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Kaminski M, Brown JI, Seibert SR, Hernández F, Duya MV, Fontanilla IKC, Roshier D, Miles A, Joseph L, Peters JL, Lavretsky P. Determining evolutionary origin and phylogenetic relationships of mallard-like ducks of Oceania, greater Indonesia, and the Philippines with ddRAD-seq data. Mol Phylogenet Evol 2024; 197:108085. [PMID: 38688441 DOI: 10.1016/j.ympev.2024.108085] [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: 12/04/2023] [Revised: 04/12/2024] [Accepted: 04/24/2024] [Indexed: 05/02/2024]
Abstract
AIM We aim to determine the evolutionary origins and population genetics of mallard-like ducks of Oceania, greater Indonesia, and the Philippines. LOCATION Oceania, greater Indonesia, and the Philippines. TAXON Mallard (Anas platyrhynchos), Pacific black duck (A. superciliosa spp.), and Philippine duck (A. luzonica) METHODS: Thousands of nuclear ddRAD-seq loci and the mitochondrial DNA control region were assayed across individuals representative of each species' range. We assessed population structure and phylogenetic relationships, as well as estimated demographic histories to reconstruct the biogeographical history of each species. RESULTS Philippine and Pacific black ducks represent unique genetic lineages that diverged from the mallard 1-2 million years ago. We find no support for the Philippine duck representing a hybrid species as once posited; however, their low levels of genetic diversity requires further attention. We find a lack of substructure among Philippine ducks. However, we found pronounced differentiation between subspecies of Pacific black ducks, especially between A. s. superciliosa from New Zealand and A. s. rogersi from Australia, Papua New Guinea, and Timor-Leste, Indonesia. Anas superciliosa pelewensis gave mixed results; individuals from the Solomon Islands were differentiated from the other subspecies, but those from the island of Aunu'u, American Samoa, were genetically more similar to A. s. rogersi than A. s. pelewensis samples from the Solomon Islands. Finally, we find limited evidence of interspecific gene flow at evolutionary scales, and mallard introgression among contemporary samples. MAIN CONCLUSIONS Mallard-like ducks radiated across Oceania, greater Indonesia, and the Philippines within the last 2 million years. Only the Pacific black duck showed unique sub-structuring that largely followed known sub-species ranges, except for A. s. pelewensis. We posit that the high interrelatedness among Solomon Island samples suggests that their genetic distinctiveness may simply be the result of high levels of genetic drift. In contrast, we conclude that mainland Australian Pacific black ducks were the most likely source for the recent colonization of American Samoa. As a result, our findings suggest that either the A. s. pelewensis subspecies designations and/or its geographical range may require re-evaluation. Continued re-evaluation of evolutionary and taxonomic relationships is necessary when attempting to reconstruct and understand biogeographical histories, with important implications towards any attempts to implement conservation strategies.
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Affiliation(s)
- Marissa Kaminski
- Department of Biological Sciences, University of Texas at El Paso, El Paso, TX, USA; Upper Midwest Environmental Sciences Center, United States Geological Survey, La Crosse, WI, USA.
| | - Joshua I Brown
- Department of Biological Sciences, University of Texas at El Paso, El Paso, TX, USA; Department of Life, Earth, and Environmental Sciences, West Texas A&M University, Canyon, Texas, USA
| | - Sara R Seibert
- Department of Biological Sciences, Wright State University, Dayton, OH, USA
| | - Flor Hernández
- Department of Biological Sciences, University of Texas at El Paso, El Paso, TX, USA
| | - Melizar V Duya
- Department of Biological Sciences, University of Texas at El Paso, El Paso, TX, USA
| | - Ian Kendrich C Fontanilla
- Institute of Biology, College of Science, University of the Philippines Diliman, Quezon City, Philippines
| | - David Roshier
- School of Animal and Veterinary Science, University of Adelaide, Roseworthy SA, Australia
| | - Adam Miles
- Department of Marine and Wildlife Resources, Pago Pago, 96799, American Samoa
| | - Leo Joseph
- Australian National Wildlife Collection, CSIRO National Research Collections Australia, Canberra, Australia
| | - Jeffrey L Peters
- Department of Biological Sciences, Wright State University, Dayton, OH, USA
| | - Philip Lavretsky
- Department of Biological Sciences, University of Texas at El Paso, El Paso, TX, USA
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Ghimire P, Palacios C, Trimble J, Lamichhaney S. Museum genomics approach to study the taxonomy and evolution of Woolly-necked storks using historic specimens. G3 (BETHESDA, MD.) 2024; 14:jkae081. [PMID: 38626302 DOI: 10.1093/g3journal/jkae081] [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: 01/05/2024] [Revised: 03/16/2024] [Accepted: 04/05/2024] [Indexed: 04/18/2024]
Abstract
The accessibility of genomic tools in evolutionary biology has allowed for a thorough exploration of various evolutionary processes associated with adaptation and speciation. However, genomic studies in natural systems present numerous challenges, reflecting the inherent complexities of studying organisms in their native habitats. The utilization of museum specimens for genomics research has received increased attention in recent times, facilitated by advancements in ancient DNA techniques. In this study, we have utilized a museum genomics approach to analyze historic specimens of Woolly-necked storks (Ciconia spp.) and examine their genetic composition and taxonomic status and explore the evolutionary and adaptive trajectories of populations over the years. The Woolly-necked storks are distributed in Asia and Africa with a taxonomic classification that has been a matter of ambiguity. Asian and African Woollynecks were recently recognized as different species based on their morphological differences; however, their genomic validation was lacking. In this study, we have used ∼70-year-old museum samples for whole-genome population-scale sequencing. Our study has revealed that Asian and African Woollynecks are genetically distinct, consistent with the current taxonomic classification based on morphological features. However, we also found a high genetic divergence between the Asian subspecies Ciconia episcopus neglecta and Ciconia episcopus episcopus, suggesting this classification requires a detailed examination to explore processes of ongoing speciation. Because taxonomic classification directly impacts conservation efforts, and there is evidence of declining populations of Asian Woollynecks in Southeast Asia, our results highlight that population-scale studies are urgent to determine the genetic, ecological, and phylogenetic diversity of these birds.
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Affiliation(s)
- Prashant Ghimire
- Department of Biological Sciences, Kent State University, Kent, OH 44240, USA
| | - Catalina Palacios
- Department of Biological Sciences, Kent State University, Kent, OH 44240, USA
| | - Jeremiah Trimble
- Museum of Comparative Zoology, Harvard University, Cambridge, MA 02138, USA
| | - Sangeet Lamichhaney
- Department of Biological Sciences, Kent State University, Kent, OH 44240, USA
- School of Biomedical Sciences, Kent State University, Kent, OH 44240, USA
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3
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Lamb K, Debban CL, Galloway LF. Phylogeography and paleoclimatic range dynamics explain variable outcomes to contact across a species' range. Mol Ecol 2024:e17450. [PMID: 38973501 DOI: 10.1111/mec.17450] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2023] [Revised: 05/24/2024] [Accepted: 06/14/2024] [Indexed: 07/09/2024]
Abstract
Replicability of divergence after contact is a poorly characterized process, particularly in the contexts of phylogeography and postglacial range dynamics within species. Using contact zones located at the leading-, mid- and rear-edges of a species' range, we examined variation in outcomes to contact between divergent lineages of Campanula americana. We investigated whether contact zones vary in quantity and directionality of gene flow, how phylogeographic structure differs between contact zones, and how historic range dynamics may affect outcomes to contact. We found that all contact zones formed at similar times via primary contact yet detected significant admixture in only the rear-edge (RE) contact zone. In the northern leading-edge contact zone and the mid-range Virginia contact zone, gene flow was minimal and asymmetric. In the southern RE contact zone, gene flow was strong and symmetric. Asymmetric admixture in the leading-edge and Virginia contact zones matches the directionality of a known cosmopolitan cytonuclear incompatibility between lineages of C. americana. Our results emphasize the dependence of speciation processes on phylogeographic structure, evolutionary history and range dynamics.
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Affiliation(s)
- Keric Lamb
- Department of Biology, University of Virginia, Charlottesville, Virginia, USA
| | - Catherine L Debban
- Center for Public Health Genomics, University of Virginia, Charlottesville, Virginia, USA
| | - Laura F Galloway
- Department of Biology, University of Virginia, Charlottesville, Virginia, USA
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4
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Tian R, Zhang Y, Kang H, Zhang F, Jin Z, Wang J, Zhang P, Zhou X, Lanyon JM, Sneath HL, Woolford L, Fan G, Li S, Seim I. Sirenian genomes illuminate the evolution of fully aquatic species within the mammalian superorder afrotheria. Nat Commun 2024; 15:5568. [PMID: 38956050 PMCID: PMC11219930 DOI: 10.1038/s41467-024-49769-x] [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: 08/23/2023] [Accepted: 06/12/2024] [Indexed: 07/04/2024] Open
Abstract
Sirenians of the superorder Afrotheria were the first mammals to transition from land to water and are the only herbivorous marine mammals. Here, we generated a chromosome-level dugong (Dugong dugon) genome. A comparison of our assembly with other afrotherian genomes reveals possible molecular adaptations to aquatic life by sirenians, including a shift in daily activity patterns (circadian clock) and tolerance to a high-iodine plant diet mediated through changes in the iodide transporter NIS (SLC5A5) and its co-transporters. Functional in vitro assays confirm that sirenian amino acid substitutions alter the properties of the circadian clock protein PER2 and NIS. Sirenians show evidence of convergent regression of integumentary system (skin and its appendages) genes with cetaceans. Our analysis also uncovers gene losses that may be maladaptive in a modern environment, including a candidate gene (KCNK18) for sirenian cold stress syndrome likely lost during their evolutionary shift in daily activity patterns. Genomes from nine Australian locations and the functionally extinct Okinawan population confirm and date a genetic break ~10.7 thousand years ago on the Australian east coast and provide evidence of an associated ecotype, and highlight the need for whole-genome resequencing data from dugong populations worldwide for conservation and genetic management.
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Affiliation(s)
- Ran Tian
- Integrative Biology Laboratory, Nanjing Normal University, Nanjing, 210023, China
| | - Yaolei Zhang
- BGI Research, Qingdao, 266555, China
- BGI Research, Shenzhen, 518083, China
- Qingdao Key Laboratory of Marine Genomics BGI Research, Qingdao, 266555, China
| | - Hui Kang
- Marine Mammal and Marine Bioacoustics Laboratory, Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, 572000, China
- The Innovation Research Center for Aquatic Mammals, and Key Laboratory of Aquatic Biodiversity and Conservation of the Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Fan Zhang
- Integrative Biology Laboratory, Nanjing Normal University, Nanjing, 210023, China
| | - Zhihong Jin
- Integrative Biology Laboratory, Nanjing Normal University, Nanjing, 210023, China
| | - Jiahao Wang
- BGI Research, Qingdao, 266555, China
- BGI Research, Shenzhen, 518083, China
| | - Peijun Zhang
- Marine Mammal and Marine Bioacoustics Laboratory, Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, 572000, China
| | - Xuming Zhou
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
- School of Life Sciences, University of Science and Technology of China, Hefei, 230027, China
| | - Janet M Lanyon
- School of the Environment, The University of Queensland, Lucia, 4072, Australia
| | - Helen L Sneath
- School of the Environment, The University of Queensland, Lucia, 4072, Australia
| | - Lucy Woolford
- School of Veterinary Sciences, The University of Adelaide, Roseworthy, 5371, Australia
| | - Guangyi Fan
- BGI Research, Qingdao, 266555, China.
- BGI Research, Shenzhen, 518083, China.
- Qingdao Key Laboratory of Marine Genomics BGI Research, Qingdao, 266555, China.
- State Key Laboratory of Agricultural Genomics, BGI Research, Shenzhen, 518083, China.
| | - Songhai Li
- Marine Mammal and Marine Bioacoustics Laboratory, Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, 572000, China.
- The Innovation Research Center for Aquatic Mammals, and Key Laboratory of Aquatic Biodiversity and Conservation of the Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China.
| | - Inge Seim
- Integrative Biology Laboratory, Nanjing Normal University, Nanjing, 210023, China.
- Marine Mammal and Marine Bioacoustics Laboratory, Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, 572000, China.
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Dong J, Qiu L, Zhou X, Liu S. Drivers of genomic differentiation landscapes in populations of disparate ecological and geographical settings within mainland Apis cerana. Mol Ecol 2024; 33:e17414. [PMID: 38801184 DOI: 10.1111/mec.17414] [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: 07/07/2023] [Revised: 05/07/2024] [Accepted: 05/09/2024] [Indexed: 05/29/2024]
Abstract
Elucidating the evolutionary processes that drive population divergence can enhance our understanding of the early stages of speciation and inform conservation management decisions. The honeybee Apis cerana displays extensive population divergence, providing an informative natural system for exploring these processes. The mainland lineage A. cerana includes several peripheral subspecies with disparate ecological and geographical settings radiated from a central ancestor. Under this evolutionary framework, we can explore the patterns of genome differentiation and the evolutionary models that explain them. We can also elucidate the contribution of non-genomic spatiotemporal mechanisms (extrinsic features) and genomic mechanisms (intrinsic features) that influence these genomic differentiation landscapes. Based on 293 whole genomes, a small part of the genome is highly differentiated between central-peripheral subspecies pairs, while low and partial parallelism partly reflects idiosyncratic responses to environmental differences. Combined elements of recurrent selection and speciation-with-gene-flow models generate the heterogeneous genome landscapes. These elements weight differently between central-island and other central-peripheral subspecies pairs, influenced by glacial cycles superimposed on different geomorphologies. Although local recombination rates exert a significant influence on patterns of genomic differentiation, it is unlikely that low-recombination rates regions were generated by structural variation. In conclusion, complex factors including geographical isolation, divergent ecological selection and non-uniform genome features have acted concertedly in the evolution of reproductive barriers that could reduce gene flow in part of the genome and facilitate the persistence of distinct populations within mainland lineage of A. cerana.
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Affiliation(s)
- Jiangxing Dong
- Department of Entomology, College of Plant Protection, China Agricultural University, Beijing, China
| | - Lifei Qiu
- Department of Entomology, College of Plant Protection, China Agricultural University, Beijing, China
| | - Xin Zhou
- Department of Entomology, College of Plant Protection, China Agricultural University, Beijing, China
| | - Shanlin Liu
- Department of Entomology, College of Plant Protection, China Agricultural University, Beijing, China
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
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Bolte CE, Phannareth T, Zavala-Paez M, Sutara BN, Can MF, Fitzpatrick MC, Holliday JA, Keller SR, Hamilton JA. Genomic insights into hybrid zone formation: The role of climate, landscape, and demography in the emergence of a novel hybrid lineage. Mol Ecol 2024; 33:e17430. [PMID: 38867593 DOI: 10.1111/mec.17430] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2024] [Revised: 05/24/2024] [Accepted: 05/30/2024] [Indexed: 06/14/2024]
Abstract
Population demographic changes, alongside landscape, geographic and climate heterogeneity, can influence the timing, stability and extent of introgression where species hybridise. Thus, quantifying interactions across diverged lineages, and the relative contributions of interspecific genetic exchange and selection to divergence at the genome-wide level is needed to better understand the drivers of hybrid zone formation and maintenance. We used seven latitudinally arrayed transects to quantify the contributions of climate, geography and landscape features to broad patterns of genetic structure across the hybrid zone of Populus trichocarpa and P. balsamifera and evaluated the demographic context of hybridisation over time. We found genetic structure differed among the seven transects. While ancestry was structured by climate, landscape features influenced gene flow dynamics. Demographic models indicated a secondary contact event may have influenced contemporary hybrid zone formation with the origin of a putative hybrid lineage that inhabits regions with higher aridity than either of the ancestral groups. Phylogenetic relationships based on chloroplast genomes support the origin of this hybrid lineage inferred from demographic models based on the nuclear data. Our results point towards the importance of climate and landscape patterns in structuring the contact zones between P. trichocarpa and P. balsamifera and emphasise the value whole genome sequencing can have to advancing our understanding of how neutral processes influence divergence across space and time.
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Affiliation(s)
- Constance E Bolte
- Department of Ecosystem Science and Management, Pennsylvania State University, University Park, Pennsylvania, USA
| | - Tommy Phannareth
- Department of Forest Resources and Environmental Conservation, Virginia Tech, Blacksburg, Virginia, USA
| | - Michelle Zavala-Paez
- Department of Ecosystem Science and Management, Pennsylvania State University, University Park, Pennsylvania, USA
| | - Brianna N Sutara
- Department of Biology, Pennsylvania State University, University Park, Pennsylvania, USA
| | | | - Matthew C Fitzpatrick
- Appalachian Laboratory, University of Maryland Center for Environmental Science, Frostburg, Maryland, USA
| | - Jason A Holliday
- Department of Forest Resources and Environmental Conservation, Virginia Tech, Blacksburg, Virginia, USA
| | - Stephen R Keller
- Department of Plant Biology, University of Vermont, Burlington, Vermont, USA
| | - Jill A Hamilton
- Department of Ecosystem Science and Management, Pennsylvania State University, University Park, Pennsylvania, USA
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7
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Filatov DA. ProSeq4: A user-friendly multiplatform program for preparation and analysis of large-scale DNA polymorphism datasets. Mol Ecol Resour 2024; 24:e13962. [PMID: 38646687 DOI: 10.1111/1755-0998.13962] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Revised: 03/28/2024] [Accepted: 04/08/2024] [Indexed: 04/23/2024]
Abstract
Preparation of DNA polymorphism datasets for analysis is an important step in evolutionary genetic and molecular ecology studies. Ever-growing dataset sizes make this step time consuming, but few convenient software tools are available to facilitate processing of large-scale datasets including thousands of sequence alignments. Here I report "processor of sequences v4" (proSeq4)-a user-friendly multiplatform software for preparation and evolutionary genetic analyses of genome- or transcriptome-scale sequence polymorphism datasets. The program has an easy-to-use graphic user interface and is designed to process and analyse many thousands of datasets. It supports over two dozen file formats, includes a flexible sequence editor and various tools for data visualization, quality control and most commonly used evolutionary genetic analyses, such as NJ-phylogeny reconstruction, DNA polymorphism analyses and coalescent simulations. Command line tools (e.g. vcf2fasta) are also provided for easier integration into bioinformatic pipelines. Apart of molecular ecology and evolution research, proSeq4 may be useful for teaching, e.g. for visual illustration of different shapes of phylogenies generated with coalescent simulations in different scenarios. ProSeq4 source code and binaries for Windows, MacOS and Ubuntu are available from https://sourceforge.net/projects/proseq/.
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Garner AG, Goulet-Scott BE, Hopkins R. Phylogenomic analyses re-examine the evolution of reinforcement and hypothesized hybrid speciation in Phlox wildflowers. THE NEW PHYTOLOGIST 2024; 243:451-465. [PMID: 38764373 DOI: 10.1111/nph.19802] [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: 10/06/2023] [Accepted: 03/22/2024] [Indexed: 05/21/2024]
Abstract
The tree of life is riddled with reticulate evolutionary histories, and some clades, such as the eastern standing Phlox, appear to be hotspots of hybridization. In this group, there are two cases of reinforcement and nine hypothesized hybrid species. Given their historical importance in our understanding of plant speciation, the relationships between these taxa and the role of hybridization in their diversification require genomic validation. Using phylogenomic analyses, we resolve the evolutionary relationships of the eastern standing Phlox and evaluate hypotheses about whether and how hybridization and gene flow played a role in their diversification. Our results provide novel resolution of the phylogenetic relationships in this group, including paraphyly across some taxa. We identify gene flow during one case of reinforcement and find genomic support for a hybrid lineage underlying one of the five hypothesized homoploid hybrid speciation events. Additionally, we estimate the ancestries of four allotetraploid hybrid species. Our results are consistent with hybridization contributing to diverse evolutionary outcomes within this group; although, not as extensively as previously hypothesized. This study demonstrates the importance of phylogenomics in evaluating hypothesized evolutionary histories of non-model systems and adds to the growing support of interspecific genetic exchange in the generation of biodiversity.
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Affiliation(s)
- Austin G Garner
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, 02138, USA
- The Arnold Arboretum, Harvard University, Boston, MA, 02131, USA
| | - Benjamin E Goulet-Scott
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, 02138, USA
- The Arnold Arboretum, Harvard University, Boston, MA, 02131, USA
| | - Robin Hopkins
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, 02138, USA
- The Arnold Arboretum, Harvard University, Boston, MA, 02131, USA
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Xin X, Li P, Zhao X, Yu Y, Wang W, Jin G, Wang J, Sun L, Zhang D, Zhang F, Yu S, Su T. Temperature-dependent jumonji demethylase modulates flowering time by targeting H3K36me2/3 in Brassica rapa. Nat Commun 2024; 15:5470. [PMID: 38937441 PMCID: PMC11211497 DOI: 10.1038/s41467-024-49721-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2023] [Accepted: 06/12/2024] [Indexed: 06/29/2024] Open
Abstract
Global warming has a severe impact on the flowering time and yield of crops. Histone modifications have been well-documented for their roles in enabling plant plasticity in ambient temperature. However, the factor modulating histone modifications and their involvement in habitat adaptation have remained elusive. In this study, through genome-wide pattern analysis and quantitative-trait-locus (QTL) mapping, we reveal that BrJMJ18 is a candidate gene for a QTL regulating thermotolerance in thermotolerant B. rapa subsp. chinensis var. parachinensis (or Caixin, abbreviated to Par). BrJMJ18 encodes an H3K36me2/3 Jumonji demethylase that remodels H3K36 methylation across the genome. We demonstrate that the BrJMJ18 allele from Par (BrJMJ18Par) influences flowering time and plant growth in a temperature-dependent manner via characterizing overexpression and CRISPR/Cas9 mutant plants. We further show that overexpression of BrJMJ18Par can modulate the expression of BrFLC3, one of the five BrFLC orthologs. Furthermore, ChIP-seq and transcriptome data reveal that BrJMJ18Par can regulate chlorophyll biosynthesis under high temperatures. We also demonstrate that three amino acid mutations may account for function differences in BrJMJ18 between subspecies. Based on these findings, we propose a working model in which an H3K36me2/3 demethylase, while not affecting agronomic traits under normal conditions, can enhance resilience under heat stress in Brassica rapa.
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Affiliation(s)
- Xiaoyun Xin
- State Key Laboratory of Vegetable Biobreeding, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Science, Beijing, China
- National Engineering Research Center for Vegetables, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Science, Beijing, China
- Beijing Key Laboratory of Vegetable Germplasms Improvement, Beijing, China
- Key Laboratory of Biology and Genetics Improvement of Horticultural Crops (North China), Beijing, China
| | - Peirong Li
- State Key Laboratory of Vegetable Biobreeding, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Science, Beijing, China
- National Engineering Research Center for Vegetables, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Science, Beijing, China
- Beijing Key Laboratory of Vegetable Germplasms Improvement, Beijing, China
- Key Laboratory of Biology and Genetics Improvement of Horticultural Crops (North China), Beijing, China
| | - Xiuyun Zhao
- State Key Laboratory of Vegetable Biobreeding, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Science, Beijing, China
- National Engineering Research Center for Vegetables, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Science, Beijing, China
- Beijing Key Laboratory of Vegetable Germplasms Improvement, Beijing, China
- Key Laboratory of Biology and Genetics Improvement of Horticultural Crops (North China), Beijing, China
| | - Yangjun Yu
- State Key Laboratory of Vegetable Biobreeding, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Science, Beijing, China
- National Engineering Research Center for Vegetables, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Science, Beijing, China
- Beijing Key Laboratory of Vegetable Germplasms Improvement, Beijing, China
- Key Laboratory of Biology and Genetics Improvement of Horticultural Crops (North China), Beijing, China
| | - Weihong Wang
- State Key Laboratory of Vegetable Biobreeding, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Science, Beijing, China
- National Engineering Research Center for Vegetables, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Science, Beijing, China
- Beijing Key Laboratory of Vegetable Germplasms Improvement, Beijing, China
- Key Laboratory of Biology and Genetics Improvement of Horticultural Crops (North China), Beijing, China
| | - Guihua Jin
- State Key Laboratory of Vegetable Biobreeding, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Science, Beijing, China
- National Engineering Research Center for Vegetables, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Science, Beijing, China
| | - Jiao Wang
- State Key Laboratory of Vegetable Biobreeding, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Science, Beijing, China
- National Engineering Research Center for Vegetables, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Science, Beijing, China
| | - Liling Sun
- State Key Laboratory of Vegetable Biobreeding, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Science, Beijing, China
- National Engineering Research Center for Vegetables, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Science, Beijing, China
| | - Deshuang Zhang
- State Key Laboratory of Vegetable Biobreeding, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Science, Beijing, China
- National Engineering Research Center for Vegetables, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Science, Beijing, China
- Beijing Key Laboratory of Vegetable Germplasms Improvement, Beijing, China
- Key Laboratory of Biology and Genetics Improvement of Horticultural Crops (North China), Beijing, China
| | - Fenglan Zhang
- State Key Laboratory of Vegetable Biobreeding, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Science, Beijing, China.
- National Engineering Research Center for Vegetables, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Science, Beijing, China.
- Beijing Key Laboratory of Vegetable Germplasms Improvement, Beijing, China.
- Key Laboratory of Biology and Genetics Improvement of Horticultural Crops (North China), Beijing, China.
| | - Shuancang Yu
- State Key Laboratory of Vegetable Biobreeding, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Science, Beijing, China.
- National Engineering Research Center for Vegetables, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Science, Beijing, China.
- Beijing Key Laboratory of Vegetable Germplasms Improvement, Beijing, China.
- Key Laboratory of Biology and Genetics Improvement of Horticultural Crops (North China), Beijing, China.
| | - Tongbing Su
- State Key Laboratory of Vegetable Biobreeding, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Science, Beijing, China.
- National Engineering Research Center for Vegetables, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Science, Beijing, China.
- Beijing Key Laboratory of Vegetable Germplasms Improvement, Beijing, China.
- Key Laboratory of Biology and Genetics Improvement of Horticultural Crops (North China), Beijing, China.
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10
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Liu Y, Hu X, Lu H, Liu Y, Wang C, Dai X. Population genetics of Todarodes pacificus (Cephalopoda: Ommastrephidae) in the northwest Pacific Ocean via GBS sequencing. Open Life Sci 2024; 19:20220876. [PMID: 38947770 PMCID: PMC11211871 DOI: 10.1515/biol-2022-0876] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2024] [Revised: 04/05/2024] [Accepted: 04/29/2024] [Indexed: 07/02/2024] Open
Abstract
The common squid, Todarodes pacificus, is an important commercial species that inhabits the northwest Pacific Ocean, particularly the East Japan Sea, the Pacific coast of Japan, and the East China Sea. In this study, we chose 29 individuals from three areas: one type from the Sea of Japan and two types from the East China Sea. A total of 43,529 SNPs were obtained using genotyping-by-sequencing (GBS). Our analyses revealed low genetic diversity and genetic differentiation in each type. Heterozygote deficiency and inbreeding have caused this low level of genetic diversity. Population structure analysis indicated that the three types were genetically similar, which may be attributed to strong gene flow combined with the demographic history events during the last 2 million years. This new GBS application technique provides valuable information for the conservation of marine species genetics and could be useful for the effective management of this resource.
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Affiliation(s)
- Yang Liu
- College of Marine Living Resource Sciences and Management, Shanghai Ocean University, Shanghai, 201306, China
- Marine Biomedical Science and Technology Innovation Platform of Lin-gang Special Area, Ministry of Agriculture and Rural Affairs, Shanghai, 201306, P.R. China
| | - Xingxing Hu
- Scientific Research Department, Qingdao Technical College, Qingdao, Shandong, 266229, P.R. China
| | - Huajie Lu
- College of Marine Living Resource Sciences and Management, Shanghai Ocean University, Shanghai, 201306, China
- National Distant-Water Fisheries Engineering Research Center, Shanghai Ocean University, Shanghai, 201306, P.R. China
- Key Laboratory of Sustainable Exploitation of Oceanic Fisheries Resources, Ministry of Education, Shanghai, 201306, P.R. China
| | - Yimeng Liu
- College of Marine Living Resource Sciences and Management, Shanghai Ocean University, Shanghai, 201306, China
| | - Congcong Wang
- College of Marine Living Resource Sciences and Management, Shanghai Ocean University, Shanghai, 201306, China
- National Distant-Water Fisheries Engineering Research Center, Shanghai Ocean University, Shanghai, 201306, P.R. China
- Key Laboratory of Sustainable Exploitation of Oceanic Fisheries Resources, Ministry of Education, Shanghai, 201306, P.R. China
| | - Xiaojie Dai
- College of Marine Living Resource Sciences and Management, Shanghai Ocean University, Shanghai, 201306, China
- Key Laboratory of Sustainable Exploitation of Oceanic Fisheries Resources, Ministry of Education, Shanghai, 201306, P.R. China
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11
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Patel RA, Weiß CL, Zhu H, Mostafavi H, Simons YB, Spence JP, Pritchard JK. Conditional frequency spectra as a tool for studying selection on complex traits in biobanks. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.15.599126. [PMID: 38948697 PMCID: PMC11212903 DOI: 10.1101/2024.06.15.599126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/02/2024]
Abstract
Natural selection on complex traits is difficult to study in part due to the ascertainment inherent to genome-wide association studies (GWAS). The power to detect a trait-associated variant in GWAS is a function of frequency and effect size - but for traits under selection, the effect size of a variant determines the strength of selection against it, constraining its frequency. To account for GWAS ascertainment, we propose studying the joint distribution of allele frequencies across populations, conditional on the frequencies in the GWAS cohort. Before considering these conditional frequency spectra, we first characterized the impact of selection and non-equilibrium demography on allele frequency dynamics forwards and backwards in time. We then used these results to understand conditional frequency spectra under realistic human demography. Finally, we investigated empirical conditional frequency spectra for GWAS variants associated with 106 complex traits, finding compelling evidence for either stabilizing or purifying selection. Our results provide insight into polygenic score portability and other properties of variants ascertained with GWAS, highlighting the utility of conditional frequency spectra.
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Affiliation(s)
- Roshni A. Patel
- Department of Genetics, Stanford University School of Medicine, Stanford, CA
| | - Clemens L. Weiß
- Stanford Cancer Institute Core, Stanford University School of Medicine, Stanford, CA
| | - Huisheng Zhu
- Department of Biology, Stanford University, Stanford, CA
| | - Hakhamanesh Mostafavi
- Center for Human Genetics and Genomics, New York University School of Medicine, New York, NY
- Division of Biostatistics, Department of Population Health, New York University School of Medicine, New York, NY
| | | | - Jeffrey P. Spence
- Department of Genetics, Stanford University School of Medicine, Stanford, CA
| | - Jonathan K. Pritchard
- Department of Genetics, Stanford University School of Medicine, Stanford, CA
- Department of Biology, Stanford University, Stanford, CA
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12
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Fonseca EM, Carstens BC. Artificial intelligence enables unified analysis of historical and landscape influences on genetic diversity. Mol Phylogenet Evol 2024; 198:108116. [PMID: 38871263 DOI: 10.1016/j.ympev.2024.108116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Revised: 04/04/2024] [Accepted: 06/04/2024] [Indexed: 06/15/2024]
Abstract
While genetic variation in any species is potentially shaped by a range of processes, phylogeography and landscape genetics are largely concerned with inferring how environmental conditions and landscape features impact neutral intraspecific diversity. However, even as both disciplines have come to utilize SNP data over the last decades, analytical approaches have remained for the most part focused on either broad-scale inferences of historical processes (phylogeography) or on more localized inferences about environmental and/or landscape features (landscape genetics). Here we demonstrate that an artificial intelligence model-based analytical framework can consider both deeper historical factors and landscape-level processes in an integrated analysis. We implement this framework using data collected from two Brazilian anurans, the Brazilian sibilator frog (Leptodactylus troglodytes) and granular toad (Rhinella granulosa). Our results indicate that historical demographic processes shape most the genetic variation in the sibulator frog, while landscape processes primarily influence variation in the granular toad. The machine learning framework used here allows both historical and landscape processes to be considered equally, rather than requiring researchers to make an a priori decision about which factors are important.
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Affiliation(s)
- Emanuel M Fonseca
- Museum of Biological Diversity & Department of Evolution, Ecology and Organismal Biology, The Ohio State University, 1315 Kinnear Rd., Columbus OH 43212, USA
| | - Bryan C Carstens
- Museum of Biological Diversity & Department of Evolution, Ecology and Organismal Biology, The Ohio State University, 1315 Kinnear Rd., Columbus OH 43212, USA.
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13
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Gómez-Palacio A, Morinaga G, Turner PE, Micieli MV, Elnour MAB, Salim B, Surendran SN, Ramasamy R, Powell JR, Soghigian J, Gloria-Soria A. Robustness in population-structure and demographic-inference results derived from the Aedes aegypti genotyping chip and whole-genome sequencing data. G3 (BETHESDA, MD.) 2024; 14:jkae082. [PMID: 38626295 PMCID: PMC11152066 DOI: 10.1093/g3journal/jkae082] [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: 03/04/2024] [Revised: 03/04/2024] [Accepted: 04/04/2024] [Indexed: 04/18/2024]
Abstract
The mosquito Aedes aegypti is the primary vector of many human arboviruses such as dengue, yellow fever, chikungunya, and Zika, which affect millions of people worldwide. Population genetic studies on this mosquito have been important in understanding its invasion pathways and success as a vector of human disease. The Axiom aegypti1 SNP chip was developed from a sample of geographically diverse A. aegypti populations to facilitate genomic studies on this species. We evaluate the utility of the Axiom aegypti1 SNP chip for population genetics and compare it with a low-depth shotgun sequencing approach using mosquitoes from the native (Africa) and invasive ranges (outside Africa). These analyses indicate that results from the SNP chip are highly reproducible and have a higher sensitivity to capture alternative alleles than a low-coverage whole-genome sequencing approach. Although the SNP chip suffers from ascertainment bias, results from population structure, ancestry, demographic, and phylogenetic analyses using the SNP chip were congruent with those derived from low-coverage whole-genome sequencing, and consistent with previous reports on Africa and outside Africa populations using microsatellites. More importantly, we identified a subset of SNPs that can be reliably used to generate merged databases, opening the door to combined analyses. We conclude that the Axiom aegypti1 SNP chip is a convenient, more accurate, low-cost alternative to low-depth whole-genome sequencing for population genetic studies of A. aegypti that do not rely on full allelic frequency spectra. Whole-genome sequencing and SNP chip data can be easily merged, extending the usefulness of both approaches.
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Affiliation(s)
- Andrés Gómez-Palacio
- Department of Entomology, Center for Vector Biology & Zoonotic Diseases, The Connecticut Agricultural Experiment Station, 123 Huntington St., New Haven, CT 06511, USA
- Laboratorio de Investigación en Genética Evolutiva, Universidad Pedagógica y Tecnológica de Colombia, Avenida Central del Norte 39-115, Boyacá 150003, Colombia
| | - Gen Morinaga
- Faculty of Veterinary Medicine, University of Calgary, 2500 University Drive NW., Calgary, AB 2TN 1N4, Canada
| | - Paul E Turner
- Department of Ecology and Evolutionary Biology, Yale University, 165 Prospect St., New Haven, CT 06511, USA
- Quantitative Biology Institute, Yale University, 260 Whitney Ave., New Haven, CT 06511, USA
| | - Maria Victoria Micieli
- Centro de Estudios Parasitológicos y de Vectores (CEPAVE), CONICET, Universidad Nacional de la Plata, Boulevard 120 s/n between Av. 60 and Calle 64, La Plata 1900, Argentina
| | - Mohammed-Ahmed B Elnour
- Department of Parasitology and Medical Entomology, Tropical Medicine Research Institute, National Center for Research, Khartoum 11111, Sudan
| | - Bashir Salim
- Faculty of Veterinary Medicine, Department of Parasitology, University of Khartoum, Khartoum North 11111, Sudan
- Camel Research Center, King Faisal University, P.O. Box. 400, Al-Ahsa 31982, Saudi Arabia
| | | | - Ranjan Ramasamy
- Department of Zoology, University of Jaffna, Jaffna 40000, Sri Lanka
| | - Jeffrey R Powell
- Department of Ecology and Evolutionary Biology, Yale University, 165 Prospect St., New Haven, CT 06511, USA
| | - John Soghigian
- Faculty of Veterinary Medicine, University of Calgary, 2500 University Drive NW., Calgary, AB 2TN 1N4, Canada
| | - Andrea Gloria-Soria
- Department of Entomology, Center for Vector Biology & Zoonotic Diseases, The Connecticut Agricultural Experiment Station, 123 Huntington St., New Haven, CT 06511, USA
- Department of Ecology and Evolutionary Biology, Yale University, 165 Prospect St., New Haven, CT 06511, USA
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14
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Soni V, Jensen JD. Temporal challenges in detecting balancing selection from population genomic data. G3 (BETHESDA, MD.) 2024; 14:jkae069. [PMID: 38551137 DOI: 10.1093/g3journal/jkae069] [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: 12/21/2023] [Revised: 12/21/2023] [Accepted: 03/19/2024] [Indexed: 04/28/2024]
Abstract
The role of balancing selection in maintaining genetic variation remains an open question in population genetics. Recent years have seen numerous studies identifying candidate loci potentially experiencing balancing selection, most predominantly in human populations. There are however numerous alternative evolutionary processes that may leave similar patterns of variation, thereby potentially confounding inference, and the expected signatures of balancing selection additionally change in a temporal fashion. Here we use forward-in-time simulations to quantify expected statistical power to detect balancing selection using both site frequency spectrum- and linkage disequilibrium-based methods under a variety of evolutionarily realistic null models. We find that whilst site frequency spectrum-based methods have little power immediately after a balanced mutation begins segregating, power increases with time since the introduction of the balanced allele. Conversely, linkage disequilibrium-based methods have considerable power whilst the allele is young, and power dissipates rapidly as the time since introduction increases. Taken together, this suggests that site frequency spectrum-based methods are most effective at detecting long-term balancing selection (>25N generations since the introduction of the balanced allele) whilst linkage disequilibrium-based methods are effective over much shorter timescales (<1N generations), thereby leaving a large time frame over which current methods have little power to detect the action of balancing selection. Finally, we investigate the extent to which alternative evolutionary processes may mimic these patterns, and demonstrate the need for caution in attempting to distinguish the signatures of balancing selection from those of both neutral processes (e.g. population structure and admixture) as well as of alternative selective processes (e.g. partial selective sweeps).
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Affiliation(s)
- Vivak Soni
- School of Life Sciences, Center for Evolution & Medicine, Arizona State University, Tempe, AZ 85281, USA
| | - Jeffrey D Jensen
- School of Life Sciences, Center for Evolution & Medicine, Arizona State University, Tempe, AZ 85281, USA
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15
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Portnoy DS, O'Leary SJ, Fields AT, Hollenbeck CM, Grubbs RD, Peterson CT, Gardiner JM, Adams DH, Falterman B, Drymon JM, Higgs JM, Pulster EL, Wiley TR, Murawski SA. Complex patterns of genetic population structure in the mouthbrooding marine catfish, Bagre marinus, in the Gulf of Mexico and U.S. Atlantic. Ecol Evol 2024; 14:e11514. [PMID: 38859886 PMCID: PMC11163162 DOI: 10.1002/ece3.11514] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2024] [Revised: 05/10/2024] [Accepted: 05/13/2024] [Indexed: 06/12/2024] Open
Abstract
Patterns of genetic variation reflect interactions among microevolutionary forces that vary in strength with changing demography. Here, patterns of variation within and among samples of the mouthbrooding gafftopsail catfish (Bagre marinus, Family Ariidae) captured in the U.S. Atlantic and throughout the Gulf of Mexico were analyzed using genomics to generate neutral and non-neutral SNP data sets. Because genomic resources are lacking for ariids, linkage disequilibrium network analysis was used to examine patterns of putatively adaptive variation. Finally, historical demographic parameters were estimated from site frequency spectra. The results show four differentiated groups, corresponding to the (1) U.S. Atlantic, and the (2) northeastern, (3) northwestern, and (4) southern Gulf of Mexico. The non-neutral data presented two contrasting signals of structure, one due to increases in diversity moving west to east and north to south, and another to increased heterozygosity in the Atlantic. Demographic analysis suggested that recently reduced long-term effective population size in the Atlantic is likely an important driver of patterns of genetic variation and is consistent with a known reduction in population size potentially due to an epizootic. Overall, patterns of genetic variation resemble that of other fishes that use the same estuarine habitats as nurseries, regardless of the presence/absence of a larval phase, supporting the idea that adult/juvenile behavior and habitat are important predictors of contemporary patterns of genetic structure.
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Affiliation(s)
- David S. Portnoy
- Marine Genomics Laboratory, Department of Life SciencesTexas A&M University – Corpus ChristiCorpus ChristiTexasUSA
| | - Shannon J. O'Leary
- Department of Biological SciencesSaint Anselm CollegeManchesterNew HampshireUSA
| | - Andrew T. Fields
- Marine Genomics Laboratory, Department of Life SciencesTexas A&M University – Corpus ChristiCorpus ChristiTexasUSA
| | - Christopher M. Hollenbeck
- Marine Genomics Laboratory, Department of Life SciencesTexas A&M University – Corpus ChristiCorpus ChristiTexasUSA
| | - R. Dean Grubbs
- Florida State University Coastal and Marine LaboratorySt. TeresaFloridaUSA
| | | | | | - Douglas H. Adams
- Florida Fish and Wildlife Conservation CommissionFish and Wildlife Research Institute, Indian River Field LabMelbourneFloridaUSA
| | | | - J. Marcus Drymon
- Mississippi State University Coastal Research and Extension CenterBiloxiMississippiUSA
- Mississippi‐Alabama Sea Grant ConsortiumOcean SpringsMississippiUSA
| | - Jeremy M. Higgs
- Center for Fisheries Research and DevelopmentThe University of Southern MississippiOcean SpringsMississippiUSA
| | - Erin L. Pulster
- U.S. Geological Survey, Columbia Environmental Research CenterColumbiaMissouriUSA
- College of Marine ScienceUniversity of South FloridaSt. PetersburgFloridaUSA
| | | | - Steven A. Murawski
- College of Marine ScienceUniversity of South FloridaSt. PetersburgFloridaUSA
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16
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Fonseca EM, Pope NS, Peterman WE, Werneck FP, Colli GR, Carstens BC. Genetic structure and landscape effects on gene flow in the Neotropical lizard Norops brasiliensis (Squamata: Dactyloidae). Heredity (Edinb) 2024; 132:284-295. [PMID: 38575800 PMCID: PMC11166928 DOI: 10.1038/s41437-024-00682-5] [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: 11/15/2023] [Revised: 03/12/2024] [Accepted: 03/18/2024] [Indexed: 04/06/2024] Open
Abstract
One key research goal of evolutionary biology is to understand the origin and maintenance of genetic variation. In the Cerrado, the South American savanna located primarily in the Central Brazilian Plateau, many hypotheses have been proposed to explain how landscape features (e.g., geographic distance, river barriers, topographic compartmentalization, and historical climatic fluctuations) have promoted genetic structure by mediating gene flow. Here, we asked whether these landscape features have influenced the genetic structure and differentiation in the lizard species Norops brasiliensis (Squamata: Dactyloidae). To achieve our goal, we used a genetic clustering analysis and estimate an effective migration surface to assess genetic structure in the focal species. Optimized isolation-by-resistance models and a simulation-based approach combined with machine learning (convolutional neural network; CNN) were then used to infer current and historical effects on population genetic structure through 12 unique landscape models. We recovered five geographically distributed populations that are separated by regions of lower-than-expected gene flow. The results of the CNN showed that geographic distance is the sole predictor of genetic variation in N. brasiliensis, and that slope, rivers, and historical climate had no discernible influence on gene flow. Our novel CNN approach was accurate (89.5%) in differentiating each landscape model. CNN and other machine learning approaches are still largely unexplored in landscape genetics studies, representing promising avenues for future research with increasingly accessible genomic datasets.
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Affiliation(s)
- Emanuel M Fonseca
- Department of Evolution, Ecology and Organismal Biology, The Ohio State University, Columbus, OH, USA
| | - Nathaniel S Pope
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR, 97403, USA
| | - William E Peterman
- School of Environment and Natural Resources, The Ohio State University, Columbus, OH, USA
| | - Fernanda P Werneck
- Coordenação de Biodiversidade, Programa de Coleções Científicas Biológicas, Instituto Nacional de Pesquisas da Amazônia (INPA), Manaus, Brazil
| | - Guarino R Colli
- Departamento de Zoologia, Universidade de Brasília, Brasília, Brazil
| | - Bryan C Carstens
- Department of Evolution, Ecology and Organismal Biology, The Ohio State University, Columbus, OH, USA.
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17
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Rick JA, Brock CD, Lewanski AL, Golcher-Benavides J, Wagner CE. Reference Genome Choice and Filtering Thresholds Jointly Influence Phylogenomic Analyses. Syst Biol 2024; 73:76-101. [PMID: 37881861 DOI: 10.1093/sysbio/syad065] [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: 03/10/2022] [Revised: 09/20/2023] [Accepted: 10/20/2023] [Indexed: 10/27/2023] Open
Abstract
Molecular phylogenies are a cornerstone of modern comparative biology and are commonly employed to investigate a range of biological phenomena, such as diversification rates, patterns in trait evolution, biogeography, and community assembly. Recent work has demonstrated that significant biases may be introduced into downstream phylogenetic analyses from processing genomic data; however, it remains unclear whether there are interactions among bioinformatic parameters or biases introduced through the choice of reference genome for sequence alignment and variant calling. We address these knowledge gaps by employing a combination of simulated and empirical data sets to investigate the extent to which the choice of reference genome in upstream bioinformatic processing of genomic data influences phylogenetic inference, as well as the way that reference genome choice interacts with bioinformatic filtering choices and phylogenetic inference method. We demonstrate that more stringent minor allele filters bias inferred trees away from the true species tree topology, and that these biased trees tend to be more imbalanced and have a higher center of gravity than the true trees. We find the greatest topological accuracy when filtering sites for minor allele count (MAC) >3-4 in our 51-taxa data sets, while tree center of gravity was closest to the true value when filtering for sites with MAC >1-2. In contrast, filtering for missing data increased accuracy in the inferred topologies; however, this effect was small in comparison to the effect of minor allele filters and may be undesirable due to a subsequent mutation spectrum distortion. The bias introduced by these filters differs based on the reference genome used in short read alignment, providing further support that choosing a reference genome for alignment is an important bioinformatic decision with implications for downstream analyses. These results demonstrate that attributes of the study system and dataset (and their interaction) add important nuance for how best to assemble and filter short-read genomic data for phylogenetic inference.
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Affiliation(s)
- Jessica A Rick
- School of Natural Resources & the Environment, University of Arizona, Tucson, AZ 85719, USA
| | - Chad D Brock
- Department of Biological Sciences, Tarleton State University, Stephenville, TX 76401, USA
| | - Alexander L Lewanski
- Department of Integrative Biology and W.K. Kellogg Biological Station, Michigan State University, East Lansing, MI 48824, USA
| | - Jimena Golcher-Benavides
- Department of Natural Resource Ecology and Management, Iowa State University, Ames, IA 50011, USA
| | - Catherine E Wagner
- Program in Ecology and Evolution, University of Wyoming, Laramie, WY 82071, USA
- Department of Botany, University of Wyoming, Laramie, WY 82071, USA
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18
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Daron J, Bouafou L, Tennessen JA, Rahola N, Makanga B, Akone-Ella O, Ngangue MF, Longo Pendy NM, Paupy C, Neafsey DE, Fontaine MC, Ayala D. Genomic Signatures of Microgeographic Adaptation in Anopheles coluzzii Along an Anthropogenic Gradient in Gabon. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.16.594472. [PMID: 38798379 PMCID: PMC11118577 DOI: 10.1101/2024.05.16.594472] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2024]
Abstract
Species distributed across heterogeneous environments often evolve locally adapted populations, but understanding how these persist in the presence of homogenizing gene flow remains puzzling. In Gabon, Anopheles coluzzii, a major African malaria mosquito is found along an ecological gradient, including a sylvatic population, away of any human presence. This study identifies into the genomic signatures of local adaptation in populations from distinct environments including the urban area of Libreville, and two proximate sites 10km apart in the La Lopé National Park (LLP), a village and its sylvatic neighborhood. Whole genome re-sequencing of 96 mosquitoes unveiled ∼ 5.7millions high-quality single nucleotide polymorphisms. Coalescent-based demographic analyses suggest an ∼ 8,000-year-old divergence between Libreville and La Lopé populations, followed by a secondary contact ( ∼ 4,000 ybp) resulting in asymmetric effective gene flow. The urban population displayed reduced effective size, evidence of inbreeding, and strong selection pressures for adaptation to urban settings, as suggested by the hard selective sweeps associated with genes involved in detoxification and insecticide resistance. In contrast, the two geographically proximate LLP populations showed larger effective sizes, and distinctive genomic differences in selective signals, notably soft-selective sweeps on the standing genetic variation. Although neutral loci and chromosomal inversions failed to discriminate between LLP populations, our findings support that microgeographic adaptation can swiftly emerge through selection on standing genetic variation despite high gene flow. This study contributes to the growing understanding of evolution of populations in heterogeneous environments amid ongoing gene flow and how major malaria mosquitoes adapt to human. Significance Anopheles coluzzii , a major African malaria vector, thrives from humid rainforests to dry savannahs and coastal areas. This ecological success is linked to its close association with domestic settings, with human playing significant roles in driving the recent urban evolution of this mosquito. Our research explores the assumption that these mosquitoes are strictly dependent on human habitats, by conducting whole-genome sequencing on An. coluzzii specimens from urban, rural, and sylvatic sites in Gabon. We found that urban mosquitoes show de novo genetic signatures of human-driven vector control, while rural and sylvatic mosquitoes exhibit distinctive genetic evidence of local adaptations derived from standing genetic variation. Understanding adaptation mechanisms of this mosquito is therefore crucial to predict evolution of vector control strategies.
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19
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Diamantidis D, Fan WTL, Birkner M, Wakeley J. Bursts of coalescence within population pedigrees whenever big families occur. Genetics 2024; 227:iyae030. [PMID: 38408329 DOI: 10.1093/genetics/iyae030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Revised: 01/23/2024] [Accepted: 02/18/2024] [Indexed: 02/28/2024] Open
Abstract
We consider a simple diploid population-genetic model with potentially high variability of offspring numbers among individuals. Specifically, against a backdrop of Wright-Fisher reproduction and no selection, there is an additional probability that a big family occurs, meaning that a pair of individuals has a number of offspring on the order of the population size. We study how the pedigree of the population generated under this model affects the ancestral genetic process of a sample of size two at a single autosomal locus without recombination. Our population model is of the type for which multiple-merger coalescent processes have been described. We prove that the conditional distribution of the pairwise coalescence time given the random pedigree converges to a limit law as the population size tends to infinity. This limit law may or may not be the usual exponential distribution of the Kingman coalescent, depending on the frequency of big families. But because it includes the number and times of big families, it differs from the usual multiple-merger coalescent models. The usual multiple-merger coalescent models are seen as describing the ancestral process marginal to, or averaging over, the pedigree. In the limiting ancestral process conditional on the pedigree, the intervals between big families can be modeled using the Kingman coalescent but each big family causes a discrete jump in the probability of coalescence. Analogous results should hold for larger samples and other population models. We illustrate these results with simulations and additional analysis, highlighting their implications for inference and understanding of multilocus data.
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Affiliation(s)
| | - Wai-Tong Louis Fan
- Department of Mathematics, Indiana University, Bloomington, IN 47405, USA
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
| | - Matthias Birkner
- Institut für Mathematik, Johannes-Gutenberg-Universität, 55099 Mainz, Germany
| | - John Wakeley
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
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20
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Guo B, Takala-Harrison S, O’Connor TD. Benchmarking and Optimization of Methods for the Detection of Identity-By-Descent in Plasmodium falciparum. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.04.592538. [PMID: 38746392 PMCID: PMC11092787 DOI: 10.1101/2024.05.04.592538] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
Genomic surveillance is crucial for identifying at-risk populations for targeted malaria control and elimination. Identity-by-descent (IBD) is being used in Plasmodium population genomics to estimate genetic relatedness, effective population size ( N e ) , population structure, and positive selection. However, a comprehensive evaluation of IBD segment detection tools is lacking for species with high rates of recombination. Here, we employ genetic simulations reflecting P. falciparum's high recombination rate and decreasing N e to benchmark IBD callers, including probabilistic (hmmIBD, isoRelate), identity-by-state-based (hap-IBD, phased IBD) and others (Refined IBD), using genealogy-based true IBD and downstream inference of population characteristics. Our findings reveal that low marker density per genetic unit, related to high recombination rates relative to mutation rates, significantly affects the quality of detected IBD segments. Most IBD callers suffer from high false negative rates, which can be improved with parameter optimization. Optimized parameters allow for more accurate capture of selection signals and population structure, but hmmIBD is unique in providing less biased estimates of N e . Empirical data subsampled from the MalariaGEN Pf7 database, representing different transmission settings, confirmed these patterns. We conclude that the detection of IBD in high-recombining species requires context-specific evaluation and parameter optimization and recommend that hmmIBD be used for quality-sensitive analysis, such as estimation of N e in these species.
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Affiliation(s)
- Bing Guo
- Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, MD USA
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Shannon Takala-Harrison
- Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, MD USA
| | - Timothy D. O’Connor
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA
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21
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Gutiérrez-Valencia J, Zervakis PI, Postel Z, Fracassetti M, Losvik A, Mehrabi S, Bunikis I, Soler L, Hughes PW, Désamoré A, Laenen B, Abdelaziz M, Pettersson OV, Arroyo J, Slotte T. Genetic Causes and Genomic Consequences of Breakdown of Distyly in Linum trigynum. Mol Biol Evol 2024; 41:msae087. [PMID: 38709782 PMCID: PMC11114476 DOI: 10.1093/molbev/msae087] [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: 11/17/2023] [Revised: 03/22/2024] [Accepted: 04/29/2024] [Indexed: 05/08/2024] Open
Abstract
Distyly is an iconic floral polymorphism governed by a supergene, which promotes efficient pollen transfer and outcrossing through reciprocal differences in the position of sexual organs in flowers, often coupled with heteromorphic self-incompatibility. Distyly has evolved convergently in multiple flowering plant lineages, but has also broken down repeatedly, often resulting in homostylous, self-compatible populations with elevated rates of self-fertilization. Here, we aimed to study the genetic causes and genomic consequences of the shift to homostyly in Linum trigynum, which is closely related to distylous Linum tenue. Building on a high-quality genome assembly, we show that L. trigynum harbors a genomic region homologous to the dominant haplotype of the distyly supergene conferring long stamens and short styles in L. tenue, suggesting that loss of distyly first occurred in a short-styled individual. In contrast to homostylous Primula and Fagopyrum, L. trigynum harbors no fixed loss-of-function mutations in coding sequences of S-linked distyly candidate genes. Instead, floral gene expression analyses and controlled crosses suggest that mutations downregulating the S-linked LtWDR-44 candidate gene for male self-incompatibility and/or anther height could underlie homostyly and self-compatibility in L. trigynum. Population genomic analyses of 224 whole-genome sequences further demonstrate that L. trigynum is highly self-fertilizing, exhibits significantly lower genetic diversity genome-wide, and is experiencing relaxed purifying selection and less frequent positive selection on nonsynonymous mutations relative to L. tenue. Our analyses shed light on the loss of distyly in L. trigynum, and advance our understanding of a common evolutionary transition in flowering plants.
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Affiliation(s)
- Juanita Gutiérrez-Valencia
- Department of Ecology, Environment and Plant Sciences, Science for Life Laboratory, Stockholm University, Stockholm, Sweden
| | - Panagiotis-Ioannis Zervakis
- Department of Ecology, Environment and Plant Sciences, Science for Life Laboratory, Stockholm University, Stockholm, Sweden
| | - Zoé Postel
- Department of Ecology, Environment and Plant Sciences, Science for Life Laboratory, Stockholm University, Stockholm, Sweden
| | - Marco Fracassetti
- Department of Ecology, Environment and Plant Sciences, Science for Life Laboratory, Stockholm University, Stockholm, Sweden
| | - Aleksandra Losvik
- Department of Ecology, Environment and Plant Sciences, Science for Life Laboratory, Stockholm University, Stockholm, Sweden
| | - Sara Mehrabi
- Department of Ecology, Environment and Plant Sciences, Science for Life Laboratory, Stockholm University, Stockholm, Sweden
| | - Ignas Bunikis
- Department of Immunology, Genetics and Pathology, Uppsala Genome Center, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Lucile Soler
- Department of Medical Biochemistry and Microbiology, Uppsala University, National Bioinformatics Infrastructure Sweden (NBIS), Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - P William Hughes
- Department of Ecology, Environment and Plant Sciences, Science for Life Laboratory, Stockholm University, Stockholm, Sweden
| | - Aurélie Désamoré
- Department of Ecology, Environment and Plant Sciences, Science for Life Laboratory, Stockholm University, Stockholm, Sweden
| | - Benjamin Laenen
- Department of Ecology, Environment and Plant Sciences, Science for Life Laboratory, Stockholm University, Stockholm, Sweden
| | | | - Olga Vinnere Pettersson
- Department of Immunology, Genetics and Pathology, Uppsala Genome Center, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Juan Arroyo
- Department of Plant Biology and Ecology, University of Seville, Seville, Spain
| | - Tanja Slotte
- Department of Ecology, Environment and Plant Sciences, Science for Life Laboratory, Stockholm University, Stockholm, Sweden
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22
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Kemppainen P, Schembri R, Momigliano P. Boundary Effects Cause False Signals of Range Expansions in Population Genomic Data. Mol Biol Evol 2024; 41:msae091. [PMID: 38743590 PMCID: PMC11135943 DOI: 10.1093/molbev/msae091] [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: 12/06/2023] [Revised: 04/25/2024] [Accepted: 05/01/2024] [Indexed: 05/16/2024] Open
Abstract
Studying range expansions is central for understanding genetic variation through space and time as well as for identifying refugia and biological invasions. Range expansions are characterized by serial founder events causing clines of decreasing genetic diversity away from the center of origin and asymmetries in the two-dimensional allele frequency spectra. These asymmetries, summarized by the directionality index (ψ), are sensitive to range expansions and persist for longer than clines in genetic diversity. In continuous and finite meta-populations, genetic drift tends to be stronger at the edges of the species distribution in equilibrium populations and populations undergoing range expansions alike. Such boundary effects are expected to affect geographic patterns in genetic diversity and ψ. Here we demonstrate that boundary effects cause high false positive rates in equilibrium meta-populations when testing for range expansions. In the simulations, the absolute value of ψ (|ψ|) in equilibrium data sets was proportional to the fixation index (FST). By fitting signatures of range expansions as a function of ɛ |ψ|/FST and geographic clines in ψ, strong evidence for range expansions could be detected in data from a recent rapid invasion of the cane toad, Rhinella marina, in Australia, but not in 28 previously published empirical data sets from Australian scincid lizards that were significant for the standard range expansion tests. Thus, while clinal variation in ψ is still the most sensitive statistic to range expansions, to detect true signatures of range expansions in natural populations, its magnitude needs to be considered in relation to the overall levels of genetic structuring in the data.
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Affiliation(s)
- Petri Kemppainen
- School of Biological Sciences and Swire Institute of Marine Science, Faculty of Science, The University of Hong Kong, Hong Kong, SAR, People's Republic of China
| | - Rhiannon Schembri
- School of Natural Sciences, Faculty of Science and Engineering, Macquarie University, Sydney, Australia
- Division of Ecology and Evolution, Research School of Biology, Australian National University, Canberra, Australia
| | - Paolo Momigliano
- School of Biological Sciences and Swire Institute of Marine Science, Faculty of Science, The University of Hong Kong, Hong Kong, SAR, People's Republic of China
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23
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Tran LN, Sun CK, Struck TJ, Sajan M, Gutenkunst RN. Computationally Efficient Demographic History Inference from Allele Frequencies with Supervised Machine Learning. Mol Biol Evol 2024; 41:msae077. [PMID: 38636507 PMCID: PMC11082913 DOI: 10.1093/molbev/msae077] [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: 05/24/2023] [Revised: 04/08/2024] [Accepted: 04/12/2024] [Indexed: 04/20/2024] Open
Abstract
Inferring past demographic history of natural populations from genomic data is of central concern in many studies across research fields. Previously, our group had developed dadi, a widely used demographic history inference method based on the allele frequency spectrum (AFS) and maximum composite-likelihood optimization. However, dadi's optimization procedure can be computationally expensive. Here, we present donni (demography optimization via neural network inference), a new inference method based on dadi that is more efficient while maintaining comparable inference accuracy. For each dadi-supported demographic model, donni simulates the expected AFS for a range of model parameters then trains a set of Mean Variance Estimation neural networks using the simulated AFS. Trained networks can then be used to instantaneously infer the model parameters from future genomic data summarized by an AFS. We demonstrate that for many demographic models, donni can infer some parameters, such as population size changes, very well and other parameters, such as migration rates and times of demographic events, fairly well. Importantly, donni provides both parameter and confidence interval estimates from input AFS with accuracy comparable to parameters inferred by dadi's likelihood optimization while bypassing its long and computationally intensive evaluation process. donni's performance demonstrates that supervised machine learning algorithms may be a promising avenue for developing more sustainable and computationally efficient demographic history inference methods.
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Affiliation(s)
- Linh N Tran
- Genetics Graduate Interdisciplinary Program, University of Arizona, Tucson, AZ 85721, USA
- Department of Molecular & Cellular Biology, University of Arizona, Tucson, AZ 85721, USA
| | - Connie K Sun
- Department of Molecular & Cellular Biology, University of Arizona, Tucson, AZ 85721, USA
| | - Travis J Struck
- Department of Molecular & Cellular Biology, University of Arizona, Tucson, AZ 85721, USA
| | - Mathews Sajan
- Department of Molecular & Cellular Biology, University of Arizona, Tucson, AZ 85721, USA
| | - Ryan N Gutenkunst
- Department of Molecular & Cellular Biology, University of Arizona, Tucson, AZ 85721, USA
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24
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Liu X, Zhang W, Zhang Y, Yang J, Zeng P, Tian Z, Sun W, Cai J. Chromosome-scale genomes of Quercus sichourensis and Quercus rex provide insights into the evolution and adaptation of Fagaceae. J Genet Genomics 2024; 51:554-565. [PMID: 38575109 DOI: 10.1016/j.jgg.2024.03.012] [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: 12/26/2023] [Revised: 03/25/2024] [Accepted: 03/28/2024] [Indexed: 04/06/2024]
Abstract
The Fagaceae, a plant family with a wide distribution and diverse adaptability, has garnered significant interest as a subject of study in plant speciation and adaptation. Meanwhile, certain Fagaceae species are regarded as highly valuable wood resources due to the exceptional quality of their wood. In this study, we present two high-quality, chromosome-scale genome sequences for Quercus sichourensis (848.75 Mb) and Quercus rex (883.46 Mb). Comparative genomics analysis reveals that the difference in the number of plant disease resistance genes and the nonsynonymous and synonymous substitution ratio (Ka/Ks) of protein-coding genes among Fagaceae species are related to different environmental adaptations. Interestingly, most genes related to starch synthesis in the investigated Quercoideae species are located on a single chromosome, as compared to the outgroup species, Fagus sylvatica. Furthermore, resequencing and population analysis of Q. sichourensis and Q. rex reveal that Q. sichourensis has lower genetic diversity and higher deleterious mutations compared to Q. rex. The high-quality, chromosome-level genomes and the population genomic analysis of the critically endangered Q. sichourensis and Q. rex will provide an invaluable resource as well as insights for future study in these two species, even the genus Quercus, to facilitate their conservation.
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Affiliation(s)
- Xue Liu
- Shaanxi Key Laboratory of Qinling Ecological Intelligent Monitoring and Protection, School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, Shaanxi 710072, China
| | - Weixiong Zhang
- Shaanxi Key Laboratory of Qinling Ecological Intelligent Monitoring and Protection, School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, Shaanxi 710072, China
| | - Yongting Zhang
- Shaanxi Key Laboratory of Qinling Ecological Intelligent Monitoring and Protection, School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, Shaanxi 710072, China
| | - Jing Yang
- Yunnan Key Laboratory for Integrative Conservation of Plant Species with Extremely Small Populations, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
| | - Peng Zeng
- Shaanxi Key Laboratory of Qinling Ecological Intelligent Monitoring and Protection, School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, Shaanxi 710072, China
| | - Zunzhe Tian
- Shaanxi Key Laboratory of Qinling Ecological Intelligent Monitoring and Protection, School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, Shaanxi 710072, China
| | - Weibang Sun
- Yunnan Key Laboratory for Integrative Conservation of Plant Species with Extremely Small Populations, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China.
| | - Jing Cai
- Shaanxi Key Laboratory of Qinling Ecological Intelligent Monitoring and Protection, School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, Shaanxi 710072, China.
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25
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Kyriazis CC, Serieys LE, Bishop JM, Drouilly M, Viljoen S, Wayne RK, Lohmueller KE. The influence of gene flow on population viability in an isolated urban caracal population. Mol Ecol 2024; 33:e17346. [PMID: 38581173 PMCID: PMC11035096 DOI: 10.1111/mec.17346] [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: 07/20/2023] [Revised: 01/23/2024] [Accepted: 03/26/2024] [Indexed: 04/08/2024]
Abstract
Wildlife populations are becoming increasingly fragmented by anthropogenic development. Small and isolated populations often face an elevated risk of extinction, in part due to inbreeding depression. Here, we examine the genomic consequences of urbanization in a caracal (Caracal caracal) population that has become isolated in the Cape Peninsula region of the City of Cape Town, South Africa, and is thought to number ~50 individuals. We document low levels of migration into the population over the past ~75 years, with an estimated rate of 1.3 effective migrants per generation. As a consequence of this isolation and small population size, levels of inbreeding are elevated in the contemporary Cape Peninsula population (mean FROH = 0.20). Inbreeding primarily manifests as long runs of homozygosity >10 Mb, consistent with the effects of isolation due to the rapid recent growth of Cape Town. To explore how reduced migration and elevated inbreeding may impact future population dynamics, we parameterized an eco-evolutionary simulation model. We find that if migration rates do not change in the future, the population is expected to decline, though with a low projected risk of extinction. However, if migration rates decline or anthropogenic mortality rates increase, the potential risk of extinction is greatly elevated. To avert a population decline, we suggest that translocating migrants into the Cape Peninsula to initiate a genetic rescue may be warranted in the near future. Our analysis highlights the utility of genomic datasets coupled with computational simulation models for investigating the influence of gene flow on population viability.
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Affiliation(s)
- Christopher C. Kyriazis
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA 90095, USA
| | - Laurel E.K. Serieys
- Panthera, 8 W 40th St, 18th Floor, New York, NY 10018, USA
- Institute for Communities and Wildlife in Africa, Department of Biological Sciences, University of Cape Town, Rondebosch, 7701, South Africa
| | - Jacqueline M. Bishop
- Institute for Communities and Wildlife in Africa, Department of Biological Sciences, University of Cape Town, Rondebosch, 7701, South Africa
| | - Marine Drouilly
- Panthera, 8 W 40th St, 18th Floor, New York, NY 10018, USA
- Institute for Communities and Wildlife in Africa, Department of Biological Sciences, University of Cape Town, Rondebosch, 7701, South Africa
- Centre for Social Science Research, University of Cape Town, Rondebosch, 7701, South Africa
| | - Storme Viljoen
- Institute for Communities and Wildlife in Africa, Department of Biological Sciences, University of Cape Town, Rondebosch, 7701, South Africa
| | - Robert K. Wayne
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA 90095, USA
| | - Kirk E. Lohmueller
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA 90095, USA
- Interdepartmental Program in Bioinformatics, University of California, Los Angeles, CA 90095, USA
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA
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26
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Fan Z, Whitaker VM. Genomic signatures of strawberry domestication and diversification. THE PLANT CELL 2024; 36:1622-1636. [PMID: 38113879 PMCID: PMC11062436 DOI: 10.1093/plcell/koad314] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Revised: 11/20/2023] [Accepted: 11/25/2023] [Indexed: 12/21/2023]
Abstract
Cultivated strawberry (Fragaria × ananassa) has a brief history of less than 300 yr, beginning with the hybridization of octoploids Fragaria chiloensis and Fragaria virginiana. Here we explored the genomic signatures of early domestication and subsequent diversification for different climates using whole-genome sequences of 289 wild, heirloom, and modern varieties from two major breeding programs in the United States. Four nonadmixed wild octoploid populations were identified, with recurrent introgression among the sympatric populations. The proportion of F. virginiana ancestry increased by 20% in modern varieties over initial hybrids, and the proportion of F. chiloensis subsp. pacifica rose from 0% to 3.4%. Effective population size rapidly declined during early breeding. Meanwhile, divergent selection for distinct environments reshaped wild allelic origins in 21 out of 28 chromosomes. Overlapping divergent selective sweeps in natural and domesticated populations revealed 16 convergent genomic signatures that may be important for climatic adaptation. Despite 20 breeding cycles since initial hybridization, more than half of loci underlying yield and fruit size are still not under artificial selection. These insights add clarity to the domestication and breeding history of what is now the most widely cultivated fruit in the world.
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Affiliation(s)
- Zhen Fan
- Horticultural Sciences Department, University of Florida, IFAS Gulf Coast Research and Education Center, Wimauma, FL 33597, USA
| | - Vance M Whitaker
- Horticultural Sciences Department, University of Florida, IFAS Gulf Coast Research and Education Center, Wimauma, FL 33597, USA
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27
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Rota F, Carnicero P, Casazza G, Nascimbene J, Schönswetter P, Wellstein C. Survival in nunatak and peripheral glacial refugia of three alpine plant species is partly predicted by altitudinal segregation. Mol Ecol 2024; 33:e17343. [PMID: 38596873 DOI: 10.1111/mec.17343] [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: 09/08/2023] [Accepted: 03/12/2024] [Indexed: 04/11/2024]
Abstract
Mountain biota survived the Quaternary cold stages most probably in peripheral refugia and/or ice-free peaks within ice-sheets (nunataks). While survival in peripheral refugia has been broadly demonstrated, evidence for nunatak refugia is still scarce. We generated RADseq data from three mountain plant species occurring at different elevations in the southeastern European Alps to investigate the role of different glacial refugia during the Last Glacial Maximum (LGM). We tested the following hypotheses. (i) The deep Piave Valley forms the deepest genetic split in the species distributed across it, delimiting two peripheral refugia. (ii) The montane to alpine species Campanula morettiana and Primula tyrolensis survived the LGM in peripheral refugia, while high-alpine to subnival Saxifraga facchinii likely survived in several nunatak refugia. (iii) The lower elevation species suffered a strong population decline during the LGM. By contrast, the higher elevation species shows long-term stability of population sizes due to survival on permanently ice-free peaks and small population sizes at present. We found peripheral refugia on both sides of the Piave Valley, which acted as a major genetic barrier. Demographic modelling confirmed nunatak survival not only for S. facchinii but also for montane to alpine C. morettiana. Altitudinal segregation influenced the species' demographic fluctuations, with the lower elevation species showing a significant population increase at the end of the LGM, and the higher elevation species either showing decrease towards the present or stable population sizes with a short bottleneck. Our results highlight the role of nunatak survival and species ecology in the demographic history of mountain species.
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Affiliation(s)
- Francesco Rota
- Faculty of Agricultural, Environmental and Food Sciences, Free University of Bozen-Bolzano, Bolzano, Italy
- Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Birmensdorf, Switzerland
| | - Pau Carnicero
- Department of Botany, University of Innsbruck, Innsbruck, Austria
| | - Gabriele Casazza
- Department of Earth, Environmental and Life Sciences (DISTAV), University of Genoa, Genova, Italy
| | - Juri Nascimbene
- BIOME Group, Department of Biological, Geological and Environmental Sciences, Alma Mater Studiorum - University of Bologna, Bologna, Italy
| | | | - Camilla Wellstein
- Faculty of Agricultural, Environmental and Food Sciences, Free University of Bozen-Bolzano, Bolzano, Italy
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28
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Diaz-Recio Lorenzo C, Tran Lu Y A, Brunner O, Arbizu PM, Jollivet D, Laurent S, Gollner S. Highly structured populations of copepods at risk to deep-sea mining: Integration of genomic data with demogenetic and biophysical modelling. Mol Ecol 2024; 33:e17340. [PMID: 38605683 DOI: 10.1111/mec.17340] [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: 09/21/2023] [Revised: 02/25/2024] [Accepted: 03/04/2024] [Indexed: 04/13/2024]
Abstract
Copepoda is the most abundant taxon in deep-sea hydrothermal vents, where hard substrate is available. Despite the increasing interest in seafloor massive sulphides exploitation, there have been no population genomic studies conducted on vent meiofauna, which are known to contribute over 50% to metazoan biodiversity at vents. To bridge this knowledge gap, restriction-site-associated DNA sequencing, specifically 2b-RADseq, was used to retrieve thousands of genome-wide single-nucleotide polymorphisms (SNPs) from abundant populations of the vent-obligate copepod Stygiopontius lauensis from the Lau Basin. SNPs were used to investigate population structure, demographic histories and genotype-environment associations at a basin scale. Genetic analyses also helped to evaluate the suitability of tailored larval dispersal models and the parameterization of life-history traits that better fit the population patterns observed in the genomic dataset for the target organism. Highly structured populations were observed on both spatial and temporal scales, with divergence of populations between the north, mid, and south of the basin estimated to have occurred after the creation of the major transform fault dividing the Australian and the Niuafo'ou tectonic plate (350 kya), with relatively recent secondary contact events (<20 kya). Larval dispersal models were able to predict the high levels of structure and the highly asymmetric northward low-level gene flow observed in the genomic data. These results differ from most studies conducted on megafauna in the region, elucidating the need to incorporate smaller size when considering site prospecting for deep-sea exploitation of seafloor massive sulphides, and the creation of area-based management tools to protect areas at risk of local extinction, should mining occur.
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Affiliation(s)
- Coral Diaz-Recio Lorenzo
- Adaptation et Diversité en Milieu Marin (AD2M), Station Biologique de Roscoff, Sorbonne Université, CNRS, Roscoff, France
| | - Adrien Tran Lu Y
- UMR MARBEC, University of Montpellier, IRD, Ifremer, CNRS, Sète, France
| | - Otis Brunner
- Okinawa Institute for Science and Technology, Kunigami-gun, Okinawa, Japan
| | - Pedro Martínez Arbizu
- Senckenberg am Meer, German Centre for Marine Biodiversity Research, Wilhelmshaven, Germany
| | - Didier Jollivet
- Adaptation et Diversité en Milieu Marin (AD2M), Station Biologique de Roscoff, Sorbonne Université, CNRS, Roscoff, France
| | | | - Sabine Gollner
- NIOZ Royal Netherlands Institute for Sea Research and Utrecht University, 't Horntje (Texel), The Netherlands
- Utrecht University, Utrecht, The Netherlands
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29
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Tengstedt ANB, Liu S, Jacobsen MW, Gundlund C, Møller PR, Berg S, Bekkevold D, Hansen MM. Genomic insights on conservation priorities for North Sea houting and European lake whitefish (Coregonus spp.). Mol Ecol 2024:e17367. [PMID: 38686435 DOI: 10.1111/mec.17367] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Revised: 04/08/2024] [Accepted: 04/12/2024] [Indexed: 05/02/2024]
Abstract
Population genomics analysis holds great potential for informing conservation of endangered populations. We focused on a controversial case of European whitefish (Coregonus spp.) populations. The endangered North Sea houting is the only coregonid fish that tolerates oceanic salinities and was previously considered a species (C. oxyrhinchus) distinct from European lake whitefish (C. lavaretus). However, no firm evidence for genetic-based salinity adaptation has been available. Also, studies based on microsatellite and mitogenome data suggested surprisingly recent divergence (c. 2500 years bp) between houting and lake whitefish. These data types furthermore have provided no evidence for possible inbreeding. Finally, a controversial taxonomic revision recently classified all whitefish in the region as C. maraena, calling conservation priorities of houting into question. We used whole-genome and ddRAD sequencing to analyse six lake whitefish populations and the only extant indigenous houting population. Demographic inference indicated post-glacial expansion and divergence between lake whitefish and houting occurring not long after the Last Glaciation, implying deeper population histories than previous analyses. Runs of homozygosity analysis suggested not only high inbreeding (FROH up to 30.6%) in some freshwater populations but also FROH up to 10.6% in the houting prompting conservation concerns. Finally, outlier scans provided evidence for adaptation to high salinities in the houting. Applying a framework for defining conservation units based on current and historical reproductive isolation and adaptive divergence led us to recommend that the houting be treated as a separate conservation unit regardless of species status. In total, the results underscore the potential of genomics to inform conservation practices, in this case clarifying conservation units and highlighting populations of concern.
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Affiliation(s)
| | - Shenglin Liu
- Department of Biology, Aarhus University, Aarhus C, Denmark
| | - Magnus W Jacobsen
- National Institute of Aquatic Resources, Technical University of Denmark, Silkeborg, Denmark
| | | | - Peter Rask Møller
- Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Søren Berg
- National Institute of Aquatic Resources, Technical University of Denmark, Silkeborg, Denmark
| | - Dorte Bekkevold
- National Institute of Aquatic Resources, Technical University of Denmark, Silkeborg, Denmark
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30
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Chen J, Liu C, Li W, Zhang W, Wang Y, Clark AG, Lu J. From sub-Saharan Africa to China: Evolutionary history and adaptation of Drosophila melanogaster revealed by population genomics. SCIENCE ADVANCES 2024; 10:eadh3425. [PMID: 38630810 PMCID: PMC11023512 DOI: 10.1126/sciadv.adh3425] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2023] [Accepted: 03/13/2024] [Indexed: 04/19/2024]
Abstract
Drosophila melanogaster is a widely used model organism for studying environmental adaptation. However, the genetic diversity of populations in Asia is poorly understood, leaving a notable gap in our knowledge of the global evolution and adaptation of this species. We sequenced genomes of 292 D. melanogaster strains from various ecological settings in China and analyzed them along with previously published genome sequences. We have identified six global genetic ancestry groups, despite the presence of widespread genetic admixture. The strains from China represent a unique ancestry group, although detectable differentiation exists among populations within China. We deciphered the global migration and demography of D. melanogaster, and identified widespread signals of adaptation, including genetic changes in response to insecticides. We validated the effects of insecticide resistance variants using population cage trials and deep sequencing. This work highlights the importance of population genomics in understanding the genetic underpinnings of adaptation, an effort that is particularly relevant given the deterioration of ecosystems.
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Affiliation(s)
- Junhao Chen
- State Key Laboratory of Protein and Plant Gene Research, Center for Bioinformatics, School of Life Sciences, Peking University, Beijing 100871, China
| | - Chenlu Liu
- State Key Laboratory of Protein and Plant Gene Research, Center for Bioinformatics, School of Life Sciences, Peking University, Beijing 100871, China
| | - Weixuan Li
- State Key Laboratory of Protein and Plant Gene Research, Center for Bioinformatics, School of Life Sciences, Peking University, Beijing 100871, China
| | - Wenxia Zhang
- State Key Laboratory of Protein and Plant Gene Research, Center for Bioinformatics, School of Life Sciences, Peking University, Beijing 100871, China
| | - Yirong Wang
- College of Biology, Hunan University, Changsha 410082, China
| | - Andrew G. Clark
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Jian Lu
- State Key Laboratory of Protein and Plant Gene Research, Center for Bioinformatics, School of Life Sciences, Peking University, Beijing 100871, China
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Murga-Moreno J, Casillas S, Barbadilla A, Uricchio L, Enard D. An efficient and robust ABC approach to infer the rate and strength of adaptation. G3 (BETHESDA, MD.) 2024; 14:jkae031. [PMID: 38365205 PMCID: PMC11090462 DOI: 10.1093/g3journal/jkae031] [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: 10/10/2023] [Revised: 10/10/2023] [Accepted: 01/29/2024] [Indexed: 02/18/2024]
Abstract
Inferring the effects of positive selection on genomes remains a critical step in characterizing the ultimate and proximate causes of adaptation across species, and quantifying positive selection remains a challenge due to the confounding effects of many other evolutionary processes. Robust and efficient approaches for adaptation inference could help characterize the rate and strength of adaptation in nonmodel species for which demographic history, mutational processes, and recombination patterns are not currently well-described. Here, we introduce an efficient and user-friendly extension of the McDonald-Kreitman test (ABC-MK) for quantifying long-term protein adaptation in specific lineages of interest. We characterize the performance of our approach with forward simulations and find that it is robust to many demographic perturbations and positive selection configurations, demonstrating its suitability for applications to nonmodel genomes. We apply ABC-MK to the human proteome and a set of known virus interacting proteins (VIPs) to test the long-term adaptation in genes interacting with viruses. We find substantially stronger signatures of positive selection on RNA-VIPs than DNA-VIPs, suggesting that RNA viruses may be an important driver of human adaptation over deep evolutionary time scales.
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Affiliation(s)
- Jesús Murga-Moreno
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85719, USA
| | - Sònia Casillas
- Department of Genetics and Microbiology, Universitat Autònoma de Barcelona, Bellaterra, Barcelona 08193, Spain
- Institute of Biotechnology and Biomedicine, Universitat Autònoma de Barcelona, Bellaterra, Barcelona 08193, Spain
| | - Antonio Barbadilla
- Department of Genetics and Microbiology, Universitat Autònoma de Barcelona, Bellaterra, Barcelona 08193, Spain
- Institute of Biotechnology and Biomedicine, Universitat Autònoma de Barcelona, Bellaterra, Barcelona 08193, Spain
| | | | - David Enard
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85719, USA
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Gottscho AD, Mulcahy DG, Leaché AD, de Queiroz K, Lovich RE. Population genomics of flat-tailed horned lizards (Phrynosoma mcallii) informs conservation and management across a fragmented Colorado Desert landscape. Mol Ecol 2024; 33:e17308. [PMID: 38445567 DOI: 10.1111/mec.17308] [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: 11/05/2023] [Revised: 01/23/2024] [Accepted: 02/01/2024] [Indexed: 03/07/2024]
Abstract
Phrynosoma mcallii (flat-tailed horned lizards) is a species of conservation concern in the Colorado Desert of the United States and Mexico. We analysed ddRADseq data from 45 lizards to estimate population structure, infer phylogeny, identify migration barriers, map genetic diversity hotspots, and model demography. We identified the Colorado River as the main geographic feature contributing to population structure, with the populations west of this barrier further subdivided by the Salton Sea. Phylogenetic analysis confirms that northwestern populations are nested within southeastern populations. The best-fit demographic model indicates Pleistocene divergence across the Colorado River, with significant bidirectional gene flow, and a severe Holocene population bottleneck. These patterns suggest that management strategies should focus on maintaining genetic diversity on both sides of the Colorado River and the Salton Sea. We recommend additional lands in the United States and Mexico that should be considered for similar conservation goals as those in the Rangewide Management Strategy. We also recommend periodic rangewide genomic sampling to monitor ongoing attrition of diversity, hybridization, and changing structure due to habitat fragmentation, climate change, and other long-term impacts.
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Affiliation(s)
- Andrew D Gottscho
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
| | - Daniel G Mulcahy
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
- Museum für Naturkunde, Leibniz Institute for Evolution and Biodiversity Science, Berlin, Germany
| | - Adam D Leaché
- Department of Biology, Burke Museum of Natural History and Culture, University of Washington, Seattle, Washington, USA
| | - Kevin de Queiroz
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
| | - Robert E Lovich
- Naval Facilities Engineering Command Southwest, San Diego, California, USA
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Bedoya AM. Botany and geogenomics: Constraining geological hypotheses in the neotropics with large-scale genetic data derived from plants. AMERICAN JOURNAL OF BOTANY 2024:e16306. [PMID: 38557829 DOI: 10.1002/ajb2.16306] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2024] [Accepted: 01/24/2024] [Indexed: 04/04/2024]
Abstract
Decades of empirical research have revealed how the geological history of our planet shaped plant evolution by establishing well-known patterns (e.g., how mountain uplift resulted in high rates of diversification and replicate radiations in montane plant taxa). This follows a traditional approach where botanical data are interpreted in light of geological events. In this synthesis, I instead describe how by integrating natural history, phylogenetics, and population genetics, botanical research can be applied alongside geology and paleontology to inform our understanding of past geological and climatic processes. This conceptual shift aligns with the goals of the emerging field of geogenomics. In the neotropics, plant geogenomics is a powerful tool for the reciprocal exploration of two long standing questions in biology and geology: how the dynamic landscape of the region came to be and how it shaped the evolution of the richest flora. Current challenges that are specific to analytical approaches for plant geogenomics are discussed. I describe the scale at which various geological questions can be addressed from biological data and what makes some groups of plants excellent model systems for geogenomics research. Although plant geogenomics is discussed with reference to the neotropics, the recommendations given here for approaches to plant geogenomics can and should be expanded to exploring long-standing questions on how the earth evolved with the use of plant DNA.
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Affiliation(s)
- Ana M Bedoya
- Department of Biological Sciences, Louisiana State University, Baton Rouge, 70803, LA, USA
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Lyulina AS, Liu Z, Good BH. Linkage equilibrium between rare mutations. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.28.587282. [PMID: 38617331 PMCID: PMC11014483 DOI: 10.1101/2024.03.28.587282] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/16/2024]
Abstract
Recombination breaks down genetic linkage by reshuffling existing variants onto new genetic backgrounds. These dynamics are traditionally quantified by examining the correlations between alleles, and how they decay as a function of the recombination rate. However, the magnitudes of these correlations are strongly influenced by other evolutionary forces like natural selection and genetic drift, making it difficult to tease out the effects of recombination. Here we introduce a theoretical framework for analyzing an alternative family of statistics that measure the homoplasy produced by recombination. We derive analytical expressions that predict how these statistics depend on the rates of recombination and recurrent mutation, the strength of negative selection and genetic drift, and the present-day frequencies of the mutant alleles. We find that the degree of homoplasy can strongly depend on this frequency scale, which reflects the underlying timescales over which these mutations occurred. We show how these scaling properties can be used to isolate the effects of recombination, and discuss their implications for the rates of horizontal gene transfer in bacteria.
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Affiliation(s)
- Anastasia S Lyulina
- Department of Biology, Stanford University, Stanford, CA 94305, USA
- Department of Applied Physics, Stanford University, Stanford, CA 94305, USA
| | - Zhiru Liu
- Department of Applied Physics, Stanford University, Stanford, CA 94305, USA
| | - Benjamin H Good
- Department of Biology, Stanford University, Stanford, CA 94305, USA
- Department of Applied Physics, Stanford University, Stanford, CA 94305, USA
- Chan Zuckerberg Biohub - San Francisco, San Francisco, CA 94158, USA
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35
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Marques V, Hinojosa JC, Dapporto L, Talavera G, Stefanescu C, Gutiérrez D, Vila R. The opposed forces of differentiation and admixture across glacial cycles in the butterfly Aglais urticae. Mol Ecol 2024; 33:e17304. [PMID: 38421113 DOI: 10.1111/mec.17304] [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: 06/07/2023] [Revised: 02/13/2024] [Accepted: 02/15/2024] [Indexed: 03/02/2024]
Abstract
Glacial cycles lead to periodic population interbreeding and isolation in warm-adapted species, which impact genetic structure and evolution. However, the effects of these processes on highly mobile and more cold-tolerant species are not well understood. This study aims to shed light on the phylogeographic history of Aglais urticae, a butterfly species with considerable dispersal ability, and a wide Palearctic distribution reaching the Arctic. Through the analysis of genomic data, four main genetic lineages are identified: European, Sierra Nevada, Sicily/Calabria/Peloponnese, and Eastern. The results indicate that the Sardo-Corsican endemic taxon ichnusa is a distinct species. The split between the relict lineages in southern Europe and the main European lineage is estimated to have happened 400-450 thousand years ago, with admixture observed during the Quaternary glacial cycles, and still ongoing, albeit to a much smaller extent. These results suggest that these lineages may be better treated as subspecific parapatric taxa. Ecological niche modelling supported the existence of both Mediterranean and extra-Mediterranean refugia during the glacial periods, with the main one located on the Atlantic coast. Nevertheless, gene flow between populations was possible, indicating that both differentiation and admixture have acted continuously across glacial cycles in this cold-tolerant butterfly, generally balancing each other but producing differentiated lineages in the southern peninsulas. We conclude that the population dynamics and the processes shaping the population genetic structure of cold-adapted species during the Quaternary ice ages may be different than those classically accepted for warm-adapted species.
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Affiliation(s)
- Valéria Marques
- Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Barcelona, Spain
| | - Joan Carles Hinojosa
- Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Barcelona, Spain
| | - Leonardo Dapporto
- Dipartimento di Biologia, Università degli Studi di Firenze, Sesto Fiorentino, Italy
| | - Gerard Talavera
- Institut Botànic de Barcelona (IBB), CSIC-CMCNB, Barcelona, Spain
| | - Constantí Stefanescu
- Natural Sciences Museum of Granollers, Granollers, Spain
- CREAF, Cerdanyola del Vallès, Spain
| | - David Gutiérrez
- Instituto de Investigación en Cambio Global (IICG), Universidad Rey Juan Carlos, Madrid, Spain
- Área de Biodiversidad y Conservación, Universidad Rey Juan Carlos, Madrid, Spain
| | - Roger Vila
- Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Barcelona, Spain
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Taylor RS, Manseau M, Keobouasone S, Liu P, Mastromonaco G, Solmundson K, Kelly A, Larter NC, Gamberg M, Schwantje H, Thacker C, Polfus J, Andrew L, Hervieux D, Simmons D, Wilson PJ. High genetic load without purging in caribou, a diverse species at risk. Curr Biol 2024; 34:1234-1246.e7. [PMID: 38417444 DOI: 10.1016/j.cub.2024.02.002] [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: 09/05/2023] [Revised: 11/17/2023] [Accepted: 02/01/2024] [Indexed: 03/01/2024]
Abstract
High intra-specific genetic diversity is associated with adaptive potential, which is key for resilience to global change. However, high variation may also support deleterious alleles through genetic load, thereby increasing the risk of inbreeding depression if population sizes decrease. Purging of deleterious variation has been demonstrated in some threatened species. However, less is known about the costs of declines and inbreeding in species with large population sizes and high genetic diversity even though this encompasses many species globally that are expected to undergo population declines. Caribou is a species of ecological and cultural significance in North America with a wide distribution supporting extensive phenotypic variation but with some populations undergoing significant declines resulting in their at-risk status in Canada. We assessed intra-specific genetic variation, adaptive divergence, inbreeding, and genetic load across populations with different demographic histories using an annotated chromosome-scale reference genome and 66 whole-genome sequences. We found high genetic diversity and nine phylogenomic lineages across the continent with adaptive diversification of genes, but also high genetic load among lineages. We found highly divergent levels of inbreeding across individuals, including the loss of alleles by drift but not increased purging in inbred individuals, which had more homozygous deleterious alleles. We also found comparable frequencies of homozygous deleterious alleles between lineages regardless of nucleotide diversity. Thus, further inbreeding may need to be mitigated through conservation efforts. Our results highlight the "double-edged sword" of genetic diversity that may be representative of other species atrisk affected by anthropogenic activities.
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Affiliation(s)
- Rebecca S Taylor
- Landscape Science and Technology, Environment and Climate Change Canada, Colonel By Drive, Ottawa, ON K1S 5B6, Canada.
| | - Micheline Manseau
- Landscape Science and Technology, Environment and Climate Change Canada, Colonel By Drive, Ottawa, ON K1S 5B6, Canada
| | - Sonesinh Keobouasone
- Landscape Science and Technology, Environment and Climate Change Canada, Colonel By Drive, Ottawa, ON K1S 5B6, Canada
| | - Peng Liu
- Landscape Science and Technology, Environment and Climate Change Canada, Colonel By Drive, Ottawa, ON K1S 5B6, Canada
| | | | - Kirsten Solmundson
- Environmental & Life Sciences Graduate Program, Trent University, Peterborough, ON K9L 1Z8, Canada
| | - Allicia Kelly
- Department of Environment and Natural Resources, Government of Northwest Territories, PO Box 900, Fort Smith, NT X0E 0P0, Canada
| | - Nicholas C Larter
- Department of Environment and Natural Resources, Government of Northwest Territories, PO Box 900, Fort Smith, NT X0E 0P0, Canada
| | - Mary Gamberg
- Gamberg Consulting, Jarvis Street, Whitehorse, YK Y1A 2J2, Canada
| | - Helen Schwantje
- British Columbia Ministry of Forest, Lands, Natural Resource Operations, and Rural Development, Labieux Road, Nanaimo, BC V9T 6E9, Canada
| | - Caeley Thacker
- British Columbia Ministry of Forest, Lands, Natural Resource Operations, and Rural Development, Labieux Road, Nanaimo, BC V9T 6E9, Canada
| | - Jean Polfus
- Canadian Wildlife Service - Pacific Region, Environment and Climate Change Canada, 1238 Discovery Avenue, Kelowna, BC V1V 1V9, Canada
| | - Leon Andrew
- Ɂehdzo Got'ı̨nę Gots'ę́ Nákedı (Sahtú Renewable Resources Board), P.O. Box 134, Tulít'a, NT X0E 0K0, Canada
| | - Dave Hervieux
- Alberta Ministry of Environment and Protected Areas, Government of Alberta, 10320-99 Street, Grande Prairie, AB T8V 6J4, Canada
| | - Deborah Simmons
- Ɂehdzo Got'ı̨nę Gots'ę́ Nákedı (Sahtú Renewable Resources Board), P.O. Box 134, Tulít'a, NT X0E 0K0, Canada
| | - Paul J Wilson
- Biology Department, Trent University, East Bank Drive, Peterborough, ON K9L 1Z8, Canada
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37
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Ravikanthachari N, Steward RA, Boggs CL. Patterns of genetic variation and local adaptation of a native herbivore to a lethal invasive plant. Mol Ecol 2024:e17326. [PMID: 38515231 DOI: 10.1111/mec.17326] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Revised: 12/03/2023] [Accepted: 02/19/2024] [Indexed: 03/23/2024]
Abstract
Understanding the evolutionary processes that influence fitness is critical to predicting species' responses to selection. Interactions among evolutionary processes including gene flow, drift and the strength of selection can lead to either local adaptation or maladaptation, especially in heterogenous landscapes. Populations experiencing novel environments or resources are ideal for understanding the mechanisms underlying adaptation or maladaptation, specifically in locally co-evolved interactions. We used the interaction between a native herbivore that oviposits on a patchily distributed introduced plant that in turn causes significant mortality to the larvae to test for signatures of local adaptation in areas where the two co-occurred. We used whole-genome sequencing to explore population structure, patterns of gene flow and signatures of local adaptation. We found signatures of local adaptation in response to the introduced plant in the absence of strong population structure with no genetic differentiation and low genetic variation. Additionally, we found localized allele frequency differences within a single population between habitats with and without the lethal plant, highlighting the effects of strong selection. Finally, we identified that selection was acting on larval ability to feed on the plant rather than on females' ability to avoid oviposition, thus uncovering the specific ontogenetic target of selection. Our work highlights the potential for adaptation to occur in a fine-grained landscape in the presence of gene flow and low genetic variation.
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Affiliation(s)
- Nitin Ravikanthachari
- Department of Biological Sciences, University of South Carolina, Columbia, South Carolina, USA
- Rocky Mountain Biological Laboratory, Crested Butte, Colorado, USA
| | - Rachel A Steward
- Department of Biological Sciences, University of South Carolina, Columbia, South Carolina, USA
- Rocky Mountain Biological Laboratory, Crested Butte, Colorado, USA
- Department of Biology, Lund University, Lund, Sweden
| | - Carol L Boggs
- Department of Biological Sciences, University of South Carolina, Columbia, South Carolina, USA
- Rocky Mountain Biological Laboratory, Crested Butte, Colorado, USA
- School of Earth, Ocean & Environment, University of South Carolina, Columbia, South Carolina, USA
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38
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Caputo B, De Marco CM, Pichler V, Bottà G, Bennett KL, Clarkson CS, Tennessen JA, Weetman D, Miles A, Torre AD. Speciation within the Anopheles gambiae complex: high-throughput whole genome sequencing reveals evidence of a putative new cryptic taxon in 'far-west' Africa. RESEARCH SQUARE 2024:rs.3.rs-3914444. [PMID: 38562903 PMCID: PMC10984024 DOI: 10.21203/rs.3.rs-3914444/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
The two main Afrotropical malaria vectors - Anopheles coluzzii and An. gambiae - are genetically distinct and reproductively isolated across West Africa. However, populations at the western extreme of their range are assigned as "intermediate" between the two species by whole genome sequence (WGS) data, and as hybrid forms by conventional molecular diagnostics. By exploiting WGS data from 1,190 specimens collected across west Africa via the Anopheles gambiae 1000 Genomes network, we identify a novel putative taxon in the far-west (provisionally named Bissau molecular form), which did not arise by admixture but rather originated at the same time as the split between An. coluzzii and An. gambiae. Intriguingly, these populations lack insecticide resistance mechanisms commonly observed in the two main species. These findings lead to a change of perspective on malaria vector species in the far-west region with potential for epidemiological implications, and a new challenge for genetic-based mosquito control approaches.
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Affiliation(s)
- B Caputo
- Dipartimento di Sanità Pubblica e Malattie Infettive, Istituto Pasteur Italia-Fondazione Cenci-Bolognetti, Università di Roma "Sapienza", Rome Italy
| | - C M De Marco
- Dipartimento di Sanità Pubblica e Malattie Infettive, Istituto Pasteur Italia-Fondazione Cenci-Bolognetti, Università di Roma "Sapienza", Rome Italy
| | - V Pichler
- Dipartimento di Sanità Pubblica e Malattie Infettive, Istituto Pasteur Italia-Fondazione Cenci-Bolognetti, Università di Roma "Sapienza", Rome Italy
| | - G Bottà
- Dipartimento di Sanità Pubblica e Malattie Infettive, Istituto Pasteur Italia-Fondazione Cenci-Bolognetti, Università di Roma "Sapienza", Rome Italy
| | - K L Bennett
- Wellcome Sanger Genomic Surveillance Unit, Wellcome Sanger Institute, Hinxton, Cambridge, UK
| | - C S Clarkson
- Wellcome Sanger Genomic Surveillance Unit, Wellcome Sanger Institute, Hinxton, Cambridge, UK
| | - J A Tennessen
- Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Broad Institute, Cambridge, MA, USA
| | - D Weetman
- Liverpool School of Tropical Medicine, Liverpool, UK
| | - A Miles
- Wellcome Sanger Genomic Surveillance Unit, Wellcome Sanger Institute, Hinxton, Cambridge, UK
| | - A Della Torre
- Dipartimento di Sanità Pubblica e Malattie Infettive, Istituto Pasteur Italia-Fondazione Cenci-Bolognetti, Università di Roma "Sapienza", Rome Italy
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39
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Coelho JFR, Mendes LDF, Di Dario F, Carvalho PH, Dias RM, Lima SMQ, Verba JT, Pereira RJ. Integration of genomic and ecological methods inform management of an undescribed, yet highly exploited, sardine species. Proc Biol Sci 2024; 291:20232746. [PMID: 38444338 PMCID: PMC10915539 DOI: 10.1098/rspb.2023.2746] [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: 12/05/2023] [Accepted: 02/06/2024] [Indexed: 03/07/2024] Open
Abstract
Assessing genetic diversity within species is key for conservation strategies in the context of human-induced biotic changes. This is important in marine systems, where many species remain undescribed while being overfished, and conflicts between resource-users and conservation agencies are common. Combining niche modelling with population genomics can contribute to resolving those conflicts by identifying management units and understanding how past climatic cycles resulted in current patterns of genetic diversity. We addressed these issues on an undescribed but already overexploited species of sardine of the genus Harengula. We find that the species distribution is determined by salinity and depth, with a continuous distribution along the Brazilian mainland and two disconnected oceanic archipelagos. Genomic data indicate that such biogeographic barriers are associated with two divergent intraspecific lineages. Changes in habitat availability during the last glacial cycle led to different demographic histories among stocks. One coastal population experienced a 3.6-fold expansion, whereas an island-associated population contracted 3-fold, relative to the size of the ancestral population. Our results indicate that the island population should be managed separately from the coastal population, and that a Marine Protected Area covering part of the island population distribution can support the viability of this lineage.
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Affiliation(s)
- Jéssica Fernanda Ramos Coelho
- Departamento de Botânica e Zoologia, Universidade Federal do Rio Grande do Norte, Avenida Senador Salgado Filho S/N, Campus Universitário, 59078-970, Natal/RN, Brazil
| | - Liana de Figueiredo Mendes
- Departamento de Ecologia, Universidade Federal do Rio Grande do Norte, Avenida Senador Salgado Filho S/N, Campus Universitário, 59078-970, Natal/RN, Brazil
| | - Fabio Di Dario
- Instituto de Biodiversidade e Sustentabilidade - Universidade Federal do Rio de Janeiro, Avenida São José do Barreto, 764, 27965-045, Macaé/RJ, Brazil
| | - Pedro Hollanda Carvalho
- Instituto de Biodiversidade e Sustentabilidade - Universidade Federal do Rio de Janeiro, Avenida São José do Barreto, 764, 27965-045, Macaé/RJ, Brazil
| | - Ricardo Marques Dias
- Museu Nacional, Universidade Federal do Rio de Janeiro, Quinta da Boa Vista - São Cristóvão, 20940-040, Rio de Janeiro/RJ, Brazil
| | - Sergio Maia Queiroz Lima
- Departamento de Botânica e Zoologia, Universidade Federal do Rio Grande do Norte, Avenida Senador Salgado Filho S/N, Campus Universitário, 59078-970, Natal/RN, Brazil
| | - Julia Tovar Verba
- Evolutionary Biology, Ludwig Maximilian University of Munich, Grosshaderner Strasse 2, 82152, Planegg-Martinsried, Germany
| | - Ricardo J. Pereira
- Evolutionary Biology, Ludwig Maximilian University of Munich, Grosshaderner Strasse 2, 82152, Planegg-Martinsried, Germany
- Department of Zoology, State Museum of Natural History Stuttgart, Rosenstein 1–3, 70191, Stuttgart, Germany
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40
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Nosil P, Gompert Z, Funk DJ. Divergent dynamics of sexual and habitat isolation at the transition between stick insect populations and species. Nat Commun 2024; 15:2273. [PMID: 38480699 PMCID: PMC10937975 DOI: 10.1038/s41467-024-46294-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Accepted: 02/22/2024] [Indexed: 03/17/2024] Open
Abstract
Speciation is often viewed as a continuum along which populations diverge until they become reproductively-isolated species. However, such divergence may be heterogeneous, proceeding in fits and bursts, rather than being uniform and gradual. We show in Timema stick insects that one component of reproductive isolation evolves non-uniformly across this continuum, whereas another does not. Specifically, we use thousands of host-preference and mating trials to study habitat and sexual isolation among 42 pairs of taxa spanning a range of genomic differentiation and divergence time. We find that habitat isolation is uncoupled from genomic differentiation within species, but accumulates linearly with it between species. In contrast, sexual isolation accumulates linearly across the speciation continuum, and thus exhibits similar dynamics to morphological traits not implicated in reproductive isolation. The results show different evolutionary dynamics for different components of reproductive isolation and highlight a special relevance for species status in the process of speciation.
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Affiliation(s)
- Patrik Nosil
- CEFE, Univ Montpellier, CNRS, EPHE, IRD, Montpellier, France
| | | | - Daniel J Funk
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA.
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41
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Judson JM, Hoekstra LA, Janzen FJ. Demographic history and genomic signatures of selection in a widespread vertebrate ectotherm. Mol Ecol 2024; 33:e17269. [PMID: 38234254 PMCID: PMC10922411 DOI: 10.1111/mec.17269] [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: 09/27/2023] [Revised: 12/20/2023] [Accepted: 01/08/2024] [Indexed: 01/19/2024]
Abstract
Environmental conditions vary greatly across large geographic ranges, and yet certain species inhabit entire continents. In such species, genomic sequencing can inform our understanding of colonization history and the impact of selection on the genome as populations experience diverse local environments. As ectothermic vertebrates are among the most vulnerable to environmental change, it is critical to understand the contributions of local adaptation to population survival. Widespread ectotherms offer an opportunity to explore how species can successfully inhabit such differing environments and how future climatic shifts will impact species' survival. In this study, we investigated the widespread painted turtle (Chrysemys picta) to assess population genomic structure, demographic history, and genomic signatures of selection in the western extent of the range. We found support for a substantial role of serial founder effects in shaping population genomic structure: demographic analysis and runs of homozygosity were consistent with bottlenecks of increasing severity from eastern to western populations during and following the Last Glacial Maximum, and edge populations were more strongly diverged and had less genetic diversity than those from the centre of the range. We also detected outlier loci, but allelic patterns in many loci could be explained by either genetic surfing or selection. While range expansion complicates the identification of loci under selection, we provide candidates for future study of local adaptation in a long-lived, widespread ectotherm that faces an uncertain future as the global climate continues to rapidly change.
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Affiliation(s)
- Jessica M. Judson
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA 50011, USA
- Current Address: W. K. Kellogg Biological Station, Departments of Fisheries and Wildlife & Integrative Biology, Michigan State University, Hickory Corners, MI 49060, USA
| | - Luke A. Hoekstra
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA 50011, USA
- Current Address: Department of Integrative Biology, Oklahoma State University, Stillwater, OK 74078, USA
| | - Fredric J. Janzen
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA 50011, USA
- Current Address: W. K. Kellogg Biological Station, Departments of Fisheries and Wildlife & Integrative Biology, Michigan State University, Hickory Corners, MI 49060, USA
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Herman RW, Clucas G, Younger J, Bates J, Robinson B, Reddy S, Stepanuk J, O'Brien K, Veeramah K, Lynch HJ. Whole genome sequencing reveals stepping-stone dispersal buffered against founder effects in a range expanding seabird. Mol Ecol 2024; 33:e17282. [PMID: 38299701 DOI: 10.1111/mec.17282] [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: 06/02/2023] [Revised: 12/20/2023] [Accepted: 01/04/2024] [Indexed: 02/02/2024]
Abstract
Many species are shifting their ranges in response to climate-driven environmental changes, particularly in high-latitude regions. However, the patterns of dispersal and colonization during range shifting events are not always clear. Understanding how populations are connected through space and time can reveal how species navigate a changing environment. Here, we present a fine-scale population genomics study of gentoo penguins (Pygoscelis papua), a presumed site-faithful colonial nesting species that has increased in population size and expanded its range south along the Western Antarctic Peninsula. Using whole genome sequencing, we analysed 129 gentoo penguin individuals across 12 colonies located at or near the southern range edge. Through a detailed examination of fine-scale population structure, admixture, and population divergence, we inferred that gentoo penguins historically dispersed rapidly in a stepping-stone pattern from the South Shetland Islands leading to the colonization of Anvers Island, and then the adjacent mainland Western Antarctica Peninsula. Recent southward expansion along the Western Antarctic Peninsula also followed a stepping-stone dispersal pattern coupled with limited post-divergence gene flow from colonies on Anvers Island. Genetic diversity appeared to be maintained across colonies during the historical dispersal process, and range-edge populations are still growing. This suggests large numbers of migrants may provide a buffer against founder effects at the beginning of colonization events to maintain genetic diversity similar to that of the source populations before migration ceases post-divergence. These results coupled with a continued increase in effective population size since approximately 500-800 years ago distinguish gentoo penguins as a robust species that is highly adaptable and resilient to changing climate.
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Affiliation(s)
- Rachael W Herman
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, New York, USA
| | - Gemma Clucas
- Cornell Lab of Ornithology, Cornell University, Ithaca, New York, USA
| | - Jane Younger
- Institute for Marine and Antarctic Studies, University of Tasmania, Hobart, Tasmania, Australia
| | - John Bates
- Negaunee Integrative Research Center, The Field Museum of Natural History, Chicago, Illinois, USA
| | - Bryce Robinson
- Cornell Lab of Ornithology, Cornell University, Ithaca, New York, USA
| | - Sushma Reddy
- Bell Museum of Natural History and Department of Fisheries, Wildlife and Conservation Biology, University of Minnesota, St. Paul, Minnesota, USA
| | - Julia Stepanuk
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, New York, USA
| | - Katie O'Brien
- Milner Centre for Evolution, University of Bath, Bath, UK
| | - Krishna Veeramah
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, New York, USA
| | - Heather J Lynch
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, New York, USA
- Institute for Advanced Computational Sciences, Stony Brook University, Stony Brook, New York, USA
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43
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Jiao X, Wu L, Zhang D, Wang H, Dong F, Yang L, Wang S, Amano HE, Zhang W, Jia C, Rheindt FE, Lei F, Song G. Landscape Heterogeneity Explains the Genetic Differentiation of a Forest Bird across the Sino-Himalayan Mountains. Mol Biol Evol 2024; 41:msae027. [PMID: 38318973 PMCID: PMC10919924 DOI: 10.1093/molbev/msae027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Revised: 01/26/2024] [Accepted: 01/31/2024] [Indexed: 02/07/2024] Open
Abstract
Mountains are the world's most important centers of biodiversity. The Sino-Himalayan Mountains are global biodiversity hotspot due to their extremely high species richness and endemicity. Ample research investigated the impact of the Qinghai-Tibet Plateau uplift and Quaternary glaciations in driving species diversification in plants and animals across the Sino-Himalayan Mountains. However, little is known about the role of landscape heterogeneity and other environmental features in driving diversification in this region. We utilized whole genomes and phenotypic data in combination with landscape genetic approaches to investigate population structure, demography, and genetic diversity in a forest songbird species native to the Sino-Himalayan Mountains, the red-billed leiothrix (Leiothrix lutea). We identified 5 phylogeographic clades, including 1 in the East of China, 1 in Yunnan, and 3 in Tibet, roughly consistent with differences in song and plumage coloration but incongruent with traditional subspecies boundaries. Isolation-by-resistance model best explained population differentiation within L. lutea, with extensive secondary contact after allopatric isolation leading to admixture among clades. Ecological niche modeling indicated relative stability in the extent of suitable distribution areas of the species across Quaternary glacial cycles. Our results underscore the importance of mountains in the diversification of this species, given that most of the distinct genetic clades are concentrated in a relatively small area in the Sino-Himalayan Mountain region, while a single shallow clade populates vast lower-lying areas to the east. This study highlights the crucial role of landscape heterogeneity in promoting differentiation and provides a deep genomic perspective on the mechanisms through which diversity hotspots form.
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Affiliation(s)
- Xiaolu Jiao
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Lei Wu
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Dezhi Zhang
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Huan Wang
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Feng Dong
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
| | - Le Yang
- Tibet Plateau Institute of Biology, Lhasa 850000, China
| | - Shangyu Wang
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | | | - Weiwei Zhang
- Center for Wildlife Resources Conservation Research, Jiangxi Agricultural University, Nanchang, China
| | - Chenxi Jia
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Frank E Rheindt
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - Fumin Lei
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Gang Song
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
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44
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La Rocca LA, Frank J, Bentzen HB, Pantel JT, Gerischer K, Bovier A, Krawitz PM. Understanding recessive disease risk in multi-ethnic populations with different degrees of consanguinity. Am J Med Genet A 2024; 194:e63452. [PMID: 37921563 DOI: 10.1002/ajmg.a.63452] [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: 09/30/2023] [Accepted: 10/10/2023] [Indexed: 11/04/2023]
Abstract
Population medical genetics aims at translating clinically relevant findings from recent studies of large cohorts into healthcare for individuals. Genetic counseling concerning reproductive risks and options is still mainly based on family history, and consanguinity is viewed to increase the risk for recessive diseases regardless of the demographics. However, in an increasingly multi-ethnic society with diverse approaches to partner selection, healthcare professionals should also sharpen their intuition for the influence of different mating schemes in non-equilibrium dynamics. We, therefore, revisited the so-called out-of-Africa model and studied in forward simulations with discrete and not overlapping generations the effect of inbreeding on the average number of recessive lethals in the genome. We were able to reproduce in both frameworks the drop in the incidence of recessive disorders, which is a transient phenomenon during and after the growth phase of a population, and therefore showed their equivalence. With the simulation frameworks, we also provide the means to study and visualize the effect of different kin sizes and mating schemes on these parameters for educational purposes.
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Affiliation(s)
- Luis A La Rocca
- Institute for Applied Mathematics, University of Bonn, Bonn, Germany
| | - Julia Frank
- Institute for Genomic Statistics and Bioinformatics, University of Bonn, Bonn, Germany
| | - Heidi Beate Bentzen
- Centre for Medical Ethics, Faculty of Medicine, Univeristy of Oslo, Oslo, Norway
| | - Jean Tori Pantel
- Department of Digitalization and General Practice, University Hospital RWTH Aachen, Aachen, Germany
| | - Konrad Gerischer
- Institute for Genomic Statistics and Bioinformatics, University of Bonn, Bonn, Germany
| | - Anton Bovier
- Institute for Genomic Statistics and Bioinformatics, University of Bonn, Bonn, Germany
| | - Peter M Krawitz
- Institute for Applied Mathematics, University of Bonn, Bonn, Germany
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45
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Kessler C, Shafer ABA. Genomic Analyses Capture the Human-Induced Demographic Collapse and Recovery in a Wide-Ranging Cervid. Mol Biol Evol 2024; 41:msae038. [PMID: 38378172 PMCID: PMC10917209 DOI: 10.1093/molbev/msae038] [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: 08/15/2023] [Revised: 02/08/2024] [Accepted: 02/14/2024] [Indexed: 02/22/2024] Open
Abstract
The glacial cycles of the Quaternary heavily impacted species through successions of population contractions and expansions. Similarly, populations have been intensely shaped by human pressures such as unregulated hunting and land use changes. White-tailed and mule deer survived in different refugia through the Last Glacial Maximum, and their populations were severely reduced after the European colonization. Here, we analyzed 73 resequenced deer genomes from across their North American range to understand the consequences of climatic and anthropogenic pressures on deer demographic and adaptive history. We found strong signals of climate-induced vicariance and demographic decline; notably, multiple sequentially Markovian coalescent recovers a severe decline in mainland white-tailed deer effective population size (Ne) at the end of the Last Glacial Maximum. We found robust evidence for colonial overharvest in the form of a recent and dramatic drop in Ne in all analyzed populations. Historical census size and restocking data show a clear parallel to historical Ne estimates, and temporal Ne/Nc ratio shows patterns of conservation concern for mule deer. Signatures of selection highlight genes related to temperature, including a cold receptor previously highlighted in woolly mammoth. We also detected immune genes that we surmise reflect the changing land use patterns in North America. Our study provides a detailed picture of anthropogenic and climatic-induced decline in deer diversity and clues to understanding the conservation concerns of mule deer and the successful demographic recovery of white-tailed deer.
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Affiliation(s)
- Camille Kessler
- Environmental and Life Sciences Graduate Program, Trent University, Peterborough, Ontario, Canada
| | - Aaron B A Shafer
- Environmental and Life Sciences Graduate Program, Trent University, Peterborough, Ontario, Canada
- Department of Forensic Science, Trent University, Peterborough, Ontario, Canada
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46
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Buffalo V, Kern AD. A quantitative genetic model of background selection in humans. PLoS Genet 2024; 20:e1011144. [PMID: 38507461 PMCID: PMC10984650 DOI: 10.1371/journal.pgen.1011144] [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: 09/17/2023] [Revised: 04/01/2024] [Accepted: 01/19/2024] [Indexed: 03/22/2024] Open
Abstract
Across the human genome, there are large-scale fluctuations in genetic diversity caused by the indirect effects of selection. This "linked selection signal" reflects the impact of selection according to the physical placement of functional regions and recombination rates along chromosomes. Previous work has shown that purifying selection acting against the steady influx of new deleterious mutations at functional portions of the genome shapes patterns of genomic variation. To date, statistical efforts to estimate purifying selection parameters from linked selection models have relied on classic Background Selection theory, which is only applicable when new mutations are so deleterious that they cannot fix in the population. Here, we develop a statistical method based on a quantitative genetics view of linked selection, that models how polygenic additive fitness variance distributed along the genome increases the rate of stochastic allele frequency change. By jointly predicting the equilibrium fitness variance and substitution rate due to both strong and weakly deleterious mutations, we estimate the distribution of fitness effects (DFE) and mutation rate across three geographically distinct human samples. While our model can accommodate weaker selection, we find evidence of strong selection operating similarly across all human samples. Although our quantitative genetic model of linked selection fits better than previous models, substitution rates of the most constrained sites disagree with observed divergence levels. We find that a model incorporating selective interference better predicts observed divergence in conserved regions, but overall our results suggest uncertainty remains about the processes generating fitness variation in humans.
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Affiliation(s)
- Vince Buffalo
- Department of Integrative Biology, University of California, Berkeley, Berkeley, California, United States of America
- Institute of Ecology and Evolution and Department of Biology, University of Oregon, Eugene, Oregon, United States of America
| | - Andrew D. Kern
- Institute of Ecology and Evolution and Department of Biology, University of Oregon, Eugene, Oregon, United States of America
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47
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Hu Y, Hu Y, Zhou W, Wei F. Conservation Genomics and Metagenomics of Giant and Red Pandas in the Wild. Annu Rev Anim Biosci 2024; 12:69-89. [PMID: 37863091 DOI: 10.1146/annurev-animal-021022-054730] [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] [Indexed: 10/22/2023]
Abstract
Giant pandas and red pandas are endangered species with similar specialized bamboo diet and partial sympatric distribution in China. Over the last two decades, the rapid development of genomics and metagenomics research on these species has enriched our knowledge of their biology, ecology, physiology, genetics, and evolution, which is crucial and useful for their conservation. We describe the evolutionary history, endangerment processes, genetic diversity, and population structure of wild giant pandas and two species of red pandas (Chinese and Himalayan red pandas). In addition, we explore how genomics and metagenomics studies have provided insight into the convergent adaptation of pandas to the specialized bamboo diet. Finally, we discuss how these findings are applied to effective conservation management of giant and red pandas in the wild and in captivity to promote the long-term persistence of these species.
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Affiliation(s)
- Yisi Hu
- College of Forestry, Jiangxi Agricultural University, Nanchang, China;
- Center for Evolution and Conservation Biology, Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Yibo Hu
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Wenliang Zhou
- Center for Evolution and Conservation Biology, Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
| | - Fuwen Wei
- College of Forestry, Jiangxi Agricultural University, Nanchang, China;
- Center for Evolution and Conservation Biology, Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
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48
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Tran LN, Sun CK, Struck TJ, Sajan M, Gutenkunst RN. Computationally efficient demographic history inference from allele frequencies with supervised machine learning. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.05.24.542158. [PMID: 38405827 PMCID: PMC10888863 DOI: 10.1101/2023.05.24.542158] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/27/2024]
Abstract
Inferring past demographic history of natural populations from genomic data is of central concern in many studies across research fields. Previously, our group had developed dadi, a widely used demographic history inference method based on the allele frequency spectrum (AFS) and maximum composite likelihood optimization. However, dadi's optimization procedure can be computationally expensive. Here, we developed donni (demography optimization via neural network inference), a new inference method based on dadi that is more efficient while maintaining comparable inference accuracy. For each dadi-supported demographic model, donni simulates the expected AFS for a range of model parameters then trains a set of Mean Variance Estimation neural networks using the simulated AFS. Trained networks can then be used to instantaneously infer the model parameters from future input data AFS. We demonstrated that for many demographic models, donni can infer some parameters, such as population size changes, very well and other parameters, such as migration rates and times of demographic events, fairly well. Importantly, donni provides both parameter and confidence interval estimates from input AFS with accuracy comparable to parameters inferred by dadi's likelihood optimization while bypassing its long and computationally intensive evaluation process. donni's performance demonstrates that supervised machine learning algorithms may be a promising avenue for developing more sustainable and computationally efficient demographic history inference methods.
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Affiliation(s)
- Linh N. Tran
- Genetics Graduate Interdisciplinary Program, University of Arizona, Tucson, AZ, USA
- Department of Molecular & Cellular Biology, University of Arizona, Tucson, AZ, USA
| | - Connie K. Sun
- Department of Molecular & Cellular Biology, University of Arizona, Tucson, AZ, USA
| | - Travis J. Struck
- Department of Molecular & Cellular Biology, University of Arizona, Tucson, AZ, USA
| | - Mathews Sajan
- Department of Molecular & Cellular Biology, University of Arizona, Tucson, AZ, USA
| | - Ryan N. Gutenkunst
- Department of Molecular & Cellular Biology, University of Arizona, Tucson, AZ, USA
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49
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Filatov DA, Kirkpatrick M. How does evolution work in superabundant microbes? Trends Microbiol 2024:S0966-842X(24)00024-6. [PMID: 38360431 DOI: 10.1016/j.tim.2024.01.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Revised: 01/24/2024] [Accepted: 01/26/2024] [Indexed: 02/17/2024]
Abstract
Marine phytoplankton play crucial roles in the Earth's ecological, chemical, and geological processes. They are responsible for about half of global primary production and drive the ocean biological carbon pump. Understanding how plankton species may adapt to the Earth's rapidly changing environments is evidently an urgent priority. This problem requires evolutionary genetic approaches as evolution occurs at the level of allele frequency change within populations driven by genetic drift and natural selection (microevolution). Plankters such as the coccolithophore Gephyrocapsa huxleyi and the cyanobacterium Prochlorococcus 'marinus' are among Earth's most abundant organisms. In this opinion paper we discuss how evolution in astronomically large populations of superabundant microbes (SAMs) may act fundamentally differently than it does in the populations of more modest size found in well-studied organisms. This offers exciting opportunities to study evolution in the conditions that have yet to be explored and also leads to unique challenges. Exploring these opportunities and challenges is the goal of this article.
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Affiliation(s)
- Dmitry A Filatov
- Department of Biology, University of Oxford, Oxford, OX1 3RB, UK.
| | - Mark Kirkpatrick
- Department of Integrative Biology, University of Texas, Austin, TX 78712, USA
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50
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Zurita AMI, Kyriazis CC, Lohmueller KE. The impact of non-neutral synonymous mutations when inferring selection on non-synonymous mutations. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.07.579314. [PMID: 38370782 PMCID: PMC10871344 DOI: 10.1101/2024.02.07.579314] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/20/2024]
Abstract
The distribution of fitness effects (DFE) describes the proportions of new mutations that have different effects on reproductive fitness. Accurate measurements of the DFE are important because the DFE is a fundamental parameter in evolutionary genetics and has implications for our understanding of other phenomena like complex disease or inbreeding depression. Current computational methods to infer the DFE for nonsynonymous mutations from natural variation first estimate demographic parameters from synonymous variants to control for the effects of demography and background selection. Then, conditional on these parameters, the DFE is then inferred for nonsynonymous mutations. This approach relies on the assumption that synonymous variants are neutrally evolving. However, some evidence points toward synonymous mutations having measurable effects on fitness. To test whether selection on synonymous mutations affects inference of the DFE of nonsynonymous mutations, we simulated several possible models of selection on synonymous mutations using SLiM and attempted to recover the DFE of nonsynonymous mutations using Fit∂a∂i, a common method for DFE inference. Our results show that the presence of selection on synonymous variants leads to incorrect inferences of recent population growth. Furthermore, under certain parameter combinations, inferences of the DFE can have an inflated proportion of highly deleterious nonsynonymous mutations. However, this bias can be eliminated if the correct demographic parameters are used for DFE inference instead of the biased ones inferred from synonymous variants. Our work demonstrates how unmodeled selection on synonymous mutations may affect downstream inferences of the DFE.
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Affiliation(s)
- Aina Martinez I Zurita
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, USA
| | - Christopher C Kyriazis
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, USA
| | - Kirk E Lohmueller
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, USA
- Interdepartmental Program in Bioinformatics, University of California, Los Angeles, USA
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, USA
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