empirically estimated temporal migration rates and temporal genetic structure in four populations of E. mediohispanicum during three consecutive years using nuclear microsatellites markers. Second, we developed a demographic genetic simulation model to assess genetic structure for different migration scenarios differing in temporal migration rates and their occurrence probabilities. We hypothesized that genetic structure decreased with increasing temporal migration rates due to the homogenizing effect of migration. Empirical and modelling results were consistent and indicated a U-shape relationship between genetic structure and temporal migration rates. Overall, they indicated the existence of temporal genetic structure and that such genetic structure indeed decreased with increasing temporal migration rates. However, genetic structure increased again at high temporal migration rates. The results shed light into the effects of reproductive asynchrony on important population genetic parameters. Our study contributes to unravel the complexity of some processes that may account for genetic diversity and genetic structure of natural populations.
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Affiliation(s)
- A Jesús Muñoz-Pajares
- Departamento de Genética, Universidad de Granada, Granada, Spain
- Research Center in Biodiversity and Genetic Resources (CIBIO), Campus Agrário de Vairão, Vairão, Portugal
- Corresponding author’s e-mail address:
| | - Mohamed Abdelaziz
- Departamento de Genética, Universidad de Granada, Granada, Spain
- Biological and Environmental Sciences, School of Natural Sciences, University of Stirling, Stirling, UK
| | - F Xavier Picó
- Departamento de Ecología Integrativa, Estación Biológica de Doñana (EBD), Consejo Superior de Investigaciones Científicas (CSIC), Sevilla, Spain
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16
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Asao S, Hayes L, Aspinwall MJ, Rymer PD, Blackman C, Bryant CJ, Cullerne D, Egerton JJG, Fan Y, Innes P, Millar AH, Tucker J, Shah S, Wright IJ, Yvon-Durocher G, Tissue D, Atkin OK. Leaf trait variation is similar among genotypes of Eucalyptus camaldulensis from differing climates and arises in plastic responses to the seasons rather than water availability. THE NEW PHYTOLOGIST 2020; 227:780-793. [PMID: 32255508 DOI: 10.1111/nph.16579] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Accepted: 03/20/2020] [Indexed: 06/11/2023]
Abstract
We used a widely distributed tree Eucalyptus camaldulensis subsp. camaldulensis to partition intraspecific variation in leaf functional traits to genotypic variation and phenotypic plasticity. We examined if genotypic variation is related to the climate of genotype provenance and whether phenotypic plasticity maintains performance in a changing environment. Ten genotypes from different climates were grown in a common garden under watering treatments reproducing the wettest and driest edges of the subspecies' distribution. We measured functional traits reflecting leaf metabolism and associated with growth (respiration rate, nitrogen and phosphorus concentrations, and leaf mass per area) and performance proxies (aboveground biomass and growth rate) each season over a year. Genotypic variation contributed substantially to the variation in aboveground biomass but much less in growth rate and leaf traits. Phenotypic plasticity was a large source of the variation in leaf traits and performance proxies and was greater among sampling dates than between watering treatments. The variation in leaf traits was weakly correlated to performance proxies, and both were unrelated to the climate of genotype provenance. Intraspecific variation in leaf traits arises similarly among genotypes in response to seasonal environmental variation, instead of long-term water availability or climate of genotype provenance.
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Affiliation(s)
- Shinichi Asao
- Australian Research Council Centre of Excellence in Plant Energy Biology, Research School of Biology, The Australian National University, Building 134, Canberra, ACT, 2601, Australia
| | - Lucy Hayes
- Australian Research Council Centre of Excellence in Plant Energy Biology, Research School of Biology, The Australian National University, Building 134, Canberra, ACT, 2601, Australia
| | - Michael J Aspinwall
- Hawkesbury Institute for the Environment, Western Sydney University, Locked Bag 1797, Penrith, NSW, 2751, Australia
- Department of Biology, University of North Florida, 1 UNF Drive, Jacksonville, FL, 32224, USA
| | - Paul D Rymer
- Hawkesbury Institute for the Environment, Western Sydney University, Locked Bag 1797, Penrith, NSW, 2751, Australia
| | - Chris Blackman
- Hawkesbury Institute for the Environment, Western Sydney University, Locked Bag 1797, Penrith, NSW, 2751, Australia
| | - Callum J Bryant
- Australian Research Council Centre of Excellence in Plant Energy Biology, Research School of Biology, The Australian National University, Building 134, Canberra, ACT, 2601, Australia
| | - Darren Cullerne
- Australian Research Council Centre of Excellence in Plant Energy Biology, Research School of Biology, The Australian National University, Building 134, Canberra, ACT, 2601, Australia
| | - John J G Egerton
- Australian Research Council Centre of Excellence in Plant Energy Biology, Research School of Biology, The Australian National University, Building 134, Canberra, ACT, 2601, Australia
| | - Yuzhen Fan
- Australian Research Council Centre of Excellence in Plant Energy Biology, Research School of Biology, The Australian National University, Building 134, Canberra, ACT, 2601, Australia
| | - Peter Innes
- Australian Research Council Centre of Excellence in Plant Energy Biology, Research School of Biology, The Australian National University, Building 134, Canberra, ACT, 2601, Australia
| | - A Harvey Millar
- Australian Research Council Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, University of Western Australia, Perth, WA, 6009, Australia
| | - Josephine Tucker
- Australian Research Council Centre of Excellence in Plant Energy Biology, Research School of Biology, The Australian National University, Building 134, Canberra, ACT, 2601, Australia
| | - Shahen Shah
- Australian Research Council Centre of Excellence in Plant Energy Biology, Research School of Biology, The Australian National University, Building 134, Canberra, ACT, 2601, Australia
- The University of Agriculture Peshawar, Khyber Pakhtunkhwa, 25130, Pakistan
| | - Ian J Wright
- Department of Biological Sciences, Macquarie University, North Ryde, NSW, 2109, Australia
| | - Gabriel Yvon-Durocher
- Environment and Sustainability Institute, University of Exeter, Penryn, Cornwall, TR10 9EZ, UK
| | - David Tissue
- Hawkesbury Institute for the Environment, Western Sydney University, Locked Bag 1797, Penrith, NSW, 2751, Australia
| | - Owen K Atkin
- Australian Research Council Centre of Excellence in Plant Energy Biology, Research School of Biology, The Australian National University, Building 134, Canberra, ACT, 2601, Australia
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Meléndez-Rosa J, Bi K, Lacey EA. Mating system is correlated with immunogenetic diversity in sympatric species of Peromyscine mice. PLoS One 2020; 15:e0236084. [PMID: 32701975 PMCID: PMC7377423 DOI: 10.1371/journal.pone.0236084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Accepted: 06/29/2020] [Indexed: 11/18/2022] Open
Abstract
The number of reproductive partners per individual varies markedly across animal mating systems. This variation may be an important determinant of patterns of immunogenetic diversity, particularly at Major Histocompatibility Complex (MHC) Class I and II loci. To compare immunogenetic variation in taxa with markedly different mating systems, we used RNAseq-generated data to quantify genotypic diversity in three species of Peromyscine rodents: the monogamous California mouse (Peromyscus californicus) and the polygynandrous deer mouse (P. maniculatus) and brush mouse (P. boylii). By sampling populations of these species from multiple localities in California, we were able to conduct replicated analyses of the relationship between mating system and immunogenetic variation. Across the four localities sampled, diversity at MHC Class I and II genes was consistently higher in the two polygynandrous species. We found no evidence that sampling location (i.e., variation in habitat conditions) contributed to observed differences in MHC variation among populations or species. Collectively, our data indicate that immunogenetic variation in Peromyscine mice is associated with reproductive behavior, rather than geographic locality or habitat type. The consistently greater variability detected in the polygynandrous species examined suggests that balancing selection imposed by behaviorally-mediated pathogen exposure is important in maintaining variation at MHC genes in these animals.
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Affiliation(s)
- Jesyka Meléndez-Rosa
- Department of Integrative Biology, University of California, Berkeley, California, United States of America
- Museum of Vertebrate Zoology, University of California, Berkeley, California, United States of America
| | - Ke Bi
- Museum of Vertebrate Zoology, University of California, Berkeley, California, United States of America
- Computational Genomics Resource Laboratory, University of California, Berkeley, California, United States of America
| | - Eileen A. Lacey
- Department of Integrative Biology, University of California, Berkeley, California, United States of America
- Museum of Vertebrate Zoology, University of California, Berkeley, California, United States of America
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Mansour H, Alsamadany H, Al-Hasawi ZM. Genetic diversity and genetic structure of Salvadora persica L., rare plant species in Rabigh province, Saudi Arabia: implications for conservation. JOURNAL OF TAIBAH UNIVERSITY FOR SCIENCE 2020. [DOI: 10.1080/16583655.2020.1787640] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Affiliation(s)
- Hassan Mansour
- Department of Biological Sciences, Rabigh-College of Science & Art, King Abdulaziz University, Rabigh, Saudi Arabia
- Department of Botany, Faculty of Science, Suez Canal University, Ismailia, Egypt
| | - Hameed Alsamadany
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Zaki M. Al-Hasawi
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
- Department of Biological Sciences, Rabigh-College of Science & Art, King Abdulaziz University, Rabigh, Saudi Arabia
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19
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Macrogeographic genetic structure of Lutzomyia longipalpis complex populations using Next Generation Sequencing. PLoS One 2019; 14:e0223277. [PMID: 31581227 PMCID: PMC6776309 DOI: 10.1371/journal.pone.0223277] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Accepted: 09/17/2019] [Indexed: 01/15/2023] Open
Abstract
Lutzomyia longipalpis is the main vector of Leishmania infantum, the causative agent of visceral leishmaniasis in the Neotropical realm. Its taxonomic status has been widely discussed once it encompasses a complex of species. The knowledge about the genetic structure of insect vector populations helps the elucidation of components and interactions of the disease ecoepidemiology. Thus, the objective of this study was to genotypically analyze populations of the Lu. longipalpis complex from a macrogeographic perspective using Next Generation Sequencing. Polymorphism analysis of three molecular markers was used to access the levels of population genetic structure among nine different populations of sand flies. Illumina Amplicon Sequencing Protocol® was used to identify possible polymorphic sites. The library was sequenced on paired-end Illumina MiSeq platform. Significant macrogeographical population differentiation was observed among Lu. longipalpis populations via PCA and DAPC analyses. Our results revealed that populations of Lu. longipalpis from the nine municipalities were grouped into three clusters. In addition, it was observed that the levels of Lu. longipalpis population structure could be associated with distance isolation. This new sequencing method allowed us to study different molecular markers after a single sequencing run, and to evaluate population and inter-species differences on a macrogeographic scale.
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21
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Korinsak S, Tangphatsornruang S, Pootakham W, Wanchana S, Plabpla A, Jantasuriyarat C, Patarapuwadol S, Vanavichit A, Toojinda T. Genome-wide association mapping of virulence gene in rice blast fungus Magnaporthe oryzae using a genotyping by sequencing approach. Genomics 2018; 111:661-668. [PMID: 29775784 DOI: 10.1016/j.ygeno.2018.05.011] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2018] [Revised: 05/04/2018] [Accepted: 05/11/2018] [Indexed: 01/22/2023]
Abstract
Magnaporthe oryzae is a fungal pathogen causing blast disease in many plant species. In this study, seventy three isolates of M. oryzae collected from rice (Oryza sativa) in 1996-2014 were genotyped using a genotyping-by-sequencing approach to detect genetic variation. An association study was performed to identify single nucleotide polymorphisms (SNPs) associated with virulence genes using 831 selected SNP and infection phenotypes on local and improved rice varieties. Population structure analysis revealed eight subpopulations. The division into eight groups was not related to the degree of virulence. Association mapping showed five SNPs associated with fungal virulence on chromosome 1, 2, 3, 4 and 7. The SNP on chromosome 1 was associated with virulence against RD6-Pi7 and IRBL7-M which might be linked to the previously reported AvrPi7.
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Affiliation(s)
- Siripar Korinsak
- Plant Breeding Program, Faculty of Agriculture at Kamphaeng Saen, Kesetsart University, Nakhon Pathom 73140, Thailand
| | - Sithichoke Tangphatsornruang
- National Center for Genetic Engineering and Biotechnology (BIOTEC), 113 Thailand Science Park, Pahonyothin Road, Khlong Nueng, Khlong Luang, PathumThani 12120, Thailand
| | - Wirulda Pootakham
- National Center for Genetic Engineering and Biotechnology (BIOTEC), 113 Thailand Science Park, Pahonyothin Road, Khlong Nueng, Khlong Luang, PathumThani 12120, Thailand
| | - Samart Wanchana
- National Center for Genetic Engineering and Biotechnology (BIOTEC), 113 Thailand Science Park, Pahonyothin Road, Khlong Nueng, Khlong Luang, PathumThani 12120, Thailand
| | - Anucha Plabpla
- Interdisciplinary Graduate Program in Genetic Engineering, Kasetsart University, Bangkok 10900, Thailand
| | | | - Sujin Patarapuwadol
- Department of Plant Pathology, Faculty of Agriculture at Kamphaeng Saen, Kasetsart University, Kamphaeng Saen Campus, Nakhon Pathom 73140, Thailand
| | - Apichart Vanavichit
- Department of Agronomy, Faculty of Agriculture at Kamphaeng Saen, Kasetsart University, Kamphaeng Saen Campus, Nakhon Pathom 73140, Thailand; Rice Science Center, Kasetsart University, Kamphaeng Saen, Nakhon Pathom 73140, Thailand
| | - Theerayut Toojinda
- National Center for Genetic Engineering and Biotechnology (BIOTEC), 113 Thailand Science Park, Pahonyothin Road, Khlong Nueng, Khlong Luang, PathumThani 12120, Thailand.
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22
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Gubili C, Mariani S, Weckworth BV, Galpern P, McDevitt AD, Hebblewhite M, Nickel B, Musiani M. Environmental and anthropogenic drivers of connectivity patterns: A basis for prioritizing conservation efforts for threatened populations. Evol Appl 2016; 10:199-211. [PMID: 28127396 PMCID: PMC5253427 DOI: 10.1111/eva.12443] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2016] [Accepted: 10/10/2016] [Indexed: 01/07/2023] Open
Abstract
Ecosystem fragmentation and habitat loss have been the focus of landscape management due to restrictions on contemporary connectivity and dispersal of populations. Here, we used an individual approach to determine the drivers of genetic differentiation in caribou of the Canadian Rockies. We modelled the effects of isolation by distance, landscape resistance and predation risk and evaluated the consequences of individual migratory behaviour (seasonally migratory vs. sedentary) on gene flow in this threatened species. We applied distance-based and reciprocal causal modelling approaches, testing alternative hypotheses on the effects of geographic, topographic, environmental and local population-specific variables on genetic differentiation and relatedness among individuals. Overall, gene flow was restricted to neighbouring local populations, with spatial coordinates, local population size, groups and elevation explaining connectivity among individuals. Landscape resistance, geographic distances and predation risk were correlated with genetic distances, with correlations threefold higher for sedentary than for migratory caribou. As local caribou populations are increasingly isolated, our results indicate the need to address genetic connectivity, especially for populations with individuals displaying different migratory behaviours, whilst maintaining quality habitat both within and across the ranges of threatened populations.
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Affiliation(s)
- Chrysoula Gubili
- School of Environment and Life Sciences University of Salford Salford UK; Faculties of Environmental Design and Veterinary Medicine University of Calgary Calgary AB Canada
| | - Stefano Mariani
- School of Environment and Life Sciences University of Salford Salford UK
| | | | - Paul Galpern
- Faculties of Environmental Design and Veterinary Medicine University of Calgary Calgary AB Canada
| | - Allan D McDevitt
- School of Environment and Life Sciences University of Salford Salford UK
| | - Mark Hebblewhite
- Wildlife Biology Program Department of Ecosystem and Conservation Sciences College of Forestry and Conservation University of Montana Missoula MT USA
| | - Barry Nickel
- Environmental Studies Department Center for Integrated Spatial Research University of California Santa Cruz CA USA
| | - Marco Musiani
- Faculties of Environmental Design and Veterinary Medicine University of Calgary Calgary AB Canada
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Abstract
Population geneticists have long been interested in the ability of natural selection to maintain the levels of standing variation observed in natural populations. Here, we study the polymorphism-maintaining properties of maternal selection, in which the fitness of an individual is a function of its own and its mother’s genotype. Using a model proposed by Gavrilets, we first estimate the proportion of parameter/state space that preserves allelic variation, before investigating the construction of polymorphism over time through the joint action of mutation and selection. These two methods, the “parameter-space” and “constructionist” approaches, respectively, enable us to draw some general conclusions. We argue that, even though the proportion of parameter-state space allowing multiallele polymorphism is greater under maternal selection than under the standard model of constant viability selection, the former is, in fact, less likely to maintain large numbers of alleles. Nevertheless, variation that is balanced by maternal selection is likely to show elements of heterozygous advantage and be resistant to depletion by genetic drift. We observe that the population mean fitness frequently decreases after the successful invasion of a new mutation, but such declines are usually temporary.
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