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Genetic Diversity of Oxytropis Species from the Center of the Genus Origin: Insight from Molecular Studies. DIVERSITY 2023. [DOI: 10.3390/d15020244] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/12/2023]
Abstract
The genus Oxytropis (Fabaceae) was formed from the ancient species of Astragalus presumably approximately 5.6 Ma ago in Southern Siberia. Our study summarized data on the genetic diversity of 69 populations of 31 Oxytropis species in the center of origin of the genus based on the sequencing of plastid genome markers. Most of the populations (82.6%) are characterized by high gene diversity (0.600–1.000), which indicates a relatively stable state. Phylogenetic relationships between most Oxytropis species remain unresolved. Three genetic complexes and four phyletic lineages have been identified. Some species form weakly differentiated complexes, which is probably caused by their relatively recent divergence and the demography processes, as well as interspecific hybridization and polyploidy characteristic of Oxytropis species.
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Guzmán S, Giudicelli GC, Turchetto C, Bombarely A, Freitas LB. Neutral and outlier single nucleotide polymorphisms disentangle the evolutionary history of a coastal Solanaceae species. Mol Ecol 2022; 31:2847-2864. [PMID: 35332594 DOI: 10.1111/mec.16441] [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: 06/08/2021] [Revised: 03/11/2022] [Accepted: 03/16/2022] [Indexed: 11/30/2022]
Abstract
Speciation begins with the isolation of some individuals or subpopulations due to drivers promoting a diverging genetic distribution. Such isolation may occur, followed by different processes and pressures. Isolation-by-distance (IBD), isolation-by-adaptation (IBA), and isolation-by-colonization (IBC) have been recognized as the main divergence patterns. Still, it is not easy to distinguish which one is the main pattern as each one may act at different points in time or even simultaneously. Using an extensive genome coverage from a Petunia species complex with coastal and inland distribution and multiple analytical approaches on population genomics and phylogeography, we showed a complex interplay between neutral and selective forces acting on the divergence process. We found 18,887 SNPs potentially neutral and 924 potentially under selection (outlier) loci. All analyses pointed that each subspecies displays its own genetic component and evolutionary history. We suggested plausible ecologic drivers for such divergence in a southernmost South Atlantic coastal plain in Brazil and Uruguay and identified a connection between adaptation and environment heterogeneity.
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Affiliation(s)
- Sebastián Guzmán
- Department of Genetics, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Giovanna C Giudicelli
- Department of Genetics, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Caroline Turchetto
- Department of Genetics, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil.,Department of Botany, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | | | - Loreta B Freitas
- Department of Genetics, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
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Kholina A, Kozyrenko M, Artyukova E, Sandanov D, Selyutina I. Genetic diversity of Oxytropis section Xerobia (Fabaceae) in one of the centres of speciation. Genetica 2021; 149:89-101. [PMID: 33713007 DOI: 10.1007/s10709-021-00115-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Accepted: 02/18/2021] [Indexed: 11/28/2022]
Abstract
The genetic diversity and phylogenetic relationships of Oxytropis caespitosa, O. grandiflora, O. eriocarpa, O. mixotriche, O. nitens, O. peschkovae and O. triphylla, section Xerobia subgenus Oxytropis, in one of the main speciation centres of the genus Oxytropis (Baikal Siberia and adjacent territories of Northeastern Mongolia) were studied based on sequence analysis of the psbA-trnH, trnL-trnF and trnS-trnG intergenic spacers of cpDNA, as well as the ITS nrDNA. Most populations are characterized by a high level of chloroplast genetic diversity (h varied from 0.327 to 1.000 and π from 0.0001 to 0.0090) due to the ancient origin for some species and to hybridization and polyploidy for others. 67 haplotypes were identified, of which six were shared. Phylogenetic relationships among species could not be satisfactorily resolved. Only the haplotypes of O. triphylla formed a group with rather high support. Probably, O. caespitosa, O. grandiflora, O. mixotriche and O. nitens constitute a single genetic complex. As regards the ITS nrDNA polymorphism, we detected only two ribotypes (RX1, RX2). Both were found in O. caespitosa, O. eriocarpa, O. mixotriche and O. peschkovae, while RX1 was present in O. nitens and O. triphylla, RX2 in O. grandiflora. The absence of diagnostic species-specific variants for the markers studied, together with the sharing of cpDNA haplotypes and nrDNA ribotypes between species, and the resulting polytomies on the phylogenetic trees, confirm the hypothesis on the hybrid origin of some of them. Obviously, the reproductive barriers within the sect. Xerobia are weak. However, morphological differences between the species of the sect. Xerobia are clearly pronounced, even when they grow in sympatry.
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Affiliation(s)
- Alla Kholina
- Federal Scientific Centre of the East Asia Terrestrial Biodiversity, Far Eastern Branch of the Russian Academy of Sciences, Vladivostok, Russia.
| | - Marina Kozyrenko
- Federal Scientific Centre of the East Asia Terrestrial Biodiversity, Far Eastern Branch of the Russian Academy of Sciences, Vladivostok, Russia
| | - Elena Artyukova
- Federal Scientific Centre of the East Asia Terrestrial Biodiversity, Far Eastern Branch of the Russian Academy of Sciences, Vladivostok, Russia
| | - Denis Sandanov
- Institute of General and Experimental Biology, Siberian Branch of the Russian Academy of Sciences, Ulan-Ude, Russia
| | - Inessa Selyutina
- Central Siberian Botanical Garden, Siberian Branch of the Russian Academy of Science, Novosibirsk, Russia
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Schnitzler CK, Turchetto C, Teixeira MC, Freitas LB. What could be the fate of secondary contact zones between closely related plant species? Genet Mol Biol 2020; 43:e20190271. [PMID: 32556035 PMCID: PMC7299303 DOI: 10.1590/1678-4685-gmb-2019-0271] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Accepted: 03/24/2020] [Indexed: 11/26/2022] Open
Abstract
Interspecific hybridization has been fundamental in plant evolution.
Nevertheless, the fate of hybrid zones throughout the generations remains poorly
addressed. We analyzed a pair of recently diverged, interfertile, and sympatric
Petunia species to ask what fate the interspecific hybrid
population has met over time. We analyzed the genetic diversity in two
generations from two contact sites and evaluated the effect of introgression. To
do this, we collected all adult plants from the contact zones, including
canonicals and intermediary colored individuals, and compared them with purebred
representatives of both species based on seven highly informative microsatellite
loci. We compared the genetic diversity observed in the contact zones with what
is seen in isolated populations of each species, considering two generations of
these annual species. Our results have confirmed the genetic differentiation
between the species and the hybrid origin of the majority of the intermediary
colored individuals. We also observed a differentiation related to genetic
variability and inbreeding levels among the populations. Over time, there were
no significant differences per site related to genetic diversity or phenotype
composition. We found two stable populations kept by high inbreeding and
backcross rates that influence the genetic diversity of their parental species
through introgression.
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Affiliation(s)
- Carolina K Schnitzler
- Universidade Federal do Rio Grande do Sul, Departamento de Genética, Laboratório de Evolução Molecular, Porto Alegre, RS, Brazil
| | - Caroline Turchetto
- Universidade Federal do Rio Grande do Sul, Departamento de Genética, Laboratório de Evolução Molecular, Porto Alegre, RS, Brazil
| | - Marcelo C Teixeira
- Universidade Federal do Rio Grande do Sul, Departamento de Genética, Laboratório de Evolução Molecular, Porto Alegre, RS, Brazil
| | - Loreta B Freitas
- Universidade Federal do Rio Grande do Sul, Departamento de Genética, Laboratório de Evolução Molecular, Porto Alegre, RS, Brazil
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Mäder G, Freitas LB. Biogeographical, ecological, and phylogenetic analyses clarifying the evolutionary history of Calibrachoa in South American grasslands. Mol Phylogenet Evol 2019; 141:106614. [PMID: 31518694 DOI: 10.1016/j.ympev.2019.106614] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Revised: 09/09/2019] [Accepted: 09/09/2019] [Indexed: 11/29/2022]
Abstract
Calibrachoa is a charismatic South American genus of Solanaceae, closely related to Petunia, which encompasses approximately 30 species. Studies that were based solely on plastid molecular markers indicated the monophyly of the genus and distributed its species in two subgenera; to date no phylogeny has included a broad morphological variants and nuclear markers. Here, we present a phylogenetic analysis based on eight plastid and eight nuclear markers that cover the most extensive geographic distribution for the genus. We use this phylogeny to infer the biogeographic history of the genus and to understand the primary drivers for species diversification. Our results yield a fully supported tree where monophyly is confirmed to genus and subgenera. The species of Stimomphis subgenus that were previously considered uncertain, here emerge in four highly supported clades. The hypothesis of niche conservatism is confirmed, and adaptive radiation explains the species diversification. The lowlands are the most likely ancestral area of the genus, subgenera, and two clades of Stimomphis subgenus. Our results constitute an excellent starting point for further evolutionary and taxonomic studies and explain several uncertain evolutionary relationships in the group and the evolution of their distribution.
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Affiliation(s)
- Geraldo Mäder
- Laboratory of Molecular Evolution, Department of Genetics, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS 91501-970, Brazil
| | - Loreta B Freitas
- Laboratory of Molecular Evolution, Department of Genetics, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS 91501-970, Brazil.
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Genetic status of the endangered plant species Gladiolus palustris in the western part of its distribution area. CONSERV GENET 2019. [DOI: 10.1007/s10592-019-01213-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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HD-AGPs as Speciation Genes: Positive Selection on a Proline-Rich Domain in Non-Hybridizing Species of Petunia, Solanum, and Nicotiana. PLANTS 2019; 8:plants8070211. [PMID: 31288469 PMCID: PMC6681252 DOI: 10.3390/plants8070211] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Revised: 06/18/2019] [Accepted: 07/04/2019] [Indexed: 11/16/2022]
Abstract
Transmitting tissue-specific proteins (TTS proteins) are abundant in the extracellular matrix of Nicotiana pistils, and vital for optimal pollen tube growth and seed set. We have identified orthologs from several species in the Solanaceae, including Petunia axillaris axillaris and Petunia integrifolia. We refer to TTS proteins and their orthologs as histidine domain-arabinogalactan proteins (HD-AGPs). HD-AGPs have distinctive domains, including a small histidine-rich region and a C-terminal PAC domain. Pairwise comparisons between HD-AGPs of 15 species belonging to Petunia, Nicotiana, and Solanum show that the his-domain and PAC domain are under purifying selection. In contrast, a proline-rich domain (HV2) is conserved among cross-hybridizing species, but variant in species-pairs that are reproductively isolated by post-pollination pre-fertilization reproductive barriers. In particular, variation in a tetrapeptide motif (XKPP) is systematically correlated with the presence of an interspecific reproductive barrier. Ka/Ks ratios are not informative at the infrageneric level, but the ratios reveal a clear signature of positive selection on two hypervariable domains (HV1 and HV2) when HD-AGPs from five solanaceous genera are compared. We propose that sequence divergence in the hypervariable domains of HD-AGPs reinforces sympatric speciation in incipient species that may have first diverged as a consequence of pollinator preferences or other ecological factors.
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Aguiar-Melo C, Zanella CM, Goetze M, Palma-Silva C, Hirsch LD, Neves B, da Costa AF, Bered F. Ecological niche modeling and a lack of phylogeographic structure in Vriesea incurvata suggest historically stable areas in the southern Atlantic Forest. AMERICAN JOURNAL OF BOTANY 2019; 106:971-983. [PMID: 31247130 DOI: 10.1002/ajb2.1317] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Accepted: 04/18/2019] [Indexed: 06/09/2023]
Abstract
PREMISE Despite the efforts to understand the processes that shape neotropical biodiversity, the complexity of certain biomes, such as the Atlantic Forest (AF), prevents the generalization of patterns. Initially, ecological niche modeling (ENM), with phylogeographic studies, identified past stable areas in the central and northern portions of the AF, while the southern portion was thought to be highly fragmented. Here, we examined the phylogeography, historical patterns, genetic diversity, and population structure of Vriesea incurvata, an endemic species of the southern portion of the AF. METHODS We evaluated 149 individuals using two plastid DNA regions (cpDNA) and 13 nuclear microsatellite markers (nuSSRs) to access the historical patterns, genetic diversity, and structure of V. incurvata populations. We also conducted historical demography and ENM analyses. RESULTS We found moderate to high genetic diversity and low population structure for both genomes. The cpDNA network revealed high haplotype sharing. The ENM suggested no drastic changes in suitable areas for V. incurvata occurrence, corroborating the finding of no phylogeographic structure. CONCLUSIONS Contrary to some studies, our results indicate that the southern AF was a historically stable climate region for V. incurvata occupation after southward colonization by the species. Past climatic changes probably did not cause structuring among its populations.
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Affiliation(s)
- Camila Aguiar-Melo
- Universidade Federal do Rio Grande do Sul, Instituto de Biociências, Programa de Pós-graduação em Genética e Biologia Molecular, Avenida Bento Gonçalves 9500, P.O. Box 15053, 91501-970, Porto Alegre, RS, Brazil
| | - Camila M Zanella
- Universidade Federal do Rio Grande do Sul, Instituto de Biociências, Programa de Pós-graduação em Genética e Biologia Molecular, Avenida Bento Gonçalves 9500, P.O. Box 15053, 91501-970, Porto Alegre, RS, Brazil
- National Institute of Agricultural Botany (NIAB), Huntingdon Road, CB30LE, Cambridge, UK
| | - Márcia Goetze
- Universidade Federal do Rio Grande do Sul, Instituto de Biociências, Programa de Pós-graduação em Genética e Biologia Molecular, Avenida Bento Gonçalves 9500, P.O. Box 15053, 91501-970, Porto Alegre, RS, Brazil
| | - Clarisse Palma-Silva
- Departamento de Biologia Vegetal, Instituto de Biologia, Universidade Estadual de Campinas, 13083-862, Campinas, SP, Brazil
| | - Luiza D Hirsch
- Universidade Federal do Rio Grande do Sul, Instituto de Biociências, Programa de Pós-graduação em Genética e Biologia Molecular, Avenida Bento Gonçalves 9500, P.O. Box 15053, 91501-970, Porto Alegre, RS, Brazil
| | - Beatriz Neves
- Departamento de Botânica, Museu Nacional, Universidade Federal do Rio de Janeiro, Quinta da Boa Vista, São Cristóvão 20940-040, Rio de Janeiro, RJ, Brazil
| | - Andrea F da Costa
- Departamento de Botânica, Museu Nacional, Universidade Federal do Rio de Janeiro, Quinta da Boa Vista, São Cristóvão 20940-040, Rio de Janeiro, RJ, Brazil
| | - Fernanda Bered
- Universidade Federal do Rio Grande do Sul, Instituto de Biociências, Programa de Pós-graduação em Genética e Biologia Molecular, Avenida Bento Gonçalves 9500, P.O. Box 15053, 91501-970, Porto Alegre, RS, Brazil
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Variation in plant functional groups indicates land degradation on the Tibetan Plateau. Sci Rep 2018; 8:17606. [PMID: 30514965 PMCID: PMC6279773 DOI: 10.1038/s41598-018-36028-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2017] [Accepted: 11/15/2018] [Indexed: 12/28/2022] Open
Abstract
Plant functional groups (PFGs) have been increasingly introduced in land degradation (LD) studies; however, it is unclear whether PFGs can indicate LD. Here, we selected five different degraded lands (i.e., pristine and, lightly, moderately, seriously and extremely degraded) higher than 4650 m on the Tibetan Plateau. In addition, we investigated floristic metrics (i.e., composition, height, cover, biomass and abundance) and soil conditions (e.g., moisture, temperature and gravel ratio) by sampling 225 subplots. We found 75 vascular plants that consist of sedges (Cyperaceae), grasses (Gramineae), legumes, forbs, cushion plants and shrubs PFGs. LD dramatically deteriorated soil conditions, vegetation cover and productivity, however, improved species diversity. Moreover, cover and productivity showed a hump-shaped relationship with LD intensification in legumes, grasses and forbs and decreased mainly in sedges. Productivity increased considerably in cushion plants and shrubs on the extremely degraded land. Major characteristics of the LD process were the replacement of Kobresia spp. by Carex spp. in sedges; cushion plants significantly expanded, and shrubs appeared on the extremely degraded land. We, thus, confirm that the PFG variations are likely to indicate a LD process and demonstrate ways of using PFGs to assess LD status on the Tibetan Plateau.
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