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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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Bradbury D, Binks RM, van Leeuwen S, Coates DJ, McArthur SL, Macdonald BM, Hankinson M, Byrne M. The nuanced nature of mesic refugia in arid landscapes: a tale of two peas. ANNALS OF BOTANY 2022; 130:901-916. [PMID: 36219678 PMCID: PMC9758307 DOI: 10.1093/aob/mcac126] [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: 07/14/2022] [Accepted: 10/11/2022] [Indexed: 06/16/2023]
Abstract
BACKGROUND AND AIMS Understanding how genetic diversity is distributed and maintained within species is a central tenet of evolutionary and conservation biology, yet is understudied in arid regions of the globe. In temperate, glaciated environments, high genetic diversity in plant species is frequently found in refugial areas, which are often associated with southern non-glaciated landscapes. In arid, unglaciated environments, landscape features providing mesic conditions are likely to be refugia, although our understanding needs more refinement in these biomes. We test whether refugia and nuclear diversity hotspots occur in high-elevation, topographically complex areas for co-distributed shrubs (Petalostylis labicheoides and Indigofera monophylla; Fabaceae) in the ancient, arid Pilbara bioregion of north-western Australia. METHODS We conducted extensive sampling of the Pilbara (>1400 individuals from 62 widespread populations) to detect patterns in nuclear diversity and structure based on 13-16 microsatellite loci. Evidence of historical refugia was investigated based on patterns of diversity in three non-coding chloroplast (cp) sequence regions for approx. 240 individuals per species. Haplotype relationships were defined with median-joining networks and maximum likelihood phylogenetic trees. KEY RESULTS We found cpDNA evidence for a high-elevation refugium in P. labicheoides but not for I. monophylla that instead exhibited extraordinary haplotype diversity and evidence for persistence across a widespread area. Nuclear diversity hotspots occurred in, but were not exclusive to, high-elevation locations and extended to adjacent, low-elevation riparian areas in both species. CONCLUSIONS Phylogeographic refugia in arid environments may occur in high-elevation areas for some species but not all, and may be influenced by species-specific traits: a mesic montane refugium in P. labicheoides could be related to its preference for growth in water-gaining areas, while a lack of such evidence in I. monophylla could be related to maintenance of cpDNA diversity in a large soil seed bank and dynamic evolutionary history. Mesic environments created by the intersection of topographically complex landscapes with riparian zones can be contemporary reservoirs of genetic diversity in arid landscapes.
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Affiliation(s)
- Donna Bradbury
- Biodiversity and Conservation Science, Department of Biodiversity, Conservation and Attractions, 17 Dick Perry Avenue, Kensington, Perth, WA 6151, Australia
| | - Rachel M Binks
- Biodiversity and Conservation Science, Department of Biodiversity, Conservation and Attractions, 17 Dick Perry Avenue, Kensington, Perth, WA 6151, Australia
| | - Stephen van Leeuwen
- Biodiversity and Conservation Science, Department of Biodiversity, Conservation and Attractions, 17 Dick Perry Avenue, Kensington, Perth, WA 6151, Australia
- School of Molecular and Life Sciences, Curtin University, GPO Box U1987, Perth, WA 6845, Australia
| | - David J Coates
- Biodiversity and Conservation Science, Department of Biodiversity, Conservation and Attractions, 17 Dick Perry Avenue, Kensington, Perth, WA 6151, Australia
| | - Shelley L McArthur
- Biodiversity and Conservation Science, Department of Biodiversity, Conservation and Attractions, 17 Dick Perry Avenue, Kensington, Perth, WA 6151, Australia
| | - Bronwyn M Macdonald
- Biodiversity and Conservation Science, Department of Biodiversity, Conservation and Attractions, 17 Dick Perry Avenue, Kensington, Perth, WA 6151, Australia
| | - Margaret Hankinson
- Biodiversity and Conservation Science, Department of Biodiversity, Conservation and Attractions, 17 Dick Perry Avenue, Kensington, Perth, WA 6151, Australia
| | - Margaret Byrne
- Biodiversity and Conservation Science, Department of Biodiversity, Conservation and Attractions, 17 Dick Perry Avenue, Kensington, Perth, WA 6151, Australia
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Raskar S, Purkar V, Sardesai M, Mitra S. Assessing the Impact of Geographical Distribution and Genetic Diversity on Metabolic Profiles of a Medicinal Plant, Embelia ribes Burm. f. PLANTS (BASEL, SWITZERLAND) 2022; 11:2861. [PMID: 36365314 PMCID: PMC9653573 DOI: 10.3390/plants11212861] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 10/08/2022] [Accepted: 10/20/2022] [Indexed: 06/16/2023]
Abstract
The extensive use of Embelia ribes Burm. f. (Embelia) in tribal medicine proclaimed global attention as a promising candidate in complementary and alternative medicine. The knowledge of chemical blends is a prerequisite for the selection of raw materials for herbal medicine formulations; however, the influence of geographical distance and genetic diversity on the metabolome of Embelia fruits is unknown. Therefore, we collected Embelia fruits from four locations across the Western Ghats of India and analyzed the metabolic profile and genotypic diversity of Embelia fruits by liquid chromatography-tandem mass spectrometry (LC-MS/MS) and inter simple sequence repeats (ISSR), respectively. LC-MS/MS analysis yielded 583 compounds; however, the trimmed data resulted in 149 compounds. Further, MS/MS analysis identified 36 compounds, among which we reported 30 compounds for the first time from Embelia. These compounds belong to 11 compound classes that suggest location-specific chemical blends of Embelia fruits. Multivariate analysis showed 94% compound diversity across the accessions. ISSR analysis suggests 95% polymorphism across the accessions. A significant positive correlation (80%) between metabolomics and genotypic data matrices validates the genotype's influence in tuning Embelia's metabolic profiles. We conclude that the chemical profiles of Embelia are location-specific, which can be explored for the selection of herbal trade sustainably.
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Millar MA, Binks RM, Tapper S, Macdonald BM, McArthur SL, Hankinson M, Coates DJ, van Leeuwen S, Byrne M. Limited phylogeographic and genetic connectivity in
Acacia
species of low stature in an arid landscape. Ecol Evol 2022; 12:e9052. [PMID: 35813908 PMCID: PMC9257521 DOI: 10.1002/ece3.9052] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Revised: 05/02/2022] [Accepted: 06/08/2022] [Indexed: 11/24/2022] Open
Abstract
Widespread plant species are expected to maintain genetic diversity and gene flow via pollen and seed dispersal. Stature is a key life history trait that affects seed and potentially pollen dispersal, with limited stature associated with limited dispersal and greater genetic differentiation. We sampled Hill’s tabletop wattle (Acacia hilliana) and curry wattle (Acacia spondylophylla), two co‐distributed, widespread, Acacia shrubs of low stature, across the arid Pilbara region of north‐western Australia. Using chloroplast sequence and nuclear microsatellite data we evaluated patterns of population genetic and phylogeographic diversity and structure, demographic signals, ratios of pollen to seed dispersal, evidence for historical refugia, and association between elevation and diversity. Results showed strong phylogeographic (chloroplast, GST = 0.831 and 0.898 for A. hilliana and A. spondylophylla, respectively) and contemporary (nuclear, FST = 0.260 and 0.349 for A. hilliana and A. spondylophylla, respectively) genetic structure in both species. This indicates limited genetic connectivity via seed and pollen dispersal associated with Acacia species of small stature compared to taller tree and shrub acacias across the Pilbara bioregion. This effect of stature on genetic structure is superimposed on moderate levels of genetic diversity that were expected based on widespread ranges (haplotype diversity h = 25 and 12; nuclear diversity He = 0.60 and 0.47 for A. hilliana and A. spondylophylla, respectively). Contemporary genetic structure was congruent at the greater landscape scale, especially in terms of strong genetic differentiation among geographically disjunct populations in less elevated areas. Measures of diversity and connectivity were associated with traits of greater geographic population proximity, population density, population size, and greater individual longevity, and some evidence for range expansion in A. hilliana. Results illustrate that low stature is associated with limited dispersal and greater patterns of genetic differentiation for congenerics in a common landscape and highlight the complex influence of taxon‐specific life history and ecological traits to seed and pollen dispersal.
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Affiliation(s)
- Melissa A. Millar
- Department of Biodiversity, Conservation and Attractions Biodiversity and Conservation Science Bentley Western Australia Australia
| | - Rachel M. Binks
- Department of Biodiversity, Conservation and Attractions Biodiversity and Conservation Science Bentley Western Australia Australia
| | - Sarah‐Louise Tapper
- Department of Biodiversity, Conservation and Attractions Biodiversity and Conservation Science Bentley Western Australia Australia
| | - Bronwyn M. Macdonald
- Department of Biodiversity, Conservation and Attractions Biodiversity and Conservation Science Bentley Western Australia Australia
| | - Shelley L. McArthur
- Department of Biodiversity, Conservation and Attractions Biodiversity and Conservation Science Bentley Western Australia Australia
| | - Margaret Hankinson
- Department of Biodiversity, Conservation and Attractions Biodiversity and Conservation Science Bentley Western Australia Australia
| | - David J. Coates
- Department of Biodiversity, Conservation and Attractions Biodiversity and Conservation Science Bentley Western Australia Australia
| | - Stephen van Leeuwen
- Department of Biodiversity, Conservation and Attractions Biodiversity and Conservation Science Bentley Western Australia Australia
- School of Molecular and Life Sciences Curtin University Perth Western Australia Australia
| | - Margaret Byrne
- Department of Biodiversity, Conservation and Attractions Biodiversity and Conservation Science Bentley Western Australia Australia
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Zhang G, Han Y, Wang H, Wang Z, Xiao H, Sun M. Phylogeography of Iris loczyi (Iridaceae) in Qinghai-Tibet Plateau revealed by chloroplast DNA and microsatellite markers. AOB PLANTS 2021; 13:plab070. [PMID: 34876969 PMCID: PMC8643446 DOI: 10.1093/aobpla/plab070] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Accepted: 10/28/2021] [Indexed: 06/13/2023]
Abstract
Quaternary climate oscillations and complex topography have tremendous effects on current distribution and genetic structure of species, and hence the Qinghai-Tibet Plateau (QTP), the largest plateau in the world, has become a hotspot for many phylogeographic studies. However, little is known about the phylogeographic pattern of herbaceous plants in QTP. Here, we investigate the genetic diversity, population structure and historical dynamics of Iris loczyi, using five chloroplast DNA (cpDNA) fragments and seven microsatellite markers. A total of 15 populations, and 149 individuals were sampled throughout the QTP. High genetic diversity was detected both in cpDNA (H d = 0.820) and SSR (H o = 0.689, H e = 0.699). Ten cpDNA haplotypes and 163 alleles were identified. AMOVA and clustering analyses revealed obvious differentiation between regions. The N st, G st and Mantel test showed significant phylogeographic structure of I. loczyi. The neutrality test and mismatch distribution analyses indicated that I. loczyi could not have undergone a historical population expansion, but population XS from the Qilian Mountain area could have experienced a local expansion. Bottleneck analyses indicated that I. loczyi had not experienced bottleneck recently. Based on cpDNA and SSR results, the Qilian Mountain area was inferred as a potential glacial refuge, and the southern Tibet valley was considered as a 'microrefugia' for I. loczyi. These findings provided new insights into the location of glacial refuges for the species distributed in QTP, and supplemented more plant species data for the response of QTP species to the Quaternary climate.
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Affiliation(s)
- Guoli Zhang
- Key Laboratory of Molecular Epigenetics of Ministry of Education, Northeast Normal University, Changchun 130024, China
| | - Yan Han
- Qian’an No. 1 Middle School, Tangshan 063000, China
| | - Huan Wang
- Key Laboratory of Molecular Epigenetics of Ministry of Education, Northeast Normal University, Changchun 130024, China
| | - Ziyang Wang
- Key Laboratory of Molecular Epigenetics of Ministry of Education, Northeast Normal University, Changchun 130024, China
| | - Hongxing Xiao
- Key Laboratory of Molecular Epigenetics of Ministry of Education, Northeast Normal University, Changchun 130024, China
| | - Mingzhou Sun
- Key Laboratory of Molecular Epigenetics of Ministry of Education, Northeast Normal University, Changchun 130024, China
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Vicente S, Máguas C, Richardson DM, Trindade H, Wilson JRU, Le Roux JJ. Highly diverse and highly successful: invasive Australian acacias have not experienced genetic bottlenecks globally. ANNALS OF BOTANY 2021; 128:149-157. [PMID: 33876193 PMCID: PMC8324033 DOI: 10.1093/aob/mcab053] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Accepted: 04/15/2021] [Indexed: 05/04/2023]
Abstract
BACKGROUND AND AIMS Invasive species may undergo rapid evolution despite very limited standing genetic diversity. This so-called genetic paradox of biological invasions assumes that an invasive species has experienced (and survived) a genetic bottleneck and then underwent local adaptation in the new range. In this study, we test how often Australian acacias (genus Acacia), one of the world's most problematic invasive tree groups, have experienced genetic bottlenecks and inbreeding. METHODS We collated genetic data from 51 different genetic studies on Acacia species to compare genetic diversity between native and invasive populations. These studies analysed 37 different Acacia species, with genetic data from the invasive ranges of 11 species, and data from the native range for 36 species (14 of these 36 species are known to be invasive somewhere in the world, and the other 22 are not known to be invasive). KEY RESULTS Levels of genetic diversity are similar in native and invasive populations, and there is little evidence of invasive populations being extensively inbred. Levels of genetic diversity in native range populations also did not differ significantly between species that have and that do not have invasive populations. CONCLUSION We attribute our findings to the impressive movement, introduction effort and human usage of Australian acacias around the world.
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Affiliation(s)
- Sara Vicente
- Centro de Estudos do Ambiente e do Mar (CESAM), Faculdade de Ciências da Universidade de Lisboa, Campo Grande, Lisboa, Portugal
- Centre for Ecology, Evolution and Environmental Changes (cE3c), Faculdade de Ciências da Universidade de Lisboa, Campo Grande, Lisboa, Portugal
- Department of Biological Sciences, Macquarie University, North Ryde, NSW, Australia
| | - Cristina Máguas
- Centre for Ecology, Evolution and Environmental Changes (cE3c), Faculdade de Ciências da Universidade de Lisboa, Campo Grande, Lisboa, Portugal
| | - David M Richardson
- Centre for Invasion Biology, Department of Botany & Zoology, Stellenbosch University, Stellenbosch, South Africa
| | - Helena Trindade
- Centro de Estudos do Ambiente e do Mar (CESAM), Faculdade de Ciências da Universidade de Lisboa, Campo Grande, Lisboa, Portugal
| | - John R U Wilson
- Centre for Invasion Biology, Department of Botany & Zoology, Stellenbosch University, Stellenbosch, South Africa
- South African National Biodiversity Institute, Kirstenbosch Research Centre, Cape Town, South Africa
| | - Johannes J Le Roux
- Department of Biological Sciences, Macquarie University, North Ryde, NSW, Australia
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Díaz BG, Zucchi MI, Alves‐Pereira A, de Almeida CP, Moraes ACL, Vianna SA, Azevedo-Filho J, Colombo CA. Genome-wide SNP analysis to assess the genetic population structure and diversity of Acrocomia species. PLoS One 2021; 16:e0241025. [PMID: 34283830 PMCID: PMC8291712 DOI: 10.1371/journal.pone.0241025] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Accepted: 07/05/2021] [Indexed: 01/01/2023] Open
Abstract
Acrocomia (Arecaceae) is a genus widely distributed in tropical and subtropical America that has been achieving economic interest due to the great potential of oil production of some of its species. In particular A. aculeata, due to its vocation to supply oil with the same productive capacity as the oil palm (Elaeis guineenses) even in areas with water deficit. Although eight species are recognized in the genus, the taxonomic classification based on morphology and geographic distribution is still controversial. Knowledge about the genetic diversity and population structure of the species is limited, which has limited the understanding of the genetic relationships and the orientation of management, conservation, and genetic improvement activities of species of the genus. In the present study, we analyzed the genomic diversity and population structure of Acrocomia genus, including 172 samples from seven species, with a focus on A. aculeata with 117 samples covering a wide geographical area of occurrence of the species, using Single Nucleotide Polymorphism (SNP) markers originated from Genotyping By Sequencing (GBS).The genetic structure of the Acrocomia species were partially congruent with the current taxonomic classification based on morphological characters, recovering the separation of the species A. aculeata, A. totai, A. crispa and A. intumescens as distinct taxonomic groups. However, the species A. media was attributed to the cluster of A. aculeata while A. hassleri and A. glauscescens were grouped together with A. totai. The species that showed the highest and lowest genetic diversity were A. totai and A. media, respectively. When analyzed separately, the species A. aculeata showed a strong genetic structure, forming two genetic groups, the first represented mainly by genotypes from Brazil and the second by accessions from Central and North American countries. Greater genetic diversity was found in Brazil when compared to the other countries. Our results on the genetic diversity of the genus are unprecedented, as is also establishes new insights on the genomic relationships between Acrocomia species. It is also the first study to provide a more global view of the genomic diversity of A. aculeata. We also highlight the applicability of genomic data as a reference for future studies on genetic diversity, taxonomy, evolution and phylogeny of the Acrocomia genus, as well as to support strategies for the conservation, exploration and breeding of Acrocomia species and in particular A. aculeata.
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Affiliation(s)
| | - Maria Imaculada Zucchi
- Biology Institute, University of Campinas UNICAMP, Campinas-SP, Brazil
- Centro de Pesquisa de Recursos Genéticos Vegetais, Instituto Agronômico-IAC, Campinas-SP, Brazil
| | | | - Caléo Panhoca de Almeida
- Centro de Pesquisa de Recursos Genéticos Vegetais, Instituto Agronômico-IAC, Campinas-SP, Brazil
| | | | - Suelen Alves Vianna
- Centro de Pesquisa de Recursos Genéticos Vegetais, Instituto Agronômico-IAC, Campinas-SP, Brazil
| | - Joaquim Azevedo-Filho
- Centro de Pesquisa de Recursos Genéticos Vegetais, Instituto Agronômico-IAC, Campinas-SP, Brazil
| | - Carlos Augusto Colombo
- Centro de Pesquisa de Recursos Genéticos Vegetais, Instituto Agronômico-IAC, Campinas-SP, Brazil
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Więcław H, Szenejko M, Kull T, Sotek Z, Rębacz-Maron E, Koopman J. Morphological variability and genetic diversity in Carex buxbaumii and Carex hartmaniorum (Cyperaceae) populations. PeerJ 2021; 9:e11372. [PMID: 34026355 PMCID: PMC8121068 DOI: 10.7717/peerj.11372] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Accepted: 04/07/2021] [Indexed: 11/20/2022] Open
Abstract
Background Carex buxbaumii and C. hartmaniorum are sister species of the clade Papilliferae within the monophyletic section Racemosae. An unambiguous identification of these species is relatively difficult due to the interspecific continuum of some morphological characters as well as the intraspecific variability. The study was aimed at determining the range of variability, both morphological and genetic, within and between these two closely related and similar species. Methods The sedges were collected during botanical expeditions to Armenia, Estonia, the Netherlands, and Poland. The morphological separation of the two species and their populations was tested using the Discriminant Function Analysis (DFA). The genetic variability of the 19 Carex populations was assessed in the presence of eight Inter Simple Sequence Repeat (ISSR) primers. Results Results of the study indicate a considerable genetic affinity between the two sedge species (mean Si = 0.619). However, the populations of C. hartmaniorum are, morphologically and genetically, more homogenous than the populations of C. buxbaumii. Compared to C. hartmaniorum, C. buxbaumii usually has wider leaf blades, a shorter inflorescence, a lower number of spikes which are shorter, but wider, and longer bracts and utricles. The AMOVA showed a larger variation between the populations of C. buxbaumii, representing 25.65% of the total variation in the taxon. Two populations of C. buxbaumii (from Poland and Estonia) are separated from the remaining populations, both genetically and morphologically; their individuals show shorter utricles and glumes, compared to the typical specimens of C. buxbaumii, and correspond with the morphology of putative infraspecific taxa described by Cajander (var. brevisquamosa and var. confusa). Conclusions The taxonomic status of the putative infraspecific taxa within C. buxbaumii requires further studies throughout the distribution range of C. buxbaumii, addressing habitats, morphology and genetics (including a chromosome count or a combination of different genetic methods), particularly as the variability in C. buxbaumii may be associated with the species’ polyploid origin.
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Affiliation(s)
- Helena Więcław
- Institute of Marine and Environmental Sciences, University of Szczecin, Szczecin, Poland
| | - Magdalena Szenejko
- Institute of Marine and Environmental Sciences, University of Szczecin, Szczecin, Poland.,Molecular Biology and Biotechnology Center, University of Szczecin, Szczecin, Poland
| | - Thea Kull
- Institute of Agricultural and Environmental Sciences, Estonian University of Life Sciences, Tartu, Estonia
| | - Zofia Sotek
- Institute of Marine and Environmental Sciences, University of Szczecin, Szczecin, Poland
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9
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Reynes L, Thibaut T, Mauger S, Blanfuné A, Holon F, Cruaud C, Couloux A, Valero M, Aurelle D. Genomic signatures of clonality in the deep water kelp Laminaria rodriguezii. Mol Ecol 2021; 30:1806-1822. [PMID: 33629449 DOI: 10.1111/mec.15860] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 02/18/2021] [Accepted: 02/19/2021] [Indexed: 12/17/2022]
Abstract
The development of population genomic approaches in non-model species allows for renewed studies of the impact of reproductive systems and genetic drift on population diversity. Here, we investigate the genomic signatures of partial clonality in the deep water kelp Laminaria rodriguezii, known to reproduce by both sexual and asexual means. We compared these results with the species Laminaria digitata, a closely related species that differs by different traits, in particular its reproductive mode (no clonal reproduction). We analysed genome-wide variation with dd-RAD sequencing using 4,077 SNPs in L. rodriguezii and 7,364 SNPs in L. digitata. As predicted for partially clonal populations, we show that the distribution of FIS within populations of L. rodriguezii is shifted toward negative values, with a high number of loci showing heterozygote excess. This finding is the opposite of what we observed within sexual populations of L. digitata, characterized by a generalized deficit in heterozygotes. Furthermore, we observed distinct distributions of FIS among populations of L. rodriguezii, which is congruent with the predictions of theoretical models for different levels of clonality and genetic drift. These findings highlight that the empirical distribution of FIS is a promising feature for the genomic study of asexuality in natural populations. Our results also show that the populations of L. rodriguezii analysed here are genetically differentiated and probably isolated. Our study provides a conceptual framework to investigate partial clonality on the basis of RAD-sequencing SNPs. These results could be obtained without any reference genome, and are therefore of interest for various non-model species.
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Affiliation(s)
- Lauric Reynes
- CNRS, IRD, MIO, Aix Marseille Université, Université de Toulon, Marseille, France
| | - Thierry Thibaut
- CNRS, IRD, MIO, Aix Marseille Université, Université de Toulon, Marseille, France
| | - Stéphane Mauger
- IRL 3614, Evolutionary Biology and Ecology of Algae, CNRS, UC, UACH, Sorbonne Université, Roscoff, France
| | - Aurélie Blanfuné
- CNRS, IRD, MIO, Aix Marseille Université, Université de Toulon, Marseille, France
| | | | - Corinne Cruaud
- Genoscope, Institut de Biologie François-Jacob, Commissariat à l'Energie Atomique (CEA), Université Paris-Saclay, Evry, France
| | - Arnaud Couloux
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, France
| | - Myriam Valero
- IRL 3614, Evolutionary Biology and Ecology of Algae, CNRS, UC, UACH, Sorbonne Université, Roscoff, France
| | - Didier Aurelle
- CNRS, IRD, MIO, Aix Marseille Université, Université de Toulon, Marseille, France
- Institut de Systématique Évolution Biodiversité (ISYEB, UMR 7205), Muséum National d'Histoire Naturelle, CNRS, EPHE, Sorbonne Université, Paris, France
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10
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Vega-Polo P, Cobo MM, Argudo A, Gutierrez B, Rowntree J, Torres MDL. Characterizing the genetic diversity of the Andean blueberry (Vaccinium floribundum Kunth.) across the Ecuadorian Highlands. PLoS One 2020; 15:e0243420. [PMID: 33284832 PMCID: PMC7721170 DOI: 10.1371/journal.pone.0243420] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Accepted: 11/22/2020] [Indexed: 11/18/2022] Open
Abstract
The Ecuadorian páramo, a high altitude tundra-like ecosystem, is a unique source of various ecosystem services and distinct biodiversity. Anthropogenic activities are associated with its fragmentation, which alters ecological factors and directly threatens resident species. Vaccinium floribundum Kunth., commonly known as Andean blueberry or mortiño, is a wild shrub endemic to the Andean region and highly valued in Ecuador for its berries, which are widely used in food preparations and hold an important cultural value. Since it is a wild species, mortiño could be vulnerable to environmental changes, resulting in a reduction of the size and distribution of its populations. To evaluate the extent of these effects on the mortiño populations, we assessed the genetic diversity and population structure of the species along the Ecuadorian highlands. We designed and developed a set of 30 species-specific SSR (simple sequence repeats) markers and used 16 of these to characterize 100 mortiño individuals from 27 collection sites. Our results revealed a high degree of genetic diversity (HE = 0.73) for the Ecuadorian mortiño, and a population structure analyses suggested the existence of distinct genetic clusters present in the northern, central and southern highlands. A fourth, clearly differentiated cluster was also found and included individuals from locations at higher elevations. We suggest that the population structure of the species could be explained by an isolation-by-distance model and can be associated with the geological history of the Andean region. Our results suggest that elevation could also be a key factor in the differentiation of mortiño populations. This study provides an extensive overview of the species across its distribution range in Ecuador, contributing to a better understanding of its conservation status. These results can assist in the development of conservation programs for this valuable biological and cultural resource and for the páramo ecosystem as a whole.
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Affiliation(s)
- Pamela Vega-Polo
- Laboratorio de Biotecnología Vegetal, Colegio de Ciencias Biológicas y Ambientales, Universidad San Francisco de Quito (USFQ), Quito, Ecuador
| | - Maria Mercedes Cobo
- Laboratorio de Biotecnología Vegetal, Colegio de Ciencias Biológicas y Ambientales, Universidad San Francisco de Quito (USFQ), Quito, Ecuador
- Department of Paediatrics, University of Oxford, Oxford, United Kingdom
| | - Andrea Argudo
- Laboratorio de Biotecnología Vegetal, Colegio de Ciencias Biológicas y Ambientales, Universidad San Francisco de Quito (USFQ), Quito, Ecuador
| | - Bernardo Gutierrez
- Laboratorio de Biotecnología Vegetal, Colegio de Ciencias Biológicas y Ambientales, Universidad San Francisco de Quito (USFQ), Quito, Ecuador
- Department of Zoology, University of Oxford, Oxford, United Kingdom
| | - Jennifer Rowntree
- Department of Natural Sciences, Ecology and Environment Research Centre, Manchester Metropolitan University, Oxford, United Kingdom
| | - Maria de Lourdes Torres
- Laboratorio de Biotecnología Vegetal, Colegio de Ciencias Biológicas y Ambientales, Universidad San Francisco de Quito (USFQ), Quito, Ecuador
- * E-mail:
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11
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Li S, Liu SL, Pei SY, Ning MM, Tang SQ. Genetic diversity and population structure of Camellia huana (Theaceae), a limestone species with narrow geographic range, based on chloroplast DNA sequence and microsatellite markers. PLANT DIVERSITY 2020; 42:343-350. [PMID: 33134617 PMCID: PMC7584792 DOI: 10.1016/j.pld.2020.06.003] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2019] [Revised: 05/30/2020] [Accepted: 06/01/2020] [Indexed: 05/23/2023]
Abstract
Camellia huana is an endangered species with a narrow distribution in limestone hills of northern Guangxi and southern Guizhou provinces, China. We used one chloroplast DNA (cpDNA) fragment and 12 pairs of microsatellite (simple sequence repeat; SSR) markers to assess the genetic diversity and structure of 12 C. huana populations. A total of 99 alleles were detected for 12 polymorphic loci, and eight haplotypes and nine polymorphic sites were detected within 5200 bp of cpDNA. C. huana populations showed a low level of genetic diversity (n = 8, Hd = 0.759, Pi = 0.00042 for cpDNA, N A = 3.931, H E = 0.466 for SSRs), but high genetic differentiation between populations (F ST = 0.2159 for SSRs, F ST = 0.9318 for cpDNA). This can be attributed to the narrow distribution and limestone habitat of C. huana. STRUCTURE analysis divided natural C. huana populations into two groups, consistent with their geographical distribution. Thus, we suggest that five natural C. huana populations should be split into two units to be managed effectively.
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Affiliation(s)
- Shuang Li
- Guangxi Key Laboratory of Rare and Endangered Animal Ecology, College of Life Science, Guangxi Normal University, Guilin, China
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection, Ministry of Education, Guangxi Normal University, Guilin, China
| | - Shang-Li Liu
- Guangxi Key Laboratory of Rare and Endangered Animal Ecology, College of Life Science, Guangxi Normal University, Guilin, China
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection, Ministry of Education, Guangxi Normal University, Guilin, China
| | - Si-Yu Pei
- Guangxi Key Laboratory of Rare and Endangered Animal Ecology, College of Life Science, Guangxi Normal University, Guilin, China
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection, Ministry of Education, Guangxi Normal University, Guilin, China
| | - Man-Man Ning
- Longtan Nature Reserve Management Center, Hechi, China
| | - Shao-Qing Tang
- Guangxi Key Laboratory of Rare and Endangered Animal Ecology, College of Life Science, Guangxi Normal University, Guilin, China
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection, Ministry of Education, Guangxi Normal University, Guilin, China
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12
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Nistelberger HM, Binks RM, van Leeuwen S, Coates DJ, McArthur SL, Macdonald BM, Hankinson M, Byrne M. Extensive Genetic Connectivity and Historical Persistence Are Features of Two Widespread Tree Species in the Ancient Pilbara Region of Western Australia. Genes (Basel) 2020; 11:E863. [PMID: 32751318 PMCID: PMC7465080 DOI: 10.3390/genes11080863] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2020] [Revised: 07/27/2020] [Accepted: 07/27/2020] [Indexed: 11/29/2022] Open
Abstract
Phylogeographic studies can be used as a tool to understand the evolutionary history of a landscape, including the major drivers of species distributions and diversity. Extensive research has been conducted on phylogeographic patterns of species found in northern hemisphere landscapes that were affected by glaciations, yet the body of literature for older, unaffected landscapes is still underrepresented. The Pilbara region of north-western Australia is an ancient and vast landscape that is topographically complex, consisting of plateaus, gorges, valleys, and ranges, and experiences extreme meteorological phenomena including seasonal cyclonic activity. These features are expected to influence patterns of genetic structuring throughout the landscape either by promoting or restricting the movement of pollen and seed. Whilst a growing body of literature exists for the fauna endemic to this region, less is known about the forces shaping the evolution of plant taxa. In this study we investigate the phylogeography of two iconic Pilbara tree species, the Hamersley Bloodwood (Corymbia hamersleyana) and Western Gidgee (Acacia pruinocarpa), by assessing patterns of variation and structure in several chloroplast DNA regions and nuclear microsatellite loci developed for each species. Gene flow was found to be extensive in both taxa and there was evidence of long-distance seed dispersal across the region (pollen to seed ratios of 6.67 and 2.96 for C. hamersleyana and A. pruinocarpa, respectively), which may result from flooding and strong wind gusts associated with extreme cyclonic activity. Both species possessed high levels of cpDNA genetic diversity in comparison to those from formerly glaciated landscapes (C. hamersleyana = 14 haplotypes, A. pruinocarpa = 37 haplotypes) and showed evidence of deep lineage diversification occurring from the late Miocene, a time of intensifying aridity in this landscape that appears to be a critical driver of evolution in Pilbara taxa. In contrast to another study, we did not find evidence for topographic features acting as refugia for the widely sampled C. hamersleyana.
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Affiliation(s)
- Heidi M. Nistelberger
- Department of Biodiversity, Conservation and Attractions, Biodiversity and Conservation Science, Locked Bag 104, Bentley Delivery Centre, Perth, WA 6983, Australia; (R.M.B.); (S.v.L.); (D.J.C.); (S.L.M.); (B.M.M.); (M.H.); (M.B.)
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13
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Ntuli NN, Nicastro KR, Zardi GI, Assis J, McQuaid CD, Teske PR. Rejection of the genetic implications of the "Abundant Centre Hypothesis" in marine mussels. Sci Rep 2020; 10:604. [PMID: 31953497 PMCID: PMC6969206 DOI: 10.1038/s41598-020-57474-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2019] [Accepted: 12/26/2019] [Indexed: 11/09/2022] Open
Abstract
The ‘Abundant-Centre Hypothesis’ is a well-established but controversial hypothesis stating that the abundance of a species is highest at the centre of its range and decreases towards the edges, where conditions are unfavourable. As genetic diversity depends on population size, edge populations are expected to show lower intra-population genetic diversity than core populations, while showing high inter-population genetic divergence. Here, the genetic implications of the Abundant-Centre Hypothesis were tested on two coastal mussels from South Africa that disperse by means of planktonic larvae, the native Perna perna and the invasive Mytilus galloprovincialis. Genetic structure was found within P. perna, which, together with evidence from Lagrangian particle simulations, points to significant reductions in gene flow between sites. Despite this, the expected diversity pattern between centre and edge populations was not found for either species. We conclude that the genetic predictions of the Abundant-Centre Hypothesis are unlikely to be met by high-dispersal species with large population sizes, and may only become evident in species with much lower levels of connectivity.
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Affiliation(s)
- Noxolo N Ntuli
- Centre for Ecological Genomics and Wildlife Conservation, Department of Zoology, University of Johannesburg, Auckland Park, 2006, South Africa
| | - Katy R Nicastro
- CCMAR - Centro de Ciências do Mar, Universidade do Algarve, Faro, Portugal.,Department of Zoology and Entomology, Rhodes University, Grahamstown, 6140, South Africa
| | - Gerardo I Zardi
- Department of Zoology and Entomology, Rhodes University, Grahamstown, 6140, South Africa
| | - Jorge Assis
- CCMAR - Centro de Ciências do Mar, Universidade do Algarve, Faro, Portugal
| | - Christopher D McQuaid
- Department of Zoology and Entomology, Rhodes University, Grahamstown, 6140, South Africa
| | - Peter R Teske
- Centre for Ecological Genomics and Wildlife Conservation, Department of Zoology, University of Johannesburg, Auckland Park, 2006, South Africa.
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Thatte P, Chandramouli A, Tyagi A, Patel K, Baro P, Chhattani H, Ramakrishnan U. Human footprint differentially impacts genetic connectivity of four wide‐ranging mammals in a fragmented landscape. DIVERS DISTRIB 2019. [DOI: 10.1111/ddi.13022] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Affiliation(s)
- Prachi Thatte
- National Center for Biological Sciences Tata Institute of Fundamental Research Bangalore India
| | - Anuradha Chandramouli
- National Center for Biological Sciences Tata Institute of Fundamental Research Bangalore India
| | - Abhinav Tyagi
- National Center for Biological Sciences Tata Institute of Fundamental Research Bangalore India
| | - Kaushal Patel
- National Center for Biological Sciences Tata Institute of Fundamental Research Bangalore India
| | - Phulmani Baro
- National Center for Biological Sciences Tata Institute of Fundamental Research Bangalore India
| | - Himanshu Chhattani
- National Center for Biological Sciences Tata Institute of Fundamental Research Bangalore India
| | - Uma Ramakrishnan
- National Center for Biological Sciences Tata Institute of Fundamental Research Bangalore India
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15
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Farris E, Filigheddu R, Mameli G, Falanga V, Vanetti I, Rosati L, Binelli G. Is population genetic structure of vascular plants shaped more by ecological or geographic factors? A study case on the Mediterranean endemic Centaurea filiformis (Asteraceae). PLANT BIOLOGY (STUTTGART, GERMANY) 2018; 20:936-947. [PMID: 29873892 DOI: 10.1111/plb.12853] [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: 02/08/2018] [Accepted: 06/01/2018] [Indexed: 06/08/2023]
Abstract
All known populations of the Sardinian endemic Centaurea filiformis Viv. (Asteraceae) were studied in order to understand the impact of both geographic and ecological factors on the genetic structuring of this species. Fourteen populations and 234 individuals were sampled. The demographic structure of the populations and the reproductive ecology were estimated in 28 plots. Population genetic analyses were based on SSR markers. Genetic structure was investigated by spatial Bayesian methods. Average densities of 0.51 individuals m-2 were detected, with a prevalence of adults. Ten species of pollinators were identified; C. filiformis ability to self-pollinate and myrmecochory were demonstrated experimentally. The populations displayed an average heterozygosity value of He = 0.576 and high genetic differentiation (overall FST = 0.218). Bayesian analysis suggests that five is the most probable number of gene pools of origin. A strong correlation between geographic distances and genetic distances among populations was highlighted. The demographic population structure of C. filiformis is dominated by adults, suggesting that it is a stable-regressive or senile species, investing more in local persistence than colonisation ability. Despite the scattered distribution, the populations studied do not present evidence of genetic erosion. The analysis of genetic differentiation reveals very high differentiation levels among populations, thus indicating that effective barriers exist against gene flow. A general conclusion is that population distribution results in a clear genetic structure for the populations studied, and that geography and not ecology is shaping the present distribution of this species.
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Affiliation(s)
- E Farris
- Department of Chemistry and Pharmacy, University of Sassari, Sassari, Italy
| | - R Filigheddu
- Department of Chemistry and Pharmacy, University of Sassari, Sassari, Italy
| | - G Mameli
- Department of Chemistry and Pharmacy, University of Sassari, Sassari, Italy
| | - V Falanga
- Dipartimento di Biotecnologie e Scienze della Vita, Università dell'Insubria, Varese, Italy
| | - I Vanetti
- Dipartimento di Biotecnologie e Scienze della Vita, Università dell'Insubria, Varese, Italy
| | - L Rosati
- School of Agricultural, Forestry, Food and Environmental Sciences, University of Basilicata, Potenza, Italy
| | - G Binelli
- Dipartimento di Biotecnologie e Scienze della Vita, Università dell'Insubria, Varese, Italy
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