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Cauz-Santos LA, Samuel R, Metschina D, Christenhusz MJM, Dodsworth S, Dixon KW, Conran JG, Paun O, Chase MW. Recent speciation and adaptation to aridity in the ecologically diverse Pilbara region of Australia enabled the native tobaccos (Nicotiana; Solanaceae) to colonize all Australian deserts. Mol Ecol 2024:e17498. [PMID: 39152668 DOI: 10.1111/mec.17498] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Revised: 08/01/2024] [Accepted: 08/05/2024] [Indexed: 08/19/2024]
Abstract
Over the last 6 million years, the arid Australian Eremaean Zone (EZ) has remained as dry as it is today. A widely accepted hypothesis suggests that the flora and fauna of arid regions were more broadly distributed before aridification began. In Australia, this process started around 20 million years ago (Ma), leading to gradual speciation as the climate became increasingly arid. Here, we use genomic data to investigate the biogeography and timing of divergence of native allotetraploid tobaccos, Nicotiana section Suaveolentes (Solanaceae). The original allotetraploid migrants from South America were adapted to mesic areas of Australia and recently radiated in the EZ, including in sandy dune fields (only 1.2 Ma old), after developing drought adaptations. Coalescent and maximum likelihood analyses suggest that Nicotiana section Suaveolentes arrived on the continent around 6 Ma, with the ancestors of the Pilbara (Western Australian) lineages radiating there at the onset of extreme aridity 5 Ma by locally adapting to these various ancient, highly stable habitats. The Pilbara thus served as both a mesic refugium and cradle for adaptations to harsher conditions, due to its high topographical diversity, providing microhabitats with varying moisture levels and its proximity to the ocean, which buffers against extreme aridity. This enabled species like Nicotiana to survive in mesic refugia and subsequently adapt to more arid conditions. These results demonstrate that initially poorly adapted plant groups can develop novel adaptations in situ, permitting extensive and rapid dispersal despite the highly variable and unpredictable extreme conditions of the EZ.
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Affiliation(s)
- Luiz A Cauz-Santos
- Department of Botany and Biodiversity Research, University of Vienna, Vienna, Austria
| | - Rosabelle Samuel
- Department of Botany and Biodiversity Research, University of Vienna, Vienna, Austria
| | - Dominik Metschina
- Department of Botany and Biodiversity Research, University of Vienna, Vienna, Austria
| | - Maarten J M Christenhusz
- Royal Botanic Gardens, Kew, Richmond, UK
- Department of Environment and Agriculture, Curtin University, Perth, Western Australia, Australia
| | - Steven Dodsworth
- School of Biological Sciences, University of Portsmouth, Portsmouth, UK
| | - Kingsley W Dixon
- Department of Environment and Agriculture, Curtin University, Perth, Western Australia, Australia
| | - John G Conran
- Environment Institute, School of Biological Sciences, The University of Adelaide, Adelaide, South Australia, Australia
| | - Ovidiu Paun
- Department of Botany and Biodiversity Research, University of Vienna, Vienna, Austria
| | - Mark W Chase
- Department of Botany and Biodiversity Research, University of Vienna, Vienna, Austria
- Royal Botanic Gardens, Kew, Richmond, UK
- Department of Environment and Agriculture, Curtin University, Perth, Western Australia, Australia
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2
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Wimalarathna NA, Wickramasuriya AM, Metschina D, Cauz-Santos LA, Bandupriya D, Ariyawansa KGSU, Gopallawa B, Chase MW, Samuel R, Silva TD. Genetic diversity and population structure of Piper nigrum (black pepper) accessions based on next-generation SNP markers. PLoS One 2024; 19:e0305990. [PMID: 38924027 PMCID: PMC11207170 DOI: 10.1371/journal.pone.0305990] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2024] [Accepted: 06/07/2024] [Indexed: 06/28/2024] Open
Abstract
Despite the economic importance of Piper nigrum (black pepper), a highly valued crop worldwide, development and utilization of genomic resources have remained limited, with diversity assessments often relying on only a few samples or DNA markers. Here we employed restriction-site associated DNA sequencing to analyze 175 P. nigrum accessions from eight main black pepper growing regions in Sri Lanka. The sequencing effort resulted in 1,976 million raw reads, averaging 11.3 million reads per accession, revealing 150,356 high-quality single nucleotide polymorphisms (SNPs) distributed across 26 chromosomes. Population structure analysis revealed two subpopulations (K = 2): a dominant group consisting of 152 accessions sourced from both home gardens and large-scale cultivations, and a smaller group comprising 23 accessions exclusively from native collections in home gardens. This clustering was further supported by principal component analysis, with the first two principal components explaining 35.2 and 12.1% of the total variation. Genetic diversity analysis indicated substantial gene flow (Nm = 342.21) and a low fixation index (FST = 0.00073) between the two subpopulations, with no clear genetic differentiation among accessions from different agro-climatic regions. These findings demonstrate that most current black pepper genotypes grown in Sri Lanka share a common genetic background, emphasizing the necessity to broaden the genetic base to enhance resilience to biotic and abiotic stresses. This study represents the first attempt at analyzing black pepper genetic diversity using high-resolution SNP markers, laying the foundation for future genome-wide association studies for SNP-based gene discovery and breeding.
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Affiliation(s)
- Nilni A. Wimalarathna
- Department of Plant Sciences, Faculty of Science, University of Colombo, Colombo, Sri Lanka
| | | | - Dominik Metschina
- Department of Botany and Biodiversity of Research, University of Vienna, Vienna, Austria
| | - Luiz A. Cauz-Santos
- Department of Botany and Biodiversity of Research, University of Vienna, Vienna, Austria
| | - Dharshani Bandupriya
- Department of Plant Sciences, Faculty of Science, University of Colombo, Colombo, Sri Lanka
| | | | - Bhathiya Gopallawa
- Department of Botany, Faculty of Science, University of Peradeniya, Peradeniya, Sri Lanka
| | - Mark W. Chase
- Department of Botany and Biodiversity of Research, University of Vienna, Vienna, Austria
- Royal Botanic Gardens, Kew, United Kingdom
- Department of Environment and Agriculture, Curtin University, Perth, Western Australia, Australia
| | - Rosabelle Samuel
- Department of Botany and Biodiversity of Research, University of Vienna, Vienna, Austria
| | - Tara D. Silva
- Department of Plant Sciences, Faculty of Science, University of Colombo, Colombo, Sri Lanka
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3
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Pérez-Calle V, Bellot S, Kuhnhäuser BG, Pillon Y, Forest F, Leitch IJ, Baker WJ. Phylogeny, biogeography and ecological diversification of New Caledonian palms (Arecaceae). ANNALS OF BOTANY 2024; 134:85-100. [PMID: 38527418 PMCID: PMC11161567 DOI: 10.1093/aob/mcae043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Accepted: 03/24/2024] [Indexed: 03/27/2024]
Abstract
BACKGROUND AND AIMS The geographical origin and evolutionary mechanisms underpinning the rich and distinctive New Caledonian flora remain poorly understood. This is attributable to the complex geological past of the island and to the scarcity of well-resolved species-level phylogenies. Here, we infer phylogenetic relationships and divergence times of New Caledonian palms, which comprise 40 species. We use this framework to elucidate the biogeography of New Caledonian palm lineages and to explore how extant species might have formed. METHODS A phylogenetic tree including 37 New Caledonian palm species and 77 relatives from tribe Areceae was inferred from 151 nuclear genes obtained by targeted sequencing. Fossil-calibrated divergence times were estimated and ancestral ranges inferred. Ancestral and extant ecological preferences in terms of elevation, precipitation and substrate were compared between New Caledonian sister species to explore their possible roles as drivers of speciation. KEY RESULTS New Caledonian palms form four well-supported clades, inside which relationships are well resolved. Our results support the current classification but suggest that Veillonia and Campecarpus should be resurrected and fail to clarify whether Rhopalostylidinae is sister to or nested in Basseliniinae. New Caledonian palm lineages are derived from New Guinean and Australian ancestors, which reached the island through at least three independent dispersal events between the Eocene and Miocene. Palms then dispersed out of New Caledonia at least five times, mainly towards Pacific islands. Geographical and ecological transitions associated with speciation events differed across time and genera. Substrate transitions were more frequently associated with older events than with younger ones. CONCLUSIONS Neighbouring areas and a mosaic of local habitats shaped the palm flora of New Caledonia, and the island played a significant role in generating palm diversity across the Pacific region. This new spatio-temporal framework will enable population-level ecological and genetic studies to unpick the mechanisms underpinning New Caledonian palm endemism.
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Affiliation(s)
- Victor Pérez-Calle
- Department of Biology, Memorial University of Newfoundland, St John’s, Newfoundland A1B 3X9, Canada
| | | | | | - Yohan Pillon
- DIADE, Univ Montpellier, CIRAD, IRD, Montpellier, France
| | - Félix Forest
- Royal Botanic Gardens, Kew, Richmond TW9 3AE, UK
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Rota F, Carnicero P, Casazza G, Nascimbene J, Schönswetter P, Wellstein C. Survival in nunatak and peripheral glacial refugia of three alpine plant species is partly predicted by altitudinal segregation. Mol Ecol 2024; 33:e17343. [PMID: 38596873 DOI: 10.1111/mec.17343] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Accepted: 03/12/2024] [Indexed: 04/11/2024]
Abstract
Mountain biota survived the Quaternary cold stages most probably in peripheral refugia and/or ice-free peaks within ice-sheets (nunataks). While survival in peripheral refugia has been broadly demonstrated, evidence for nunatak refugia is still scarce. We generated RADseq data from three mountain plant species occurring at different elevations in the southeastern European Alps to investigate the role of different glacial refugia during the Last Glacial Maximum (LGM). We tested the following hypotheses. (i) The deep Piave Valley forms the deepest genetic split in the species distributed across it, delimiting two peripheral refugia. (ii) The montane to alpine species Campanula morettiana and Primula tyrolensis survived the LGM in peripheral refugia, while high-alpine to subnival Saxifraga facchinii likely survived in several nunatak refugia. (iii) The lower elevation species suffered a strong population decline during the LGM. By contrast, the higher elevation species shows long-term stability of population sizes due to survival on permanently ice-free peaks and small population sizes at present. We found peripheral refugia on both sides of the Piave Valley, which acted as a major genetic barrier. Demographic modelling confirmed nunatak survival not only for S. facchinii but also for montane to alpine C. morettiana. Altitudinal segregation influenced the species' demographic fluctuations, with the lower elevation species showing a significant population increase at the end of the LGM, and the higher elevation species either showing decrease towards the present or stable population sizes with a short bottleneck. Our results highlight the role of nunatak survival and species ecology in the demographic history of mountain species.
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Affiliation(s)
- Francesco Rota
- Faculty of Agricultural, Environmental and Food Sciences, Free University of Bozen-Bolzano, Bolzano, Italy
- Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Birmensdorf, Switzerland
| | - Pau Carnicero
- Department of Botany, University of Innsbruck, Innsbruck, Austria
| | - Gabriele Casazza
- Department of Earth, Environmental and Life Sciences (DISTAV), University of Genoa, Genova, Italy
| | - Juri Nascimbene
- BIOME Group, Department of Biological, Geological and Environmental Sciences, Alma Mater Studiorum - University of Bologna, Bologna, Italy
| | | | - Camilla Wellstein
- Faculty of Agricultural, Environmental and Food Sciences, Free University of Bozen-Bolzano, Bolzano, Italy
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Kirschner P, Záveská E, Hülber K, Wessely J, Willner W, Schönswetter P, Frajman B. Evolutionary dynamics of Euphorbia carniolica suggest a complex Plio-Pleistocene history of understorey species of deciduous forest in southeastern Europe. Mol Ecol 2023; 32:5350-5368. [PMID: 37632417 PMCID: PMC10946815 DOI: 10.1111/mec.17102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Revised: 06/22/2023] [Accepted: 07/19/2023] [Indexed: 08/28/2023]
Abstract
Deciduous forests form the dominant natural vegetation of Europe today, but were restricted to small refugia during Pleistocene cold stages, implying an evolutionary past shaped by recurrent range contractions and expansions. Cold-stage forest refugia were probably widespread in southern and central Europe, with the northwestern Balkan Peninsula being of particular importance. However, the actual number and location of deciduous forest refugia, as well as the connections between them, remain disputed. Here, we address the evolutionary dynamics of the deciduous forest understorey species Euphorbia carniolica as a proxy for past forest dynamics. To do so, we obtained genomic and morphometric data from populations representing the species' entire range, investigated phylogenetic position and intraspecific genetic variation, tested explicit demographic scenarios and applied species distribution models. Our data support two disjoint groups linked to separate refugia on the northwestern and central Balkan Peninsula. We find that genetic differentiation between groups started in the early Pleistocene via vicariance, suggesting a larger distribution in the past. Both refugia acted as sources for founder events to the southeastern Alps and the Carpathians; the latter were likely colonised before the last cold stage. In line with traditional views on the pre-Pleistocene origin of many southeastern European deciduous forest species, the origin of E. carniolica was dated to the late Pliocene. The fact that E. carniolica evolved at a time when a period of continuous forestation was ending in much of Eurasia provides an interesting biogeographical perspective on the past links between Eurasian deciduous forests and their biota.
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Affiliation(s)
- Philipp Kirschner
- Department of BotanyUniversity of InnsbruckInnsbruckAustria
- Faculty of Agricultural, Environmental and Food SciencesFree University of Bozen‐BolzanoBolzanoItaly
| | - Eliška Záveská
- Department of BotanyUniversity of InnsbruckInnsbruckAustria
- Institute of Botany of the Czech Academy of SciencesPrůhoniceCzechia
| | - Karl Hülber
- Department of Botany and Biodiversity ResearchUniversity of ViennaViennaAustria
| | - Johannes Wessely
- Department of Botany and Biodiversity ResearchUniversity of ViennaViennaAustria
| | - Wolfgang Willner
- Department of Botany and Biodiversity ResearchUniversity of ViennaViennaAustria
| | | | - Božo Frajman
- Department of BotanyUniversity of InnsbruckInnsbruckAustria
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6
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Tonin R, Wilhelmi S, Gültas M, Gerdol R, Paun O, Trucchi E, Schmitt AO, Wellstein C. Ice holes microrefugia harbor genetically and functionally distinct populations of Vaccinium vitis-idaea (Ericaceae). Sci Rep 2023; 13:13055. [PMID: 37567871 PMCID: PMC10421893 DOI: 10.1038/s41598-023-39772-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Accepted: 07/31/2023] [Indexed: 08/13/2023] Open
Abstract
In the mountain terrain, ice holes are little depressions between rock boulders that are characterized by the exit of cold air able to cool down the rock surface even in summer. This cold air creates cold microrefugia in warmer surroundings that preserve plant species probably over thousands of years under extra-zonal climatic conditions. We hypothesized that ice hole populations of the model species Vaccinium vitis-idaea (Ericaceae) show genetic differentiation from nearby zonal subalpine populations, and high functional trait distinctiveness, in agreement with genetic patterns. We genotyped almost 30,000 single nucleotide polymorphisms using restriction site-associated DNA sequencing and measured eight functional traits indicative of individual performance and ecological strategies. Genetic results showed high differentiation among the six populations suggesting isolation. On siliceous bedrock, ice hole individuals exhibited higher levels of admixture than those from subalpine populations which could have experienced more bottlenecks during demographic fluctuations related to glacial cycles. Ice hole and subalpine calcareous populations clearly separated from siliceous populations, indicating a possible effect of bedrock in shaping genetic patterns. Trait analysis reflected the bedrock effect on populations' differentiation. The significant correlation between trait and genetic distances suggests the genetic contribution in shaping intraspecific functional differentiation. In conclusion, extra-zonal populations reveal a prominent genetic and phenotypic differentiation determined by history and ecological contingency. Therefore, microrefugia populations can contribute to the overall variability of the species and lead to intraspecific-driven responses to upcoming environmental changes.
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Affiliation(s)
- Rita Tonin
- Faculty of Agricultural, Environmental and Food Sciences, Free University of Bozen-Bolzano, 39100, Bozen, Italy
| | - Selina Wilhelmi
- Breeding Informatics Group, Department of Animal Sciences, University of Göttingen, 37075, Göttingen, Germany
- Center for Integrated Breeding Research (CiBreed), 37075, Göttingen, Germany
- Department of Forest Genetics and Forest Tree Breeding, University of Göttingen, 37077, Göttingen, Germany
| | - Mehmet Gültas
- Center for Integrated Breeding Research (CiBreed), 37075, Göttingen, Germany
- Faculty of Agriculture, South Westphalia University of Applied Sciences, 59494, Soest, Germany
| | - Renato Gerdol
- Department of Environmental and Prevention Sciences, University of Ferrara, 44121, Ferrara, Italy
| | - Ovidiu Paun
- Department for Botany and Biodiversity Research, University of Vienna, 1030, Vienna, Austria
| | - Emiliano Trucchi
- Department of Life and Environmental Science, Università Politecnica delle Marche, 60131, Ancona, Italy
| | - Armin Otto Schmitt
- Breeding Informatics Group, Department of Animal Sciences, University of Göttingen, 37075, Göttingen, Germany
- Center for Integrated Breeding Research (CiBreed), 37075, Göttingen, Germany
| | - Camilla Wellstein
- Faculty of Agricultural, Environmental and Food Sciences, Free University of Bozen-Bolzano, 39100, Bozen, Italy.
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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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8
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Carnicero P, Kröll J, Schönswetter P. Homoploid hybrids are common but evolutionary dead ends, whereas polyploidy is not linked to hybridization in a group of Pyrenean saxifrages. Mol Phylogenet Evol 2023; 180:107703. [PMID: 36632928 DOI: 10.1016/j.ympev.2023.107703] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 12/28/2022] [Accepted: 01/06/2023] [Indexed: 01/09/2023]
Abstract
Hybridization and polyploidy are major forces in plant evolution. Homoploid hybridization can generate new species via hybrid speciation, or modify extant evolutionary lineages through introgression. Polyploidy enables instantaneous reproductive isolation from the parental lineage(s) and is often coupled with evolutionary innovations, especially when linked to hybridization. While allopolyploidy is a well-known and common mechanism of plant speciation, the evolutionary role of autopolyploidy might have been underestimated. Here, we studied the saxifrages of Saxifraga subsection Saxifraga in the Pyrenees, which easily hybridise and include polyploid populations of uncertain origin, as a model to unravel evolutionary consequences and origin of hybridization and polyploidy. Additionally, we investigate the phylogenetic relationship between the two subspecies of the endemic S. pubescens to ascertain whether they should rather be treated as different species. For these purposes, we combined ploidy-informed restriction associated DNA analyses, plastid DNA sequences and morphological data on a comprehensive population sample of seven species. Our results unravel multiple homoploid hybridization events at the diploid level between different species pairs, but with limited evolutionary impact. The ploidy-informed analyses reveal that all tetraploid populations detected in the present study belong to the widespread alpine species S. moschata. Although of autopolyploid origin, they are to some extent morphologically differentiated and underwent a different evolutionary pathway than their diploid parent. However, the high plastid DNA diversity and the internal structure within eastern and western population groups suggest multiple origins of the polyploids. Finally, our phylogenetic analyses show that S. pubescens and S. iratiana are clearly not sister lineages, and should consequently be considered as independent species.
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Affiliation(s)
- Pau Carnicero
- Department of Botany, University of Innsbruck, Sternwartestraße 15, 6020 Innsbruck, Austria.
| | - Joelle Kröll
- Department of Botany, University of Innsbruck, Sternwartestraße 15, 6020 Innsbruck, Austria
| | - Peter Schönswetter
- Department of Botany, University of Innsbruck, Sternwartestraße 15, 6020 Innsbruck, Austria
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9
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Chase MW, Samuel R, Leitch AR, Guignard MS, Conran JG, Nollet F, Fletcher P, Jakob A, Cauz-Santos LA, Vignolle G, Dodsworth S, Christenhusz MJM, Buril MT, Paun O. Down, then up: non-parallel genome size changes and a descending chromosome series in a recent radiation of the Australian allotetraploid plant species, Nicotiana section Suaveolentes (Solanaceae). ANNALS OF BOTANY 2023; 131:123-142. [PMID: 35029647 PMCID: PMC9904355 DOI: 10.1093/aob/mcac006] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Accepted: 01/11/2022] [Indexed: 05/25/2023]
Abstract
BACKGROUND AND AIMS The extent to which genome size and chromosome numbers evolve in concert is little understood, particularly after polyploidy (whole-genome duplication), when a genome returns to a diploid-like condition (diploidization). We study this phenomenon in 46 species of allotetraploid Nicotiana section Suaveolentes (Solanaceae), which formed <6 million years ago and radiated in the arid centre of Australia. METHODS We analysed newly assessed genome sizes and chromosome numbers within the context of a restriction site-associated nuclear DNA (RADseq) phylogenetic framework. KEY RESULTS RADseq generated a well-supported phylogenetic tree, in which multiple accessions from each species formed unique genetic clusters. Chromosome numbers and genome sizes vary from n = 2x = 15 to 24 and 2.7 to 5.8 pg/1C nucleus, respectively. Decreases in both genome size and chromosome number occur, although neither consistently nor in parallel. Species with the lowest chromosome numbers (n = 15-18) do not possess the smallest genome sizes and, although N. heterantha has retained the ancestral chromosome complement, n = 2x = 24, it nonetheless has the smallest genome size, even smaller than that of the modern representatives of ancestral diploids. CONCLUSIONS The results indicate that decreases in genome size and chromosome number occur in parallel down to a chromosome number threshold, n = 20, below which genome size increases, a phenomenon potentially explained by decreasing rates of recombination over fewer chromosomes. We hypothesize that, more generally in plants, major decreases in genome size post-polyploidization take place while chromosome numbers are still high because in these stages elimination of retrotransposons and other repetitive elements is more efficient. Once such major genome size change has been accomplished, then dysploid chromosome reductions take place to reorganize these smaller genomes, producing species with small genomes and low chromosome numbers such as those observed in many annual angiosperms, including Arabidopsis.
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Affiliation(s)
- Mark W Chase
- Royal Botanic Gardens, Kew, Richmond TW9 3DS, UK
- Department of Environment and Agriculture, Curtin University, Perth, Western Australia, Australia
- Department of Botany and Biodiversity Research, University of Vienna, Rennweg 14, A-1030 Vienna, Austria
| | - Rosabelle Samuel
- Department of Botany and Biodiversity Research, University of Vienna, Rennweg 14, A-1030 Vienna, Austria
| | - Andrew R Leitch
- School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK
| | | | - John G Conran
- ACEBB & SGC, School of Biological Sciences, The University of Adelaide, SA 5005Australia
| | - Felipe Nollet
- Universidade Federal Rural de Pernambuco, Centro de Ciências Biológicas, Departamento de Botânica, Rua Manuel de Medeiros, S/N, Dois Irmãos, 52171-900 Recife, Pernambuco, Brazil
| | - Paul Fletcher
- School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK
| | - Aljaž Jakob
- Department of Botany and Biodiversity Research, University of Vienna, Rennweg 14, A-1030 Vienna, Austria
| | - Luiz A Cauz-Santos
- Department of Botany and Biodiversity Research, University of Vienna, Rennweg 14, A-1030 Vienna, Austria
| | - Gabriel Vignolle
- Department of Botany and Biodiversity Research, University of Vienna, Rennweg 14, A-1030 Vienna, Austria
| | - Steven Dodsworth
- School of Biological Sciences, University of Portsmouth, Portsmouth PO1 2DY, UK
| | - Maarten J M Christenhusz
- Department of Environment and Agriculture, Curtin University, Perth, Western Australia, Australia
| | - Maria Teresa Buril
- ACEBB & SGC, School of Biological Sciences, The University of Adelaide, SA 5005Australia
| | - Ovidiu Paun
- Department of Botany and Biodiversity Research, University of Vienna, Rennweg 14, A-1030 Vienna, Austria
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10
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Okuno S, Yin T, Nanami S, Matsuyama S, Kamiya K, Tan S, Davies SJ, Mohamad M, Yamakura T, Itoh A. Community phylogeny and spatial scale affect phylogenetic diversity metrics in a species-rich rainforest in Borneo. Ecol Evol 2022; 12:e9536. [PMID: 36440315 PMCID: PMC9682210 DOI: 10.1002/ece3.9536] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 11/04/2022] [Accepted: 11/04/2022] [Indexed: 11/24/2022] Open
Abstract
Community phylogenetic analysis is an effective approach to understanding the process of community formation. The phylogenetic tree of the species pool is reconstructed in the first step, and the phylogenetic tree obtained in the second step is used to analyze phylogenetic diversity. Sythetic trees have often been used in the construction of phylogenentic trees; however, in tropical rainforests with many closely related species, synthetic trees contain many unresolved nodes, which may affect the results of phylogenetic structure analysis. Here, we constructed a phylogenetic tree using DNA barcode sequences (rbcL, matK, trnH-psbA) for 737 tree species from the rainforests of Borneo, which have a high-species diversity and many closely related species. The phylogenetic tree had fewer polytomies and more branch length variations than the Phylocom synthetic trees. Comparison of community phylogenetic analyses indicated that values of the standardized effect size of mean pairwise distance (SES-MPD) were highly correlated between Phylocom and DNA barcode trees, but less so for the standardized effect size of mean nearest taxon distance (SES-MNTD), suggesting that caution is needed when using synthetic trees for communities containing many congeneric species, especially when using SES-MNTD. Simulation analysis suggested that spatial dependence on phylogenetic diversity is related to the phylogenetic signal of the species' habitat niche and the spatial structure of habitat, indicating the importance of detailed phylogeny in understanding community assembly processes.
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Affiliation(s)
- Seiya Okuno
- Graduate School of ScienceOsaka City UniversityOsakaJapan
| | - Tingting Yin
- Graduate School of ScienceOsaka City UniversityOsakaJapan
| | - Satoshi Nanami
- Graduate School of ScienceOsaka City UniversityOsakaJapan
- Graduate School of ScienceOsaka Metropolitan UniversityOsakaJapan
| | - Shuhei Matsuyama
- College of Agriculture, Food and Environmental SciencesRakuno Gakuen UniversityEbetsuJapan
| | - Koichi Kamiya
- Graduate School of AgricultureEhime UniversityMatsuyamaJapan
| | - Sylvester Tan
- Global Earth Observatory (ForestGEO)Smithsonian Tropical Research InstituteWashingtonUSA
| | - Stuart J. Davies
- Global Earth Observatory (ForestGEO)Smithsonian Tropical Research InstituteWashingtonUSA
| | | | - Takuo Yamakura
- Graduate School of ScienceOsaka City UniversityOsakaJapan
| | - Akira Itoh
- Graduate School of ScienceOsaka City UniversityOsakaJapan
- Graduate School of ScienceOsaka Metropolitan UniversityOsakaJapan
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11
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Trethowan LA, Arvidsson C, Bramley GLC. Environmental stress influences Malesian Lamiaceae distributions. Ecol Evol 2022; 12:e9467. [PMID: 36340815 PMCID: PMC9627225 DOI: 10.1002/ece3.9467] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Revised: 09/20/2022] [Accepted: 10/12/2022] [Indexed: 11/07/2022] Open
Abstract
Dual effects of spatial distance and environment shape archipelagic floras. In Malesia, there are multiple environmental stressors associated with increasing uplands, drought, and metal-rich ultramafic soils. Here, we examine the contrasting impacts of multifactorial environmental stress and spatial distance upon Lamiaceae species distributions. We used a phylogenetic generalized mixed effects model of species occurrence across Malesia's taxonomic database working group areas from Peninsular Malaysia to New Guinea. Predictor variables were environmental stress, spatial distance between areas and two trait principal component axes responsible for increasing fruit and leaf size and a negative correlation between flower size and plant height. We found that Lamiaceae species with smaller fruits and leaves are more likely to tolerate environmental stress and become widely distributed across megadiverse Malesian islands. How global species distribution and diversification are shaped by multifactorial environmental stress requires further examination.
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Affiliation(s)
| | - Camilla Arvidsson
- Herbarium KewRoyal Botanic Gardens KewLondonUK
- Department of BiosciencesUniversity of ExeterExeterUK
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12
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Palombo NE, Carrizo García C. Geographical Patterns of Genetic Variation in Locoto Chile ( Capsicum pubescens) in the Americas Inferred by Genome-Wide Data Analysis. PLANTS (BASEL, SWITZERLAND) 2022; 11:2911. [PMID: 36365364 PMCID: PMC9656212 DOI: 10.3390/plants11212911] [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: 10/02/2022] [Revised: 10/22/2022] [Accepted: 10/27/2022] [Indexed: 06/16/2023]
Abstract
The locoto chile (Capsicum pubescens) is a regionally important food crop grown and marketed throughout the mid-highlands of South andCentral America, but little is known about its evolution and the diversity it harbours. An initial scan of genetic diversity and structure across its cultivation range was conducted, the first one using a genomic approach. The RAD-sequencing methodology was applied to a sampling of C. pubescens germplasm consisting of 67 accessions from different American countries, covering its range of distribution/cultivation on the continent. The RAD-seq SNP data obtained clustered the accessions into three major groups, with a high degree of admixture/reticulation among them. Moderate but significant differentiation and geographic structuration were found, depicting a south-north pattern in the distribution of genetic variation. The highest levels of diversity were found among central-western Bolivian individuals, while the lowest was found across Central America-Mexican germplasm. This study provides new genome-wide supported insights into the diversity and differentiation of C. pubescens, as well as a starting point for more efficient use of its genetic variation and germplasm conservation efforts. The findings also contribute to understanding the evolutionary history of C. pubescens, but further investigation is needed to disentangle its origin and diversification under domestication.
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Affiliation(s)
- Nahuel E. Palombo
- Instituto Multidisciplinario de Biología Vegetal, Universidad Nacional de Córdoba, CONICET, Córdoba 5000, Argentina
| | - Carolina Carrizo García
- Instituto Multidisciplinario de Biología Vegetal, Universidad Nacional de Córdoba, CONICET, Córdoba 5000, Argentina
- Department of Botany and Biodiversity Research, University of Vienna, 1030 Vienna, Austria
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13
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Carrizo García C, Barboza GE, Palombo N, Weiss-Schneeweiss H. Diversification of chiles ( Capsicum, Solanaceae) through time and space: New insights from genome-wide RAD-seq data. Front Genet 2022; 13:1030536. [PMID: 36330443 PMCID: PMC9622771 DOI: 10.3389/fgene.2022.1030536] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Accepted: 09/20/2022] [Indexed: 11/25/2022] Open
Abstract
Capsicum L. encompasses 43 American species, including the five domesticated worldwide consumed sweet and hot chiles. This study presents new, updated and age-calibrated phylogenetic hypothesis on the genus evolution incorporating nearly all currently accepted Capsicum species. A new model of spatial diversification of Capsicum is proposed based on analyses of several thousands of genome-wide RAD-seq derived SNPs. Maximum likelihood approaches were used to reconstruct phylogenies and to estimate dates of all major splits. Ancestral ranges were inferred and diversification events were modeled in a time frame using a Bayesian approach. Nine clades corresponding to genetically and (mostly) geographically well-defined lineages, which diversified starting around mid-upper Miocene, were recovered with strong support. The Northern and Central Andes were inferred to represent the most likely ancestral range of the genus Capsicum. A few early vicariant and dispersal events were estimated to have driven the geographic divergence of the main Capsicum clades. Each lineage was inferred to have diversified within a distinct region of South America and expanded geographically to different extent. Extant species diversification was inferred to have begun at the beginning of Pliocene and continued through the Pleistocene. The Central Andes, represented mainly by the territory of present-day Bolivia, were proposed to play a central role in the diversification of lineages comprising domesticated capsicums and their wild allies. The genome-wide approach allowed for high resolution and support of deep phylogenetic nodes providing novel insights into the affinities of major lineages and clades as well as on the geographic expansion of Capsicum. This study provides the first dated evolutionary history of the genus encompassing most of the chile species diversity.
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Affiliation(s)
- Carolina Carrizo García
- Multidisciplinary Institute of Plant Biology, Cordoba, Argentina
- Department of Botany and Biodiversity Research, University of Vienna, Vienna, Austria
| | | | - Nahuel Palombo
- Multidisciplinary Institute of Plant Biology, Cordoba, Argentina
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14
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Carnicero P, Wessely J, Moser D, Font X, Dullinger S, Schönswetter P. Postglacial range expansion of high-elevation plants is restricted by dispersal ability and habitat specialization. JOURNAL OF BIOGEOGRAPHY 2022; 49:1739-1752. [PMID: 36245965 PMCID: PMC9541807 DOI: 10.1111/jbi.14390] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 04/01/2022] [Accepted: 04/06/2022] [Indexed: 06/16/2023]
Abstract
Aim Species' ecological traits influence their spatial genetic patterns. Bedrock preference strongly shapes the phylogeography of alpine plants, but its interactions with other ecological traits have rarely been disentangled. Here, we explore whether dispersal ability and degree of habitat specialization account for divergent postglacial expansion patterns of high-elevation plants in spite of similar bedrock preference. Location The Pyrenees, southwestern Europe. Taxon Cirsium glabrum (Asteraceae), Salix pyrenaica (Salicaceae) and Silene borderei (Caryophyllaceae). Methods Phylogenetic, genetic structure and demographic modelling analyses based on restriction-site-associated DNA sequencing (RADseq) data from a range-wide populational sampling were conducted. Occurrence data and environmental variables were used to construct species distribution models, which were projected under current and Last Glacial Maximum conditions, and were combined with RADseq data to reconstruct the postglacial history of the study species. The degree of habitat specialization of each species was estimated based on the plant communities within which they occur, and their climatic niche breadth. Results Salix pyrenaica, which occupies a broad range of habitats, shows a high level of range filling, a blurred genetic structure and an admixture cline between the two main genetic groups, congruent with rapid postglacial expansion. The microsite specialists C. glabrum and S. borderei exhibit a strong genetic structure and low levels of range filling, indicative of slow postglacial expansion. The good disperser C. glabrum shows higher levels of admixture between genetic groups and weaker population differentiation than the poor disperser S. borderei. Main Conclusions Factors other than bedrock preference have a strong impact on the postglacial range dynamics of high-elevation species. Habitat specialization plays an important role, allowing species occupying a broad range of habitats to more rapidly expand their ranges after environmental change. The effect of dispersal ability is lower than expected for the study species.
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Affiliation(s)
- Pau Carnicero
- Department of BotanyUniversity of InnsbruckInnsbruckAustria
| | - Johannes Wessely
- Department of Botany and Biodiversity ResearchUniversity of ViennaViennaAustria
| | - Dietmar Moser
- Department of Botany and Biodiversity ResearchUniversity of ViennaViennaAustria
| | - Xavier Font
- Department of Evolutionary Biology, Ecology and Environmental SciencesUniversity of BarcelonaBarcelonaSpain
| | - Stefan Dullinger
- Department of Botany and Biodiversity ResearchUniversity of ViennaViennaAustria
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15
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Xia M, Cai M, Comes HP, Zheng L, Ohi-Toma T, Lee J, Qi Z, Konowalik K, Li P, Cameron KM, Fu C. An overlooked dispersal route of Cardueae (Asteraceae) from the Mediterranean to East Asia revealed by phylogenomic and biogeographical analyses of Atractylodes. ANNALS OF BOTANY 2022; 130:53-64. [PMID: 35533344 PMCID: PMC9295924 DOI: 10.1093/aob/mcac059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Accepted: 05/06/2022] [Indexed: 05/11/2023]
Abstract
BACKGROUND AND AIMS The East Asian-Tethyan disjunction pattern and its mechanisms of formation have long been of interest to researchers. Here, we studied the biogeographical history of Asteraceae tribe Cardueae, with a particular focus on the temperate East Asian genus Atractylodes DC., to understand the role of tectonic and climatic events in driving the diversification and disjunctions of the genus. METHODS A total of 76 samples of Atractylodes from 36 locations were collected for RAD-sequencing. Three single nucleotide polymorphism (SNP) datasets based on different filtering strategies were used for phylogenetic analyses. Molecular dating and ancestral distribution reconstruction were performed using both chloroplast DNA sequences (127 Cardueae samples) and SNP (36 Atractylodes samples) datasets. KEY RESULTS Six species of Atractylodes were well resolved as individually monophyletic, although some introgression was identified among accessions of A. chinensis, A. lancea and A. koreana. Dispersal of the subtribe Carlininae from the Mediterranean to East Asia occurred after divergence between Atractylodes and Carlina L. + Atractylis L. + Thevenotia DC. at ~31.57 Ma, resulting in an East Asian-Tethyan disjunction. Diversification of Atractylodes in East Asia mainly occurred from the Late Miocene to the Early Pleistocene. CONCLUSIONS Aridification of Asia and the closure of the Turgai Strait in the Late Oligocene promoted the dispersal of Cardueae from the Mediterranean to East China. Subsequent uplift of the Qinghai-Tibet Plateau as well as changes in Asian monsoon systems resulted in an East Asian-Tethyan disjunction between Atractylodes and Carlina + Atractylis + Thevenotia. In addition, Late Miocene to Quaternary climates and sea level fluctuations played major roles in the diversification of Atractylodes. Through this study of different taxonomic levels using genomic data, we have revealed an overlooked dispersal route between the Mediterranean and far East Asia (Japan/Korea) via Central Asia and East China.
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Affiliation(s)
| | | | - Hans Peter Comes
- Department of Biosciences, Salzburg University, Salzburg, Austria
| | - Li Zheng
- Systematic & Evolutionary Botany and Biodiversity Group, MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, China
- Key Laboratory of Jiaxing Second Hospital, Jiaxing, Zhejiang, China
| | - Tetsuo Ohi-Toma
- Nature Fieldwork Center, Okayama University of Science, Okayama, Japan
| | - Joongku Lee
- Department of Environment and Forest Resources, Chungnam National University, Daejeon, South Korea
| | - Zhechen Qi
- College of Life Sciences, Zhejiang Sci-Tech University, Hangzhou, China
| | - Kamil Konowalik
- Department of Plant Biology, Institute of Environmental Biology, Wrocław University of Environmental and Life Sciences, Kożuchowska 5b, 51-631, Wroclaw, Poland
| | - Pan Li
- For correspondence. E-email
| | | | - Chengxin Fu
- Systematic & Evolutionary Botany and Biodiversity Group, MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, China
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16
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Cauz‐Santos LA, Dodsworth S, Samuel R, Christenhusz MJM, Patel D, Shittu T, Jakob A, Paun O, Chase MW. Genomic insights into recent species divergence in Nicotiana benthamiana and natural variation in Rdr1 gene controlling viral susceptibility. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 111:7-18. [PMID: 35535507 PMCID: PMC9543217 DOI: 10.1111/tpj.15801] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Revised: 05/05/2022] [Accepted: 05/07/2022] [Indexed: 05/31/2023]
Abstract
One of the most commonly encountered and frequently cited laboratory organisms worldwide is classified taxonomically as Nicotiana benthamiana (Solanaceae), an accession of which, typically referred to as LAB, is renowned for its unique susceptibility to a wide range of plant viruses and hence capacity to be transformed using a variety of methods. This susceptibility is the result of an insertion and consequent loss of function in the RNA-dependent RNA polymerase 1 (Rdr1) gene. However, the origin and age of LAB and the evolution of N. benthamiana across its wide distribution in Australia remain relatively underexplored. Here, we have used multispecies coalescent methods on genome-wide single nucleotide polymorphisms (SNPs) to assess species limits, phylogenetic relationships and divergence times within N. benthamiana. Our results show that the previous taxonomic concept of this species in fact comprises five geographically, morphologically and genetically distinct species, one of which includes LAB. We provide clear evidence that LAB is closely related to accessions collected further north in the Northern Territory; this species split much earlier, c. 1.1 million years ago, from their common ancestor than the other four in this clade and is morphologically the most distinctive. We also found that the Rdr1 gene insertion is variable among accessions from the northern portions of the Northern Territory. Furthermore, this long-isolated species typically grows in sheltered sites in subtropical/tropical monsoon areas of northern Australia, contradicting the previously advanced hypothesis that this species is an extremophile that has traded viral resistance for precocious development.
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Affiliation(s)
- Luiz A. Cauz‐Santos
- Department of Botany and Biodiversity ResearchUniversity of ViennaRennweg 14A‐1030ViennaAustria
| | - Steven Dodsworth
- School of Biological SciencesUniversity of PortsmouthKing Henry Building, King Henry 1 StreetPortsmouthPO1 2DYUK
- School of Life SciencesUniversity of Bedfordshire, University SquareLutonBedfordshireLU1 3JUUK
| | - Rosabelle Samuel
- Department of Botany and Biodiversity ResearchUniversity of ViennaRennweg 14A‐1030ViennaAustria
| | | | - Denise Patel
- School of Life SciencesUniversity of Bedfordshire, University SquareLutonBedfordshireLU1 3JUUK
| | - Taiwo Shittu
- School of Life SciencesUniversity of Bedfordshire, University SquareLutonBedfordshireLU1 3JUUK
| | - Aljaž Jakob
- Department of Botany and Biodiversity ResearchUniversity of ViennaRennweg 14A‐1030ViennaAustria
| | - Ovidiu Paun
- Department of Botany and Biodiversity ResearchUniversity of ViennaRennweg 14A‐1030ViennaAustria
| | - Mark W. Chase
- Department of Botany and Biodiversity ResearchUniversity of ViennaRennweg 14A‐1030ViennaAustria
- Royal Botanic GardensKewRichmondTW9 3DSUK
- Department of Environment and AgricultureCurtin UniversityPerthWestern AustraliaAustralia
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17
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Stojilkovič V, Záveská E, Frajman B. From Western Asia to the Mediterranean Basin: Diversification of the Widespread Euphorbia nicaeensis Alliance (Euphorbiaceae). FRONTIERS IN PLANT SCIENCE 2022; 13:815379. [PMID: 35812903 PMCID: PMC9262032 DOI: 10.3389/fpls.2022.815379] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Accepted: 05/05/2022] [Indexed: 05/19/2023]
Abstract
The Mediterranean Basin is an important biodiversity hotspot and one of the richest areas in the world in terms of plant diversity. Its flora parallels in several aspects that of the Eurasian steppes and the adjacent Irano-Turanian floristic region. The Euphorbia nicaeensis alliance spans this immense area from the western Mediterranean to Central Asia. Using an array of complementary methods, ranging from phylogenomic and phylogenetic data through relative genome size (RGS) estimation to morphometry, we explored relationships and biogeographic connections among taxa of this group. We identified the main evolutionary lineages, which mostly correspond to described taxa. However, despite the use of highly resolving Restriction Site Associated DNA (RAD) sequencing data, relationships among the main lineages remain ambiguous. This is likely due to hybridisation, lineage sorting triggered by rapid range expansion, and polyploidisation. The phylogenomic data identified cryptic diversity in the Mediterranean, which is also correlated with RGS and, partly, also, morphological divergence, rendering the description of a new species necessary. Biogeographic analyses suggest that Western Asia is the source area for the colonisation of the Mediterranean by this plant group and highlight the important contribution of the Irano-Turanian region to the high diversity in the Mediterranean Basin. The diversification of the E. nicaeensis alliance in the Mediterranean was triggered by vicariance in isolated Pleistocene refugia, morphological adaptation to divergent ecological conditions, and, to a lesser extent, by polyploidisation.
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Affiliation(s)
- Valentina Stojilkovič
- Department of Botany, University of Innsbruck, Innsbruck, Austria
- Department of Biology, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Eliška Záveská
- Department of Botany, University of Innsbruck, Innsbruck, Austria
- Institute of Botany of the Czech Academy of Sciences, Průhonice, Czechia
| | - Božo Frajman
- Department of Botany, University of Innsbruck, Innsbruck, Austria
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18
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Kirschner P, Perez MF, Záveská E, Sanmartín I, Marquer L, Schlick-Steiner BC, Alvarez N, Steiner FM, Schönswetter P. Congruent evolutionary responses of European steppe biota to late Quaternary climate change. Nat Commun 2022; 13:1921. [PMID: 35396388 PMCID: PMC8993823 DOI: 10.1038/s41467-022-29267-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Accepted: 03/08/2022] [Indexed: 11/09/2022] Open
Abstract
Quaternary climatic oscillations had a large impact on European biogeography. Alternation of cold and warm stages caused recurrent glaciations, massive vegetation shifts, and large-scale range alterations in many species. The Eurasian steppe biome and its grasslands are a noteworthy example; they underwent climate-driven, large-scale contractions during warm stages and expansions during cold stages. Here, we evaluate the impact of these range alterations on the late Quaternary demography of several phylogenetically distant plant and insect species, typical of the Eurasian steppes. We compare three explicit demographic hypotheses by applying an approach combining convolutional neural networks with approximate Bayesian computation. We identified congruent demographic responses of cold stage expansion and warm stage contraction across all species, but also species-specific effects. The demographic history of the Eurasian steppe biota reflects major paleoecological turning points in the late Quaternary and emphasizes the role of climate as a driving force underlying patterns of genetic variance on the biome level.
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Affiliation(s)
- Philipp Kirschner
- Department of Botany, University of Innsbruck, Sternwartestraße 15, 6020, Innsbruck, Austria. .,Department of Ecology, University of Innsbruck, Technikerstraße 25, 6020, Innsbruck, Austria.
| | - Manolo F Perez
- Real Jardín Botánico, CSIC, Plaza de Murillo 2, 28014, Madrid, Spain.,Departamento de Genetica e Evolucao, Universidade Federal de Sao Carlos, Rodovia Washington Luis, km 235, 13565905, Sao Carlos, Brazil
| | - Eliška Záveská
- Department of Botany, University of Innsbruck, Sternwartestraße 15, 6020, Innsbruck, Austria.,Institute of Botany of the Czech Academy of Sciences, Zámek 1, 25243, Průhonice, Czech Republic
| | - Isabel Sanmartín
- Real Jardín Botánico, CSIC, Plaza de Murillo 2, 28014, Madrid, Spain
| | - Laurent Marquer
- Department of Botany, University of Innsbruck, Sternwartestraße 15, 6020, Innsbruck, Austria
| | | | - Nadir Alvarez
- Geneva Natural History Museum of Geneva, Route de Malagnou 1, 1208, Genève, Switzerland.,Department of Genetics and Evolution, University of Geneva, Boulevard D'Yvoy 4, 1205, Genève, Switzerland
| | | | - Florian M Steiner
- Department of Ecology, University of Innsbruck, Technikerstraße 25, 6020, Innsbruck, Austria
| | - Peter Schönswetter
- Department of Botany, University of Innsbruck, Sternwartestraße 15, 6020, Innsbruck, Austria.
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19
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Dellinger AS, Paun O, Baar J, Temsch EM, Fernández‐Fernández D, Schönenberger J. Population structure in Neotropical plants: Integrating pollination biology, topography and climatic niches. Mol Ecol 2022; 31:2264-2280. [PMID: 35175652 PMCID: PMC9310734 DOI: 10.1111/mec.16403] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Revised: 02/10/2022] [Accepted: 02/11/2022] [Indexed: 11/29/2022]
Abstract
Animal pollinators mediate gene flow among plant populations, but in contrast to well-studied topographic and (Pleistocene) environmental isolating barriers, their impact on population genetic differentiation remains largely unexplored. Comparing how these multifarious factors drive microevolutionary histories is, however, crucial for better resolving macroevolutionary patterns of plant diversification. Here we combined genomic analyses with landscape genetics and niche modelling across six related Neotropical plant species (424 individuals across 33 localities) differing in pollination strategy to test the hypothesis that highly mobile (vertebrate) pollinators more effectively link isolated localities than less mobile (bee) pollinators. We found consistently higher genetic differentiation (FST ) among localities of bee- than vertebrate-pollinated species with increasing geographical distance, topographic barriers and historical climatic instability. High admixture among montane populations further suggested relative climatic stability of Neotropical montane forests during the Pleistocene. Overall, our results indicate that pollinators may differentially impact the potential for allopatric speciation, thereby critically influencing diversification histories at macroevolutionary scales.
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Affiliation(s)
- Agnes S. Dellinger
- Department of Botany and Biodiversity ResearchUniversity of ViennaWienAustria
- Ecology and Evolutionary BiologyUniversity of ColoradoBoulderUSA
| | - Ovidiu Paun
- Department of Botany and Biodiversity ResearchUniversity of ViennaWienAustria
| | - Juliane Baar
- Department of Botany and Biodiversity ResearchUniversity of ViennaWienAustria
| | - Eva M. Temsch
- Department of Botany and Biodiversity ResearchUniversity of ViennaWienAustria
| | | | - Jürg Schönenberger
- Department of Botany and Biodiversity ResearchUniversity of ViennaWienAustria
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20
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Rešetnik I, Záveská E, Grgurev M, Bogdanović S, Bartolić P, Frajman B. Stability in the South, Turbulence Toward the North: Evolutionary History of Aurinia saxatilis (Brassicaceae) Revealed by Phylogenomic and Climatic Modelling Data. FRONTIERS IN PLANT SCIENCE 2022; 13:822331. [PMID: 35360300 PMCID: PMC8964184 DOI: 10.3389/fpls.2022.822331] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Accepted: 01/31/2022] [Indexed: 06/14/2023]
Abstract
The Balkan Peninsula played an important role in the evolution of many Mediterranean plants and served as a major source for post-Pleistocene colonisation of central and northern Europe. Its complex geo-climatic history and environmental heterogeneity significantly influenced spatiotemporal diversification and resulted in intricate phylogeographic patterns. To explore the evolutionary dynamics and phylogeographic patterns within the widespread eastern Mediterranean and central European species Aurinia saxatilis, we used a combination of phylogenomic (restriction-site associated DNA sequencing, RADseq) and phylogenetic (sequences of the plastid marker ndhF) data as well as species distribution models generated for the present and the Last Glacial Maximum (LGM). The inferred phylogenies retrieved three main geographically distinct lineages. The southern lineage is restricted to the eastern Mediterranean, where it is distributed throughout the Aegean area, the southern Balkan Peninsula, and the southern Apennine Peninsula, and corresponds to the species main distribution area during the LGM. The eastern lineage extends from the eastern Balkan Peninsula over the Carpathians to central Europe, while the central lineage occupies the central Balkan Peninsula. Molecular dating places the divergence among all the three lineages to the early to middle Pleistocene, indicating their long-term independent evolutionary trajectories. Our data revealed an early divergence and stable in situ persistence of the southernmost, eastern Mediterranean lineage, whereas the mainland, south-east European lineages experienced more complex and turbulent evolutionary dynamics triggered by Pleistocene climatic oscillations. Our data also support the existence of multiple glacial refugia in southeast Europe and highlight the central Balkan Peninsula not only as a cradle of lineage diversifications but also as a source of lineage dispersal. Finally, the extant genetic variation within A. saxatilis is congruent with the taxonomic separation of peripatric A. saxatilis subsp. saxatilis and A. saxatilis subsp. orientalis, whereas the taxonomic status of A. saxatilis subsp. megalocarpa remains doubtful.
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Affiliation(s)
- Ivana Rešetnik
- Department of Biology, Faculty of Science, University of Zagreb, Zagreb, Croatia
| | - Eliška Záveská
- Institute of Botany, Czech Academy of Sciences, Prague, Czechia
| | - Marin Grgurev
- Department of Biology, Faculty of Science, University of Zagreb, Zagreb, Croatia
| | - Sandro Bogdanović
- Department of Agricultural Botany, Faculty of Agriculture, University of Zagreb, Zagreb, Croatia
- Centre of Excellence for Biodiversity and Molecular Plant Breeding, Zagreb, Croatia
| | - Paolo Bartolić
- Department of Botany, Charles University, Prague, Czechia
| | - Božo Frajman
- Department of Botany, University of Innsbruck, Innsbruck, Austria
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21
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Xue Z, Greimler J, Paun O, Ford KA, Barfuss MHJ, Chiapella JO. The Evolutionary History of New Zealand Deschampsia Is Marked by Long-Distance Dispersal, Endemism, and Hybridization. BIOLOGY 2021; 10:1001. [PMID: 34681100 PMCID: PMC8533413 DOI: 10.3390/biology10101001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 09/22/2021] [Accepted: 09/30/2021] [Indexed: 11/16/2022]
Abstract
The contrasting evolutionary histories of endemic versus related cosmopolitan species provide avenues to understand the spatial drivers and limitations of biodiversity. Here, we investigated the evolutionary history of three New Zealand endemic Deschampsia species, and how they are related to cosmopolitan D. cespitosa. We used RADseq to test species delimitations, infer a dated species tree, and investigate gene flow patterns between the New Zealand endemics and the D. cespitosa populations of New Zealand, Australia and Korea. Whole plastid DNA analysis was performed on a larger worldwide sampling. Morphometrics of selected characters were applied to New Zealand sampling. Our RADseq review of over 55 Mbp showed the endemics as genetically well-defined from each other. Their last common ancestor with D. cespitosa lived during the last ten MY. The New Zealand D. cespitosa appears in a clade with Australian and Korean samples. Whole plastid DNA analysis revealed the endemics as members of a southern hemisphere clade, excluding the extant D. cespitosa of New Zealand. Both data provided strong evidence for hybridization between D. cespitosa and D. chapmanii. Our findings provide evidence for at least two migration events of the genus Deschampsia to New Zealand and hybridization between D. cespitosa and endemic taxa.
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Affiliation(s)
- Zhiqing Xue
- Department of Botany and Biodiversity Research, Faculty of Life Sciences, University of Vienna, Rennweg 14, 1030 Vienna, Austria; (O.P.); (M.H.J.B.)
| | - Josef Greimler
- Department of Botany and Biodiversity Research, Faculty of Life Sciences, University of Vienna, Rennweg 14, 1030 Vienna, Austria; (O.P.); (M.H.J.B.)
| | - Ovidiu Paun
- Department of Botany and Biodiversity Research, Faculty of Life Sciences, University of Vienna, Rennweg 14, 1030 Vienna, Austria; (O.P.); (M.H.J.B.)
| | - Kerry A. Ford
- Allan Herbarium, Manaaki-Whenua Landcare Research, P.O. Box 69040, Lincoln 7640, New Zealand;
| | - Michael H. J. Barfuss
- Department of Botany and Biodiversity Research, Faculty of Life Sciences, University of Vienna, Rennweg 14, 1030 Vienna, Austria; (O.P.); (M.H.J.B.)
| | - Jorge O. Chiapella
- Instituto de Investigaciones en Biodiversidad y Medioambiente (INIBIOMA-CONICET-Universidad Nacional del Comahue), Quintral 1250, Bariloche R8400FRF, Argentina;
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22
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Genetic Divergence between Two Sympatric Ecotypes of Phalaenopsis pulcherrima on Hainan Island. DIVERSITY 2021. [DOI: 10.3390/d13090446] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Ecotypes are the result of ecological differentiation at the early stages of speciation. Adaptation to soil conditions offers arguably the best examples of local adaptation in plants. Two sympatric ecotypes, with either a red or green abaxial leaf surface, were found without clear geographical isolation in Phalaenopsis pulcherrima, a Southeast Asia endemic and endangered orchid. The soil of the red leaf ecotype has a higher water content and nutrient content than the green ecotype. What is the genetic structure of the two ecotypes? Is there complete or partial reproductive isolation between the two ecotypes? In this work, leaf reflection of the two ecotypes in P. pulcherrima were compared, to illustrate their difference in leaf color. The genetic differentiation between two ecotypes was examined, using ISSR and SRAP markers to determine the genetic structure of the populations. Our results showed that the green ecotype had reflectance spectrum peaks at 530 nm and 620 nm, while in the red ecotype, the peak at 530 nm was absent. A total of 165 ISSR and SRAP loci showed a high level of genetic diversity within the green ecotype, and analyses of the population structure revealed two genetic clusters that corresponded to the red and green ecotypes. The percentage of variation between the two ecotypes (24.55%) was greater than the percentage of variation among the populations (16.54%)—indicating partial reproductive isolation, high genetic differentiation, and that ecological differentiation has been more important than geographical barriers among populations within ecotypes. Most pairwise FST values between the populations within either ecotype on Hainan Island were less than 0.15; however, the FST between both the Thai and Malaysian populations and the Hainan Island population was greater than 0.25, due to South China sea isolation. Ecotypic differentiation is an important part of speciation; therefore, we must take into account the axes along which lineages sort, when formulating protection strategies.
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23
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Schmitt S, Tysklind N, Hérault B, Heuertz M. Topography drives microgeographic adaptations of closely related species in two tropical tree species complexes. Mol Ecol 2021; 30:5080-5093. [PMID: 34387001 DOI: 10.1111/mec.16116] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 07/29/2021] [Accepted: 07/30/2021] [Indexed: 11/27/2022]
Abstract
Closely related tree species that grow in sympatry are abundant in rainforests. However, little is known of the eco-evolutionary processes that govern their niches and local coexistence. We assessed genetic species delimitation in closely related sympatric species belonging to two Neotropical tree species complexes and investigated their genomic adaptation to a fine-scale topographic gradient with associated edaphic and hydrologic features. Combining LiDAR-derived topography, tree inventories, and single nucleotide polymorphisms (SNPs) from gene capture experiments, we explored genome-wide population genetic structure, covariation of environmental variables, and genotype-environment association to assess microgeographic adaptations to topography within the species complexes Symphonia (Clusiaceae), and Eschweilera (Lecythidaceae) with three species per complex and 385 and 257 individuals genotyped, respectively. Within species complexes, closely related tree species had different realized optima for topographic niches defined through the topographic wetness index or the relative elevation, and species displayed genetic signatures of adaptations to these niches. Symphonia species were genetically differentiated along water and nutrient distribution particularly in genes responding to water deprivation, whereas Eschweilera species were genetically differentiated according to soil chemistry. Our results suggest that varied topography represents a powerful driver of processes modulating tropical forest biodiversity with differential adaptations that stabilize local coexistence of closely related tree species.
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Affiliation(s)
- Sylvain Schmitt
- CNRS, UMR EcoFoG (Agroparistech, Cirad, INRAE, Université des Antilles, Université de la Guyane), Campus Agronomique, 97310, Kourou, French Guiana, France.,Univ. Bordeaux, INRAE, BIOGECO, 69 route d'Arcachon, 33610, Cestas, France
| | - Niklas Tysklind
- INRAE, UMR EcoFoG (Agroparistech, CNRS, Cirad, Université des Antilles, Université de la Guyane), Campus Agronomique, 97310, Kourou, French Guiana, France
| | - Bruno Hérault
- CIRAD, UR Forêts et Sociétés, Yamoussoukro Côte d'Ivoire, France.,Forêts et Sociétés, Univ Montpellier, CIRAD, Montpellier, France.,Institut National Polytechnique Félix Houphouët-Boigny, INP-HB, Yamoussoukro Côte d'Ivoire, France
| | - Myriam Heuertz
- Univ. Bordeaux, INRAE, BIOGECO, 69 route d'Arcachon, 33610, Cestas, France
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24
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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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25
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Genome Sequence of the Black Yeast-Like Strain Aureobasidium pullulans var. aubasidani CBS 100524. Microbiol Resour Announc 2021; 10:10/12/e01293-20. [PMID: 33766907 PMCID: PMC7996466 DOI: 10.1128/mra.01293-20] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
In this work, we present the whole-genome sequence and the complete mitochondrial sequence of the black yeast-like strain Aureobasidium pullulans var. aubasidani CBS 100524, which produces the exopolysaccharide aubasidan and was previously isolated from Betula sp. slime flux from the Leningrad Region of Russia.
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26
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Kirschner P, Arthofer W, Pfeifenberger S, Záveská E, Schönswetter P, Steiner FM, Schlick-Steiner BC. Performance comparison of two reduced-representation based genome-wide marker-discovery strategies in a multi-taxon phylogeographic framework. Sci Rep 2021; 11:3978. [PMID: 33597550 PMCID: PMC7889850 DOI: 10.1038/s41598-020-79778-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Accepted: 12/09/2020] [Indexed: 01/31/2023] Open
Abstract
Multi-locus genetic data are pivotal in phylogenetics. Today, high-throughput sequencing (HTS) allows scientists to generate an unprecedented amount of such data from any organism. However, HTS is resource intense and may not be accessible to wide parts of the scientific community. In phylogeography, the use of HTS has concentrated on a few taxonomic groups, and the amount of data used to resolve a phylogeographic pattern often seems arbitrary. We explore the performance of two genetic marker sampling strategies and the effect of marker quantity in a comparative phylogeographic framework focusing on six species (arthropods and plants). The same analyses were applied to data inferred from amplified fragment length polymorphism fingerprinting (AFLP), a cheap, non-HTS based technique that is able to straightforwardly produce several hundred markers, and from restriction site associated DNA sequencing (RADseq), a more expensive, HTS-based technique that produces thousands of single nucleotide polymorphisms. We show that in four of six study species, AFLP leads to results comparable with those of RADseq. While we do not aim to contest the advantages of HTS techniques, we also show that AFLP is a robust technique to delimit evolutionary entities in both plants and animals. The demonstrated similarity of results from the two techniques also strengthens biological conclusions that were based on AFLP data in the past, an important finding given the wide utilization of AFLP over the last decades. We emphasize that whenever the delimitation of evolutionary entities is the central goal, as it is in many fields of biodiversity research, AFLP is still an adequate technique.
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Affiliation(s)
- Philipp Kirschner
- grid.5771.40000 0001 2151 8122Department of Ecology, University of Innsbruck, Technikerstraße 25, 6020 Innsbruck, Austria ,grid.5771.40000 0001 2151 8122Department of Botany, University of Innsbruck, Sternwartestraße 15, 6020 Innsbruck, Austria
| | - Wolfgang Arthofer
- grid.5771.40000 0001 2151 8122Department of Ecology, University of Innsbruck, Technikerstraße 25, 6020 Innsbruck, Austria
| | - Stefanie Pfeifenberger
- grid.5771.40000 0001 2151 8122Department of Ecology, University of Innsbruck, Technikerstraße 25, 6020 Innsbruck, Austria
| | - Eliška Záveská
- grid.5771.40000 0001 2151 8122Department of Botany, University of Innsbruck, Sternwartestraße 15, 6020 Innsbruck, Austria
| | - Peter Schönswetter
- grid.5771.40000 0001 2151 8122Department of Botany, University of Innsbruck, Sternwartestraße 15, 6020 Innsbruck, Austria
| | | | - Florian M. Steiner
- grid.5771.40000 0001 2151 8122Department of Ecology, University of Innsbruck, Technikerstraße 25, 6020 Innsbruck, Austria
| | - Birgit C. Schlick-Steiner
- grid.5771.40000 0001 2151 8122Department of Ecology, University of Innsbruck, Technikerstraße 25, 6020 Innsbruck, Austria
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27
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Záveská E, Kirschner P, Frajman B, Wessely J, Willner W, Gattringer A, Hülber K, Lazić D, Dobeš C, Schönswetter P. Evidence for Glacial Refugia of the Forest Understorey Species Helleborus niger (Ranunculaceae) in the Southern as Well as in the Northern Limestone Alps. FRONTIERS IN PLANT SCIENCE 2021; 12:683043. [PMID: 34040627 PMCID: PMC8141911 DOI: 10.3389/fpls.2021.683043] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Accepted: 04/14/2021] [Indexed: 05/10/2023]
Abstract
Glacial refugia of alpine and subnival biota have been intensively studied in the European Alps but the fate of forests and their understory species in that area remains largely unclear. In order to fill this gap, we aimed at disentangling the spatiotemporal diversification of disjunctly distributed black hellebore Helleborus niger (Ranunculaceae). We applied a set of phylogeographic analyses based on restriction-site associated DNA sequencing (RADseq) data and plastid DNA sequences to a range-wide sampling of populations. These analyses were supplemented with species distribution models generated for the present and the Last Glacial Maximum (LGM). We used exploratory analyses to delimit genomically coherent groups and then employed demographic modeling to reconstruct the history of these groups. We uncovered a deep split between two major genetic groups with western and eastern distribution within the Southern Limestone Alps, likely reflecting divergent evolution since the mid-Pleistocene in two glacial refugia situated along the unglaciated southern margin of the Alps. Long-term presence in the Southern Limestone Alps is also supported by high numbers of private alleles, elevated levels of nucleotide diversity and the species' modeled distribution at the LGM. The deep genetic divergence, however, is not reflected in leaf shape variation, suggesting that the morphological discrimination of genetically divergent entities within H. niger is questionable. At a shallower level, populations from the Northern Limestone Alps are differentiated from those in the Southern Limestone Alps in both RADseq and plastid DNA data sets, reflecting the North-South disjunction within the Eastern Alps. The underlying split was dated to ca. 0.1 mya, which is well before the LGM. In the same line, explicit tests of demographic models consistently rejected the hypothesis that the partial distribution area in the Northern Limestone Alps is the result of postglacial colonization. Taken together, our results strongly support that forest understory species such as H. niger have survived the LGM in refugia situated along the southern, but also along the northern or northeastern periphery of the Alps. Being a slow migrator, the species has likely survived repeated glacial-interglacial circles in distributional stasis while the composition of the tree canopy changed in the meanwhile.
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Affiliation(s)
- Eliška Záveská
- Department of Botany, University of Innsbruck, Innsbruck, Austria
- Institute of Botany of the Czech Academy of Sciences, Průhonice, Czechia
| | | | - Božo Frajman
- Department of Botany, University of Innsbruck, Innsbruck, Austria
| | - Johannes Wessely
- Department of Botany and Biodiversity Research, University of Vienna, Vienna, Austria
| | - Wolfgang Willner
- Department of Botany and Biodiversity Research, University of Vienna, Vienna, Austria
| | - Andreas Gattringer
- Department of Botany and Biodiversity Research, University of Vienna, Vienna, Austria
| | - Karl Hülber
- Department of Botany and Biodiversity Research, University of Vienna, Vienna, Austria
- *Correspondence: Karl Hülber,
| | - Desanka Lazić
- Department of Forest Genetics and Forest Tree Breeding, Georg-August University of Göttingen, Göttingen, Germany
| | - Christoph Dobeš
- Institute of Forest Genetics, Austrian Research Centre for Forests, Vienna, Austria
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28
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White OW, Reyes-Betancort JA, Chapman MA, Carine MA. Geographical isolation, habitat shifts and hybridisation in the diversification of the Macaronesian endemic genus Argyranthemum (Asteraceae). THE NEW PHYTOLOGIST 2020; 228:1953-1971. [PMID: 33006142 DOI: 10.1111/nph.16980] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Accepted: 09/16/2020] [Indexed: 06/11/2023]
Abstract
Inferring the processes responsible for the rich endemic diversity of oceanic island floras is important for our understanding of plant evolution and setting practical conservation priorities. This requires an accurate knowledge of phylogenetic relationships, which have often been difficult to resolve due to a lack of genetic variation. We employed genotyping-by-sequencing (GBS) to investigate how geographical isolation, habitat shifts, and hybridisation have contributed to the evolution of diversity observed in Argyranthemum Webb (Asteraceae), the largest genus of flowering plants endemic to the Macaronesian archipelagos. Species relationships were resolved, and biogeographical stochastic mapping identified intra-island speciation as the most frequent biogeographic process underlying diversification, contrary to the prevailing view in Argyranthemum and the Canary Islands. D-statistics revealed significant evidence of hybridisation between lineages co-occurring on the same island, however there was little support for the hypothesis that hybridisation may be responsible for the occurrence of nonmonophyletic multi-island endemic (MIE) species. Geographic isolation, habitat shifts and hybridisation have all contributed to the diversification of Argyranthemum, with intra-island speciation found to be more frequent than previously thought. Morphological convergence is also proposed to explain the occurrence of nonmonophyletic MIE species. This study reveals greater complexity in the evolutionary processes generating Macaronesian endemic diversity.
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Affiliation(s)
- Oliver W White
- Algae, Fungi and Plants Division, Department of Life Sciences, The Natural History Museum, Cromwell Road, London, SW7 5BD, UK
- Biological Sciences, University of Southampton, Southampton, SO17 1BJ, UK
- Royal Botanic Gardens, Kew, Richmond, TW9 3AE, UK
| | - J Alfredo Reyes-Betancort
- Jardín de Aclimatación de La Oratava, Instituto Canario de Investigaciones Agrarias - ICIA), C/ Retama 2, Puerto de la Cruz, Tenerife, 38400, Spain
| | - Mark A Chapman
- Biological Sciences, University of Southampton, Southampton, SO17 1BJ, UK
| | - Mark A Carine
- Algae, Fungi and Plants Division, Department of Life Sciences, The Natural History Museum, Cromwell Road, London, SW7 5BD, UK
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29
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Pillon Y, Jaffré T, Birnbaum P, Bruy D, Cluzel D, Ducousso M, Fogliani B, Ibanez T, Jourdan H, Lagarde L, Léopold A, Munzinger J, Pouteau R, Read J, Isnard S. Infertile landscapes on an old oceanic island: the biodiversity hotspot of New Caledonia. Biol J Linn Soc Lond 2020. [DOI: 10.1093/biolinnean/blaa146] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Abstract
The OCBIL theory comprises a set of hypotheses to comprehend the biota of old, climatically buffered, infertile landscapes (OCBILs). Here, we review evidence from the literature to evaluate the extent to which this theory could apply to the biodiversity hotspot of New Caledonia. We present geological, pedological and climatic evidence suggesting how the island might qualify as an OCBIL. The predictions of OCBIL theory are then reviewed in the context of New Caledonia. There is evidence for a high rate of micro-endemism, accumulation of relict lineages, a high incidence of dioecy, myrmecochory and nutritional specializations in plants. New Caledonian vegetation also exhibits several types of monodominant formations that reveal the importance of disturbances on the island. Fires and tropical storms are likely to be important factors that contribute to the dynamic of New Caledonian ecosystems. Although naturally infertile, there is archaeological evidence that humans developed specific horticultural practices in the ultramafic landscapes of New Caledonia. Further comparisons between New Caledonia and other areas of the world, such as South Africa and Southwest Australia, are desirable, to develop the OCBIL theory into a more robust and generalized, testable framework and to determine the most efficient strategies to preserve their outstanding biodiversity.
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Affiliation(s)
- Yohan Pillon
- LSTM, IRD, INRAE, CIRAD, Institut Agro, Univ Montpellier, Montpellier, France
| | - Tanguy Jaffré
- AMAP, Univ Montpellier, IRD, CIRAD, CNRS, INRAE, Montpellier, France
- AMAP, IRD, CIRAD, Herbier de la Nouvelle-Calédonie, Nouméa, New Caledonia
| | - Philippe Birnbaum
- AMAP, Univ Montpellier, IRD, CIRAD, CNRS, INRAE, Montpellier, France
- AMAP, IRD, CIRAD, Herbier de la Nouvelle-Calédonie, Nouméa, New Caledonia
- Institut Agronomique Néo-Calédonien (IAC), équipe SolVeg, Nouméa, New Caledonia
| | - David Bruy
- AMAP, Univ Montpellier, IRD, CIRAD, CNRS, INRAE, Montpellier, France
- AMAP, IRD, CIRAD, Herbier de la Nouvelle-Calédonie, Nouméa, New Caledonia
| | - Dominique Cluzel
- ISEA, Université de la Nouvelle-Calédonie, Nouméa, New Caledonia
| | - Marc Ducousso
- LSTM, IRD, INRAE, CIRAD, Institut Agro, Univ Montpellier, Montpellier, France
| | - Bruno Fogliani
- ISEA, Université de la Nouvelle-Calédonie, Nouméa, New Caledonia
| | - Thomas Ibanez
- Department of Biology, University of Hawai′i at Hilo, Hilo, HI, USA
| | - Hervé Jourdan
- IMBE, Aix Marseille Université, CNRS, IRD, Avignon Université, Nouméa, New Caledonia
| | - Louis Lagarde
- TROCA, Université de la Nouvelle-Calédonie, Nouméa, New Caledonia
| | - Audrey Léopold
- Institut Agronomique Néo-Calédonien (IAC), équipe SolVeg, Nouméa, New Caledonia
| | - Jérôme Munzinger
- AMAP, Univ Montpellier, IRD, CIRAD, CNRS, INRAE, Montpellier, France
| | - Robin Pouteau
- AMAP, Univ Montpellier, IRD, CIRAD, CNRS, INRAE, Montpellier, France
| | - Jennifer Read
- School of Biological Sciences, Monash University, Victoria, Australia
| | - Sandrine Isnard
- AMAP, Univ Montpellier, IRD, CIRAD, CNRS, INRAE, Montpellier, France
- AMAP, IRD, CIRAD, Herbier de la Nouvelle-Calédonie, Nouméa, New Caledonia
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30
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The potential of genome-wide RAD sequences for resolving rapid radiations: a case study in Cactaceae. Mol Phylogenet Evol 2020; 151:106896. [PMID: 32562821 DOI: 10.1016/j.ympev.2020.106896] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Revised: 03/22/2020] [Accepted: 06/10/2020] [Indexed: 11/23/2022]
Abstract
The reconstruction of relationships within recently radiated groups is challenging even when massive amounts of sequencing data are available. The use of restriction site-associated DNA sequencing (RAD-Seq) to this end is promising. Here, we assessed the performance of RAD-Seq to infer the species-level phylogeny of the rapidly radiating genus Cereus (Cactaceae). To examine how the amount of genomic data affects resolution in this group, we used datasets and implemented different analyses. We sampled 52 individuals of Cereus, representing 18 of the 25 species currently recognized, plus members of the closely allied genera Cipocereus and Praecereus, and other 11 Cactaceae genera as outgroups. Three scenarios of permissiveness to missing data were carried out in iPyRAD, assembling datasets with 30% (333 loci), 45% (1440 loci), and 70% (6141 loci) of missing data. For each dataset, Maximum Likelihood (ML) trees were generated using two supermatrices, i.e., only SNPs and SNPs plus invariant sites. Accuracy and resolution were improved when the dataset with the highest number of loci was used (6141 loci), despite the high percentage of missing data included (70%). Coalescent trees estimated using SVDQuartets and ASTRAL are similar to those obtained by the ML reconstructions. Overall, we reconstruct a well-supported phylogeny of Cereus, which is resolved as monophyletic and composed of four main clades with high support in their internal relationships. Our findings also provide insights into the impact of missing data for phylogeny reconstruction using RAD loci.
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31
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Kirschner P, Záveská E, Gamisch A, Hilpold A, Trucchi E, Paun O, Sanmartín I, Schlick-Steiner BC, Frajman B, Arthofer W, Steiner FM, Schönswetter P. Long-term isolation of European steppe outposts boosts the biome's conservation value. Nat Commun 2020; 11:1968. [PMID: 32327640 PMCID: PMC7181837 DOI: 10.1038/s41467-020-15620-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2019] [Accepted: 03/13/2020] [Indexed: 11/10/2022] Open
Abstract
The European steppes and their biota have been hypothesized to be either young remnants of the Pleistocene steppe belt or, alternatively, to represent relicts of long-term persisting populations; both scenarios directly bear on nature conservation priorities. Here, we evaluate the conservation value of threatened disjunct steppic grassland habitats in Europe in the context of the Eurasian steppe biome. We use genomic data and ecological niche modelling to assess pre-defined, biome-specific criteria for three plant and three arthropod species. We show that the evolutionary history of Eurasian steppe biota is strikingly congruent across species. The biota of European steppe outposts were long-term isolated from the Asian steppes, and European steppes emerged as disproportionally conservation relevant, harbouring regionally endemic genetic lineages, large genetic diversity, and a mosaic of stable refugia. We emphasize that conserving what is left of Europe's steppes is crucial for conserving the biological diversity of the entire Eurasian steppe biome.
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Affiliation(s)
- Philipp Kirschner
- Department of Ecology, University of Innsbruck, Technikerstraße 25, 6020, Innsbruck, Austria.
| | - Eliška Záveská
- Department of Botany, University of Innsbruck, Sternwartestraße 15, 6020, Innsbruck, Austria
| | - Alexander Gamisch
- Department of Ecology, University of Innsbruck, Technikerstraße 25, 6020, Innsbruck, Austria.,Department of Biosciences, University of Salzburg, Hellbrunnerstrasse 34, 5020, Salzburg, Austria
| | - Andreas Hilpold
- Institute for Alpine Environment, Eurac Research, Drususallee 1/Viale Druso 1, 39100, Bozen/Bolzano, Italy
| | - Emiliano Trucchi
- Department of Life and Environmental Sciences, Marche Polytechnic University, Via Brecce Bianche, 60131, Ancona, Italy
| | - Ovidiu Paun
- Department of Botany and Biodiversity Research, University of Vienna, Rennweg 14, 1030, Vienna, Austria
| | - Isabel Sanmartín
- Real Jardín Botánico CSIC, Plaza de Murillo 2, 28014, Madrid, Spain
| | | | - Božo Frajman
- Department of Botany, University of Innsbruck, Sternwartestraße 15, 6020, Innsbruck, Austria
| | - Wolfgang Arthofer
- Department of Ecology, University of Innsbruck, Technikerstraße 25, 6020, Innsbruck, Austria
| | | | - Florian M Steiner
- Department of Ecology, University of Innsbruck, Technikerstraße 25, 6020, Innsbruck, Austria.
| | - Peter Schönswetter
- Department of Botany, University of Innsbruck, Sternwartestraße 15, 6020, Innsbruck, Austria.
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Balao F, Lorenzo MT, Sánchez-Robles JM, Paun O, García-Castaño JL, Terrab A. Early diversification and permeable species boundaries in the Mediterranean firs. ANNALS OF BOTANY 2020; 125:495-507. [PMID: 31730195 PMCID: PMC7061173 DOI: 10.1093/aob/mcz186] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Accepted: 11/14/2019] [Indexed: 05/09/2023]
Abstract
BACKGROUND AND AIMS Inferring the evolutionary relationships of species and their boundaries is critical in order to understand patterns of diversification and their historical drivers. Despite Abies (Pinaceae) being the second most diverse group of conifers, the evolutionary history of Circum-Mediterranean firs (CMFs) remains under debate. METHODS We used restriction site-associated DNA sequencing (RAD-seq) on all proposed CMF taxa to investigate their phylogenetic relationships and taxonomic status. KEY RESULTS Based on thousands of genome-wide single nucleotide polymorphisms (SNPs), we present here the first formal test of species delimitation, and the first fully resolved, complete species tree for CMFs. We discovered that all previously recognized taxa in the Mediterranean should be treated as independent species, with the exception of Abies tazaotana and Abies marocana. An unexpectedly early pulse of speciation in the Oligocene-Miocene boundary is here documented for the group, pre-dating previous hypotheses by millions of years, revealing a complex evolutionary history encompassing both ancient and recent gene flow between distant lineages. CONCLUSIONS Our phylogenomic results contribute to shed light on conifers' diversification. Our efforts to resolve the CMF phylogenetic relationships help refine their taxonomy and our knowledge of their evolution.
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Affiliation(s)
- Francisco Balao
- Departamento de Biología Vegetal y Ecología, Facultad de Biología, Universidad de Sevilla, Apdo. 1095, 41080 Sevilla, Spain
- For correspondence. E-mail
| | - María Teresa Lorenzo
- Departamento de Biología Vegetal y Ecología, Facultad de Biología, Universidad de Sevilla, Apdo. 1095, 41080 Sevilla, Spain
| | - José Manuel Sánchez-Robles
- Departamento de Biología Vegetal y Ecología, Facultad de Biología, Universidad de Sevilla, Apdo. 1095, 41080 Sevilla, Spain
| | - Ovidiu Paun
- Department of Botany and Biodiversity Research, University of Vienna, Rennweg 14, A-1030 Vienna, Austria
| | - Juan Luis García-Castaño
- Departamento de Biología Vegetal y Ecología, Facultad de Biología, Universidad de Sevilla, Apdo. 1095, 41080 Sevilla, Spain
| | - Anass Terrab
- Departamento de Biología Vegetal y Ecología, Facultad de Biología, Universidad de Sevilla, Apdo. 1095, 41080 Sevilla, Spain
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Pérez-Escobar OA, Bogarín D, Schley R, Bateman RM, Gerlach G, Harpke D, Brassac J, Fernández-Mazuecos M, Dodsworth S, Hagsater E, Blanco MA, Gottschling M, Blattner FR. Resolving relationships in an exceedingly young Neotropical orchid lineage using Genotyping-by-sequencing data. Mol Phylogenet Evol 2020; 144:106672. [DOI: 10.1016/j.ympev.2019.106672] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Revised: 10/26/2019] [Accepted: 11/05/2019] [Indexed: 01/18/2023]
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Brandrud MK, Baar J, Lorenzo MT, Athanasiadis A, Bateman RM, Chase MW, Hedrén M, Paun O. Phylogenomic Relationships of Diploids and the Origins of Allotetraploids in Dactylorhiza (Orchidaceae). Syst Biol 2020; 69:91-109. [PMID: 31127939 PMCID: PMC6902629 DOI: 10.1093/sysbio/syz035] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2018] [Revised: 05/12/2019] [Accepted: 05/17/2019] [Indexed: 12/04/2022] Open
Abstract
Disentangling phylogenetic relationships proves challenging for groups that have evolved recently, especially if there is ongoing reticulation. Although they are in most cases immediately isolated from diploid relatives, sets of sibling allopolyploids often hybridize with each other, thereby increasing the complexity of an already challenging situation. Dactylorhiza (Orchidaceae: Orchidinae) is a genus much affected by allopolyploid speciation and reticulate phylogenetic relationships. Here, we use genetic variation at tens of thousands of genomic positions to unravel the convoluted evolutionary history of Dactylorhiza. We first investigate circumscription and relationships of diploid species in the genus using coalescent and maximum likelihood methods, and then group 16 allotetraploids by maximum affiliation to their putative parental diploids, implementing a method based on genotype likelihoods. The direction of hybrid crosses is inferred for each allotetraploid using information from maternally inherited plastid RADseq loci. Starting from age estimates of parental taxa, the relative ages of these allotetraploid entities are inferred by quantifying their genetic similarity to the diploids and numbers of private alleles compared with sibling allotetraploids. Whereas northwestern Europe is dominated by young allotetraploids of postglacial origins, comparatively older allotetraploids are distributed further south, where climatic conditions remained relatively stable during the Pleistocene glaciations. Our bioinformatics approach should prove effective for the study of other naturally occurring, nonmodel, polyploid plant complexes.
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Affiliation(s)
- Marie K Brandrud
- Department of Botany and Biodiversity Research, University of Vienna, Rennweg 14, A-1030 Vienna, Austria
| | - Juliane Baar
- Department of Botany and Biodiversity Research, University of Vienna, Rennweg 14, A-1030 Vienna, Austria
| | - Maria T Lorenzo
- Department of Botany and Biodiversity Research, University of Vienna, Rennweg 14, A-1030 Vienna, Austria
| | - Alexander Athanasiadis
- Department of Botany and Biodiversity Research, University of Vienna, Rennweg 14, A-1030 Vienna, Austria
| | | | - Mark W Chase
- Royal Botanic Gardens Kew, Richmond, Surrey, TW9 3AB, UK
- Department of Environment and Agriculture, Curtin University, Bentley, Western Australia 6102, Australia
| | - Mikael Hedrén
- Department of Biology, University of Lund, Sölvegatan 37, SE-223 62 Lund, Sweden
| | - Ovidiu Paun
- Department of Botany and Biodiversity Research, University of Vienna, Rennweg 14, A-1030 Vienna, Austria
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Pan D, Hülber K, Willner W, Schneeweiss GM. An explicit test of Pleistocene survival in peripheral versus nunatak refugia in two high mountain plant species. Mol Ecol 2019; 29:172-183. [PMID: 31765501 PMCID: PMC7003806 DOI: 10.1111/mec.15316] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Revised: 11/20/2019] [Accepted: 11/22/2019] [Indexed: 01/15/2023]
Abstract
Pleistocene climate fluctuations had profound influence on the biogeographical history of many biota. As large areas in high mountain ranges were covered by glaciers, biota were forced either to peripheral refugia (and possibly beyond to lowland refugia) or to interior refugia (nunataks). However, nunatak survival remains controversial as it relies solely on correlative genetic evidence. Here, we test hypotheses of glacial survival using two high alpine plant species (the insect‐pollinated Pedicularis asplenifolia and wind‐pollinated Carex fuliginosa) in the European Alps. Employing the iDDC (integrative Distributional, Demographic and Coalescent) approach, which couples species distribution modelling, spatial and temporal demographic simulation and Approximate Bayesian Computation, we explicitly test three hypotheses of glacial survival: (a) peripheral survival only, (b) nunatak survival only and (c) peripheral plus nunatak survival. In P. asplenifolia the peripheral plus nunatak survival hypothesis was supported by Bayes factors (BF> 100), whereas in C. fuliginosa the peripheral survival only hypothesis, although best supported, could not be unambiguously distinguished from the peripheral plus nunatak survival hypothesis (BF = 5.58). These results are consistent with current habitat preferences (P. asplenifolia extends to higher elevations) and the potential for genetic swamping (i.e., replacement of local genotypes via hybridization with immigrating genotypes [expected to be higher in the wind‐pollinated C. fuliginosa]). Although the persistence of plants on nunataks during glacial periods has been debated and studied over decades, this is one of the first studies to explicitly test the hypothesis instead of solely using correlative evidence.
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Affiliation(s)
- Da Pan
- Department of Botany and Biodiversity Research, University of Vienna, Vienna, Austria
| | - Karl Hülber
- Department of Botany and Biodiversity Research, University of Vienna, Vienna, Austria
| | - Wolfgang Willner
- Department of Botany and Biodiversity Research, University of Vienna, Vienna, Austria
| | - Gerald M Schneeweiss
- Department of Botany and Biodiversity Research, University of Vienna, Vienna, Austria
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Sramkó G, Paun O, Brandrud MK, Laczkó L, Molnár A, Bateman RM. Iterative allogamy-autogamy transitions drive actual and incipient speciation during the ongoing evolutionary radiation within the orchid genus Epipactis (Orchidaceae). ANNALS OF BOTANY 2019; 124:481-497. [PMID: 31231754 PMCID: PMC6798847 DOI: 10.1093/aob/mcz103] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Accepted: 06/19/2019] [Indexed: 05/16/2023]
Abstract
BACKGROUND AND AIMS The terrestrial orchid genus Epipactis has become a model system for the study of speciation via transitions from allogamy to autogamy, but close phylogenetic relationships have proven difficult to resolve through Sanger sequencing. METHODS We analysed with restriction site-associated sequencing (RAD-seq) 108 plants representing 29 named taxa that together span the genus, focusing on section Epipactis. Our filtered matrix of 12 543 single nucleotide polymorphisms was used to generate an unrooted network and a rooted, well-supported likelihood tree. We further inferred genetic structure through a co-ancestry heat map and admixture analysis, and estimated inbreeding coefficients per sample. KEY RESULTS The 27 named taxa of the ingroup were resolved as 11 genuine, geographically widespread species: four dominantly allogamous and seven dominantly autogamous. A single comparatively allogamous species, E. helleborine, is the direct ancestor of most of the remaining species, though one of the derived autogams has generated one further autogamous species. An assessment of shared ancestry suggested only sporadic hybridization between the re-circumscribed species. Taxa with the greatest inclination towards autogamy show less, if any, admixture, whereas the gene pools of more allogamous species contain a mixture alleles found in the autogams. CONCLUSIONS This clade is presently undergoing an evolutionary radiation driven by a wide spectrum of genotypic, phenotypic and environmental factors. Epipactis helleborine has also frequently generated many local variants showing inclinations toward autogamy (and occasionally cleistogamy), best viewed as incipient speciation from within the genetic background provided by E. helleborine, which thus becomes an example of a convincingly paraphyletic species. Autogams are often as widespread and ecologically successful as allogams.
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Affiliation(s)
- Gábor Sramkó
- Department of Botany, University of Debrecen, Egyetem tér, Debrecen, Hungary
- MTA-DE ‘Lendület’ Evolutionary Phylogenomics Research Group, Debrecen, Hungary
- For correspondence. E-mail
| | - Ovidiu Paun
- Department of Botany and Biodiversity Research, University of Vienna, Vienna, Austria
| | - Marie K Brandrud
- Department of Botany and Biodiversity Research, University of Vienna, Vienna, Austria
| | - Levente Laczkó
- Department of Botany, University of Debrecen, Egyetem tér, Debrecen, Hungary
| | - Attila Molnár
- Department of Botany, University of Debrecen, Egyetem tér, Debrecen, Hungary
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Dodsworth S, Pokorny L, Johnson MG, Kim JT, Maurin O, Wickett NJ, Forest F, Baker WJ. Hyb-Seq for Flowering Plant Systematics. TRENDS IN PLANT SCIENCE 2019; 24:887-891. [PMID: 31477409 DOI: 10.1016/j.tplants.2019.07.011] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Revised: 07/15/2019] [Accepted: 07/31/2019] [Indexed: 05/21/2023]
Abstract
High-throughput DNA sequencing (HTS) presents great opportunities for plant systematics, yet genomic complexity needs to be reduced for HTS to be effectively applied. We highlight Hyb-Seq as a promising approach, especially in light of the recent development of probes enriching 353 low-copy nuclear genes from any flowering plant taxon.
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Affiliation(s)
- Steven Dodsworth
- Royal Botanic Gardens, Kew, Richmond TW9 3AE, Surrey, UK; School of Life Sciences, University of Bedfordshire, University Square, Luton LU1 3JU, UK.
| | - Lisa Pokorny
- Royal Botanic Gardens, Kew, Richmond TW9 3AE, Surrey, UK; Centre for Plant Biotechnology and Genomics (CBGP, UPM-INIA), 28223 Pozuelo de Alarcón, Madrid, Spain
| | - Matthew G Johnson
- Department of Biological Sciences, Texas Tech University, Lubbock, TX 79409, USA; Chicago Botanic Garden, Glencoe, IL 60022, USA
| | - Jan T Kim
- Royal Botanic Gardens, Kew, Richmond TW9 3AE, Surrey, UK
| | - Olivier Maurin
- Royal Botanic Gardens, Kew, Richmond TW9 3AE, Surrey, UK
| | - Norman J Wickett
- Chicago Botanic Garden, Glencoe, IL 60022, USA; Program in Plant Biology and Conservation, Northwestern University, Evanston, IL 60208, USA
| | - Felix Forest
- Royal Botanic Gardens, Kew, Richmond TW9 3AE, Surrey, UK
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Clugston JAR, Kenicer GJ, Milne R, Overcast I, Wilson TC, Nagalingum NS. RADseq as a valuable tool for plants with large genomes—A case study in cycads. Mol Ecol Resour 2019; 19:1610-1622. [DOI: 10.1111/1755-0998.13085] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Revised: 08/08/2019] [Accepted: 08/09/2019] [Indexed: 11/26/2022]
Affiliation(s)
- James A. R. Clugston
- School of Biological Sciences The University of Edinburgh Edinburgh UK
- Royal Botanic Garden Edinburgh Edinburgh UK
| | | | - Richard Milne
- School of Biological Sciences The University of Edinburgh Edinburgh UK
| | - Isaac Overcast
- The Graduate Center of the City University of New York New York NY USA
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Záveská E, Maylandt C, Paun O, Bertel C, Frajman B, The Steppe Consortium, Schönswetter P. Multiple auto- and allopolyploidisations marked the Pleistocene history of the widespread Eurasian steppe plant Astragalus onobrychis (Fabaceae). Mol Phylogenet Evol 2019; 139:106572. [PMID: 31351183 DOI: 10.1016/j.ympev.2019.106572] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Revised: 07/12/2019] [Accepted: 07/23/2019] [Indexed: 12/26/2022]
Abstract
The Eurasian steppes occupy a significant portion of the worldwide land surface and their biota have been affected by specific past range dynamics driven by ice ages-related climatic fluctuations. The dynamic alterations in conditions during the Pleistocene often triggered reticulate evolution and whole genome duplication events. Employing genomic, genetic and cytogenetic tools as well as morphometry we investigate the intricate evolution of Astragalus onobrychis, a widespread Eurasian steppe plant with diploid, tetraploid and octoploid cytotypes. To analyse the heteroploid RADseq dataset we employ both genotype-based and genotype-free methods that result in highly consistent results, and complement our inference with information from the plastid ycf1 region. We uncover a complex and reticulate evolutionary history, including at least one auto-tetraploidization event and two allo-octoploidization events; one of them involved also genetic contributions from other species, most likely A. goktschaicus. The present genetic structure points to the existence of four main clades within A. onobrychis, which only partly correspond to different ploidies. Time-calibrated diffusion models suggest that diversification within A. onobrychis was associated with ice age-related climatic fluctuations during the last million years. We finally argue for the usefulness of uniparentally inherited plastid markers, even in the genomic era, especially when investigating heteroploid systems.
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Affiliation(s)
- Eliška Záveská
- Department of Botany, University of Innsbruck, Sternwartestraße 15, 6020 Innsbruck, Austria
| | - Clemens Maylandt
- Department of Botany, University of Innsbruck, Sternwartestraße 15, 6020 Innsbruck, Austria
| | - Ovidiu Paun
- Department of Botany and Biodiversity Research, University of Vienna, Rennweg 14, 1030 Vienna, Austria
| | - Clara Bertel
- Department of Botany, University of Innsbruck, Sternwartestraße 15, 6020 Innsbruck, Austria
| | - Božo Frajman
- Department of Botany, University of Innsbruck, Sternwartestraße 15, 6020 Innsbruck, Austria
| | - The Steppe Consortium
- Department of Botany, University of Innsbruck, Sternwartestraße 15, 6020 Innsbruck, Austria; Department of Botany and Biodiversity Research, University of Vienna, Rennweg 14, 1030 Vienna, Austria; Department of Biosciences, University of Salzburg, Hellbrunnerstrasse 34, 5020 Salzburg, Austria; Department of Ecology, University of Innsbruck, Technikerstraße 25, 6020 Innsbruck, Austria; Real Jardín Botánico, CSIC, Plaza de Murillo 2, 28014 Madrid, Spain; Department of Life Sciences and Biotechnology, University of Ferrara, Via L. Borsari 46, 44121 Ferrara, Italy; Institute for Alpine Environment, Eurac Research, Drususallee 1/Viale Druso 1, 39100 Bozen/Bolzano, Italy
| | - Peter Schönswetter
- Department of Botany, University of Innsbruck, Sternwartestraße 15, 6020 Innsbruck, Austria.
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Integrating phylogenomics, phylogenetics, morphometrics, relative genome size and ecological niche modelling disentangles the diversification of Eurasian Euphorbia seguieriana s. l. (Euphorbiaceae). Mol Phylogenet Evol 2019; 134:238-252. [DOI: 10.1016/j.ympev.2018.10.046] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2018] [Revised: 10/27/2018] [Accepted: 10/31/2018] [Indexed: 12/31/2022]
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Barrabé L, Lavergne S, Karnadi-Abdelkader G, Drew BT, Birnbaum P, Gâteblé G. Changing Ecological Opportunities Facilitated the Explosive Diversification of New Caledonian Oxera (Lamiaceae). Syst Biol 2019; 68:460-481. [PMID: 30365031 PMCID: PMC6472440 DOI: 10.1093/sysbio/syy070] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Revised: 10/04/2018] [Accepted: 10/23/2018] [Indexed: 11/28/2022] Open
Abstract
Phylogenies recurrently demonstrate that oceanic island systems have been home to rapid clade diversification and adaptive radiations. The existence of adaptive radiations posits a central role of natural selection causing ecological divergence and speciation, and some plant radiations have been highlighted as paradigmatic examples of such radiations. However, neutral processes may also drive speciation during clade radiations, with ecological divergence occurring following speciation. Here, we document an exceptionally rapid and unique radiation of Lamiaceae within the New Caledonian biodiversity hotspot. Specifically, we investigated various biological, ecological, and geographical drivers of species diversification within the genus Oxera. We found that Oxera underwent an initial process of rapid cladogenesis likely triggered by a dramatic period of aridity during the early Pliocene. This early diversification of Oxera was associated with an important phase of ecological diversification triggered by significant shifts of pollination syndromes, dispersal modes, and life forms. Finally, recent diversification of Oxera appears to have been further driven by the interplay of allopatry and habitat shifts likely related to climatic oscillations. This suggests that Oxera could be regarded as an adaptive radiation at an early evolutionary stage that has been obscured by more recent joint habitat diversification and neutral geographical processes. Diversification within Oxera has perhaps been triggered by varied ecological and biological drivers acting in a leapfrog pattern, but geographic processes may have been an equally important driver. We suspect that strictly adaptive radiations may be rare in plants and that most events of rapid clade diversification may have involved a mixture of geographical and ecological divergence.
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Affiliation(s)
- Laure Barrabé
- Institut Agronomique néo-Calédonien (IAC), Equipes ARBOREAL and SOLVEG, BP 711, Mont-Dore 98810, New Caledonia.,Endemia, Plant Red List Authority, 7 rue Pierre Artigue, Nouméa 98800, New Caledonia
| | - Sébastien Lavergne
- Laboratoire d'Ecologie Alpine, CNRS - Université Grenoble Alpes, UMR 5553, Grenoble F-38000, France
| | - Giliane Karnadi-Abdelkader
- Institut Agronomique néo-Calédonien (IAC), Equipes ARBOREAL and SOLVEG, BP 711, Mont-Dore 98810, New Caledonia
| | - Bryan T Drew
- Department of Biology, University of Nebraska-Kearney, Kearney, NE 68849, USA
| | - Philippe Birnbaum
- Institut Agronomique néo-Calédonien (IAC), Equipes ARBOREAL and SOLVEG, BP 711, Mont-Dore 98810, New Caledonia.,UMR AMAP, Université de Montpellier, CIRAD, CNRS, INRA, IRD, Montpellier 34398, France
| | - Gildas Gâteblé
- Institut Agronomique néo-Calédonien (IAC), Equipes ARBOREAL and SOLVEG, BP 711, Mont-Dore 98810, New Caledonia
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Brandrud MK, Paun O, Lorenz R, Baar J, Hedrén M. Restriction-site associated DNA sequencing supports a sister group relationship of Nigritella and Gymnadenia (Orchidaceae). Mol Phylogenet Evol 2019; 136:21-28. [PMID: 30914398 DOI: 10.1016/j.ympev.2019.03.018] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2019] [Accepted: 03/22/2019] [Indexed: 11/30/2022]
Abstract
The orchid genus Nigritella is closely related to Gymnadenia and has from time to time been merged with the latter. Although Nigritella is morphologically distinct, it has been suggested that the separating characters are easily modifiable and subject to rapid evolutionary change. So far, molecular phylogenetic studies have either given support for the inclusion of Nigritella in Gymnadenia, or for their separation as different genera. To resolve this issue, we analysed data obtained from Restriction-site associated DNA sequencing, RADseq, which provides a large number of SNPs distributed across the entire genome. To analyse samples of different ploidies, we take an analytical approach of building a reduced genomic reference based on de novo RADseq loci reconstructed from diploid accessions only, which we further use to map and call variants across both diploid and polyploid accessions. We found that Nigritella is distinct from Gymnadenia forming a well-supported separate clade, and that genetic diversity within Gymnadenia is high. Within Gymnadenia, taxa characterized by an ITS-E ribotype (G. conopsea s.str. (early flowering) and G. odoratissima), are divergent from taxa characterized by ITS-L ribotype (G. frivaldii, G. densiflora and late flowering G. conopsea). Gymnigritella runei is confirmed to have an allopolyploid origin from diploid Gymnadenia conopsea and tetraploid N. nigra ssp. nigra on the basis of RADseq data. Within Nigritella the aggregation of polyploid members into three clear-cut groups as suggested by allozyme and nuclear microsatellite data was further supported.
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Affiliation(s)
- Marie K Brandrud
- Department of Botany and Biodiversity Research, University of Vienna, Rennweg 14, A-1030 Vienna, Austria
| | - Ovidiu Paun
- Department of Botany and Biodiversity Research, University of Vienna, Rennweg 14, A-1030 Vienna, Austria
| | - Richard Lorenz
- AHO Baden-Württemberg, Leibnizstrasse 1, D-69459 Weinheim, Germany
| | - Juliane Baar
- Department of Botany and Biodiversity Research, University of Vienna, Rennweg 14, A-1030 Vienna, Austria
| | - Mikael Hedrén
- Department of Biology, University of Lund, Sölvegatan 37, SE-223 62 Lund, Sweden.
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Igea J, Tanentzap AJ. Multiple macroevolutionary routes to becoming a biodiversity hotspot. SCIENCE ADVANCES 2019; 5:eaau8067. [PMID: 30775437 PMCID: PMC6365113 DOI: 10.1126/sciadv.aau8067] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Accepted: 12/21/2018] [Indexed: 05/28/2023]
Abstract
Why is species diversity so unevenly distributed across different regions on Earth? Regional differences in biodiversity may stem from differences in rates of speciation and dispersal and colonization times, but these hypotheses have rarely been tested simultaneously at a global scale. Our study reveals the macroevolutionary routes that have generated hotspots of mammal and bird biodiversity by analyzing the tempo and mode of diversification and dispersal within major biogeographic realms. Hotspots in tropical realms had higher rates of speciation, whereas those in temperate realms received more immigrant species from their surrounding regions. We also found that hotspots had higher spatial complexity and energy availability, providing a link between the environment and macroevolutionary history. Our study highlights how assessing differences in macroevolutionary history can help to explain why biodiversity varies so much worldwide.
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Affiliation(s)
- J. Igea
- Corresponding author. (J.I.); (A.J.T.)
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Crotti M, Barratt CD, Loader SP, Gower DJ, Streicher JW. Causes and analytical impacts of missing data in RADseq phylogenetics: Insights from an African frog (Afrixalus
). ZOOL SCR 2019. [DOI: 10.1111/zsc.12335] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
- Marco Crotti
- Department of Life Sciences; The Natural History Museum; London UK
- Department of Life Sciences; Imperial College London; London UK
- Institute of Biodiversity, Animal Health and Comparative Medicine; University of Glasgow; Glasgow UK
| | - Christopher D. Barratt
- Department of Environmental Sciences; University of Basel; Basel Switzerland
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig; Leipzig Germany
| | - Simon P. Loader
- Department of Life Sciences; The Natural History Museum; London UK
- Department of Environmental Sciences; University of Basel; Basel Switzerland
| | - David J. Gower
- Department of Life Sciences; The Natural History Museum; London UK
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Heckenhauer J, Samuel R, Ashton PS, Abu Salim K, Paun O. Phylogenomics resolves evolutionary relationships and provides insights into floral evolution in the tribe Shoreeae (Dipterocarpaceae). Mol Phylogenet Evol 2018; 127:1-13. [PMID: 29778722 DOI: 10.1016/j.ympev.2018.05.010] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2018] [Revised: 05/11/2018] [Accepted: 05/11/2018] [Indexed: 10/16/2022]
Abstract
A supra-annual, community-level synchronous flowering prevails in several parts of the tropical forests of Southeast Asia and its evolution has been hypothesized to be linked to pollinator shifts. The aseasonal Southeast Asian lowland rainforests are dominated by Dipterocarpaceae, which exhibit great floral diversity, a range of pollination syndromes and include species with annual and supra-annual gregarious flowering. Phylogenetic relationships within this family are still unclear, especially in the tribe Shoreeae. Here, we develop a pipeline to maximize recovery of genome-wide SNPs from restriction-site associated DNA sequencing (RADseq) in non-model organisms across wide phylogenetic scales. We then infer phylogenomic relationships in the tribe Shoreeae using both traditional and coalescent analyses. The phylogenetic trees obtained with these methods are congruent to each other and highly resolved. They allow reconstructing the evolutionary patterns of floral traits (number of stamens, anther structure and anther/appendage size) in the group. Our inferences indicate that species with many stamens, but smaller, globose anthers and longer appendages and have evolved multiple times from species with fewer stamens, but larger, oblong anthers and shorter appendages. This could have happened in parallel to iterative shifts in pollinators across the uncovered phylogeny from larger, longer generation to smaller, shorter-generation insects that can quickly build up the necessary population sizes during mass flowering episodes.
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Affiliation(s)
- Jacqueline Heckenhauer
- University of Vienna, Department of Botany and Biodiversity Research, Rennweg 14, 1030 Vienna, Austria.
| | - Rosabelle Samuel
- University of Vienna, Department of Botany and Biodiversity Research, Rennweg 14, 1030 Vienna, Austria
| | - Peter S Ashton
- Harvard University, Department of Organismic and Evolutionary Biology, 26 Oxford St, Cambridge, MA 02138, United States
| | - Kamariah Abu Salim
- University of Brunei Darussalam, Environmental and Life Sciences, Faculty of Science, Tungku Link Road, Gadong 1410, Brunei Darussalam
| | - Ovidiu Paun
- University of Vienna, Department of Botany and Biodiversity Research, Rennweg 14, 1030 Vienna, Austria
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Phylogeny, historical biogeography, and diversification of angiosperm order Ericales suggest ancient Neotropical and East Asian connections. Mol Phylogenet Evol 2018; 122:59-79. [DOI: 10.1016/j.ympev.2018.01.014] [Citation(s) in RCA: 67] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2017] [Revised: 01/08/2018] [Accepted: 01/18/2018] [Indexed: 11/18/2022]
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Niu Z, Pan J, Xue Q, Zhu S, Liu W, Ding X. Plastome-wide comparison reveals new SNV resources for the authentication of Dendrobium huoshanense and its corresponding medicinal slice (Huoshan Fengdou). Acta Pharm Sin B 2018; 8:466-477. [PMID: 29881686 PMCID: PMC5989833 DOI: 10.1016/j.apsb.2017.12.004] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2017] [Revised: 10/24/2017] [Accepted: 11/08/2017] [Indexed: 11/06/2022] Open
Abstract
Dendrobium species and their corresponding medicinal slices have been extensively used as traditional Chinese medicine (TCM) in many Asian countries. However, it is extremely difficult to identify Dendrobium species based on their morphological and chemical features. In this study, the plastomes of D. huoshanense were used as a model system to investigate the hypothesis that plastomic mutational hotspot regions could provide a useful single nucleotide variants (SNVs) resource for authentication studies. We surveyed the plastomes of 17 Dendrobium species, including the newly sequenced plastome of D. huoshanense. A total of 19 SNVs that could be used for the authentication of D. huoshanense were detected. On the basis of this comprehensive comparison, we identified the four most informative hotspot regions in the Dendrobium plastome that encompass ccsA to ndhF, matK to 3'trnG, rpoB to psbD, and trnT to rbcL. Furthermore, to established a simple and accurate method for the authentication of D. huoshanense and its medicinal slices, a total of 127 samples from 20 Dendrobium species including their corresponding medicinal slices (Fengdous) were used in this study. Our results suggest that D. huoshanense and its medicinal slices can be rapidly and unequivocally identified using this method that combines real-time PCR with the amplification refractory mutation system (ARMS).
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Affiliation(s)
| | | | | | | | | | - Xiaoyu Ding
- College of Life Sciences, Nanjing Normal University, Nanjing 210023, China
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Shih KM, Chang CT, Chung JD, Chiang YC, Hwang SY. Adaptive Genetic Divergence Despite Significant Isolation-by-Distance in Populations of Taiwan Cow-Tail Fir ( Keteleeria davidiana var. formosana). FRONTIERS IN PLANT SCIENCE 2018; 9:92. [PMID: 29449860 PMCID: PMC5799944 DOI: 10.3389/fpls.2018.00092] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2017] [Accepted: 01/17/2018] [Indexed: 05/05/2023]
Abstract
Double digest restriction site-associated DNA sequencing (ddRADseq) is a tool for delivering genome-wide single nucleotide polymorphism (SNP) markers for non-model organisms useful in resolving fine-scale population structure and detecting signatures of selection. This study performs population genetic analysis, based on ddRADseq data, of a coniferous species, Keteleeria davidiana var. formosana, disjunctly distributed in northern and southern Taiwan, for investigation of population adaptive divergence in response to environmental heterogeneity. A total of 13,914 SNPs were detected and used to assess genetic diversity, FST outlier detection, population genetic structure, and individual assignments of five populations (62 individuals) of K. davidiana var. formosana. Principal component analysis (PCA), individual assignments, and the neighbor-joining tree were successful in differentiating individuals between northern and southern populations of K. davidiana var. formosana, but apparent gene flow between the southern DW30 population and northern populations was also revealed. Fifteen of 23 highly differentiated SNPs identified were found to be strongly associated with environmental variables, suggesting isolation-by-environment (IBE). However, multiple matrix regression with randomization analysis revealed strong IBE as well as significant isolation-by-distance. Environmental impacts on divergence were found between populations of the North and South regions and also between the two southern neighboring populations. BLASTN annotation of the sequences flanking outlier SNPs gave significant hits for three of 23 markers that might have biological relevance to mitochondrial homeostasis involved in the survival of locally adapted lineages. Species delimitation between K. davidiana var. formosana and its ancestor, K. davidiana, was also examined (72 individuals). This study has produced highly informative population genomic data for the understanding of population attributes, such as diversity, connectivity, and adaptive divergence associated with large- and small-scale environmental heterogeneity in K. davidiana var. formosana.
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Affiliation(s)
- Kai-Ming Shih
- Department of Life Science, National Taiwan Normal University, Taipei, Taiwan
| | - Chung-Te Chang
- Department of Geography, National Taiwan University, Taipei, Taiwan
| | - Jeng-Der Chung
- Division of Silviculture, Taiwan Forestry Research Institute, Taipei, Taiwan
| | - Yu-Chung Chiang
- Department of Biological Sciences, National Sun Yat-Sen University, Kaohsiung, Taiwan
| | - Shih-Ying Hwang
- Department of Life Science, National Taiwan Normal University, Taipei, Taiwan
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Bateman RM, Sramkó G, Paun O. Integrating restriction site-associated DNA sequencing (RAD-seq) with morphological cladistic analysis clarifies evolutionary relationships among major species groups of bee orchids. ANNALS OF BOTANY 2018; 121:85-105. [PMID: 29325077 PMCID: PMC5786241 DOI: 10.1093/aob/mcx129] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2017] [Accepted: 10/02/2017] [Indexed: 05/03/2023]
Abstract
BACKGROUND AND AIMS Bee orchids (Ophrys) have become the most popular model system for studying reproduction via insect-mediated pseudo-copulation and for exploring the consequent, putatively adaptive, evolutionary radiations. However, despite intensive past research, both the phylogenetic structure and species diversity within the genus remain highly contentious. Here, we integrate next-generation sequencing and morphological cladistic techniques to clarify the phylogeny of the genus. METHODS At least two accessions of each of the ten species groups previously circumscribed from large-scale cloned nuclear ribosomal internal transcibed spacer (nrITS) sequencing were subjected to restriction site-associated sequencing (RAD-seq). The resulting matrix of 4159 single nucleotide polymorphisms (SNPs) for 34 accessions was used to construct an unrooted network and a rooted maximum likelihood phylogeny. A parallel morphological cladistic matrix of 43 characters generated both polymorphic and non-polymorphic sets of parsimony trees before being mapped across the RAD-seq topology. KEY RESULTS RAD-seq data strongly support the monophyly of nine out of ten groups previously circumscribed using nrITS and resolve three major clades; in contrast, supposed microspecies are barely distinguishable. Strong incongruence separated the RAD-seq trees from both the morphological trees and traditional classifications; mapping of the morphological characters across the RAD-seq topology rendered them far more homoplastic. CONCLUSIONS The comparatively high level of morphological homoplasy reflects extensive convergence, whereas the derived placement of the fusca group is attributed to paedomorphic simplification. The phenotype of the most recent common ancestor of the extant lineages is inferred, but it post-dates the majority of the character-state changes that typify the genus. RAD-seq may represent the high-water mark of the contribution of molecular phylogenetics to understanding evolution within Ophrys; further progress will require large-scale population-level studies that integrate phenotypic and genotypic data in a cogent conceptual framework.
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Affiliation(s)
- Richard M Bateman
- Jodrell Laboratory, Royal Botanic Gardens Kew, Richmond, Surrey, UK
- For correspondence. E-mail
| | - Gábor Sramkó
- Department of Botany, University of Debrecen, Egyetem, Debrecen, Hungary
- MTA-DE ‘Lendület’ Evolutionary Phylogenomics Research Group, Egyetem, Debrecen, Hungary
| | - Ovidiu Paun
- Department of Botany and Biodiversity Research, University of Vienna, Rennweg, Vienna, Austria
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Ibanez T, Blanchard E, Hequet V, Keppel G, Laidlaw M, Pouteau R, Vandrot H, Birnbaum P. High endemism and stem density distinguish New Caledonian from other high-diversity rainforests in the Southwest Pacific. ANNALS OF BOTANY 2018; 121:25-35. [PMID: 29077788 PMCID: PMC5786226 DOI: 10.1093/aob/mcx107] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2017] [Accepted: 08/04/2017] [Indexed: 05/15/2023]
Abstract
BACKGROUND AND AIMS The biodiversity hotspot of New Caledonia is globally renowned for the diversity and endemism of its flora. New Caledonia's tropical rainforests have been reported to have higher stem densities, higher concentrations of relictual lineages and higher endemism than other rainforests. This study investigates whether these aspects differ in New Caledonian rainforests compared to other high-diversity rainforests in the Southwest Pacific. METHODS Plants (with a diameter at breast height ≥10 cm) were surveyed in nine 1-ha rainforest plots across the main island of New Caledonia and compared with 14 1-ha plots in high-diversity rainforests of the Southwest Pacific (in Australia, Fiji, Papua New Guinea and the Solomon Islands). This facilitated a comparison of stem densities, taxonomic composition and diversity, and species turnover among plots and countries. KEY RESULTS The study inventoried 11 280 stems belonging to 335 species (93 species ha-1 on average) in New Caledonia. In comparison with other rainforests in the Southwest Pacific, New Caledonian rainforests exhibited higher stem density (1253 stems ha-1 on average) including abundant palms and tree ferns, with the high abundance of the latter being unparalleled outside New Caledonia. In all plots, the density of relictual species was ≥10 % for both stems and species, with no discernible differences among countries. Species endemism, reaching 89 % on average, was significantly higher in New Caledonia. Overall, species turnover increased with geographical distance, but not among New Caledonian plots. CONCLUSIONS High stem density, high endemism and a high abundance of tree ferns with stem diameters ≥10 cm are therefore unique characteristics of New Caledonian rainforests. High endemism and high spatial species turnover imply that the current system consisting of a few protected areas is inadequate, and that the spatial distribution of plant species needs to be considered to adequately protect the exceptional flora of New Caledonian rainforests.
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Affiliation(s)
- Thomas Ibanez
- Institut Agronomique néo-Calédonien (IAC), Diversité biologique et fonctionnelle des écosystèmes terrestres, Nouméa, New Caledonia
- For correspondence. Email
| | - E Blanchard
- Institut Agronomique néo-Calédonien (IAC), Diversité biologique et fonctionnelle des écosystèmes terrestres, Nouméa, New Caledonia
| | - V Hequet
- Institut de Recherche pour le Développement (IRD), UMR AMAP, Nouméa, New Caledonia
| | - G Keppel
- School of Natural and Built Environments, University of South Australia, GPO, Adelaide, South Australia, Australia
| | - M Laidlaw
- Queensland Herbarium, Department of Science, Information Technology and Innovation, Toowong, Queensland, Australia
| | - R Pouteau
- Institut Agronomique néo-Calédonien (IAC), Diversité biologique et fonctionnelle des écosystèmes terrestres, Nouméa, New Caledonia
| | - H Vandrot
- Institut Agronomique néo-Calédonien (IAC), Diversité biologique et fonctionnelle des écosystèmes terrestres, Nouméa, New Caledonia
| | - P Birnbaum
- Institut Agronomique néo-Calédonien (IAC), Diversité biologique et fonctionnelle des écosystèmes terrestres, Nouméa, New Caledonia
- Cirad, UMR AMAP, Montpellier, France
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