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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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Guzmán S, Giudicelli GC, Turchetto C, Bombarely A, Freitas LB. Neutral and outlier single nucleotide polymorphisms disentangle the evolutionary history of a coastal Solanaceae species. Mol Ecol 2022; 31:2847-2864. [PMID: 35332594 DOI: 10.1111/mec.16441] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Revised: 03/11/2022] [Accepted: 03/16/2022] [Indexed: 11/30/2022]
Abstract
Speciation begins with the isolation of some individuals or subpopulations due to drivers promoting a diverging genetic distribution. Such isolation may occur, followed by different processes and pressures. Isolation-by-distance (IBD), isolation-by-adaptation (IBA), and isolation-by-colonization (IBC) have been recognized as the main divergence patterns. Still, it is not easy to distinguish which one is the main pattern as each one may act at different points in time or even simultaneously. Using an extensive genome coverage from a Petunia species complex with coastal and inland distribution and multiple analytical approaches on population genomics and phylogeography, we showed a complex interplay between neutral and selective forces acting on the divergence process. We found 18,887 SNPs potentially neutral and 924 potentially under selection (outlier) loci. All analyses pointed that each subspecies displays its own genetic component and evolutionary history. We suggested plausible ecologic drivers for such divergence in a southernmost South Atlantic coastal plain in Brazil and Uruguay and identified a connection between adaptation and environment heterogeneity.
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Affiliation(s)
- Sebastián Guzmán
- Department of Genetics, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Giovanna C Giudicelli
- Department of Genetics, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Caroline Turchetto
- Department of Genetics, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil.,Department of Botany, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | | | - Loreta B Freitas
- Department of Genetics, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
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Merklinger FF, Böhnert T, Arakaki M, Weigend M, Quandt D, Luebert F. Quaternary diversification of a columnar cactus in the driest place on earth. AMERICAN JOURNAL OF BOTANY 2021; 108:184-199. [PMID: 33580531 DOI: 10.1002/ajb2.1608] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Accepted: 09/28/2020] [Indexed: 06/12/2023]
Abstract
PREMISE The cactus family (Cactaceae) is a speciose lineage with an almost entirely New World distribution. The genus Eulychnia with eight currently recognized species is endemic to the Atacama and Peruvian Deserts. Here we investigated the phylogeny of this group based on a complete taxon sampling to elucidate species delimitation and biogeographic history of the genus. METHODS A family-wide Bayesian molecular clock dating based on plastid sequence data was conducted to estimate the age of Eulychnia and its divergence from its sister genus Austrocactus. A second data set obtained from genotyping by sequencing (GBS) was analyzed, using the family-wide age estimate as a secondary calibration to date the GBS phylogeny using a penalized likelihood approach. Ancestral ranges were inferred employing the dispersal extinction cladogenesis approach. RESULTS Our GBS phylogeny of Eulychnia was fully resolved with high support values nearly throughout the phylogeny. The split from Austrocactus occurred in the late Miocene, and Eulychnia diversified during the early Quaternary. Three lineages were retrieved: Eulychnia ritteri from Peru is sister to all Chilean species, which in turn fall into two sister clades of three and four species, respectively. Diversification in the Chilean clades started in the early Pleistocene. Eulychnia likely originated at the coastal range of its distribution and colonized inland locations several times. CONCLUSIONS Diversification of Eulychnia during the Pleistocene coincides with long periods of hyperaridity alternated with pluvial phases. Hyperaridity caused habitat fragmentation, ultimately leading to speciation and resulting in the current allopatric distribution of taxa.
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Affiliation(s)
- Felix F Merklinger
- Nees Institute for Biodiversity of Plants, University of Bonn, Germany
- Sukkulenten-Sammlung Zürich / Grün Stadt Zürich, Zürich, Switzerland
| | - Tim Böhnert
- Nees Institute for Biodiversity of Plants, University of Bonn, Germany
| | - Mónica Arakaki
- Museo de Historia Natural, Universidad Nacional Mayor de San Marcos, Lima, Peru
| | | | - Dietmar Quandt
- Nees Institute for Biodiversity of Plants, University of Bonn, Germany
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
| | - Federico Luebert
- Nees Institute for Biodiversity of Plants, University of Bonn, Germany
- Departamento de Silvicultura y Conservación de la Naturaleza, Universidad de Chile, Santiago, Chile
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