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Almeida TE, Santos Leal BS. Recurrent allopolyploidy and its implications for conservation in vascular plants: a commentary on 'Population genomics of the Isoetes appalachiana (Isoetaceae) complex supports a "diploids-first" approach to conservation'. ANNALS OF BOTANY 2024; 133:i-ii. [PMID: 38183619 PMCID: PMC11005762 DOI: 10.1093/aob/mcad201] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/08/2024]
Abstract
This article comments on:
David Wickell, Jacob Landis, Elizabeth Zimmer and Fay-Wei Li, Population genomics of the Isoetes appalachiana (Isoetaceae) complex supports a ‘diploids-first’ approach to conservation, Annals of Botany, Volume 133, Issue 2, 01 February 2024, Pages 261–272, https://doi.org/10.1093/aob/mcad180
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Affiliation(s)
- Thaís Elias Almeida
- Universidade Federal de Pernambuco, Centro de Biociências, Departamento de Botânica, Avenida Professor Moraes Rego – 1235, 50.670-420, Recife, PE, Brazil
| | - Bárbara Simões Santos Leal
- Instituto Tecnológico Vale Desenvolvimento Sustentável, Grupo de Biodiversidade e Serviços Ecossistêmicos, Rua Boaventura da Silva – 955, 66.055-090, Belém, PA, Brazil
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Aihara T, Araki K, Onuma Y, Cai Y, Paing AMM, Goto S, Hisamoto Y, Tomaru N, Homma K, Takagi M, Yoshida T, Iio A, Nagamatsu D, Kobayashi H, Hirota M, Uchiyama K, Tsumura Y. Divergent mechanisms of reduced growth performance in Betula ermanii saplings from high-altitude and low-latitude range edges. Heredity (Edinb) 2023; 131:387-397. [PMID: 37940658 PMCID: PMC10673911 DOI: 10.1038/s41437-023-00655-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Revised: 10/13/2023] [Accepted: 10/13/2023] [Indexed: 11/10/2023] Open
Abstract
The reduced growth performance of individuals from range edges is a common phenomenon in various taxa, and considered to be an evolutionary factor that limits the species' range. However, most studies did not distinguish between two mechanisms that can lead to this reduction: genetic load and adaptive selection to harsh conditions. To address this lack of understanding, we investigated the climatic and genetic factors underlying the growth performance of Betula ermanii saplings transplanted from 11 populations including high-altitude edge and low-latitude edge population. We estimated the climatic position of the populations within the overall B. ermanii's distribution, and the genetic composition and diversity using restriction-site associated DNA sequencing, and measured survival, growth rates and individual size of the saplings. The high-altitude edge population (APW) was located below the 95% significance interval for the mean annual temperature range, but did not show any distinctive genetic characteristics. In contrast, the low-latitude edge population (SHK) exhibited a high level of linkage disequilibrium, low genetic diversity, a distinct genetic composition from the other populations, and a high relatedness coefficient. Both APW and SHK saplings displayed lower survival rates, heights and diameters, while SHK saplings also exhibited lower growth rates than the other populations' saplings. The low heights and diameters of APW saplings was likely the result of adaptive selection to harsh conditions, while the low survival and growth rates of SHK saplings was likely the result of genetic load. Our findings shed light on the mechanisms underlying the reduced growth performance of range-edge populations.
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Affiliation(s)
- Takaki Aihara
- Graduate School of Life and Environmental Sciences, University of Tsukuba, 1-1-1, Tennodai, Tsukuba, Ibaraki, 305-8577, Japan
| | - Kyoko Araki
- Garden Division, Maintenance and Works Department, the Imperial Household Agency, 1-1, Chiyoda, Chiyoda-ku, Tokyo, 100-8111, Japan
- Graduate School of Science and Technology, University of Tsukuba, 1-1-1, Tennodai, Tsukuba, Ibaraki, 305-8577, Japan
| | - Yunosuke Onuma
- Graduate School of Life and Environmental Sciences, University of Tsukuba, 1-1-1, Tennodai, Tsukuba, Ibaraki, 305-8577, Japan
| | - Yihan Cai
- Graduate School of Environmental Science, Hokkaido University, Kita 10 Nishi 5, Kita-ku, Sapporo, 060-0810, Japan
| | - Aye Myat Myat Paing
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1, Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Susumu Goto
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1, Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Yoko Hisamoto
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1, Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Nobuhiro Tomaru
- Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Cikusa-ku, Nagoya, Aichi, 464-0804, Japan
| | - Kosuke Homma
- Sado Island Center for Ecological Sustainability, Niigata University, 1101-1, Niibokatagami, Sado, Niigata, 952-0103, Japan
| | - Masahiro Takagi
- Faculty of Agriculture, University of Miyazaki, 1-1, Gakuen kibanadai nishi, Miyazaki, Miyazaki, 889-2192, Japan
| | - Toshiya Yoshida
- Field Science Center for Northern Biosphere, Hokkaido University, Kita 10 Nishi 5, Kita-ku, Sapporo, 060-0810, Japan
| | - Atsuhiro Iio
- Graduate School of Integrated Science and Technology, Shizuoka University, 836, Ohtani, Suruga-ku, Shizuoka, Shizuoka, 422-8017, Japan
| | - Dai Nagamatsu
- Faculty of Agriculture, Tottori University, 4-101, Koyama-cho, Tottori, Tottori, 680-8553, Japan
| | - Hajime Kobayashi
- Faculty of Agriculture, Shinshu University, 8304, Minamiminowa-mura, Kamiina-gun, Nagano, 399-4598, Japan
| | - Mitsuru Hirota
- Faculty of Life and Environmental Sciences, University of Tsukuba, 1-1-1, Tennodai, Tsukuba, Ibaraki, 305-8577, Japan
| | - Kentaro Uchiyama
- Department of Forest Molecular Genetics and Biotechnology, Forestry and Forest Products Research Institute, 1, Matsunosato, Tsukuba, Ibaraki, 305-8687, Japan
| | - Yoshihiko Tsumura
- Faculty of Life and Environmental Sciences, University of Tsukuba, 1-1-1, Tennodai, Tsukuba, Ibaraki, 305-8577, Japan.
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Regmi B, Douglas MR, Wangchuk K, Zbinden ZD, Edds DR, Tshering S, Douglas ME. The Himalayan uplift and evolution of aquatic biodiversity across Asia: Snowtrout (Cyprininae: Schizothorax) as a test case. PLoS One 2023; 18:e0289736. [PMID: 37874844 PMCID: PMC10597529 DOI: 10.1371/journal.pone.0289736] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Accepted: 07/26/2023] [Indexed: 10/26/2023] Open
Abstract
Global biodiversity hotspots are often remote, tectonically active areas undergoing climatic fluctuations, such as the Himalaya Mountains and neighboring Qinghai-Tibetan Plateau (QTP). They provide biogeographic templates upon which endemic biodiversity can be mapped to infer diversification scenarios. Yet, this process can be somewhat opaque for the Himalaya, given substantial data gaps separating eastern and western regions. To help clarify, we evaluated phylogeographic and phylogenetic hypotheses for a widespread fish (Snowtrout: Cyprininae; Schizothorax) by sequencing 1,140 base pair of mtDNA cytochrome-b (cytb) from Central Himalaya samples (Nepal: N = 53; Bhutan: N = 19), augmented with 68 GenBank sequences (N = 60 Schizothorax/N = 8 outgroups). Genealogical relationships (N = 132) were analyzed via maximum likelihood (ML), Bayesian (BA), and haplotype network clustering, with clade divergence estimated via TimeTree. Snowtrout seemingly originated in Central Asia, dispersed across the QTP, then into Bhutan via southward-flowing tributaries of the east-flowing Yarlung-Tsangpo River (YLTR). Headwaters of five large Asian rivers provided dispersal corridors from Central into eastern/southeastern Asia. South of the Himalaya, the YLTR transitions into the Brahmaputra River, facilitating successive westward colonization of Himalayan drainages first in Bhutan, then Nepal, followed by far-western drainages subsequently captured by the (now) westward-flowing Indus River. Two distinct Bhutanese phylogenetic groups were recovered: Bhutan-1 (with three subclades) seemingly represents southward dispersal from the QTP; Bhutan-2 apparently illustrates northward colonization from the Lower Brahmaputra. The close phylogenetic/phylogeographic relationships between the Indus River (Pakistan) and western tributaries of the Upper Ganges (India/Nepal) potentially implicate an historic, now disjunct connection. Greater species-divergences occurred across rather than within-basins, suggesting vicariance as a driver. The Himalaya is a component of the Earth's largest glacial reservoir (i.e., the "third-pole") separate from the Arctic/Antarctic. Its unique aquatic biodiversity must be defined and conserved through broad, trans-national collaborations. Our study provides an initial baseline for this process.
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Affiliation(s)
- Binod Regmi
- Department of Biological Sciences, University of Arkansas, Fayetteville, Arkansas, United States of America
| | - Marlis R. Douglas
- Department of Biological Sciences, University of Arkansas, Fayetteville, Arkansas, United States of America
| | - Karma Wangchuk
- Department of Biological Sciences, University of Arkansas, Fayetteville, Arkansas, United States of America
- National Research & Development Centre for Riverine and Lake Fisheries, Ministry of Agriculture & Forests, Royal Government of Bhutan, Thimphu, Bhutan
| | - Zachery D. Zbinden
- Department of Biological Sciences, University of Arkansas, Fayetteville, Arkansas, United States of America
| | - David R. Edds
- Department of Biological Sciences, Emporia State University, Emporia, Kansas, United States of America
| | - Singye Tshering
- National Research & Development Centre for Riverine and Lake Fisheries, Ministry of Agriculture & Forests, Royal Government of Bhutan, Thimphu, Bhutan
| | - Michael E. Douglas
- Department of Biological Sciences, University of Arkansas, Fayetteville, Arkansas, United States of America
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Reichel K, Herklotz V, Smolka A, Nybom H, Kellner A, De Riek J, Smulders MJM, Wissemann V, Ritz CM. Untangling the hedge: Genetic diversity in clonally and sexually transmitted genomes of European wild roses, Rosa L. PLoS One 2023; 18:e0292634. [PMID: 37797054 PMCID: PMC10553836 DOI: 10.1371/journal.pone.0292634] [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: 06/09/2023] [Accepted: 09/25/2023] [Indexed: 10/07/2023] Open
Abstract
While European wild roses are abundant and widely distributed, their morphological taxonomy is complicated and ambiguous. In particular, the polyploid Rosa section Caninae (dogroses) is characterised by its unusual meiosis, causing simultaneous clonal and sexual transmission of sub-genomes. This hemisexual reproduction, which often co-occurs with vegetative reproduction, defies the standard definition of species boundaries. We analysed seven highly polymorphic microsatellite loci, scored for over 2 600 Rosa samples of differing ploidy, collected across Europe within three independent research projects. Based on their morphology, these samples had been identified as belonging to 21 dogrose and five other native rose species. We quantified the degree of clonality within species and at individual sampling sites. We then compared the genetic structure within our data to current rose morpho-systematics and searched for hemisexually co-inherited sets of alleles at individual loci. We found considerably fewer copies of identical multi-locus genotypes in dogroses than in roses with regular meiosis, with some variation recorded among species. While clonality showed no detectable geographic pattern, some genotypes appeared to be more widespread. Microsatellite data confirmed the current classification of subsections, but they did not support most of the generally accepted dogrose microspecies. Under canina meiosis, we found co-inherited sets of alleles as expected, but could not distinguish between sexually and clonally inherited sub-genomes, with only some of the detected allele combinations being lineage-specific.
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Affiliation(s)
- Katja Reichel
- Institute of Biology, Dahlem Center of Plant Sciences, Freie Universität Berlin, Berlin, Germany
| | - Veit Herklotz
- Department of Botany, Senckenberg Museum for Natural History Görlitz, Senckenberg–Member of the Leibniz Association, Görlitz, Germany
| | - Alisia Smolka
- Institute of Biology, Dahlem Center of Plant Sciences, Freie Universität Berlin, Berlin, Germany
- Department of Botany, Senckenberg Museum for Natural History Görlitz, Senckenberg–Member of the Leibniz Association, Görlitz, Germany
| | - Hilde Nybom
- Department of Plant Breeding, Balsgård, Swedish University of Agricultural Sciences, Kristianstad, Sweden
| | - Alexandra Kellner
- Institute of Botany, Systematic Botany Group, Justus-Liebig-University, Gießen, Germany
| | - Jan De Riek
- Flanders Research Institute for Agricultural, Fisheries and Food Research (ILVO), Plant Sciences Unit, Melle, Belgium
| | | | - Volker Wissemann
- Institute of Botany, Systematic Botany Group, Justus-Liebig-University, Gießen, Germany
| | - Christiane M. Ritz
- Department of Botany, Senckenberg Museum for Natural History Görlitz, Senckenberg–Member of the Leibniz Association, Görlitz, Germany
- International Institute (IHI) Zittau, Chair of Biodiversity of Higher Plants, Technical University Dresden, Zittau, Germany
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Sullivan TJ, Roberts H, Bultman TL. Genetic Covariation Between the Vertically Transmitted Endophyte Epichloë canadensis and Its Host Canada Wildrye. MICROBIAL ECOLOGY 2023; 86:1686-1695. [PMID: 36725749 DOI: 10.1007/s00248-022-02166-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Accepted: 12/26/2022] [Indexed: 06/18/2023]
Abstract
Symbiotic mutualisms are thought to be stabilized by correlations between the interacting genotypes which may be strengthened via vertical transmission and/or reduced genetic variability within each species. Vertical transmission, however, may weaken interactions over time as the endosymbionts would acquire mutations that could not be purged. Additionally, temporal variation in a conditional mutualism could create genetic variation and increased variation in the interaction outcome. In this study, we assessed genetic variation in both members of a symbiosis, the endosymbiotic fungal endophyte Epichloë canadensis and its grass host Canada wildrye (Elymus canadensis). Both species exhibited comparable levels of diversity, mostly within populations rather than between. There were significant differences between populations, although not in the same pattern for the two species, and the differences were not correlated with geographic distance for either species. Interindividual genetic distance matrices for the two species were significantly correlated, although all combinations of discriminant analysis of principle components (DAPC) defined multilocus genotype groups were found suggesting that strict genotype matching is not necessary. Variation in interaction outcome is common in grass/endophyte interactions, and our results suggest that the accumulation of mutations overtime combined with temporal variation in selection pressures increasing genetic variation in the symbiosis may be the cause.
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Affiliation(s)
- T J Sullivan
- School of Sciences, Indiana University Kokomo, 2300 S. Washington St, Kokomo, IN, 46902, USA.
| | - Holly Roberts
- School of Sciences, Indiana University Kokomo, 2300 S. Washington St, Kokomo, IN, 46902, USA
| | - Thomas L Bultman
- Department of Biology, Hope College, 35 E. 12th St., Holland, MI, 49423, USA
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Gerard D. Double reduction estimation and equilibrium tests in natural autopolyploid populations. Biometrics 2023; 79:2143-2156. [PMID: 35848417 DOI: 10.1111/biom.13722] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Accepted: 07/11/2022] [Indexed: 11/27/2022]
Abstract
Many bioinformatics pipelines include tests for equilibrium. Tests for diploids are well studied and widely available, but extending these approaches to autopolyploids is hampered by the presence of double reduction, the comigration of sister chromatid segments into the same gamete during meiosis. Though a hindrance for equilibrium tests, double reduction rates are quantities of interest in their own right, as they provide insights about the meiotic behavior of autopolyploid organisms. Here, we develop procedures to (i) test for equilibrium while accounting for double reduction, and (ii) estimate the double reduction rate given equilibrium. To do so, we take two approaches: a likelihood approach, and a novel U-statistic minimization approach that we show generalizes the classical equilibrium χ2 test in diploids. For small sample sizes and uncertain genotypes, we further develop a bootstrap procedure based on our U-statistic to test for equilibrium. We validate our methods on both simulated and real data.
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Affiliation(s)
- David Gerard
- Department of Mathematics and Statistics, American University, Washington, District of Columbia, USA
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Skubic M, Záveská E, Frajman B. Meeting in Liguria: hybridisation between Apennine endemic Euphorbia barrelieri and western Mediterranean E. nicaeensis led to the allopolyploid origin of E. ligustica. Mol Phylogenet Evol 2023; 185:107805. [PMID: 37127112 DOI: 10.1016/j.ympev.2023.107805] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 04/17/2023] [Accepted: 04/25/2023] [Indexed: 05/03/2023]
Abstract
The Mediterranean Basin is renowned for its extremely rich biota and is considered as one of the 25 Global Biodiversity Hotspots, but its diversity is not homogeneously distributed. Outstanding in the number of (endemic) species are the Ligurian Alps (Italy). At the foot of the Ligurian Alps, little above the Mediterranean Sea, a disjunct occurrence of Italian endemic Euphorbia barrelieri was reported. Using an array of integrative methods ranging from cytogenetic (chromosome number and relative genome size estimation), over phylogenetic approaches (plastid, ITS and RAD sequencing) to multivariate morphometrics we disentangled the origin of these populations that were shown to be tetraploid. We performed phylogenetic analyses of the nuclear ITS and plastid regions of a broad taxonomic sampling of Euphorbia sect. Pithyusa to identify possible species involved in the origin of the tetraploid populations and then applied various analyses of RADseq data to identify the putative parental species. Our results have shown that the Ligurian populations of E. barrelieri are of allotetraploid origin that involved E. barrelieri and western Mediterranean E. nicaeensis as parental species. We thus describe a new species, E. ligustica, and hypothesise that its adaptation to similar environments in which E. barrelieri occurs, triggered development of similar morphology, whereas its genetic composition appears to be closer to that of E. nicaeensis. Our study emphasises the importance of polyploidisation for plant diversification, highlights the value of the Ligurian Alps as a hotspot of biodiversity and endemism and underlines the importance of integrative taxonomic approaches in uncovering cryptic diversity.
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Affiliation(s)
- Maruša Skubic
- Department of Botany, University of Innsbruck, Sternwartestrasse 15, 6020 Innsbruck, Austria; Department of Agronomy, Biotechnical Faculty, University of Ljubljana, Jamnikarjeva ulica 101, 1000 Ljubljana, Slovenia
| | - Eliška Záveská
- Institute of Botany of the Czech Academy of Sciences, Zámek 1, 25243 Průhonice, Czech Republic
| | - Božo Frajman
- Department of Botany, University of Innsbruck, Sternwartestrasse 15, 6020 Innsbruck, Austria.
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Tong H, Deng H, Han Z. Genetic differentiation and genetic structure of mixed-ploidy Camellia hainanica populations. PeerJ 2023; 11:e14756. [PMID: 36852222 PMCID: PMC9961093 DOI: 10.7717/peerj.14756] [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: 09/12/2022] [Accepted: 12/27/2022] [Indexed: 02/24/2023] Open
Abstract
Camellia hainanica, which is common in China's Hainan Province, is an important woody olive tree species. Due to many years of geographic isolation, C. hainanica has not received the attention it deserves, which limits the exploitation of germplasm resources. Therefore, it is necessary to study population genetic characteristics for further utilization and conservation of C. hainanica. In this study, 96 individuals in six wild Camellia hainanica populations were used for ploidy analysis of the chromosome number, and the genetic diversity and population structure were investigated using 12 pairs of SSR primers. The results show complex ploidy differentiation in C. hainanica species. The ploidy of wild C. hainanica includes tetraploid, pentaploid, hexaploid, heptaploid, octoploid and decaploid species. Genetic analysis shows that genetic diversity and genetic differentiation among populations are low. Populations can be divided into two clusters based on their genetic structure, which matches their geographic location. Finally, to further maintain the genetic diversity of C. hainanica, ex-situ cultivation and in-situ management measures should be considered to protect it in the future.
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Affiliation(s)
- Hailang Tong
- Central South University of Forestry and Technology, The College of Forestry, Changsha, China,Central South University of Forestry and Technology, The Laboratory of Forestry Genetics, Changsha, China
| | - Hongda Deng
- Central South University of Forestry and Technology, The College of Forestry, Changsha, China,Central South University of Forestry and Technology, The Laboratory of Forestry Genetics, Changsha, China
| | - Zhiqiang Han
- Central South University of Forestry and Technology, The College of Forestry, Changsha, China,Central South University of Forestry and Technology, The Laboratory of Forestry Genetics, Changsha, China
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Bohutínská M, Vlček J, Monnahan P, Kolář F. Population Genomic Analysis of Diploid-Autopolyploid Species. Methods Mol Biol 2023; 2545:297-324. [PMID: 36720820 DOI: 10.1007/978-1-0716-2561-3_16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
This chapter outlines an empirical analysis of genome-wide single-nucleotide polymorphism (SNP) variation and its underlying drivers among multiple natural populations within a diploid-autopolyploid species. The aim is to reconstruct the genetic structure among natural populations of varying ploidy and infer footprints of selection in these populations, framed around specific questions that are typically encountered when analyzing a mixed-ploidy data set,e.g., addressing the relevance of natural whole-genome duplication for speciation and adaptation. We briefly review the options for the analysis of polyploid population genomic data involving variant calling, population structure, demographic history inference, and selection scanning approaches. Further, we provide suggestions for methods and associated software, possible caveats, and examples of their application to mixed-ploidy and autopolyploid data sets.
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Affiliation(s)
- Magdalena Bohutínská
- Department of Botany, Faculty of Science, Charles University, Prague, Czech Republic.,Institute of Botany of the Czech Academy of Sciences, Průhonice, Czech Republic
| | - Jakub Vlček
- Department of Botany, Faculty of Science, Charles University, Prague, Czech Republic
| | - Patrick Monnahan
- Department of Pediatrics, University of Minnesota, Minneapolis, MN, USA
| | - Filip Kolář
- Department of Botany, Faculty of Science, Charles University, Prague, Czech Republic. .,Institute of Botany of the Czech Academy of Sciences, Průhonice, Czech Republic.
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10
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Mairal M, García-Verdugo C, Le Roux JJ, Chau JH, van Vuuren BJ, Hui C, Münzbergová Z, Chown SL, Shaw JD. Multiple introductions, polyploidy and mixed reproductive strategies are linked to genetic diversity and structure in the most widespread invasive plant across Southern Ocean archipelagos. Mol Ecol 2023; 32:756-771. [PMID: 36478264 DOI: 10.1111/mec.16809] [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: 07/08/2022] [Revised: 11/30/2022] [Accepted: 12/01/2022] [Indexed: 12/12/2022]
Abstract
Biological invasions in remote areas that experience low human activity provide unique opportunities to elucidate processes responsible for invasion success. Here we study the most widespread invasive plant species across the isolated islands of the Southern Ocean, the annual bluegrass, Poa annua. To analyse geographical variation in genome size, genetic diversity and reproductive strategies, we sampled all major sub-Antarctic archipelagos in this region and generated microsatellite data for 470 individual plants representing 31 populations. We also estimated genome sizes for a subset of individuals using flow cytometry. Occasional events of island colonization are expected to result in high genetic structure among islands, overall low genetic diversity and increased self-fertilization, but we show that this is not the case for P. annua. Microsatellite data indicated low population genetic structure and lack of isolation by distance among the sub-Antarctic archipelagos we sampled, but high population structure within each archipelago. We identified high levels of genetic diversity, low clonality and low selfing rates in sub-Antarctic P. annua populations (contrary to rates typical of continental populations). In turn, estimates of selfing declined in populations as genetic diversity increased. Additionally, we found that most P. annua individuals are probably tetraploid and that only slight variation exists in genome size across the Southern Ocean. Our findings suggest multiple independent introductions of P. annua into the sub-Antarctic, which promoted the establishment of genetically diverse populations. Despite multiple introductions, the adoption of convergent reproductive strategies (outcrossing) happened independently in each major archipelago. The combination of polyploidy and a mixed reproductive strategy probably benefited P. annua in the Southern Ocean by increasing genetic diversity and its ability to cope with the novel environmental conditions.
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Affiliation(s)
- Mario Mairal
- Departamento de Biodiversidad, Ecología y Evolución, Universidad Complutense de Madrid, Madrid, Spain.,Department of Botany and Zoology, Stellenbosch University, Stellenbosch, South Africa
| | - Carlos García-Verdugo
- Departamento de Botánica, Facultad de Ciencias, Universidad de Granada, Granada, Spain.,Departamento de Biología, Universitat de les Illes Balears - Institut Mediterrani d'Estudis Avançats (CSIC-UIB), Mallorca, Spain
| | - Johannes J Le Roux
- Departamento de Biodiversidad, Ecología y Evolución, Universidad Complutense de Madrid, Madrid, Spain.,School of Natural Sciences, Macquarie University, New South Wales, Sydney, Australia
| | - John H Chau
- Department of Zoology, Centre for Ecological Genomics and Wildlife Conservation, University of Johannesburg, Auckland Park, South Africa
| | - Bettine Jansen van Vuuren
- Department of Zoology, Centre for Ecological Genomics and Wildlife Conservation, University of Johannesburg, Auckland Park, South Africa
| | - Cang Hui
- Department of Mathematical Sciences, Centre for Invasion Biology, Stellenbosch University, Stellenbosch, South Africa.,Biodiversity Informatics Unit, African Institute for Mathematical Sciences, Cape Town, South Africa
| | - Zuzana Münzbergová
- Faculty of Science, Department of Botany, Charles University, Prague, Czech Republic.,Institute of Botany, Czech Academy of Science, Průhonice, Czech Republic
| | - Steven L Chown
- Securing Antarctica's Environmental Future, School of Biological Sciences, Monash University, Melbourne, Victoria, Australia
| | - Justine D Shaw
- Securing Antarctica's Environmental Future, School of Biology and Environmental Sciences, Queensland University of Technology, Brisbane, Queensland, Australia.,Australian Antarctic Division, Tasmania, Kingston, Australia
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Xiang N, Lu B, Yuan T, Yang T, Guo J, Wu Z, Liu H, Liu X, Qin R. De Novo Transcriptome Assembly and EST-SSR Marker Development and Application in Chrysosplenium macrophyllum. Genes (Basel) 2023; 14:genes14020279. [PMID: 36833206 PMCID: PMC9956384 DOI: 10.3390/genes14020279] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Revised: 01/16/2023] [Accepted: 01/17/2023] [Indexed: 01/26/2023] Open
Abstract
Chrysosplenium macrophyllum Oliv., belonging to the family Saxifragaceae, is a traditional and unique Chinese herbal medicine. However, the lack of adequate molecular markers has hampered the progress regarding population genetics and evolution within this species. In this research, we used the DNBSEQ-T7 Sequencer (MGI) sequencing assay to analyze the transcriptome profiles of C. macrophyllum. SSR markers were developed on the basis of transcriptomic sequences and further validated on C. macrophyllum and other Chrysosplenium species. The genetic diversity and structure of the 12 populations were analyzed by using polymorphic expressed sequence tag simple sequence repeat (EST-SSR) markers. A potential pool of 3127 non-redundant EST-SSR markers were identified for C. macrophyllum in this study. The developed EST-SSR markers had high amplification rates and cross-species transferability in Chrysosplenium. Our results also showed that the natural populations of C. macrophyllum had a high level of genetic diversity. Genetic distance, principal component analysis, and popular structure analysis revealed that all 60 samples clustered into two major groups that were consistent with their geographical origins. This study provided a batch of highly polymorphic EST-SSR molecular markers that were developed via transcriptome sequencing. These markers will be of great significance for the study of the genetic diversity and evolutionary history of C. macrophyllum and other Chrysosplenium species.
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Affiliation(s)
- Niyan Xiang
- Laboratory of Extreme Environmental Biological Resources and Adaptive Evolution, Research Center for Ecology, School of Sciences, Tibet University, Lhasa 850000, China
- Hubei Provincial Key Laboratory for Protection and Application of Special Plant Germplasm in Wuling Area of China, College of Life Sciences, South-Central Minzu University, Wuhan 430074, China
| | - Bojie Lu
- Hubei Provincial Key Laboratory for Protection and Application of Special Plant Germplasm in Wuling Area of China, College of Life Sciences, South-Central Minzu University, Wuhan 430074, China
| | - Tao Yuan
- Laboratory of Extreme Environmental Biological Resources and Adaptive Evolution, Research Center for Ecology, School of Sciences, Tibet University, Lhasa 850000, China
| | - Tiange Yang
- Hubei Provincial Key Laboratory for Protection and Application of Special Plant Germplasm in Wuling Area of China, College of Life Sciences, South-Central Minzu University, Wuhan 430074, China
| | - Jiani Guo
- Laboratory of Extreme Environmental Biological Resources and Adaptive Evolution, Research Center for Ecology, School of Sciences, Tibet University, Lhasa 850000, China
| | - Zhihua Wu
- College of Life Sciences, Zhejiang Normal University, Jinhua 321004, China
| | - Hong Liu
- Hubei Provincial Key Laboratory for Protection and Application of Special Plant Germplasm in Wuling Area of China, College of Life Sciences, South-Central Minzu University, Wuhan 430074, China
| | - Xing Liu
- Laboratory of Extreme Environmental Biological Resources and Adaptive Evolution, Research Center for Ecology, School of Sciences, Tibet University, Lhasa 850000, China
- State Key Laboratory of Hybrid Rice, Laboratory of Plant Systematics and Evolutionary Biology, College of Life Sciences, Wuhan University, Wuhan 430072, China
- Correspondence: (X.L.); (R.Q.)
| | - Rui Qin
- Hubei Provincial Key Laboratory for Protection and Application of Special Plant Germplasm in Wuling Area of China, College of Life Sciences, South-Central Minzu University, Wuhan 430074, China
- Correspondence: (X.L.); (R.Q.)
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Pina-Martins F, Caperta AD, Conceição SIR, Nunes VL, Marques I, Paulo OS. A first look at sea-lavenders genomics - can genome wide SNP information tip the scales of controversy in the Limonium vulgare species complex? BMC PLANT BIOLOGY 2023; 23:34. [PMID: 36642719 PMCID: PMC9841708 DOI: 10.1186/s12870-022-03974-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Accepted: 12/01/2022] [Indexed: 06/17/2023]
Abstract
BACKGROUND Sea-lavenders (Limonium Mill., Plumbaginaceae) are a cosmopolitan group of diploid and polyploid plants often adapted to extreme saline environments, with a mostly Tethyan distribution, occurring in the Mediterranean, Irano-Turanian, Euro-Siberian and in the New World. The halophylic Limonium vulgare polyploid complex in particular, presents a large distribution throughout extreme salt-marsh habitats and shows little morphological but high taximetric variation, frequently blurring species delimitation. In this work we pursue three main goals: assert whether SNP data from polyploid individuals has the resolution to distinguish the seven sampled species, to better understand how genetically structured Limonium vulgare is, and attempt to identify specific molecular mechanisms for the differentiation between L. maritimum and L. vulgare. For this purpose, 95 individuals were genotyped using Genotyping by Sequencing (GBS), which were assembled as two independent datasets using IPYRAD. All analyses performed downstream of assembly were fully automated. Phylogenetic inference, PCA, and admixture plots were used to infer answers to the study's main goals. RESULTS Close to 10,000 SNPs were obtained for each dataset. Phylogenetic analyses reveal that polyploid data can be used to infer species relationships. Population structure analyses suggest a genetically structured L. vulgare. A set of 34 SNPs were found to be fully segregated between L. vulgare and L. maritimum, two of which are potentially linked to proteins that might be involved in the speciation process. CONCLUSION Despite polyploid data analyses shortcomings, GBS generated SNPs have the resolution to discern all seven included species. Limonium vulgare revealed pronounced genetic structure along a geographical north-south cline. L. maritimum always appears as a distinct genetic entity. Segregated SNPs between L. vulgare and L. maritimum indicate salinity response and morphological trait control genes as potentially interesting to follow up for studying these species' divergence process.
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Affiliation(s)
- Francisco Pina-Martins
- cE3c - Centre for Ecology, Evolution and Environmental Changes & CHANGE - Global Change and Sustainability Institute, Departamento de Biologia Animal Faculdade de Ciências, Universidade de Lisboa, Campo Grande, 1749-016, Lisbon, Portugal.
| | - Ana D Caperta
- LEAF-Linking Landscape, Environment, Agriculture and Food, Associated Laboratory TERRA, Instituto Superior de Agronomia (ISA), Universidade de Lisboa, Tapada da Ajuda, 1349-017, Lisbon, Portugal
| | - Sofia I R Conceição
- LEAF-Linking Landscape, Environment, Agriculture and Food, Associated Laboratory TERRA, Instituto Superior de Agronomia (ISA), Universidade de Lisboa, Tapada da Ajuda, 1349-017, Lisbon, Portugal
- LASIGE Computer Science and Engineering Research Centre, Faculdade de Ciências, Universidade de Lisboa, 1749-016, Lisbon, Portugal
| | - Vera L Nunes
- cE3c - Centre for Ecology, Evolution and Environmental Changes & CHANGE - Global Change and Sustainability Institute, Departamento de Biologia Animal Faculdade de Ciências, Universidade de Lisboa, Campo Grande, 1749-016, Lisbon, Portugal
| | - Isabel Marques
- cE3c - Centre for Ecology, Evolution and Environmental Changes & CHANGE - Global Change and Sustainability Institute, Departamento de Biologia Animal Faculdade de Ciências, Universidade de Lisboa, Campo Grande, 1749-016, Lisbon, Portugal
- Forest Research Centre (CEF) & Associated Laboratory TERRA, Instituto Superior de Agronomia (ISA), Universidade de Lisboa, 1349-017, Lisbon, Portugal
| | - Octávio S Paulo
- cE3c - Centre for Ecology, Evolution and Environmental Changes & CHANGE - Global Change and Sustainability Institute, Departamento de Biologia Animal Faculdade de Ciências, Universidade de Lisboa, Campo Grande, 1749-016, Lisbon, Portugal
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Population Structure of White Sturgeon (Acipenser transmontanus) in the Columbia River Inferred from Single-Nucleotide Polymorphisms. DIVERSITY 2022. [DOI: 10.3390/d14121045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
White sturgeon (Acipenser transmontanus) are the largest freshwater fish in North America, with reproducing populations in the Sacramento-San Joaquin, Fraser, and Columbia River Basins. Of these, the Columbia River is the largest, but it is also highly fragmented by hydroelectric dams, and many segments are characterized by declining abundance and persistent recruitment failure. Efforts to conserve and supplement these fish requires an understanding of their spatial genetic structure. Here, we assembled a large set of samples from throughout the Columbia River Basin, along with representative collections from adjacent basins, and genotyped them using a panel of 325 single-nucleotide markers. Results from individual- and group-based analyses of these data indicate that white sturgeon in the uppermost Columbia River Basin, in the Kootenai and upper Snake Rivers, are the most distinct, while the remaining populations downstream in the basin can be described as a genetic gradient consistent with an isolation-by-distance effect. Notably, the population in the lowest reaches of the Columbia River is more distinct from the middle or upper reaches than from outside basins, and suggests historically a higher or more recent gene exchange through coastal routes than with populations in the interior Columbia Basin. Nonetheless, proximal reaches were generally only marginally or non-significantly divergent, suggesting that transplanting larvae or juveniles from nearby sources poses relatively little risk of outbreeding depression. Indeed, we inferred examples of dispersal between reaches via close-kin mark-recapture and genetic mark-recapture that indicate movement between nearby reaches is not unusual. Samples from the Kootenai and upper Snake Rivers exhibited notably lower genetic diversity than the remaining samples as a result of population bottlenecks, genetic drift, and/or historical divergence. Conservation actions, such as supplementation, are underway to maintain population viability and will require balanced efforts to increase demographic abundance while maintaining genetic diversity.
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14
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Assessment of the Genetic Distinctiveness and Uniformity of Pre-Basic Seed Stocks of Italian Ryegrass Varieties. Genes (Basel) 2022; 13:genes13112097. [DOI: 10.3390/genes13112097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 11/03/2022] [Accepted: 11/09/2022] [Indexed: 11/16/2022] Open
Abstract
Lolium multiflorum Lam., commonly known as Italian ryegrass, is a forage grass mostly valued for its high palatability and digestibility, along with its high productivity. However, Italian ryegrass has an outbreeding nature and therefore has high genetic heterogeneity within each variety. Consequently, the exclusive use of morphological descriptors in the existing varietal identification and registration process based on the Distinctness, Uniformity, and Stability (DUS) test results in an inadequately precise assessment. The primary objective of this work was to effectively test whether the uniformity observed at the phenological level within each population of Italian ryegrass was confirmed at the genetic level through an SSR marker analysis. In this research, using 12 polymorphic SSR loci, we analyzed 672 samples belonging to 14 different Italian ryegrass commercial varieties to determine the pairwise genetic similarity (GS), verified the distribution of genetic diversity within and among varieties, and investigated the population structure. Although the fourteen commercial varieties did not show elevated genetic differentiation, with only 13% of the total variation attributable to among-cultivar genetic variation, when analyzed as a core, each variety constitutes a genetic cluster on its own, resulting in distinct characteristics from the others, except for two varieties. In this way, by combining a genetic tool with the traditional morphological approach, we were able to limit biases linked to the environmental effect of field trials, assessing the real source of diversity among varieties and concretely answering the key requisites of the Plant Variety Protection (PVP) system.
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Spring JF, Revolinski SR, Young FL, Lyon DJ, Burke IC. Weak population differentiation and high diversity in Salsola tragus in the inland Pacific Northwest, USA. PEST MANAGEMENT SCIENCE 2022; 78:4728-4740. [PMID: 35872633 DOI: 10.1002/ps.7093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Revised: 07/13/2022] [Accepted: 07/25/2022] [Indexed: 06/15/2023]
Abstract
BACKGROUND Salsola tragus is a widespread and problematic weed of semi-arid wheat production globally, and in the inland Pacific Northwest region of the USA. The species exhibits high levels of phenotypic diversity across its range and, at least in California USA, previous work has described cryptic diversity comprising a multi-species complex. Such cryptic diversity could suggest the potential for a differential response to management inputs between groups, and have important implications for the spread of herbicide resistance or other adaptive traits within populations. We used a genotyping-by-sequencing approach to characterize the population structure of S. tragus in the inland Pacific Northwest. RESULTS Our results indicated that the population in this region is comprised of a single, tetraploid species (S. tragus sensu latu) with weak population structure on a regional scale. Isolation-by-distance appears to be the primary pattern of structure, but an independent set of weakly differentiated clusters of unknown origin were also apparent, along with a mixed mating system and high levels of largely unstructured genetic diversity. CONCLUSIONS Despite considerable phenotypic variability within S. tragus in the region, agronomic weed managers can likely consider it as a single entity across the region, rather than a collection of cryptic subgroups with possible differential responses to management inputs or agroecosystem conditions. A lack of strong barriers to migration and gene flow mean that adaptive traits, such as herbicide resistance, can be expected to spread rapidly through populations across the region. © 2022 Society of Chemical Industry.
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Affiliation(s)
- John F Spring
- Oregon State University Central Oregon Agricultural Research and Extension Center, Madras, OR, USA
| | - Samuel R Revolinski
- Washington State University Department of Crop and Soil Sciences, Pullman, WA, USA
| | - Frank L Young
- USDA-ARS Northwest Sustainable Agroecosystems Research Unit, Pullman, WA, USA
| | - Drew J Lyon
- Washington State University Department of Crop and Soil Sciences, Pullman, WA, USA
| | - Ian C Burke
- Washington State University Department of Crop and Soil Sciences, Pullman, WA, USA
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Feigs JT, Holzhauer SIJ, Huang S, Brunet J, Diekmann M, Hedwall PO, Kramp K, Naaf T. Pollinator movement activity influences genetic diversity and differentiation of spatially isolated populations of clonal forest herbs. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.908258] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
In agricultural landscapes, forest herbs live in small, spatially isolated forest patches. For their long-term survival, their populations depend on animals as genetic linkers that provide pollen- or seed-mediated gene flow among different forest patches. However, whether insect pollinators serve as genetic linkers among spatially isolated forest herb populations in agricultural landscapes remains to be shown. Here, we used population genetic methods to analyze: (A) the genetic diversity and genetic differentiation of populations of two common, slow-colonizing temperate forest herb species [Polygonatum multiflorum (L.) All. and Anemone nemorosa L.] in spatially isolated populations within three agricultural landscapes in Germany and Sweden and (B) the movement activity of their most relevant associated pollinator species, i.e., the bumblebee Bombus pascuorum (Scopoli, 1,763) and the hoverfly Melanostoma scalare (Fabricus, 1,794), respectively, which differ in their mobility. We tested whether the indicated pollinator movement activity affected the genetic diversity and genetic differentiation of the forest herb populations. Bumblebee movement indicators that solely indicated movement activity between the forest patches affected both genetic diversity and genetic differentiation of the associated forest herb P. multiflorum in a way that can be explained by pollen-mediated gene flow among the forest herb populations. In contrast, movement indicators reflecting the total movement activity at a forest patch (including within-forest patch movement activity) showed unexpected effects for both plant-pollinator pairs that might be explained by accelerated genetic drift due to enhanced sexual reproduction. Our integrated approach revealed that bumblebees serve as genetic linkers of associated forest herb populations, even if they are more than 2 km apart from each other. No such evidence was found for the forest associated hoverfly species which showed significant genetic differentiation among forest patches itself. Our approach also indicated that a higher within-forest patch movement activity of both pollinator species might enhance sexual recruitment and thus diminishes the temporal buffer that clonal growth provides against habitat fragmentation effects.
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Hu J, Mei M, Jin F, Xu J, Duan S, Bian C, Li G, Wang X, Jin L. Phenotypic variability and genetic diversity analysis of cultivated potatoes in China. FRONTIERS IN PLANT SCIENCE 2022; 13:954162. [PMID: 36212356 PMCID: PMC9541749 DOI: 10.3389/fpls.2022.954162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Accepted: 09/02/2022] [Indexed: 06/16/2023]
Abstract
Phenotypic evaluation and molecular biotechnology are both important in the identification and utilization of crop germplasm resources. In this study, the phenotypic variation and genetic diversity of 149 main potato cultivars in China were investigated with 12 phenotypic traits and 24 SSR markers. The coefficient of variation of 12 phenotypic traits ranged from 12.11% to 156.93%. The results of SSR markers exhibited a relatively high level of genetic variation (Na =5.458 ± 1.499, Ne =3.300 ± 1.087, I =1.397 ± 0.298, Ho =0.797 ± 0.178, He = 0.660 ± 0.117, and PIC=0.702 ± 0.087). Population structure and phylogenetic tree analysis divided the varieties into three subgroups. The results indicated that ninety percent of the molecular variance was attributed to within-group differences, and the remaining 10% was attributed to variation among groups. Consistent with previous report, alleles of the STI032 marker were significantly associated with tuber starch content and growth period traits in the population. The results of this study could facilitate the utilization of potato germplasm resources, molecular genetic breeding and improvement.
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Affiliation(s)
- Jun Hu
- Key Laboratory of Biology and Genetic Improvement of Tuber and Root Crops, Ministry of Agriculture and Rural Affairs of the People’s Republic of China, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Meng Mei
- College of Agronomy, Sichuan Agricultural University, Chengdu, China
| | - Fang Jin
- National Agro-Tech Extension and Service Center, Ministry of Agriculture and Rural Affairs of the People’s Republic of China, Beijing, China
| | - Jianfei Xu
- Key Laboratory of Biology and Genetic Improvement of Tuber and Root Crops, Ministry of Agriculture and Rural Affairs of the People’s Republic of China, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Shaoguang Duan
- Key Laboratory of Biology and Genetic Improvement of Tuber and Root Crops, Ministry of Agriculture and Rural Affairs of the People’s Republic of China, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Chunsong Bian
- Key Laboratory of Biology and Genetic Improvement of Tuber and Root Crops, Ministry of Agriculture and Rural Affairs of the People’s Republic of China, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Guangcun Li
- Key Laboratory of Biology and Genetic Improvement of Tuber and Root Crops, Ministry of Agriculture and Rural Affairs of the People’s Republic of China, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xiyao Wang
- College of Agronomy, Sichuan Agricultural University, Chengdu, China
| | - Liping Jin
- Key Laboratory of Biology and Genetic Improvement of Tuber and Root Crops, Ministry of Agriculture and Rural Affairs of the People’s Republic of China, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
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Genotyping-by-Sequencing and Morphology Revealed the Role of Polyploidization and Hybridization in the Diversification of the Centaurea aspera L. Complex of Section Seridia (Juss.) DC. (Asteraceae). PLANTS 2022; 11:plants11151919. [PMID: 35893623 PMCID: PMC9332712 DOI: 10.3390/plants11151919] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Revised: 07/11/2022] [Accepted: 07/19/2022] [Indexed: 12/03/2022]
Abstract
Hybridization and polyploidy are major drivers of plant evolution. In Centaurea (Asteraceae), both mechanisms are frequent and lead to reticulate evolutions. However, in the Western Mediterranean section, Seridia studies are scarce. In this section, Centaurea aspera forms a complex including four European diploid and one Moroccan autotetraploid subspecies, an allopolyploid, and hybrids among them. Here, we aimed to delimit the different taxa, identify any introgressions, and discuss their evolutionary history. Samples of all taxa were analysed using 1688 SNPs obtained through GBS and were morphologically characterized. Three genetically well-differentiated clusters were observed, corresponding to the allopolyploid C. seridis, the diploid C. aspera and the cryptic autotetraploid C. aspera ssp. gentilii, which is proposed to be considered as a species. Centaurea seridis showed a high isolation by distance, a greater morphological variability, and a lack of interspecific gene flow. Diploid and autotetraploid C. aspera individuals were morphologically similar, and some introgressions were detected in Southern Spain, where new forms may promote diversification. This gene flow might have taken place during the Messinian and before autopolyploidization occurred in Morocco. In the C. aspera complex, current interspecific barriers are strong, while polyploidization may provide a better adaptation to drier environments.
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Wang J, Feng L, Mu S, Dong A, Gan J, Wen Z, Meng J, Li M, Wu R, Sun L. Asymptotic tests for Hardy-Weinberg equilibrium in hexaploids. HORTICULTURE RESEARCH 2022; 9:uhac104. [PMID: 35795385 PMCID: PMC9250657 DOI: 10.1093/hr/uhac104] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/25/2021] [Accepted: 04/20/2022] [Indexed: 06/15/2023]
Abstract
Hexaploids, a group of organisms containing three complete sets of chromosomes in a single nucleus, are of utmost importance to evolutionary studies and breeding programs. Many studies have focused on hexaploid linkage analysis and QTL mapping in controlled crosses, but little methodology has been developed to reveal how hexaploids diversify and evolve in natural populations. We formulate a general framework for studying the pattern of genetic variation in autohexaploid populations through testing deviation from Hardy-Weinberg equilibrium (HWE) at individual molecular markers. We confirm that hexaploids cannot reach exact HWE but can approach asymptotic HWE at 8-9 generations of random mating. We derive a statistical algorithm for testing HWE and the occurrence of double reduction for autopolyploids, a phenomenon that affects population variation during long evolutionary processes. We perform computer simulation to validate the statistical behavior of our test procedure and demonstrate its usefulness by analyzing a real data set for autohexaploid chrysanthemum. When extended to allohexaploids, our test procedure will provide a generic tool for illustrating the genome structure of hexaploids in the quest to infer their evolutionary status and design association studies of complex traits.
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Affiliation(s)
- Jing Wang
- Center for Computational Biology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
| | - Li Feng
- Center for Computational Biology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
| | - Shuaicheng Mu
- Center for Computational Biology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
| | - Ang Dong
- Center for Computational Biology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
| | - Jinwen Gan
- Center for Computational Biology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
| | - Zhenying Wen
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, School of Landscape Architecture, Beijing Forestry University, Beijing 100083, China
| | - Juan Meng
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, School of Landscape Architecture, Beijing Forestry University, Beijing 100083, China
| | - Mingyu Li
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, School of Landscape Architecture, Beijing Forestry University, Beijing 100083, China
| | - Rongling Wu
- Center for Computational Biology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
- Center for Statistical Genetics, Departments of Public Health Sciences and Statistics, The Pennsylvania State University, Hershey, PA 17033, USA
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de Oliveira Bernardes C, Tuler AC, Canal D, Carvalho MS, Ferreira A, da Silva Ferreira MF. Genetic Diversity and Population Structure of Psidium Species from Restinga: A Coastal and Disturbed Ecosystem of the Brazilian Atlantic Forest. Biochem Genet 2022; 60:2503-2514. [PMID: 35577994 DOI: 10.1007/s10528-022-10222-7] [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: 07/05/2021] [Accepted: 03/09/2022] [Indexed: 11/30/2022]
Abstract
The Atlantic Forest is one of the most threatened biomes in the world. Here, we use a common set of microsatellite markers to assess the genetic diversity and population structure of three species from the genus Psidium (P. guajava, P. macahense, and P. guineense), located in a disturbed environment of the Atlantic Forest, the restinga, in Espírito Santo, Brazil. Psidium guajava populations presented the highest number of alleles (95) followed by P. guineense (81) and P. macahense (68). The genetic variability was high (P. guajava = 0.71; P. guineense = 0.74; P. macahense = 0.63), with greater variation within populations (72 to 84%) than among populations (15 to 27%), reflecting elevated values of genetic differentiation (P. guajava, FST: 0.15; P. macahense, ØST: 0.27; P. guineense, ØST: 0.21). The populations were clustered into two main groups and considered moderately structured. This is the first report of genetic studies and evidence of polyploidy to P. macahense. Our results may provide information that can be used in management and conservation strategies, to preserve the diversity of Psidium populations.
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Affiliation(s)
- Carolina de Oliveira Bernardes
- Laboratório de Genética e Melhoramento Vegetal, Centro de Ciências Agrárias E Engenharias, Universidade Federal do Espírito Santo, Alegre, Espírito Santo, Brazil
| | - Amélia Carlos Tuler
- Universidade Federal de Roraima, Campus Paricana, Boa Vista, RR, 69304-000, Brazil
| | - Drielli Canal
- Laboratório de Genética e Melhoramento Vegetal, Centro de Ciências Agrárias E Engenharias, Universidade Federal do Espírito Santo, Alegre, Espírito Santo, Brazil
| | - Marina Santos Carvalho
- Laboratório de Genética e Melhoramento Vegetal, Centro de Ciências Agrárias E Engenharias, Universidade Federal do Espírito Santo, Alegre, Espírito Santo, Brazil
| | - Adésio Ferreira
- Laboratório de Genética e Melhoramento Vegetal, Centro de Ciências Agrárias E Engenharias, Universidade Federal do Espírito Santo, Alegre, Espírito Santo, Brazil
| | - Marcia Flores da Silva Ferreira
- Laboratório de Genética e Melhoramento Vegetal, Centro de Ciências Agrárias E Engenharias, Universidade Federal do Espírito Santo, Alegre, Espírito Santo, Brazil.
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Graffelman J, Weir BS. The transitivity of the Hardy-Weinberg law. Forensic Sci Int Genet 2022; 58:102680. [PMID: 35313226 PMCID: PMC10693928 DOI: 10.1016/j.fsigen.2022.102680] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Revised: 02/12/2022] [Accepted: 02/20/2022] [Indexed: 11/27/2022]
Abstract
The Hardy-Weinberg law is shown to be transitive in the sense that a multi-allelic polymorphism that is in equilibrium will retain its equilibrium status if any allele together with its corresponding genotypes is deleted from the population. Similarly, the transitivity principle also applies if alleles are joined, which leads to the summation of allele frequencies and their corresponding genotype frequencies. These basic polymorphism properties are intuitive, but they have apparently not been formalized or investigated. This article provides a straightforward proof of the transitivity principle, and its usefulness in genetic data analysis is explored, using high-quality autosomal microsatellite databases from the US National Institute of Standards and Technology. We address the reduction of multi-allelic polymorphisms to variants with fewer alleles, two in the limit. Equilibrium test results obtained with the original and reduced polymorphisms are generally observed to be coherent, in particular when results obtained with length-based and sequence-based microsatellites are compared. We exploit the transitivity principle in order to identify disequilibrium-related alleles, and show its usefulness for detecting population substructure and genotyping problems that relate to null alleles and allele imbalance.
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Affiliation(s)
- Jan Graffelman
- Department of Statistics and Operations Research, Universitat Politècnica de Catalunya, Carrer Jordi Girona, 1-3, 08034, Barcelona, Spain; Department of Biostatistics, University of Washington, University Tower, 15th Floor, 4333 Brooklyn Avenue, Seattle, WA 98105-9461, United States of America.
| | - Bruce S Weir
- Department of Biostatistics, University of Washington, University Tower, 15th Floor, 4333 Brooklyn Avenue, Seattle, WA 98105-9461, United States of America
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22
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Wang Z, Hu G, Li Z, Zhong C, Yao X. Characterizing Tetraploid Populations of Actinidia chinensis for Kiwifruit Genetic Improvement. PLANTS 2022; 11:plants11091154. [PMID: 35567155 PMCID: PMC9102457 DOI: 10.3390/plants11091154] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Revised: 04/11/2022] [Accepted: 04/19/2022] [Indexed: 11/24/2022]
Abstract
Understanding genetic diversity and structure in natural populations and their suitable habitat response to environmental changes is critical for the protection and utilization of germplasm resources. We evaluated the genetic diversity and structure of 24 A. chinensis populations using simple sequence repeat (SSR) molecular markers. The potential suitable distribution of tetraploid A. chinensis estimated under the current climate and predicted for the future climate was generated with ecological niche modeling (ENM). The results indicated that the polyploid populations of A.chinensis have high levels of genetic diversity and that there are distinct eastern and western genetic clusters. The population structure of A. chinensis can be explained by an isolation-by-distance model. The results also revealed that potentially suitable areas of tetraploids will likely be gradually lost and the habitat will likely be increasingly fragmented in the future. This study provides an extensive overview of tetraploid A. chinensis across its distribution range, contributing to a better understanding of its germplasm resources. These results can also provide the scientific basis for the protection and sustainable utilization of kiwifruit wild resources.
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Affiliation(s)
- Zhi Wang
- Institute of Fruit and Tea, Hubei Academy of Agricultural Sciences, Wuhan 430064, China;
- CAS Key Laboratory of Plant Germplasm Enhancement and Speciality Agriculture, Wuhan Botanical Garden, the Chinese Academy of Sciences, Wuhan 430074, China; (G.H.); (Z.L.)
| | - Guangming Hu
- CAS Key Laboratory of Plant Germplasm Enhancement and Speciality Agriculture, Wuhan Botanical Garden, the Chinese Academy of Sciences, Wuhan 430074, China; (G.H.); (Z.L.)
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zuozhou Li
- CAS Key Laboratory of Plant Germplasm Enhancement and Speciality Agriculture, Wuhan Botanical Garden, the Chinese Academy of Sciences, Wuhan 430074, China; (G.H.); (Z.L.)
| | - Caihong Zhong
- CAS Key Laboratory of Plant Germplasm Enhancement and Speciality Agriculture, Wuhan Botanical Garden, the Chinese Academy of Sciences, Wuhan 430074, China; (G.H.); (Z.L.)
- Correspondence: (C.Z.); (X.Y.); Tel.: +86-27-8770884 (C.Z. & X.Y.); Fax: +86-27-87510567 (C.Z. & X.Y.)
| | - Xiaohong Yao
- CAS Key Laboratory of Plant Germplasm Enhancement and Speciality Agriculture, Wuhan Botanical Garden, the Chinese Academy of Sciences, Wuhan 430074, China; (G.H.); (Z.L.)
- Correspondence: (C.Z.); (X.Y.); Tel.: +86-27-8770884 (C.Z. & X.Y.); Fax: +86-27-87510567 (C.Z. & X.Y.)
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23
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Boyd JN, Odell J, Cruse‐Sanders J, Rogers W, Anderson JT, Baskauf C, Brzyski J. Phenotypic plasticity and genetic diversity elucidate rarity and vulnerability of an endangered riparian plant. Ecosphere 2022. [DOI: 10.1002/ecs2.3996] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- Jennifer Nagel Boyd
- Department of Biology, Geology, and Environmental Science University of Tennessee at Chattanooga Chattanooga Tennessee USA
| | - Jared Odell
- Department of Biology, Geology, and Environmental Science University of Tennessee at Chattanooga Chattanooga Tennessee USA
| | - Jennifer Cruse‐Sanders
- Department of Genetics Odum School of Ecology, Davison Life Sciences, University of Georgia Athens Georgia USA
| | - Will Rogers
- Department of Biology, Geology, and Environmental Science University of Tennessee at Chattanooga Chattanooga Tennessee USA
- State Botanical Garden of Georgia University of Georgia Athens Georgia USA
| | - Jill T. Anderson
- Department of Biology, Geology, and Environmental Science University of Tennessee at Chattanooga Chattanooga Tennessee USA
- Department of Genetics Odum School of Ecology, Davison Life Sciences, University of Georgia Athens Georgia USA
- State Botanical Garden of Georgia University of Georgia Athens Georgia USA
| | - Carol Baskauf
- Department of Biology Austin Peay State University Clarksville Tennessee USA
| | - Jessica Brzyski
- Department of Biology Seton Hill University Greensburg Pennsylvania USA
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24
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A generalist-specialist trade-off between switchgrass cytotypes impacts climate adaptation and geographic range. Proc Natl Acad Sci U S A 2022; 119:e2118879119. [PMID: 35377798 PMCID: PMC9169841 DOI: 10.1073/pnas.2118879119] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Polyploidy, which occurs in roughly half of all flowering plants and an even higher percentage of grasses, is thought to be a major driver of adaptation. Higher numbers of copies of each gene in polyploid genomes can increase genetic diversity, which could drive shifts in habitat preference, adaptability, and fitness. To test the effects of increased ploidy, we compared genomic diversity, environmental niche, and fitness responses across climatic gradients between tetraploid and octoploid switchgrass. We found that the octoploids contained novel combinations of the ancestral tetraploid genetic diversity, which was linked to the expansion of switchgrass into unsuitable habitats for tetraploid populations. Our experiments revealed evidence of niche divergence, differential fitness, and a generalist–specialist trade-off between cytotypes. Polyploidy results from whole-genome duplication and is a unique form of heritable variation with pronounced evolutionary implications. Different ploidy levels, or cytotypes, can exist within a single species, and such systems provide an opportunity to assess how ploidy variation alters phenotypic novelty, adaptability, and fitness, which can, in turn, drive the development of unique ecological niches that promote the coexistence of multiple cytotypes. Switchgrass, Panicum virgatum, is a widespread, perennial C4 grass in North America with multiple naturally occurring cytotypes, primarily tetraploids (4×) and octoploids (8×). Using a combination of genomic, quantitative genetic, landscape, and niche modeling approaches, we detect divergent levels of genetic admixture, evidence of niche differentiation, and differential environmental sensitivity between switchgrass cytotypes. Taken together, these findings support a generalist (8×)–specialist (4×) trade-off. Our results indicate that the 8× represent a unique combination of genetic variation that has allowed the expansion of switchgrass’ ecological niche and thus putatively represents a valuable breeding resource.
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25
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Salvado P, Aymerich Boixader P, Parera J, Vila Bonfill A, Martin M, Quélennec C, Lewin J, Delorme‐Hinoux V, Bertrand JAM. Little hope for the polyploid endemic Pyrenean Larkspur (
Delphinium montanum
): Evidences from population genomics and Ecological Niche Modeling. Ecol Evol 2022; 12:e8711. [PMID: 35342590 PMCID: PMC8932081 DOI: 10.1002/ece3.8711] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Revised: 02/11/2022] [Accepted: 02/18/2022] [Indexed: 11/17/2022] Open
Abstract
Species endemic to restricted geographical ranges represent a particular conservation issue, be it for their heritage interest. In a context of global change, this is particularly the case for plants which belong to high‐mountain ecosystems and, because of their ecological requirements, are doomed to survive or disappear on their “sky islands”. The Pyrenean Larkspur (Delphinium montanum, Ranunculaceae) is endemic to the Eastern part of the Pyrenees (France and Spain). It is now only observable at a dozen of localities and some populations show signs of decline, such as a recurrent lack of flowering. Implementing population genomics approach (e.g., RAD‐seq like) is particularly useful to understand genomic patterns of diversity and differentiation in order to provide recommendations in term of conservation. However, it remains challenging for species such as D. montanum that are autotetraploid with a large genome size (1C‐value >10 pg) as most methods currently available were developed for diploid species. A Bayesian framework able to call genotypes with uncertainty allowed us to assess genetic diversity and population structure in this system. Our results show evidence for inbreeding (mean GIS = 0.361) within all the populations and substantial population structure (mean GST = 0.403) at the metapopulation level. In addition to a lack of connectivity between populations, spatial projections of Ecological Niche Modeling (ENM) analyses under different climatic scenarios predict a dramatic decrease of suitable habitat for D. montanum in the future. Based on these results, we discuss the relevance and feasibility of different conservation measures.
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Affiliation(s)
- Pascaline Salvado
- Laboratoire Génome et Développement des Plantes (LGDP, UMR 5096 UPVD/CNRS) Université de Perpignan Via Domitia Perpignan France
| | | | - Josep Parera
- Fédération des Réserves Naturelles Catalanes Prades France
| | | | - Maria Martin
- Fédération des Réserves Naturelles Catalanes Prades France
| | | | | | - Valérie Delorme‐Hinoux
- Laboratoire Génome et Développement des Plantes (LGDP, UMR 5096 UPVD/CNRS) Université de Perpignan Via Domitia Perpignan France
- Association Charles Flahault Toulouges France
| | - Joris A. M. Bertrand
- Laboratoire Génome et Développement des Plantes (LGDP, UMR 5096 UPVD/CNRS) Université de Perpignan Via Domitia Perpignan France
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26
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Varela-Álvarez E, Meirmans PG, Guiry MD, Serrão EA. Biogeographic Population Structure of Chimeric Blades of Porphyra in the Northeast Atlantic Reveals Southern Rich Gene Pools, Introgression and Cryptic Plasticity. FRONTIERS IN PLANT SCIENCE 2022; 13:818368. [PMID: 35283864 PMCID: PMC8908385 DOI: 10.3389/fpls.2022.818368] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Accepted: 02/04/2022] [Indexed: 06/14/2023]
Abstract
The genus Porphyra sensu lato (Bangiaceae, Rhodophyta), an important seaweed grown in aquaculture, is the most genetically diverse group of the Class Bangiophyceae, but has poorly understood genetic variability linked to complex evolutionary processes. Genetic studies in the last decades have largely focused on resolving gene phylogenies; however, there is little information on historical population biogeography, structure and gene flow in the Bangiaceae, probably due to their cryptic nature, chimerism and polyploidy, which render analyses challenging. This study aims to understand biogeographic population structure in the two abundant Porphyra species in the Northeast Atlantic: Porphyra dioica (a dioecious annual) and Porphyra linearis (protandrous hermaphroditic winter annual), occupying distinct niches (seasonality and position on the shore). Here, we present a large-scale biogeographic genetic analysis across their distribution in the Northeast Atlantic, using 10 microsatellites and cpDNA as genetic markers and integrating chimerism and polyploidy, including simulations considering alleles derived from different ploidy levels and/or from different genotypes within the chimeric blade. For P. linearis, both markers revealed strong genetic differentiation of north-central eastern Atlantic populations (from Iceland to the Basque region of Northeast Iberia) vs. southern populations (Galicia in Northwest Iberia, and Portugal), with higher genetic diversity in the south vs. a northern homogenous low diversity. For. P. dioica, microsatellite analyses also revealed two genetic regions, but with weaker differentiation, and cpDNA revealed little structure with all the haplotypes mixed across its distribution. The southern cluster in P. linearis also included introgressed individuals with cpDNA from P. dioica and a winter form of P. dioica occurred spatially intermixed with P. linearis. This third entity had a similar morphology and seasonality as P. linearis but genomes (either nuclear or chloroplast) from P. dioica. We hypothesize a northward colonization from southern Europe (where the ancestral populations reside and host most of the gene pool of these species). In P. linearis recently established populations colonized the north resulting in homogeneous low diversity, whereas for P. dioica the signature of this colonization is not as obvious due to hypothetical higher gene flow among populations, possibly linked to its reproductive biology and annual life history.
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Affiliation(s)
| | - Patrick G. Meirmans
- Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, Netherlands
| | - Michael D. Guiry
- AlgaeBase, Ryan Institute, National University of Ireland, Galway, Ireland
| | - Ester A. Serrão
- CCMAR Centro de Ciências do Mar, CIMAR, Universidade do Algarve, Faro, Portugal
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27
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de Almeida Miranda D, Araripe J, de Morais Magalhães NG, de Siqueira LS, de Abreu CC, Pereira PDC, Henrique EP, da Silva Chira PAC, de Melo MAD, do Rêgo PS, Diniz DG, Sherry DF, Diniz CWP, Guerreiro-Diniz C. Shorebirds' Longer Migratory Distances Are Associated With Larger ADCYAP1 Microsatellites and Greater Morphological Complexity of Hippocampal Astrocytes. Front Psychol 2022; 12:784372. [PMID: 35185684 PMCID: PMC8855117 DOI: 10.3389/fpsyg.2021.784372] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Accepted: 12/29/2021] [Indexed: 12/12/2022] Open
Abstract
For the epic journey of autumn migration, long-distance migratory birds use innate and learned information and follow strict schedules imposed by genetic and epigenetic mechanisms, the details of which remain largely unknown. In addition, bird migration requires integrated action of different multisensory systems for learning and memory, and the hippocampus appears to be the integration center for this task. In previous studies we found that contrasting long-distance migratory flights differentially affected the morphological complexity of two types of hippocampus astrocytes. Recently, a significant association was found between the latitude of the reproductive site and the size of the ADCYAP1 allele in long distance migratory birds. We tested for correlations between astrocyte morphological complexity, migratory distances, and size of the ADCYAP1 allele in three long-distance migrant species of shorebird and one non-migrant. Significant differences among species were found in the number and morphological complexity of the astrocytes, as well as in the size of the microsatellites of the ADCYAP1 gene. We found significant associations between the size of the ADCYAP1 microsatellites, the migratory distances, and the degree of morphological complexity of the astrocytes. We suggest that associations between astrocyte number and morphological complexity, ADCYAP1 microsatellite size, and migratory behavior may be part of the adaptive response to the migratory process of shorebirds.
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Affiliation(s)
- Diego de Almeida Miranda
- Instituto Federal de Educação Ciência e Tecnologia do Pará, Campus Bragança, Laboratório de Biologia Molecular e Neuroecologia, Bragança, Brazil.,Laboratório de Genética e Conservação, Instituto de Estudos Costeiros (IECOS), Universidade Federal do Pará, Bragança, Brazil
| | - Juliana Araripe
- Laboratório de Genética e Conservação, Instituto de Estudos Costeiros (IECOS), Universidade Federal do Pará, Bragança, Brazil
| | - Nara G de Morais Magalhães
- Instituto Federal de Educação Ciência e Tecnologia do Pará, Campus Bragança, Laboratório de Biologia Molecular e Neuroecologia, Bragança, Brazil
| | - Lucas Silva de Siqueira
- Instituto Federal de Educação Ciência e Tecnologia do Pará, Campus Bragança, Laboratório de Biologia Molecular e Neuroecologia, Bragança, Brazil
| | - Cintya Castro de Abreu
- Instituto Federal de Educação Ciência e Tecnologia do Pará, Campus Bragança, Laboratório de Biologia Molecular e Neuroecologia, Bragança, Brazil
| | - Patrick Douglas Corrêa Pereira
- Instituto Federal de Educação Ciência e Tecnologia do Pará, Campus Bragança, Laboratório de Biologia Molecular e Neuroecologia, Bragança, Brazil
| | - Ediely Pereira Henrique
- Instituto Federal de Educação Ciência e Tecnologia do Pará, Campus Bragança, Laboratório de Biologia Molecular e Neuroecologia, Bragança, Brazil
| | - Pedro Arthur Campos da Silva Chira
- Instituto Federal de Educação Ciência e Tecnologia do Pará, Campus Bragança, Laboratório de Biologia Molecular e Neuroecologia, Bragança, Brazil
| | - Mauro A D de Melo
- Instituto Federal de Educação Ciência e Tecnologia do Pará, Campus Bragança, Laboratório de Biologia Molecular e Neuroecologia, Bragança, Brazil
| | - Péricles Sena do Rêgo
- Laboratório de Genética e Conservação, Instituto de Estudos Costeiros (IECOS), Universidade Federal do Pará, Bragança, Brazil
| | - Daniel Guerreiro Diniz
- Laboratório de Investigações em Neurodegeneração e Infecção, Instituto de Ciências Biológicas, Universidade Federal do Pará, Hospital Universitário João de Barros Barreto, Belém, Brazil.,Laboratório de Microscopia Eletrônica, Instituto Evandro Chagas, Belém, Brazil
| | - David Francis Sherry
- Department of Psychology, Advanced Facility for Avian Research, University of Western Ontario, London, ON, Canada
| | - Cristovam W P Diniz
- Laboratório de Investigações em Neurodegeneração e Infecção, Instituto de Ciências Biológicas, Universidade Federal do Pará, Hospital Universitário João de Barros Barreto, Belém, Brazil
| | - Cristovam Guerreiro-Diniz
- Instituto Federal de Educação Ciência e Tecnologia do Pará, Campus Bragança, Laboratório de Biologia Molecular e Neuroecologia, Bragança, Brazil
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28
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Guagliardo SAJ, Thiele E, Unterwegner K, Narcisse Nanguita N, Dossou L, Tchindebet Ouakou P, Zirimwabagabo H, Ruiz-Tiben E, Hopkins DR, Roy SL, Cama V, Bishop H, Sapp S, Yerian S, Weiss AJ. Epidemiological and molecular investigations of a point-source outbreak of Dracunculus medinensis infecting humans and dogs in Chad: a cross-sectional study. THE LANCET MICROBE 2022; 3:e105-e112. [DOI: 10.1016/s2666-5247(21)00209-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Revised: 07/21/2021] [Accepted: 07/28/2021] [Indexed: 11/17/2022] Open
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29
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Wang J, Lv X, Feng L, Dong A, Liang D, Wu R. A Tracing Model for the Evolutionary Equilibrium of Octoploids. Front Genet 2022; 12:794907. [PMID: 35154248 PMCID: PMC8831725 DOI: 10.3389/fgene.2021.794907] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Accepted: 12/30/2021] [Indexed: 11/19/2022] Open
Abstract
Testing Hardy-Weinberg equilibrium (HWE) is a fundamental approach for inferring population diversity and evolution, but its application to octoploids containing eight chromosome sets has not well been justified. We derive a mathematical model to trace how genotype frequencies transmit from parental to offspring generations in the natural populations of autooctoploids. We find that octoploids, including autooctolpoids undergoing double reduction, attach asymptotic HWE (aHWE) after 15 generations of random mating, in a contrast to diploids where one generation can assure exact equilibrium and, also, different from tetraploids that use 5 generations to reach aHWE. We develop a statistical procedure for testing aHWE in octoploids and apply it to analyze a real data set from octoploid switchgrass distributed in two ecologically different regions, demonstrating the usefulness of the test procedure. Our model provides a tool for studying the population genetic diversity of octoploids, inferring their evolutionary history, and identifying the ecological relationship of octoploid-genome structure with environmental adaptation.
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Affiliation(s)
- Jing Wang
- National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, Center for Computational Biology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Xuemin Lv
- National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, Center for Computational Biology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Li Feng
- National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, Center for Computational Biology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Ang Dong
- National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, Center for Computational Biology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Dan Liang
- National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, Center for Computational Biology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- *Correspondence: Dan Liang, ; Rongling Wu,
| | - Rongling Wu
- Departments of Public Health Sciences and Statistics, Center for Statistical Genetics, The Pennsylvania State University, Hershey, PA, United States
- *Correspondence: Dan Liang, ; Rongling Wu,
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30
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Li M, Hu M, Xiao Y, Wu X, Wang J. The activation of gene expression and alternative splicing in the formation and evolution of allopolyploid Brassica napus. HORTICULTURE RESEARCH 2022; 9:uhab075. [PMID: 35043208 PMCID: PMC8923814 DOI: 10.1093/hr/uhab075] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Revised: 11/09/2021] [Accepted: 11/12/2021] [Indexed: 06/14/2023]
Abstract
Allopolyploids contain two or more sets of subgenomes. To establish a compatible relationship between subgenomes, a series of gene expression changes occurred in allopolyploids. What evolutionary changes of transcripts have taken place in Brassica napus during the early establishment and subsequent evolution was a fascinating scientific question. Here, we study this issue using a set of materials (natural, resynthesized B. napus and their progenitors/parents) by long-read RNA sequencing technology. The results showed that more genes were up-regulated in resynthesized B. napus compared with its two parents, and more up-regulated expressed genes were observed in natural B. napus compared with resynthesized B. napus. The presence of up-regulation genes in organism may help it adapt to the influence of "genomic shock" and cope with natural environment. Isoforms are produced from precursor mRNAs by alternative splicing (AS) events, and more than 60% of novel isoforms were identified in all materials, which could improve the reference genome information of B. napus. We found that the isoform numbers, the number of genes potentially involved in AS and alternative polyadenylation increased in B. napus after evolution, which may involve in the adaptation of plants to natural environment. In addition, all identified isoforms were functional annotated by searching 7 databases. In general, this study could improve our overall understanding of the full-length transcriptome of B. napus, and help us recognize the significant gene expression changes and isoform abundance changes occurred in allopolyploid B. napus during evolution.
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Affiliation(s)
- Mengdi Li
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, China
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi’an, Shaanxi 710069, China
| | - Meimei Hu
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Yafang Xiao
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Xiaoming Wu
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of CAAS, Wuhan 430062, China
| | - Jianbo Wang
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, China
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31
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Jighly A. When do autopolyploids need poly-sequencing data? Mol Ecol 2021; 31:1021-1027. [PMID: 34875138 DOI: 10.1111/mec.16313] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Revised: 11/23/2021] [Accepted: 12/01/2021] [Indexed: 12/17/2022]
Abstract
The sequencing depth required to genotype autopolyploid populations is a very controversial topic. Different studies have adopted variable depth values without a clear guide on the optimal sequencing depth value. Many studies suggest high depth thresholds for different ploidies that may not be practical and substantially increase the overall genotyping cost for different projects. However, such conservative thresholds may not be required to achieve the most common research goals. In fact, some recent reports in the field of quantitative genetics found that much lower sequencing depth thresholds could achieve the same accuracy as high depth thresholds. In this manuscript, I discuss when researchers need to use stringent sequencing depth thresholds and when they can use more relaxed ones. I support my argument by calculating the probabilities of sampling different homologues at a given sequencing depth. I also discuss the uses and the uncertainty in calculating a continuous allelic dosage as the proportion of sequencing reads that hold the alternative allele, which is becoming a common method now in quantitative genetics to replace discrete dosage estimation.
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Affiliation(s)
- Abdulqader Jighly
- AgriBio, Centre for AgriBiosciences, Agriculture Victoria, Bundoora, Victoria, Australia
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32
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Yang D, Li F, Wang J, Dong A, Wu R. A framework to model a web of linkage disequilibria for natural allotetraploid populations. Methods Ecol Evol 2021. [DOI: 10.1111/2041-210x.13757] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Dengcheng Yang
- Center for Computational Biology College of Biological Sciences and Technology Beijing Forestry University Beijing China
| | - Fan Li
- Center for Computational Biology College of Biological Sciences and Technology Beijing Forestry University Beijing China
| | - Jing Wang
- Center for Computational Biology College of Biological Sciences and Technology Beijing Forestry University Beijing China
| | - Ang Dong
- Center for Computational Biology College of Biological Sciences and Technology Beijing Forestry University Beijing China
| | - Rongling Wu
- Center for Computational Biology College of Biological Sciences and Technology Beijing Forestry University Beijing China
- Center for Statistical Genetics Departments of Public Health Sciences and Statistics The Pennsylvania State University Hershey PA USA
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33
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Chafin TK, Regmi B, Douglas MR, Edds DR, Wangchuk K, Dorji S, Norbu P, Norbu S, Changlu C, Khanal GP, Tshering S, Douglas ME. Parallel introgression, not recurrent emergence, explains apparent elevational ecotypes of polyploid Himalayan snowtrout. ROYAL SOCIETY OPEN SCIENCE 2021; 8:210727. [PMID: 34729207 PMCID: PMC8548808 DOI: 10.1098/rsos.210727] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Accepted: 10/01/2021] [Indexed: 06/13/2023]
Abstract
The recurrence of similar evolutionary patterns within different habitats often reflects parallel selective pressures acting upon either standing or independently occurring genetic variation to produce a convergence of phenotypes. This interpretation (i.e. parallel divergences within adjacent streams) has been hypothesized for drainage-specific morphological 'ecotypes' observed in polyploid snowtrout (Cyprinidae: Schizothorax). However, parallel patterns of differential introgression during secondary contact are a viable alternative hypothesis. Here, we used ddRADseq (N = 35 319 de novo and N = 10 884 transcriptome-aligned SNPs), as derived from Nepali/Bhutanese samples (N = 48 each), to test these competing hypotheses. We first employed genome-wide allelic depths to derive appropriate ploidy models, then a Bayesian approach to yield genotypes statistically consistent under the inferred expectations. Elevational 'ecotypes' were consistent in geometric morphometric space, but with phylogenetic relationships at the drainage level, sustaining a hypothesis of independent emergence. However, partitioned analyses of phylogeny and admixture identified subsets of loci under selection that retained genealogical concordance with morphology, suggesting instead that apparent patterns of morphological/phylogenetic discordance are driven by widespread genomic homogenization. Here, admixture occurring in secondary contact effectively 'masks' previous isolation. Our results underscore two salient factors: (i) morphological adaptations are retained despite hybridization and (ii) the degree of admixture varies across tributaries, presumably concomitant with underlying environmental or anthropogenic factors.
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Affiliation(s)
- Tyler K. Chafin
- Department of Biological Sciences, University of Arkansas, Fayetteville, AR 72701, USA
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder 80309, USA
| | - Binod Regmi
- Department of Biological Sciences, University of Arkansas, Fayetteville, AR 72701, USA
- National Institute of Arthritis, Musculoskeletal and Skin Diseases (NIAMS), National Institutes of Health, Bethesda, MD 20892, USA
| | - Marlis R. Douglas
- Department of Biological Sciences, University of Arkansas, Fayetteville, AR 72701, USA
| | - David R. Edds
- Department of Biological Sciences, Emporia State University, Emporia, KS 66801, USA
| | - Karma Wangchuk
- Department of Biological Sciences, University of Arkansas, Fayetteville, AR 72701, USA
- National Research and Development Centre for Riverine and Lake Fisheries, Ministry of Agriculture and Forests, Royal Government of Bhutan, Haa, Bhutan
| | - Sonam Dorji
- National Research and Development Centre for Riverine and Lake Fisheries, Ministry of Agriculture and Forests, Royal Government of Bhutan, Haa, Bhutan
| | - Pema Norbu
- National Research and Development Centre for Riverine and Lake Fisheries, Ministry of Agriculture and Forests, Royal Government of Bhutan, Haa, Bhutan
| | - Sangay Norbu
- National Research and Development Centre for Riverine and Lake Fisheries, Ministry of Agriculture and Forests, Royal Government of Bhutan, Haa, Bhutan
| | - Changlu Changlu
- National Research and Development Centre for Riverine and Lake Fisheries, Ministry of Agriculture and Forests, Royal Government of Bhutan, Haa, Bhutan
| | - Gopal Prasad Khanal
- National Research and Development Centre for Riverine and Lake Fisheries, Ministry of Agriculture and Forests, Royal Government of Bhutan, Haa, Bhutan
| | - Singye Tshering
- National Research and Development Centre for Riverine and Lake Fisheries, Ministry of Agriculture and Forests, Royal Government of Bhutan, Haa, Bhutan
| | - Michael E. Douglas
- Department of Biological Sciences, University of Arkansas, Fayetteville, AR 72701, USA
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Comparative Transcriptome Analysis Revealed Genes Involved in Sexual and Polyploid Growth Dimorphisms in Loach ( Misgurnus anguillicaudatus). BIOLOGY 2021; 10:biology10090935. [PMID: 34571812 PMCID: PMC8468957 DOI: 10.3390/biology10090935] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Revised: 09/05/2021] [Accepted: 09/13/2021] [Indexed: 11/16/2022]
Abstract
Simple Summary Misgurnus anguillicaudatus not only exhibits sexual size dimorphism, but also shows polyploid size dimorphism. Here, we performed comparative transcriptome integration analysis of multiple tissues of diploid and tetraploid M. anguillicaudatus of both sexes. We found that differences in energy metabolism and steroid hormone synthesis levels may be the main causes of sexual and polyploidy growth dimorphisms of M. anguillicaudatus. Fast-growing M. anguillicaudatus (tetraploids, females) have higher levels of energy metabolism and lower steroid hormone synthesis and fatty acid degradation abilities than slow-growing M. anguillicaudatus (diploids, males). Abstract Sexual and polyploidy size dimorphisms are widespread phenomena in fish, but the molecular mechanisms remain unclear. Loach (Misgurnus anguillicaudatus) displays both sexual and polyploid growth dimorphism phenomena, and are therefore ideal models to study these two phenomena. In this study, RNA-seq was used for the first time to explore the differentially expressed genes (DEGs) between both sexes of diploid and tetraploid loaches in four tissues (brain, gonad, liver, and muscle). Results showed that 21,003, 17, and 1 DEGs were identified in gonad, liver, and muscle tissues, respectively, between females and males in both diploids and tetraploids. Regarding the ploidy levels, 4956, 1496, 2187, and 1726 DEGs were identified in the brain, gonad, liver, and muscle tissues, respectively, between tetraploids and diploids of the same sex. When both sexual and polyploid size dimorphisms were considered simultaneously in the four tissues, only 424 DEGs were found in the gonads, indicating that these gonadal DEGs may play an important regulatory role in regulating sexual and polyploid size dimorphisms. Regardless of the sex or ploidy comparison, the significant DEGs involved in glycolysis/gluconeogenesis and oxidative phosphorylation pathways were upregulated in faster-growing individuals, while steroid hormone biosynthesis-related genes and fatty acid degradation and elongation-related genes were downregulated. This suggests that fast-growing loaches (tetraploids, females) have higher energy metabolism levels and lower steroid hormone synthesis and fatty acid degradation abilities than slow-growing loaches (diploids, males). Our findings provide an archive for future systematic research on fish sexual and polyploid dimorphisms.
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VanWallendael A, Alvarez M. Alignment-free methods for polyploid genomes: Quick and reliable genetic distance estimation. Mol Ecol Resour 2021; 22:612-622. [PMID: 34478242 DOI: 10.1111/1755-0998.13499] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Accepted: 08/20/2021] [Indexed: 01/10/2023]
Abstract
Polyploid genomes pose several inherent challenges to population genetic analyses. While alignment-based methods are fundamentally limited in their applicability to polyploids, alignment-free methods bypass most of these limits. We investigated the use of Mash, a k-mer analysis tool that uses the MinHash method to reduce complexity in large genomic data sets, for basic population genetic analyses of polyploid sequences. We measured the degree to which Mash correctly estimated pairwise genetic distance in simulated haploid and polyploid short-read sequences with various levels of missing data. Mash-based estimates of genetic distance were comparable to alignment-based estimates, and were less impacted by missing data. We also used Mash to analyse publicly available short-read data for three polyploid and one diploid species, then compared Mash results to published results. For both simulated and real data, Mash accurately estimated pairwise genetic differences for polyploids as well as diploids as much as 476 times faster than alignment-based methods, though we found that Mash genetic distance estimates could be biased by per-sample read depth. Mash may be a particularly useful addition to the toolkit of polyploid geneticists for rapid confirmation of alignment-based results and for basic population genetics in reference-free systems or those with only poor-quality sequence data available.
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Affiliation(s)
- Acer VanWallendael
- Department of Plant Biology, Michigan State University, East Lansing, MI, USA
| | - Mariano Alvarez
- Biology Department, Wesleyan University, Middletown, CT, USA
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36
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Cui X, Li C, Qin S, Huang Z, Gan B, Jiang Z, Huang X, Yang X, Li Q, Xiang X, Chen J, Zhao Y, Rong J. High-throughput sequencing-based microsatellite genotyping for polyploids to resolve allele dosage uncertainty and improve analyses of genetic diversity, structure and differentiation: A case study of the hexaploid Camellia oleifera. Mol Ecol Resour 2021; 22:199-211. [PMID: 34260828 DOI: 10.1111/1755-0998.13469] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Revised: 07/08/2021] [Accepted: 07/12/2021] [Indexed: 11/30/2022]
Abstract
Conventional microsatellite (simple sequence repeat, SSR) genotyping methods cannot accurately identify polyploid genotypes leading to allele dosage uncertainty, introducing biases in population genetic analysis. Here, a new SSR genotyping method was developed to directly infer accurate polyploid genotypes. The frequency distribution of SSR sequences was obtained based on deep-coverage high-throughput sequencing data. Corrections were performed accounting for the "stutter peak" and amplification efficiency of SSR sequences. Perl scripts and an online SSR genotyping tool "SSRSeq" were provided to process the sequencing data and output genotypes with corrected allele dosages. Hexaploid Camellia oleifera is the dominant woody oilseed crop in China. Understanding the geographical pattern of genetic variation in wild C. oleifera is essential for the conservation and utilization of genetic resources. Six wild C. oleifera populations were sampled across geographical ranges in subtropical evergreen broadleaf forests of China. Using 35 SSR markers, the high-throughput sequencing-based SSRSeq method was applied to obtain accurate hexaploid genotypes of wild C. oleifera. The results demonstrated that the new method could resolve allele dosage uncertainty and considerably improve genetic diversity, structure and differentiation analyses for polyploids. The genetic variation patterns of wild C. oleifera across geographical ranges agree with the "central-marginal hypothesis", stating that genetic diversity is high in the central population and declines from the central to the peripheral populations, and genetic differentiation increases from the centre to the periphery. This method and findings can facilitate the utilization of wild C. oleifera genetic resources for the breeding of cultivated C. oleifera.
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Affiliation(s)
- Xiangyan Cui
- Jiangxi Province Key Laboratory of Watershed Ecosystem Change and Biodiversity, Center for Watershed Ecology, Institute of Life Science and School of Life Sciences, Nanchang University, Nanchang, China
| | - Caihua Li
- Center for Genetic & Genomic Analysis, Genesky Biotechnologies Inc, Shanghai, China
| | - Shengyuan Qin
- Jiangxi Province Key Laboratory of Watershed Ecosystem Change and Biodiversity, Center for Watershed Ecology, Institute of Life Science and School of Life Sciences, Nanchang University, Nanchang, China
| | - Zebin Huang
- Center for Genetic & Genomic Analysis, Genesky Biotechnologies Inc, Shanghai, China
| | - Bin Gan
- Center for Genetic & Genomic Analysis, Genesky Biotechnologies Inc, Shanghai, China
| | | | - Xiaomao Huang
- Jiangxi Province Key Laboratory of Watershed Ecosystem Change and Biodiversity, Center for Watershed Ecology, Institute of Life Science and School of Life Sciences, Nanchang University, Nanchang, China
| | - Xiaoqiang Yang
- Jiangxi Province Key Laboratory of Watershed Ecosystem Change and Biodiversity, Center for Watershed Ecology, Institute of Life Science and School of Life Sciences, Nanchang University, Nanchang, China
| | - Qin Li
- Fudan Development Institute, Fudan University, Shanghai, China
| | - Xiaoguo Xiang
- Jiangxi Province Key Laboratory of Watershed Ecosystem Change and Biodiversity, Center for Watershed Ecology, Institute of Life Science and School of Life Sciences, Nanchang University, Nanchang, China
| | - Jiakuan Chen
- Jiangxi Province Key Laboratory of Watershed Ecosystem Change and Biodiversity, Center for Watershed Ecology, Institute of Life Science and School of Life Sciences, Nanchang University, Nanchang, China.,Fudan Development Institute, Fudan University, Shanghai, China
| | - Yao Zhao
- Jiangxi Province Key Laboratory of Watershed Ecosystem Change and Biodiversity, Center for Watershed Ecology, Institute of Life Science and School of Life Sciences, Nanchang University, Nanchang, China.,Lushan Botanical Garden, Chinese Academy of Sciences, Lushan, China
| | - Jun Rong
- Jiangxi Province Key Laboratory of Watershed Ecosystem Change and Biodiversity, Center for Watershed Ecology, Institute of Life Science and School of Life Sciences, Nanchang University, Nanchang, China.,Lushan Botanical Garden, Chinese Academy of Sciences, Lushan, China
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Ahmad M, Leroy T, Krigas N, Temsch EM, Weiss-Schneeweiss H, Lexer C, Sehr EM, Paun O. Spatial and Ecological Drivers of Genetic Structure in Greek Populations of Alkanna tinctoria (Boraginaceae), a Polyploid Medicinal Herb. FRONTIERS IN PLANT SCIENCE 2021; 12:706574. [PMID: 34335669 PMCID: PMC8317432 DOI: 10.3389/fpls.2021.706574] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Accepted: 06/16/2021] [Indexed: 06/08/2023]
Abstract
Background and Aims: Quantifying genetic variation is fundamental to understand a species' demographic trajectory and its ability to adapt to future changes. In comparison with diploids, however, genetic variation and factors fostering genetic divergence remain poorly studied in polyploids due to analytical challenges. Here, by employing a ploidy-aware framework, we investigated the genetic structure and its determinants in polyploid Alkanna tinctoria (Boraginaceae), an ancient medicinal herb that is the source of bioactive compounds known as alkannin and shikonin (A/S). From a practical perspective, such investigation can inform biodiversity management strategies. Methods: We collected 14 populations of A. tinctoria within its main distribution range in Greece and genotyped them using restriction site-associated DNA sequencing. In addition, we included two populations of A. sieberi. By using a ploidy-aware genotype calling based on likelihoods, we generated a dataset of 16,107 high-quality SNPs. Classical and model-based analysis was done to characterize the genetic structure within and between the sampled populations, complemented by genome size measurements and chromosomal counts. Finally, to reveal the drivers of genetic structure, we searched for associations between allele frequencies and spatial and climatic variables. Key Results: We found support for a marked regional structure in A. tinctoria along a latitudinal gradient in line with phytogeographic divisions. Several analyses identified interspecific admixture affecting both mainland and island populations. Modeling of spatial and climatic variables further demonstrated a larger contribution of neutral processes and a lesser albeit significant role of selection in shaping the observed genetic structure in A. tinctoria. Conclusion: Current findings provide evidence of strong genetic structure in A. tinctoria mainly driven by neutral processes. The revealed natural genomic variation in Greek Alkanna can be used to further predict variation in A/S production, whereas our bioinformatics approach should prove useful for the study of other non-model polyploid species.
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Affiliation(s)
- Muhammad Ahmad
- Center for Health & Bioresources, AIT Austrian Institute of Technology GmbH, Tulln, Austria
- Department of Botany and Biodiversity Research, University of Vienna, Vienna, Austria
| | - Thibault Leroy
- Department of Botany and Biodiversity Research, University of Vienna, Vienna, Austria
| | - Nikos Krigas
- Institute of Plant Breeding and Genetic Resources, Hellenic Agricultural Organization Demeter, Thessaloniki, Greece
| | - Eva M. Temsch
- Department of Botany and Biodiversity Research, University of Vienna, Vienna, Austria
| | | | - Christian Lexer
- Department of Botany and Biodiversity Research, University of Vienna, Vienna, Austria
| | - Eva Maria Sehr
- Center for Health & Bioresources, AIT Austrian Institute of Technology GmbH, Tulln, Austria
| | - Ovidiu Paun
- Department of Botany and Biodiversity Research, University of Vienna, Vienna, Austria
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Garreta L, Cerón‐Souza I, Palacio MR, Reyes‐Herrera PH. MultiGWAS: An integrative tool for Genome Wide Association Studies in tetraploid organisms. Ecol Evol 2021; 11:7411-7426. [PMID: 34188823 PMCID: PMC8216910 DOI: 10.1002/ece3.7572] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Revised: 03/22/2021] [Accepted: 03/23/2021] [Indexed: 12/27/2022] Open
Abstract
The genome-wide association studies (GWASs) are essential to determine the genetic bases of either ecological or economic phenotypic variation across individuals within populations of the model and nonmodel organisms. For this research question, the GWAS replication testing different parameters and models to validate the results' reproducibility is common. However, straightforward methodologies that manage both replication and tetraploid data are still missing. To solve this problem, we designed the MultiGWAS, a tool that does GWAS for diploid and tetraploid organisms by executing in parallel four software packages, two designed for polyploid data (GWASpoly and SHEsis) and two designed for diploid data (GAPIT and TASSEL). MultiGWAS has several advantages. It runs either in the command line or in a graphical interface; it manages different genotype formats, including VCF. Moreover, it allows control for population structure, relatedness, and several quality control checks on genotype data. Besides, MultiGWAS can test for additive and dominant gene action models, and, through a proprietary scoring function, select the best model to report its associations. Finally, it generates several reports that facilitate identifying false associations from both the significant and the best-ranked association Single Nucleotide Polymorphisms (SNPs) among the four software packages. We tested MultiGWAS with public tetraploid potato data for tuber shape and several simulated data under both additive and dominant models. These tests demonstrated that MultiGWAS is better at detecting reliable associations than using each of the four software packages individually. Moreover, the parallel analysis of polyploid and diploid software that only offers MultiGWAS demonstrates its utility in understanding the best genetic model behind the SNP association in tetraploid organisms. Therefore, MultiGWAS probed to be an excellent alternative for wrapping GWAS replication in diploid and tetraploid organisms in a single analysis environment.
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Affiliation(s)
- Luis Garreta
- Corporación Colombiana de Investigación Agropecuaria (AGROSAVIA)CI TibaitatáBogotaColombia
| | - Ivania Cerón‐Souza
- Corporación Colombiana de Investigación Agropecuaria (AGROSAVIA)CI TibaitatáBogotaColombia
| | | | - Paula H. Reyes‐Herrera
- Corporación Colombiana de Investigación Agropecuaria (AGROSAVIA)CI TibaitatáBogotaColombia
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39
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Recursive Test of Hardy-Weinberg Equilibrium in Tetraploids. Trends Genet 2021; 37:504-513. [DOI: 10.1016/j.tig.2020.11.006] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Revised: 11/15/2020] [Accepted: 11/17/2020] [Indexed: 02/08/2023]
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40
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VanWallendael A, Alvarez M, Franks SJ. Patterns of population genomic diversity in the invasive Japanese knotweed species complex. AMERICAN JOURNAL OF BOTANY 2021; 108:857-868. [PMID: 33942283 DOI: 10.1002/ajb2.1653] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2020] [Accepted: 12/22/2020] [Indexed: 06/12/2023]
Abstract
PREMISE Invasive species are expected to undergo a reduction in genetic diversity due to founder effects, which should limit their ability to adapt to new habitats. Still, many invasive species achieve widespread distributions and dense populations. This paradox of invasions could potentially be overcome through multiple introductions or hybridization, both of which increase genetic diversity. We conducted a population genomics study of Japanese knotweed (Reynoutria japonica), which is a polyploid, clonally reproducing invasive species that has been notoriously successful worldwide despite supposedly low genetic diversity. METHODS We used genotyping by sequencing to collect 12,912 SNP markers from 88 samples collected at 38 locations across North America for the species complex. We used alignment-free k-mer hashing analysis in addition to traditional population genetic analyses to account for the challenges of genotyping polyploids. RESULTS Genotypes conformed to three genetic clusters, likely representing Japanese knotweed, giant knotweed, and hybrid bohemian knotweed. We found that, contrary to previous findings, the Japanese knotweed cluster had substantial genetic diversity, though it had no apparent genetic structure across the landscape. In contrast, giant knotweed and hybrids showed distinct population groups. We did not find evidence of isolation by distance in the species complex, likely reflecting the stochastic introduction history of this species complex. CONCLUSIONS The results indicate that clonal invasive species can show substantial genetic diversity and can be successful at colonizing a variety of habitats without showing evidence of local adaptation or genetic structure.
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Affiliation(s)
- Acer VanWallendael
- Biology Department, Fordham University, 441 E. Fordham Road, Bronx, NY, 10458, USA
- Biology Department, Duke University, 130 Science Drive, Durham, NC, 27708, USA
| | - Mariano Alvarez
- Biology Department, Duke University, 130 Science Drive, Durham, NC, 27708, USA
| | - Steven J Franks
- Biology Department, Fordham University, 441 E. Fordham Road, Bronx, NY, 10458, USA
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41
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Olofsson JK, Curran EV, Nyirenda F, Bianconi ME, Dunning LT, Milenkovic V, Sotelo G, Hidalgo O, Powell RF, Lundgren MR, Leitch IJ, Nosil P, Osborne CP, Christin PA. Low dispersal and ploidy differences in a grass maintain photosynthetic diversity despite gene flow and habitat overlap. Mol Ecol 2021; 30:2116-2130. [PMID: 33682242 DOI: 10.1111/mec.15871] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2020] [Revised: 02/26/2021] [Accepted: 03/01/2021] [Indexed: 12/15/2022]
Abstract
Geographical isolation facilitates the emergence of distinct phenotypes within a single species, but reproductive barriers or selection are needed to maintain the polymorphism after secondary contact. Here, we explore the processes that maintain intraspecific variation of C4 photosynthesis, a complex trait that results from the combined action of multiple genes. The grass Alloteropsis semialata includes C4 and non-C4 populations, which have coexisted as a polyploid series for more than 1 million years in the miombo woodlands of Africa. Using population genomics, we show that there is genome-wide divergence for the photosynthetic types, but the current geographical distribution does not reflect a simple habitat displacement scenario as the genetic clusters overlap, being occasionally mixed within a given habitat. Despite evidence of recurrent introgression between non-C4 and C4 groups, in both diploids and polyploids, the distinct genetic lineages retain their identity, potentially because of selection against hybrids. Coupled with strong isolation by distance within each genetic group, this selection created a geographical mosaic of photosynthetic types. Diploid C4 and non-C4 types never grew together, and the C4 type from mixed populations constantly belonged to the hexaploid lineage. By limiting reproductive interactions between photosynthetic types, the ploidy difference probably allows their co-occurrence, reinforcing the functional diversity within this species. Together, these factors enabled the persistence of divergent physiological traits of ecological importance within a single species despite gene flow and habitat overlap.
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Affiliation(s)
- Jill K Olofsson
- Department of Animal and Plant Science, University of Sheffield, Sheffield, UK
| | - Emma V Curran
- Department of Animal and Plant Science, University of Sheffield, Sheffield, UK
| | - Florence Nyirenda
- Department of Biological Sciences, University of Zambia, Lusaka, Zambia
| | - Matheus E Bianconi
- Department of Animal and Plant Science, University of Sheffield, Sheffield, UK
| | - Luke T Dunning
- Department of Animal and Plant Science, University of Sheffield, Sheffield, UK
| | - Vanja Milenkovic
- Department of Animal and Plant Science, University of Sheffield, Sheffield, UK
| | - Graciela Sotelo
- Department of Animal and Plant Science, University of Sheffield, Sheffield, UK
| | | | | | - Marjorie R Lundgren
- Department of Animal and Plant Science, University of Sheffield, Sheffield, UK
| | | | - Patrik Nosil
- Department of Animal and Plant Science, University of Sheffield, Sheffield, UK
| | - Colin P Osborne
- Department of Animal and Plant Science, University of Sheffield, Sheffield, UK
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42
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Jiang L, Ren X, Wu R. Computational characterization of double reduction in autotetraploid natural populations. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 105:1703-1709. [PMID: 33295001 DOI: 10.1111/tpj.15126] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Accepted: 12/03/2020] [Indexed: 06/12/2023]
Abstract
Population genetic theory has been well developed for diploid species, but its extension to study genetic diversity, variation and evolution in autopolyploids, a class of polyploids derived from the genome doubling of a single ancestral species, requires the incorporation of multisomic inheritance. Double reduction, which is characteristic of autopolyploidy, has long been believed to shape the evolutionary consequence of organisms in changing environments. Here, we develop a computational model for testing and estimating double reduction and its genomic distribution in autotetraploids. The model is implemented with the expectation-maximization (EM) algorithm to dissect unobservable allelic recombinations among multiple chromosomes, enabling the simultaneous estimation of allele frequencies and double reduction in natural populations. The framework fills an important gap in the population genetic theory of autopolyploids.
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Affiliation(s)
- Libo Jiang
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, 100083, China
- Center for Computational Biology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Xiangyu Ren
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, 100083, China
- Center for Computational Biology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Rongling Wu
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, 100083, China
- Center for Computational Biology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
- Center for Statistical Genetics, Departments of Public Health Sciences and Statistics, Pennsylvania State University, Hershey, PA, 17033, USA
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43
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Shastry V, Adams PE, Lindtke D, Mandeville EG, Parchman TL, Gompert Z, Buerkle CA. Model-based genotype and ancestry estimation for potential hybrids with mixed-ploidy. Mol Ecol Resour 2021; 21:1434-1451. [PMID: 33482035 DOI: 10.1111/1755-0998.13330] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 12/11/2020] [Accepted: 01/11/2021] [Indexed: 11/29/2022]
Abstract
Non-random mating among individuals can lead to spatial clustering of genetically similar individuals and population stratification. This deviation from panmixia is commonly observed in natural populations. Consequently, individuals can have parentage in single populations or involving hybridization between differentiated populations. Accounting for this mixture and structure is important when mapping the genetics of traits and learning about the formative evolutionary processes that shape genetic variation among individuals and populations. Stratified genetic relatedness among individuals is commonly quantified using estimates of ancestry that are derived from a statistical model. Development of these models for polyploid and mixed-ploidy individuals and populations has lagged behind those for diploids. Here, we extend and test a hierarchical Bayesian model, called entropy, which can use low-depth sequence data to estimate genotype and ancestry parameters in autopolyploid and mixed-ploidy individuals (including sex chromosomes and autosomes within individuals). Our analysis of simulated data illustrated the trade-off between sequencing depth and genome coverage and found lower error associated with low-depth sequencing across a larger fraction of the genome than with high-depth sequencing across a smaller fraction of the genome. The model has high accuracy and sensitivity as verified with simulated data and through analysis of admixture among populations of diploid and tetraploid Arabidopsis arenosa.
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Affiliation(s)
| | - Paula E Adams
- Department of Biological Sciences, University of Alabama, Tuscaloosa, AL, USA
| | - Dorothea Lindtke
- Institute of Plant Sciences, University of Bern, Bern, Switzerland
| | | | | | | | - C Alex Buerkle
- Department of Botany, University of Wyoming, Laramie, WY, USA
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44
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Lozada-Gobilard S, Schwarzer C, Dyer R, Tiedemann R, Joshi J. Genetic Diversity and Connectivity in Plant Species Differing in Clonality and Dispersal Mechanisms in Wetland Island Habitats. J Hered 2021; 112:108-121. [PMID: 33555304 DOI: 10.1093/jhered/esaa059] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2020] [Accepted: 12/15/2020] [Indexed: 11/14/2022] Open
Abstract
In plants, long-distance dispersal is both attenuated and directed by specific movement vectors, including animals, wind, and/or water. Hence, movement vectors partly shape metapopulation genetic patterns that are, however, also influenced by other life-history traits such as clonal growth. We studied the relationship between area, isolation, plant-species richness, reproduction, and dispersal mechanisms with genetic diversity and divergence in 4 widespread wetland plant-species in a total of 20 island-like kettle-hole habitats surrounded by an intensive agricultural landscape. Our results showed that genetic parameters reflect the reproduction strategies with the highest genetic diversity being observed in the non-clonal, outcrossing Oenanthe aquatica compared to the clonal Lycopus europaeus, Typha latifolia, and Phragmites australis. Lycopus showed a positive relationship between genetic diversity and kettle-hole area, but a negative relationship with the number of neighboring kettle holes (less isolation). Genetic diversity increased with plant-species richness in the clonal species Phragmites and Lycopus; while it decreased in the non-clonal Oenanthe. Finally, genetic divergence and, therefore, connectivity differed between alternative dispersal strategies, where wind-dispersed Typha and Phragmites had a higher gene flow between the analyzed kettle holes compared with the insect-pollinated, hydrochorous Lycopus and Oenanthe. Our study provides information on genetic patterns related to reproduction and dispersal mechanisms of 4 common wetland species contributing to the understanding of the functioning of plant metacommunities occurring in kettle holes embedded in agricultural landscapes.
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Affiliation(s)
- Sissi Lozada-Gobilard
- Unit of Evolutionary Biology/Systematic Zoology, University of Potsdam, Karl-Liebknecht-Str. 24-25, Potsdam, Germany.,The Botanical Garden, School of Plant Sciences and Food Security, G.S. Wise Faculty of Life Science, Tel Aviv University, Israel
| | - Christian Schwarzer
- Plant Systematics and Biodiversity, Humboldt University of Berlin, Späth-Arboretum, Späthstr. 80/81, Berlin, Germany
| | - Rodney Dyer
- Center of Environmental Studies, Virginia Commonwealth University, Richmond, VA
| | - Ralph Tiedemann
- Unit of Evolutionary Biology/Systematic Zoology, University of Potsdam, Karl-Liebknecht-Str. 24-25, Potsdam, Germany
| | - Jasmin Joshi
- Institute for Landscape and Open Space, Eastern Switzerland University of Applied Sciences, Seestrasse 10, Rapperswil, Switzerland.,Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), Altensteinstr. 6, Berlin, Germany
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Bigey F, Segond D, Friedrich A, Guezenec S, Bourgais A, Huyghe L, Agier N, Nidelet T, Sicard D. Evidence for Two Main Domestication Trajectories in Saccharomyces cerevisiae Linked to Distinct Bread-Making Processes. Curr Biol 2021; 31:722-732.e5. [DOI: 10.1016/j.cub.2020.11.016] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Revised: 09/07/2020] [Accepted: 11/05/2020] [Indexed: 10/22/2022]
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Emel SL, Wang S, Metz RP, Spigler RB. Type and intensity of surrounding human land use, not local environment, shape genetic structure of a native grassland plant. Mol Ecol 2021; 30:639-655. [PMID: 33245827 DOI: 10.1111/mec.15753] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2019] [Revised: 11/01/2020] [Accepted: 11/13/2020] [Indexed: 12/28/2022]
Abstract
Landscape heterogeneity can shape genetic structure and functional connectivity of populations. When this heterogeneity imposes variable costs of moving across the landscape, populations can be structured according to a pattern of "isolation by resistance" (IBR). At the same time, divergent local environmental filters can limit gene flow, creating an alternative pattern of "isolation by environment" (IBE). Here, we evaluate IBR and IBE in the insect-pollinated, biennial plant Sabatia angularis (L.) Pursh (Gentianaceae) across serpentine grasslands in the fragmented landscape of SE Pennsylvania, USA using ~4500 neutral SNP loci. Specifically, we test the extent to which radical alteration of the landscape matrix by humans has fundamentally altered the cost of movement, imprinting a pattern of IBR dictated by land use type and intensity, and the potential for IBE in relation to a gradient of heavy metal concentrations found in serpentine soil. We reveal a strong signal of IBR and a weak signal of IBE across sites, indicating the greater importance of the landscape matrix in shaping genetic structure of S. angularis populations in the study region. Based on Circuitscape and least cost path approaches, we find that both low- and high-intensity urbanization resist gene flow by orders of magnitude greater than "natural" habitats, although resistance to low-intensity urbanization weakens at larger spatial scales. While cropland presents a substantially lower barrier than urban development, cumulative human land use surrounding populations predicts within-population genetic diversity and inbreeding in S. angularis. Our results emphasize the role of forest buffers and corridors in facilitating gene flow between serpentine grassland patches and averting local extinction of plant populations.
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Affiliation(s)
- Sarah L Emel
- Department of Biology, Temple University, Philadelphia, PA, USA.,Department of Biology, Indiana University of Pennsylvania, Indiana, PA, USA
| | - Shichen Wang
- Genomics and Bioinformatics Service, Texas A&M AgriLife Research, TX, USA
| | - Richard P Metz
- Genomics and Bioinformatics Service, Texas A&M AgriLife Research, TX, USA
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Abstract
A suitable pairwise relatedness estimation is key to genetic studies. Several methods are proposed to compute relatedness in autopolyploids based on molecular data. However, unlike diploids, autopolyploids still need further studies considering scenarios with many linked molecular markers with known dosage. In this study, we provide guidelines for plant geneticists and breeders to access trustworthy pairwise relatedness estimates. To this end, we simulated populations considering different ploidy levels, meiotic pairings patterns, number of loci and alleles, and inbreeding levels. Analysis were performed to access the accuracy of distinct methods and to demonstrate the usefulness of molecular marker in practical situations. Overall, our results suggest that at least 100 effective biallelic molecular markers are required to have good pairwise relatedness estimation if methods based on correlation is used. For this number of loci, current methods based on multiallelic markers show lower performance than biallelic ones. To estimate relatedness in cases of inbreeding or close relationships (as parent-offspring, full-sibs, or half-sibs) is more challenging. Methods to estimate pairwise relatedness based on molecular markers, for different ploidy levels or pedigrees were implemented in the AGHmatrix R package.
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Manco R, Chiaiese P, Basile B, Corrado G. Comparative analysis of genomic- and EST-SSRs in European plum ( Prunus domestica L.): implications for the diversity analysis of polyploids. 3 Biotech 2020; 10:543. [PMID: 33235823 PMCID: PMC7679426 DOI: 10.1007/s13205-020-02513-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Accepted: 10/27/2020] [Indexed: 11/23/2022] Open
Abstract
Simple sequence repeats (SSRs) are among the most useful DNA markers in plant science. The aim of this study was to compare the features and usefulness of genomic SSR (gSSR) and EST-SSRs in European plum (Prunus domestica L.), an economically important, hexaploid stone fruit crop globally cultivated to produce fleshy fruits and derived foodstuff. The analysis of an ample set of morphologically diverse varieties indicated that gSSRs and EST-SSRs provide different estimates of some of the locus-based indicators of diversity. Moreover, the two classes of SSRs gave different, weakly correlated, estimations of distance-based parameters with gSSRs being more powerful for discriminating purposes. The two SSR classes provide complementary information in European plum, making the contribution of EST-SSRs useful not only as non-neutral markers. The differences between SSR classes are discussed considering the neutral and non-neutral evolution, and the polyploidy and asexual propagation of the cultivated tree varieties.
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Mizeriene G, Cerny K, Zyka V, Bakonyi J, Nagy ZÁ, Oliva J, Redondo MA, Corcobado T, Martín-García J, Prospero S. Patterns of Genetic Diversification in the Invasive Hybrid Plant Pathogen Phytophthora × alni and Its Parental Species P. uniformis. PHYTOPATHOLOGY 2020; 110:1959-1969. [PMID: 32633698 DOI: 10.1094/phyto-12-19-0475-r] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
In pathogenic fungi and oomycetes, interspecific hybridization may lead to the formation of new species having a greater impact on natural ecosystems than the parental species. From the early 1990s, a severe alder (Alnus spp.) decline due to an unknown Phytophthora species was observed in several European countries. Genetic analyses revealed that the disease was caused by the triploid hybrid P. × alni, which originated in Europe from the hybridization of P. uniformis and P. × multiformis. Here, we investigated the population structure of P. × alni (158 isolates) and P. uniformis (85 isolates) in several European countries using microsatellite markers. Our analyses confirmed the genetic structure previously observed in other European populations, with P. uniformis populations consisting of at most two multilocus genotypes (MLGs) and P. × alni populations dominated by MLG Pxa-1. The genetic structure of P. × alni populations in the Czech Republic, Hungary and Sweden seemed to reflect the physical isolation of river systems. Most rare P. × alni MLGs showed a loss of heterozygosity (LOH) at one or a few microsatellite loci compared with other MLGs. This LOH may allow a stabilization within the P. × alni genome or a rapid adaptation to stress situations. Alternatively, alleles may be lost because of random genetic drift in small, isolated populations, with no effect on fitness of P. × alni. Additional studies would be necessary to confirm these patterns of population diversification and to better understand the factors driving it.
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Affiliation(s)
- Goda Mizeriene
- Swiss Federal Research Institute WSL, Zuercherstrasse 111, CH-8903 Birmensdorf, Switzerland
- Institute of Botany at The Lithuanian State Research Institute Nature Research Centre, Žaliųjų Ežerų Str. 49, LT-08406 Vilnius, Lithuania
| | - Karel Cerny
- The Silva Tarouca Research Institute for Landscape and Ornamental Gardening (RILOG), Květnové náměstí 391, Průhonice 252 43, The Czech Republic
| | - Vladimir Zyka
- The Silva Tarouca Research Institute for Landscape and Ornamental Gardening (RILOG), Květnové náměstí 391, Průhonice 252 43, The Czech Republic
| | - József Bakonyi
- Plant Protection Institute, Centre for Agricultural Research, Herman Ottó Str. 15, H-1022 Budapest, Hungary
| | - Zoltán Árpád Nagy
- Phytophthora Research Centre, Department of Forest Protection and Wildlife Management, Faculty of Forestry and Wood Technology, Mendel University in Brno, Zemědělská 3, 61300 Brno, Czech Republic
| | - Jonas Oliva
- Department Crop and Forest Sciences, University of Lleida, Alcalde Rovira Roure 191, 25198, Lleida, Spain
- Joint Research Unit CTFC-Agrotecnio, Alcalde Rovira Roure 191 Lleida, 25198, Spain
| | - Miguel Angel Redondo
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Box 7026, 750 07 Uppsala, Sweden
| | - Tamara Corcobado
- Phytophthora Research Centre, Department of Forest Protection and Wildlife Management, Faculty of Forestry and Wood Technology, Mendel University in Brno, Zemědělská 3, 61300 Brno, Czech Republic
- Federal Research and Training Centre for Forests, Natural Hazards and Landscape (BFW), Seckendorff-Gudent-Weg 8, 1131 Vienna, Austria
| | - Jorge Martín-García
- Department of Biology, CESAM (Centre for Environmental and Marine Studies), University of Aveiro, Campus Universitario de Santiago, 3810-193 Aveiro, Portugal
- Department of Plant Production and Forest Resources, University of Valladolid, Avenida de Madrid 44, 34071 Palencia, Spain
| | - Simone Prospero
- Swiss Federal Research Institute WSL, Zuercherstrasse 111, CH-8903 Birmensdorf, Switzerland
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Understanding the genetic diversity of the guayabillo (Psidium galapageium), an endemic plant of the Galapagos Islands. Glob Ecol Conserv 2020. [DOI: 10.1016/j.gecco.2020.e01350] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
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