1
|
Gómez Quijano MJ, Gross BL, Etterson JR. Genetic differentiation across a steep and narrow environmental gradient: Quantitative genetic and genomic insights into Lake Superior populations of Quercus rubra. Mol Ecol 2024; 33:e17483. [PMID: 39056407 DOI: 10.1111/mec.17483] [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: 07/06/2023] [Revised: 07/05/2024] [Accepted: 07/12/2024] [Indexed: 07/28/2024]
Abstract
Adaptive differentiation of traits and underlying loci can occur at a small geographical scale if natural selection is stronger than countervailing gene flow and drift. We investigated this hypothesis using coupled quantitative genetic and genomic approaches for a wind-pollinated tree species, Quercus rubra, along the steep, narrow gradient of the Lake Superior coast that encompasses four USDA Hardiness Zones within 100 km. For the quantitative genetic component of this study, we examined phenotypic differentiation among eight populations in a common garden, measuring seed mass, germination, height, stem diameter, leaf number, specific leaf area and survival. For the genomic component, we quantified genetic differentiation for 26 populations from the same region using RAD-seq. Because hybridisation with Quercus ellipsoidalis occurs in other parts of the species' range, we included two populations of this congener for comparison. In the common garden study, we found a strong signal of population differentiation that was significantly associated with at least one climate factor for nine of 10 measured traits. In contrast, we found no evidence of genomic differentiation among populations based on FST or any other measures. However, both distance-based and genotype-environment association analyses identified loci showing the signature of selection, with one locus in common across five analyses. This locus was associated with the minimum temperature of the coldest month, a factor that defines the climate zones and was also significant in the common garden analyses. In addition, we documented introgression from Q. ellipsoidalis into Q. rubra, with rates of introgression correlated with the climate gradient. In sum, this study reveals signatures of selection at the quantitative trait and genomic level consistent with climate adaptation, a pattern that is more often documented at a much broader geographical scale, especially in long-lived wind-pollinated species.
Collapse
Affiliation(s)
- María José Gómez Quijano
- Department of Biology, Queen's University, Kingston, Ontario, Canada
- Department of Biology, University of Minnesota Duluth, Duluth, Minnesota, USA
| | - Briana L Gross
- Department of Biology, University of Minnesota Duluth, Duluth, Minnesota, USA
| | - Julie R Etterson
- Department of Biology, University of Minnesota Duluth, Duluth, Minnesota, USA
| |
Collapse
|
2
|
Antonio AS, Franco LO, Cardoso SRS, Dos Santos GRC, Pereira HMG, Wiedemann LSM, Ferreira PCG, Veiga-Junior VF. Chemical variability of Copaifera langsdorffii Desf. from environmentally contrasting populations. Nat Prod Res 2022:1-5. [PMID: 35236187 DOI: 10.1080/14786419.2022.2043856] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Copaifera langsdorffii Desf. is recognised as one of most famous medicinal and economic species of Copaiba, occurring in several distinct biomes. An untargeted metabolomic approach was used to evaluate the chemical variability of C. langsdorffii from contrasting climates biomes (Atlantic Rainflorest and the semiarid Cerrado). Metabolomic analysis enabled the identification of 11 compounds, including glycosylated flavonoids and galloylquinic acid derivatives. Multivariate analysis highlighted that Cerrado population had a significantly higher concentrations of galloylquinic acid derivatives in comparison to the rainforest biome. Meanwhile, Atlantic Rainforest populations presented higher content of flavonols. Semiarid biome, reduced the concentration of flavonoids, mainly concerning quercetin and kaempferol derivatives, however, in this biome flavonoids were more diverse. Both chemical classes presented relevance to be used as geographical origin chemical markers by qualitative and quantitative features.
Collapse
Affiliation(s)
- Ananda S Antonio
- Departmento de Química, Instituto de Ciências Exatas, Universidade Federal do Amazonas, Coroado, Manaus, AM, Brazil.,Instituto de Química, Laboratório Brasileiro de Controle de Doping (LBCD - LADETEC, Universidade Federal do Rio de Janeiro, Avenida Horácio Macedo, Ilha do Fundão, Rio de Janeiro, RJ, Brazil
| | - Luciana O Franco
- Instituto de Pesquisas Jardim Botânico do Rio de Janeiro, Diretoria de Pesquisa Científica, Rio de Janeiro, RJ, Brazil
| | - Sérgio Ricardo S Cardoso
- Instituto de Pesquisas Jardim Botânico do Rio de Janeiro, Diretoria de Pesquisa Científica, Rio de Janeiro, RJ, Brazil
| | - Gustavo R C Dos Santos
- Instituto de Química, Laboratório Brasileiro de Controle de Doping (LBCD - LADETEC, Universidade Federal do Rio de Janeiro, Avenida Horácio Macedo, Ilha do Fundão, Rio de Janeiro, RJ, Brazil
| | - Henrique Marcelo G Pereira
- Instituto de Química, Laboratório Brasileiro de Controle de Doping (LBCD - LADETEC, Universidade Federal do Rio de Janeiro, Avenida Horácio Macedo, Ilha do Fundão, Rio de Janeiro, RJ, Brazil
| | - Larissa S M Wiedemann
- Departmento de Química, Instituto de Ciências Exatas, Universidade Federal do Amazonas, Coroado, Manaus, AM, Brazil
| | - Paulo C G Ferreira
- Instituto de Bioquímica Médica, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - Valdir F Veiga-Junior
- Departmento de Química, Instituto de Ciências Exatas, Universidade Federal do Amazonas, Coroado, Manaus, AM, Brazil.,Seção de Engenharia Química, Instituto Militar de Engenharia, Praça General Tibúrcio, Rio de Janeiro, RJ, Brazil
| |
Collapse
|
3
|
de Aquino SO, Kiwuka C, Tournebize R, Gain C, Marraccini P, Mariac C, Bethune K, Couderc M, Cubry P, Andrade AC, Lepelley M, Darracq O, Crouzillat D, Anten N, Musoli P, Vigouroux Y, de Kochko A, Manel S, François O, Poncet V. Adaptive potential of
Coffea canephora
from Uganda in response to climate change. Mol Ecol 2022; 31:1800-1819. [DOI: 10.1111/mec.16360] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Revised: 11/12/2021] [Accepted: 01/06/2022] [Indexed: 11/28/2022]
Affiliation(s)
| | - Catherine Kiwuka
- NARO Kampala Uganda
- Centre for Crop Systems Analysis Wageningen Univ. Wageningen Netherlands
| | | | - Clément Gain
- U. Grenoble‐Alpes, TIMC‐IMAG, CNRS UMR 5525, Grenoble, France and LJK, Inria, CNRS UMR 5224 Grenoble France
| | | | - Cédric Mariac
- DIADE, Univ. Montpellier, CIRAD, IRD Montpellier France
| | - Kévin Bethune
- DIADE, Univ. Montpellier, CIRAD, IRD Montpellier France
| | - Marie Couderc
- DIADE, Univ. Montpellier, CIRAD, IRD Montpellier France
| | | | | | | | | | | | - Niels Anten
- Centre for Crop Systems Analysis Wageningen Univ. Wageningen Netherlands
| | | | | | | | - Stéphanie Manel
- CEFE, Univ Montpellier, CNRS, EPHE‐PSL University, IRD Montpellier France
| | - Olivier François
- U. Grenoble‐Alpes, TIMC‐IMAG, CNRS UMR 5525, Grenoble, France and LJK, Inria, CNRS UMR 5224 Grenoble France
| | | |
Collapse
|
4
|
Blyth C, Christmas MJ, Bickerton DC, Breed MF, Foster NR, Guerin GR, Mason ARG, Lowe AJ. Genomic, Habitat, and Leaf Shape Analyses Reveal a Possible Cryptic Species and Vulnerability to Climate Change in a Threatened Daisy. Life (Basel) 2021; 11:553. [PMID: 34208381 PMCID: PMC8231295 DOI: 10.3390/life11060553] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Revised: 06/08/2021] [Accepted: 06/09/2021] [Indexed: 12/01/2022] Open
Abstract
Olearia pannosa is a plant species listed as vulnerable in Australia. Two subspecies are currently recognised (O. pannosa subsp. pannosa (silver daisy) and O. pannosa subsp. cardiophylla (velvet daisy)), which have overlapping ranges but distinct leaf shape. Remnant populations face threats from habitat fragmentation and climate change. We analysed range-wide genomic data and leaf shape variation to assess population diversity and divergence and to inform conservation management strategies. We detected three distinct genetic groupings and a likely cryptic species. Samples identified as O. pannosa subsp. cardiophylla from the Flinders Ranges in South Australia were genetically distinct from all other samples and likely form a separate, range-restricted species. Remaining samples formed two genetic clusters, which aligned with leaf shape differences but not fully with current subspecies classifications. Levels of genetic diversity and inbreeding differed between the three genetic groups, suggesting each requires a separate management strategy. Additionally, we tested for associations between genetic and environmental variation and carried out habitat suitability modelling for O. pannosa subsp. pannosa populations. We found mean annual maximum temperature explained a significant proportion of genomic variance. Habitat suitability modelling identified mean summer maximum temperature, precipitation seasonality and mean annual rainfall as constraints on the distribution of O. pannosa subsp. pannosa, highlighting increasing aridity as a threat for populations located near suitability thresholds. Our results suggest maximum temperature is an important agent of selection on O. pannosa subsp. pannosa and should be considered in conservation strategies. We recommend taxonomic revision of O. pannosa and provide conservation management recommendations.
Collapse
Affiliation(s)
- Colette Blyth
- School of Biological Sciences, University of Adelaide, Adelaide 5005, Australia; (N.R.F.); (G.R.G.); (A.R.G.M.); (A.J.L.)
| | - Matthew J. Christmas
- Department of Medical Biochemistry and Microbiology, Uppsala University, 751 23 Uppsala, Sweden
| | | | - Martin F. Breed
- College of Science and Engineering, Flinders University, Bedford Park 5042, Australia;
| | - Nicole R. Foster
- School of Biological Sciences, University of Adelaide, Adelaide 5005, Australia; (N.R.F.); (G.R.G.); (A.R.G.M.); (A.J.L.)
- College of Science and Engineering, Flinders University, Bedford Park 5042, Australia;
| | - Greg R. Guerin
- School of Biological Sciences, University of Adelaide, Adelaide 5005, Australia; (N.R.F.); (G.R.G.); (A.R.G.M.); (A.J.L.)
- Terrestrial Ecosystem Research Network (TERN), University of Adelaide, Adelaide 5005, Australia
| | - Alex R. G. Mason
- School of Biological Sciences, University of Adelaide, Adelaide 5005, Australia; (N.R.F.); (G.R.G.); (A.R.G.M.); (A.J.L.)
| | - Andrew J. Lowe
- School of Biological Sciences, University of Adelaide, Adelaide 5005, Australia; (N.R.F.); (G.R.G.); (A.R.G.M.); (A.J.L.)
| |
Collapse
|
5
|
Chen Y, Gao Y, Huang X, Li S, Zhan A. Local environment-driven adaptive evolution in a marine invasive ascidian ( Molgula manhattensis). Ecol Evol 2021; 11:4252-4266. [PMID: 33976808 PMCID: PMC8093682 DOI: 10.1002/ece3.7322] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Revised: 01/21/2021] [Accepted: 01/26/2021] [Indexed: 12/04/2022] Open
Abstract
Elucidating molecular mechanisms of environment-driven adaptive evolution in marine invaders is crucial for understanding invasion success and further predicting their future invasions. Although increasing evidence suggests that adaptive evolution could contribute to organisms' adaptation to varied environments, there remain knowledge gaps regarding how environments influence genomic variation in invaded habitats and genetic bases underlying local adaptation for most marine invaders. Here, we performed restriction-site-associated DNA sequencing (RADseq) to assess population genetic diversity and further investigate genomic signatures of local adaptation in the marine invasive ascidian, Molgula manhattensis. We revealed that most invasive populations exhibited significant genetic differentiation, low recent gene flow, and no signal of significant population bottleneck. Based on three genome scan approaches, we identified 109 candidate loci potentially under environmental selection. Redundancy analysis and variance partitioning analysis suggest that local environmental factors, particularly the salinity-related variables, represent crucial evolutionary forces in driving adaptive divergence. Using the newly developed transcriptome as a reference, 14 functional genes were finally obtained with potential roles in salinity adaptation, including SLC5A1 and SLC9C1 genes from the solute carrier gene (SLC) superfamily. Our findings confirm that differed local environments could rapidly drive adaptive divergence among invasive populations and leave detectable genomic signatures in marine invaders.
Collapse
Affiliation(s)
- Yiyong Chen
- Research Center for Eco‐Environmental SciencesChinese Academy of SciencesHaidian DistrictBeijingChina
- University of Chinese Academy of SciencesChinese Academy of SciencesShijingshan DistrictBeijingChina
| | - Yangchun Gao
- Research Center for Eco‐Environmental SciencesChinese Academy of SciencesHaidian DistrictBeijingChina
- University of Chinese Academy of SciencesChinese Academy of SciencesShijingshan DistrictBeijingChina
- Guangdong Key Laboratory of Animal Conservation and Resource UtilizationInstitute of ZoologyGuangdong Academy of SciencesHaizhu DistrictGuangzhouChina
| | - Xuena Huang
- Research Center for Eco‐Environmental SciencesChinese Academy of SciencesHaidian DistrictBeijingChina
| | - Shiguo Li
- Research Center for Eco‐Environmental SciencesChinese Academy of SciencesHaidian DistrictBeijingChina
- University of Chinese Academy of SciencesChinese Academy of SciencesShijingshan DistrictBeijingChina
| | - Aibin Zhan
- Research Center for Eco‐Environmental SciencesChinese Academy of SciencesHaidian DistrictBeijingChina
- University of Chinese Academy of SciencesChinese Academy of SciencesShijingshan DistrictBeijingChina
| |
Collapse
|
6
|
Galliart M, Sabates S, Tetreault H, DeLaCruz A, Bryant J, Alsdurf J, Knapp M, Bello NM, Baer SG, Maricle BR, Gibson DJ, Poland J, St Amand P, Unruh N, Parrish O, Johnson L. Adaptive genetic potential and plasticity of trait variation in the foundation prairie grass Andropogon gerardii across the US Great Plains' climate gradient: Implications for climate change and restoration. Evol Appl 2020; 13:2333-2356. [PMID: 33005227 PMCID: PMC7513703 DOI: 10.1111/eva.13028] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Revised: 03/06/2020] [Accepted: 04/06/2020] [Indexed: 12/04/2022] Open
Abstract
Plant response to climate depends on a species' adaptive potential. To address this, we used reciprocal gardens to detect genetic and environmental plasticity effects on phenotypic variation and combined with genetic analyses. Four reciprocal garden sites were planted with three regional ecotypes of Andropogon gerardii, a dominant Great Plains prairie grass, using dry, mesic, and wet ecotypes originating from western KS to Illinois that span 500-1,200 mm rainfall/year. We aimed to answer: (a) What is the relative role of genetic constraints and phenotypic plasticity in controlling phenotypes? (b) When planted in the homesite, is there a trait syndrome for each ecotype? (c) How are genotypes and phenotypes structured by climate? and (d) What are implications of these results for response to climate change and use of ecotypes for restoration? Surprisingly, we did not detect consistent local adaptation. Rather, we detected co-gradient variation primarily for most vegetative responses. All ecotypes were stunted in western KS. Eastward, the wet ecotype was increasingly robust relative to other ecotypes. In contrast, fitness showed evidence for local adaptation in wet and dry ecotypes with wet and mesic ecotypes producing little seed in western KS. Earlier flowering time in the dry ecotype suggests adaptation to end of season drought. Considering ecotype traits in homesite, the dry ecotype was characterized by reduced canopy area and diameter, short plants, and low vegetative biomass and putatively adapted to water limitation. The wet ecotype was robust, tall with high biomass, and wide leaves putatively adapted for the highly competitive, light-limited Eastern Great Plains. Ecotype differentiation was supported by random forest classification and PCA. We detected genetic differentiation and outlier genes associated with primarily precipitation. We identified candidate gene GA1 for which allele frequency associated with plant height. Sourcing of climate adapted ecotypes should be considered for restoration.
Collapse
Affiliation(s)
| | | | | | | | | | | | - Mary Knapp
- State ClimatologistKansas State UniversityManhattanKSUSA
| | | | - Sara G. Baer
- Ecology and Evolutionary BiologyUniversity of KansasLawrenceKSUSA
| | - Brian R. Maricle
- Department of Biological SciencesFort Hays State UniversityHaysKSUSA
| | - David J. Gibson
- Plant Biology and Center for EcologySouthern Illinois UniversityCarbondaleILUSA
| | - Jesse Poland
- Plant PathologyKansas State UniversityManhattanKSUSA
| | - Paul St Amand
- Hard Winter Wheat Genetics Research UnitUSDA‐ARSManhattanKSUSA
| | | | | | | |
Collapse
|
7
|
Knowledge status and sampling strategies to maximize cost-benefit ratio of studies in landscape genomics of wild plants. Sci Rep 2020; 10:3706. [PMID: 32111897 PMCID: PMC7048820 DOI: 10.1038/s41598-020-60788-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Accepted: 02/11/2020] [Indexed: 11/27/2022] Open
Abstract
To avoid local extinction due to the changes in their natural ecosystems, introduced by anthropogenic activities, species undergo local adaptation. Landscape genomics approach, through genome–environment association studies, has helped evaluate the local adaptation in natural populations. Landscape genomics, is still a developing discipline, requiring refinement of guidelines in sampling design, especially for studies conducted in the backdrop of stark socioeconomic realities of the rainforest ecologies, which are global biodiversity hotspots. In this study we aimed to devise strategies to improve the cost-benefit ratio of landscape genomics studies by surveying sampling designs and genome sequencing strategies used in existing studies. We conducted meta-analyses to evaluate the importance of sampling designs, in terms of (i) number of populations sampled, (ii) number of individuals sampled per population, (iii) total number of individuals sampled, and (iv) number of SNPs used in different studies, in discerning the molecular mechanisms underlying local adaptation of wild plant species. Using the linear mixed effects model, we demonstrated that the total number of individuals sampled and the number of SNPs used, significantly influenced the detection of loci underlying the local adaptation. Thus, based on our findings, in order to optimize the cost-benefit ratio of landscape genomics studies, we suggest focusing on increasing the total number of individuals sampled and using a targeted (e.g. sequencing capture) Pool-Seq approach and/or a random (e.g. RAD-Seq) Pool-Seq approach to detect SNPs and identify SNPs under selection for a given environmental cline. We also found that the existing molecular evidences are inadequate in predicting the local adaptations to climate change in tropical forest ecosystems.
Collapse
|
8
|
Myers EA, McKelvy AD, Burbrink FT. Biogeographic barriers, Pleistocene refugia, and climatic gradients in the southeastern Nearctic drive diversification in cornsnakes (Pantherophis guttatus complex). Mol Ecol 2020; 29:797-811. [PMID: 31955477 DOI: 10.1111/mec.15358] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Revised: 01/08/2020] [Accepted: 01/13/2020] [Indexed: 12/21/2022]
Abstract
The southeastern Nearctic is a biodiversity hotspot that is also rich in cryptic species. Numerous hypotheses (e.g., vicariance, local adaptation, and Pleistocene speciation in glacial refugia) have been tested in an attempt to explain diversification and the observed pattern of extant biodiversity. However, previous phylogeographic studies have both supported and refuted these hypotheses. Therefore, while data support one or more of these diversification hypotheses, it is likely that taxa are forming within this region in species-specific ways. Here, we generate a genomic data set for the cornsnakes (Pantherophis guttatus complex), which are widespread across this region, spanning both biogeographic barriers and climatic gradients. We use phylogeographic model selection combined with hindcast ecological niche models to determine regions of habitat stability through time. This combined approach suggests that numerous drivers of population differentiation explain the current diversity of this group of snakes. The Mississippi River caused initial speciation in this species complex, with more recent divergence events linked to adaptations to ecological heterogeneity and allopatric Pleistocene refugia. Lastly, we discuss the taxonomy of this group and suggest there may be additional cryptic species in need of formal recognition.
Collapse
Affiliation(s)
- Edward A Myers
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA.,Department of Herpetology, The American Museum of Natural History, New York, NY, USA
| | - Alexander D McKelvy
- Department of Biology, The Graduate School and Center, City University of New York, New York, NY, USA
| | - Frank T Burbrink
- Department of Herpetology, The American Museum of Natural History, New York, NY, USA
| |
Collapse
|
9
|
Zhao H, Wang H, Liu T, Liu S, Jin L, Huang X, Dai W, Sun K, Feng J. Gene expression vs. sequence divergence: comparative transcriptome sequencing among natural Rhinolophus ferrumequinum populations with different acoustic phenotypes. Front Zool 2019; 16:37. [PMID: 31528181 PMCID: PMC6743130 DOI: 10.1186/s12983-019-0336-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Accepted: 09/04/2019] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND Although the sensory drive hypothesis can explain the geographic variation in echolocation frequencies of some bat species, the molecular mechanisms underlying this phenomenon are still unclear. The three lineages of greater horseshoe bat (Rhinolophus ferrumequinum) in China (northeast, central-east, and southwest) have significant geographic variation in resting frequencies (RF) of echolocation calls. Because their cochleae have an acoustic fovea that is highly sensitive to a narrow range of frequencies, we reported the transcriptomes of cochleae collected from three genetic lineages of R. ferrumequinum, which is an ideal organism for studying geographic variation in echolocation signals, and tried to understand the mechanisms behind this bat phenomenon by analyzing gene expression and sequence variation. RESULTS A total of 8190 differentially expressed genes (DEGs) were identified. We identified five modules from all DEGs that were significantly related to RF or forearm length (FL). DEGs in the RF-related modules were significantly enriched in the gene categories involved in neural activity, learning, and response to sound. DEGs in the FL-related modules were significantly enriched in the pathways related to muscle and actin functions. Using 21,945 single nucleotide polymorphisms, we identified 18 candidate unigenes associated with hearing, five of which were differentially expressed among the three populations. Additionally, the gene ERBB4, which regulates diverse cellular processes in the inner ear such as cell proliferation and differentiation, was in the largest module. We also found 49 unigenes that were under positive selection from 4105 one-to-one orthologous gene pairs between the three R. ferrumequinum lineages and three other Chiroptera species. CONCLUSIONS The variability of gene expression and sequence divergence at the molecular level might provide evidence that can help elucidate the genetic basis of geographic variation in echolocation signals of greater horseshoe bats.
Collapse
Affiliation(s)
- Hanbo Zhao
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun, 130117 China
| | - Hui Wang
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun, 130117 China
| | - Tong Liu
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun, 130117 China
| | - Sen Liu
- Institute of Resources & Environment, Henan Polytechnic University, Jiaozuo, 454000 China
| | - Longru Jin
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun, 130117 China
| | - Xiaobin Huang
- Vector Laboratory, Institute of Pathogens and Vectors, Branch of Yunnan Provincial Key Laboratory for Zoonosis Control and Prevention, Dali University, Dali, 671003 China
| | - Wentao Dai
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun, 130117 China
| | - Keping Sun
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun, 130117 China
| | - Jiang Feng
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun, 130117 China
- College of Life Science, Jilin Agricultural University, Changchun, 130118 China
| |
Collapse
|
10
|
Breed MF, Harrison PA, Blyth C, Byrne M, Gaget V, Gellie NJC, Groom SVC, Hodgson R, Mills JG, Prowse TAA, Steane DA, Mohr JJ. The potential of genomics for restoring ecosystems and biodiversity. Nat Rev Genet 2019; 20:615-628. [PMID: 31300751 DOI: 10.1038/s41576-019-0152-0] [Citation(s) in RCA: 89] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/21/2019] [Indexed: 01/12/2023]
Abstract
Billions of hectares of natural ecosystems have been degraded through human actions. The global community has agreed on targets to halt and reverse these declines, and the restoration sector faces the important but arduous task of implementing programmes to meet these objectives. Existing and emerging genomics tools offer the potential to improve the odds of achieving these targets. These tools include population genomics that can improve seed sourcing, meta-omics that can improve assessment and monitoring of restoration outcomes, and genome editing that can generate novel genotypes for restoring challenging environments. We identify barriers to adopting these tools in a restoration context and emphasize that regulatory and ethical frameworks are required to guide their use.
Collapse
Affiliation(s)
- Martin F Breed
- School of Biological Sciences and the Environment Institute, University of Adelaide, North Terrace, South Australia, Australia.
| | - Peter A Harrison
- School of Natural Sciences, Australian Research Council Training Centre for Forest Value, University of Tasmania, Hobart, Tasmania, Australia
| | - Colette Blyth
- School of Biological Sciences and the Environment Institute, University of Adelaide, North Terrace, South Australia, Australia
| | - Margaret Byrne
- Biodiversity and Conservation Science, Department of Biodiversity, Conservation and Attractions, Western Australia, Australia
| | - Virginie Gaget
- School of Biological Sciences and the Environment Institute, University of Adelaide, North Terrace, South Australia, Australia
| | - Nicholas J C Gellie
- School of Biological Sciences and the Environment Institute, University of Adelaide, North Terrace, South Australia, Australia
| | - Scott V C Groom
- School of Agriculture, Food and Wine, The University of Adelaide, Waite Campus, Urrbrae, South Australia, Australia
| | - Riley Hodgson
- School of Biological Sciences and the Environment Institute, University of Adelaide, North Terrace, South Australia, Australia
| | - Jacob G Mills
- School of Biological Sciences and the Environment Institute, University of Adelaide, North Terrace, South Australia, Australia
| | - Thomas A A Prowse
- School of Biological Sciences and the Environment Institute, University of Adelaide, North Terrace, South Australia, Australia.,School of Mathematical Sciences, University of Adelaide, North Terrace, South Australia, Australia
| | - Dorothy A Steane
- School of Natural Sciences, Australian Research Council Training Centre for Forest Value, University of Tasmania, Hobart, Tasmania, Australia
| | - Jakki J Mohr
- College of Business, Institute on Ecosystems, University of Montana, Missoula, MT, USA
| |
Collapse
|
11
|
Disentangling the evolutionary history of three related shrub species using genome-wide molecular markers. CONSERV GENET 2019. [DOI: 10.1007/s10592-019-01197-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
|
12
|
Digging for the spiny rat and hutia phylogeny using a gene capture approach, with the description of a new mammal subfamily. Mol Phylogenet Evol 2019; 136:241-253. [PMID: 30885830 DOI: 10.1016/j.ympev.2019.03.007] [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: 11/08/2018] [Revised: 03/13/2019] [Accepted: 03/14/2019] [Indexed: 02/07/2023]
Abstract
Next generation sequencing (NGS) and genomic database mining allow biologists to gather and select large molecular datasets well suited to address phylogenomics and molecular evolution questions. Here we applied this approach to a mammal family, the Echimyidae, for which generic relationships have been difficult to recover and often referred to as a star phylogeny. These South-American spiny rats represent a family of caviomorph rodents exhibiting a striking diversity of species and life history traits. Using a NGS exon capture protocol, we isolated and sequenced ca. 500 nuclear DNA exons for 35 species belonging to all major echimyid and capromyid clades. Exons were carefully selected to encompass as much diversity as possible in terms of rate of evolution, heterogeneity in the distribution of site-variation and nucleotide composition. Supermatrix inferences and coalescence-based approaches were subsequently applied to infer this family's phylogeny. The inferred topologies were the same for both approaches, and support was maximal for each node, entirely resolving the ambiguous relationships of previous analyses. Fast-evolving nuclear exons tended to yield more reliable phylogenies, as slower-evolving sequences were not informative enough to disentangle the short branches of the Echimyidae radiation. Based on this resolved phylogeny and on molecular and morphological evidence, we confirm the rank of the Caribbean hutias - formerly placed in the Capromyidae family - as Capromyinae, a clade nested within Echimyidae. We also name and define Carterodontinae, a new subfamily of Echimyidae, comprising the extant monotypic genus Carterodon from Brazil, which is the closest living relative of West Indies Capromyinae.
Collapse
|
13
|
Friis G, Fandos G, Zellmer AJ, McCormack JE, Faircloth BC, Milá B. Genome-wide signals of drift and local adaptation during rapid lineage divergence in a songbird. Mol Ecol 2018; 27:5137-5153. [PMID: 30451354 DOI: 10.1111/mec.14946] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Revised: 09/26/2018] [Accepted: 10/15/2018] [Indexed: 12/25/2022]
Abstract
The formation of independent evolutionary lineages involves neutral and selective factors, and understanding their relative roles in population divergence is a fundamental goal of speciation research. Correlations between allele frequencies and environmental variability can reveal the role of selection, yet the relative contribution of drift can be difficult to establish. Recently diversified taxa like the Oregon junco (Aves, Passerellidae, Junco hyemalis oreganus) of western North America provide ideal scenarios to apply genetic-environment association analyses (GEA) while controlling for population structure. Analysis of genome-wide SNP loci revealed marked genetic structure consisting of differentiated populations in isolated, dry southern mountain ranges, and less divergent, recently expanded populations in humid northern latitudes. We used correlations between genomic and environmental variance to test for three specific modes of evolutionary divergence: (a) drift in geographic isolation, (b) differentiation along continuous selective gradients and (c) isolation-by-adaptation. We found evidence of strong drift in southern mountains, but also signals of local adaptation driven by temperature, precipitation, elevation and vegetation, especially when controlling for population history. We identified numerous variants under selection scattered across the genome, suggesting that local adaptation can promote rapid differentiation when acting over multiple independent loci.
Collapse
Affiliation(s)
- Guillermo Friis
- National Museum of Natural Sciences, Spanish National Research Council (CSIC), Madrid, Spain
| | - Guillermo Fandos
- Department of Biodiversity, Ecology and Evolution, Complutense University of Madrid, Madrid, Spain
| | - Amanda J Zellmer
- Department of Biology, Occidental College, Los Angeles, California
| | - John E McCormack
- Department of Biology, Occidental College, Los Angeles, California.,Moore Laboratory of Zoology and Department of Biology, Occidental College, Los Angeles, California
| | - Brant C Faircloth
- Department of Biological Sciences and Museum of Natural Science, Louisiana State University, Baton Rouge, Louisiana
| | - Borja Milá
- National Museum of Natural Sciences, Spanish National Research Council (CSIC), Madrid, Spain
| |
Collapse
|
14
|
Breed MF, Harrison PA, Bischoff A, Durruty P, Gellie NJC, Gonzales EK, Havens K, Karmann M, Kilkenny FF, Krauss SL, Lowe AJ, Marques P, Nevill PG, Vitt PL, Bucharova A. Priority Actions to Improve Provenance Decision-Making. Bioscience 2018. [DOI: 10.1093/biosci/biy050] [Citation(s) in RCA: 67] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Affiliation(s)
- Martin F Breed
- All the authors have an interest in the science and practice of seed sourcing and provenance decision-making for restoration
- School of Biological Sciences and the Environment Institute at the University of Adelaide, in Australia
| | - Peter A Harrison
- All the authors have an interest in the science and practice of seed sourcing and provenance decision-making for restoration
- School of Natural Sciences and the ARC Centre for Forest Values at the University of Tasmania, in Australia
| | - Armin Bischoff
- All the authors have an interest in the science and practice of seed sourcing and provenance decision-making for restoration
- University of Avignon, in France
| | - Paula Durruty
- All the authors have an interest in the science and practice of seed sourcing and provenance decision-making for restoration
- Instituto Forestal Nacional (INFONA), in San Lorenzo, Paraguay
| | - Nick J C Gellie
- All the authors have an interest in the science and practice of seed sourcing and provenance decision-making for restoration
- School of Biological Sciences and the Environment Institute at the University of Adelaide, in Australia
| | - Emily K Gonzales
- All the authors have an interest in the science and practice of seed sourcing and provenance decision-making for restoration
- Ecological Restoration Division at Parks Canada, in Vancouver, British Columbia
| | - Kayri Havens
- All the authors have an interest in the science and practice of seed sourcing and provenance decision-making for restoration
- School of Natural Sciences and the ARC Centre for Forest Values at the University of Tasmania, in Australia
| | - Marion Karmann
- All the authors have an interest in the science and practice of seed sourcing and provenance decision-making for restoration
- Forest Stewardship Council, in Bonn, Germany
| | - Francis F Kilkenny
- All the authors have an interest in the science and practice of seed sourcing and provenance decision-making for restoration
- US Department of Agriculture, Forest Service, Rocky Mountain Research Station, in Boise, Idaho
| | - Siegfried L Krauss
- All the authors have an interest in the science and practice of seed sourcing and provenance decision-making for restoration
- Kings Park and Botanic Garden, in West Perth, Western Australia
| | - Andrew J Lowe
- All the authors have an interest in the science and practice of seed sourcing and provenance decision-making for restoration
- School of Biological Sciences and the Environment Institute at the University of Adelaide, in Australia
| | - Pedro Marques
- All the authors have an interest in the science and practice of seed sourcing and provenance decision-making for restoration
- Big Hole Watershed Committee, in Divide, Montana
| | - Paul G Nevill
- All the authors have an interest in the science and practice of seed sourcing and provenance decision-making for restoration
- Department of Environment and Agriculture at Curtin University, in Australia
| | - Pati L Vitt
- All the authors have an interest in the science and practice of seed sourcing and provenance decision-making for restoration
- Chicago Botanic Garden, in Glencoe, Illinois
| | - Anna Bucharova
- All the authors have an interest in the science and practice of seed sourcing and provenance decision-making for restoration
- Department of Plant Evolutionary Ecology at Karl Eberhard University and with the Department of Landscape Ecology and Nature Conservation at Albert Ludwigs University, in Freiburg, Germany
| |
Collapse
|
15
|
Baruch Z, Jones AR, Hill KE, McInerney FA, Blyth C, Caddy-Retalic S, Christmas MJ, Gellie NJC, Lowe AJ, Martin-Fores I, Nielson KE, Breed MF. Functional acclimation across microgeographic scales in Dodonaea viscosa. AOB PLANTS 2018; 10:ply029. [PMID: 29942458 PMCID: PMC6007226 DOI: 10.1093/aobpla/ply029] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Accepted: 05/09/2018] [Indexed: 05/11/2023]
Abstract
Intraspecific plant functional trait variation provides mechanistic insight into persistence and can infer population adaptive capacity. However, most studies explore intraspecific trait variation in systems where geographic and environmental distances co-vary. Such a design reduces the certainty of trait-environment associations, and it is imperative for studies that make trait-environment associations be conducted in systems where environmental distance varies independently of geographic distance. Here we explored trait variation in such a system, and aimed to: (i) quantify trait variation of parent and offspring generations, and associate this variation to parental environments; (ii) determine the traits which best explain population differences; (iii) compare parent and offspring trait-trait relationships. We characterized 15 plant functional traits in eight populations of a shrub with a maximum separation ca. 100 km. Populations differed markedly in aridity and elevation, and environmental distance varied independently of geographic distance. We measured traits in parent populations collected in the field, as well as their offspring reared in greenhouse conditions. Parent traits regularly associated with their environment. These associations were largely lost in the offspring generation, indicating considerable phenotypic plasticity. An ordination of parent traits showed clear structure with strong influence of leaf area, specific leaf area, stomatal traits, isotope δ13C and δ15N ratios, and Narea, whereas the offspring ordination was less structured. Parent trait-trait correlations were in line with expectations from the leaf economic spectrum. We show considerable trait plasticity in the woody shrub over microgeographic scales (<100 km), indicating it has the adaptive potential within a generation to functionally acclimate to a range of abiotic conditions. Since our study shrub is commonly used for restoration in southern Australia and local populations do not show strong genetic differentiation in functional traits, the potential risks of transferring seed across the broad environmental conditions are not likely to be a significant issue.
Collapse
Affiliation(s)
- Zdravko Baruch
- School of Biological Sciences and the Environment Institute, University of Adelaide, North Terrace, Adelaide, SA, Australia
| | - Alice R Jones
- School of Biological Sciences and the Environment Institute, University of Adelaide, North Terrace, Adelaide, SA, Australia
| | - Kathryn E Hill
- School of Biological Sciences and the Environment Institute, University of Adelaide, North Terrace, Adelaide, SA, Australia
| | - Francesca A McInerney
- Sprigg Geobiology Centre and School of Physical Sciences, University of Adelaide, Adelaide, SA, Australia
| | - Colette Blyth
- School of Biological Sciences and the Environment Institute, University of Adelaide, North Terrace, Adelaide, SA, Australia
| | - Stefan Caddy-Retalic
- School of Biological Sciences and the Environment Institute, University of Adelaide, North Terrace, Adelaide, SA, Australia
- Sprigg Geobiology Centre and School of Physical Sciences, University of Adelaide, Adelaide, SA, Australia
| | - Matthew J Christmas
- School of Biological Sciences and the Environment Institute, University of Adelaide, North Terrace, Adelaide, SA, Australia
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Nicholas J C Gellie
- School of Biological Sciences and the Environment Institute, University of Adelaide, North Terrace, Adelaide, SA, Australia
| | - Andrew J Lowe
- School of Biological Sciences and the Environment Institute, University of Adelaide, North Terrace, Adelaide, SA, Australia
| | - Irene Martin-Fores
- School of Biological Sciences and the Environment Institute, University of Adelaide, North Terrace, Adelaide, SA, Australia
- National Museum of Natural Sciences, Spanish National Research Council, Madrid, Spain
| | - Kristine E Nielson
- Sprigg Geobiology Centre and School of Physical Sciences, University of Adelaide, Adelaide, SA, Australia
| | - Martin F Breed
- School of Biological Sciences and the Environment Institute, University of Adelaide, North Terrace, Adelaide, SA, Australia
- Corresponding author’s e-mail address:
| |
Collapse
|
16
|
Harrisson KA, Amish SJ, Pavlova A, Narum SR, Telonis‐Scott M, Rourke ML, Lyon J, Tonkin Z, Gilligan DM, Ingram BA, Lintermans M, Gan HM, Austin CM, Luikart G, Sunnucks P. Signatures of polygenic adaptation associated with climate across the range of a threatened fish species with high genetic connectivity. Mol Ecol 2017; 26:6253-6269. [DOI: 10.1111/mec.14368] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2017] [Revised: 09/22/2017] [Accepted: 09/25/2017] [Indexed: 12/25/2022]
Affiliation(s)
- Katherine A. Harrisson
- School of Biological Sciences Monash University Clayton Vic. Australia
- Department of Ecology Environment and Evolution School of Life Sciences La Trobe University Bundoora Vic. Australia
- Arthur Rylah Institute for Environmental Research Heidelberg Vic. Australia
| | - Stephen J. Amish
- Conservation Genomics Group Division of Biological Sciences University of Montana Missoula MT USA
- Flathead Lake Biological Station University of Montana Polson MT USA
| | - Alexandra Pavlova
- School of Biological Sciences Monash University Clayton Vic. Australia
| | - Shawn R. Narum
- Columbia River Inter‐Tribal Fish Commission Hagerman Fish Culture Experiment Station Hagerman IDUSA
| | | | - Meaghan L. Rourke
- Department of Primary Industries DPI Fisheries Narrandera NSW Australia
| | - Jarod Lyon
- Arthur Rylah Institute for Environmental Research Heidelberg Vic. Australia
| | - Zeb Tonkin
- Arthur Rylah Institute for Environmental Research Heidelberg Vic. Australia
| | - Dean M. Gilligan
- Department of Primary Industries DPI Fisheries, Batemans Bay Fisheries Office Batemans Bay NSW Australia
| | | | - Mark Lintermans
- Institute for Applied Ecology University of Canberra Canberra ACT Australia
| | - Han Ming Gan
- Centre for Integrative Ecology School of Life and Environmental Sciences Deakin University Geelong Vic. Australia
- School of Science Monash University Malaysia Petaling Jaya Selangor Malaysia
- Genomics Facility, Tropical Medicine and Biology Platform Monash University Malaysia Petaling Jaya Selangor Malaysia
| | - Christopher M. Austin
- Centre for Integrative Ecology School of Life and Environmental Sciences Deakin University Geelong Vic. Australia
- School of Science Monash University Malaysia Petaling Jaya Selangor Malaysia
- Genomics Facility, Tropical Medicine and Biology Platform Monash University Malaysia Petaling Jaya Selangor Malaysia
| | - Gordon Luikart
- Conservation Genomics Group Division of Biological Sciences University of Montana Missoula MT USA
- Flathead Lake Biological Station University of Montana Polson MT USA
| | - Paul Sunnucks
- School of Biological Sciences Monash University Clayton Vic. Australia
| |
Collapse
|
17
|
Jordan R, Hoffmann AA, Dillon SK, Prober SM. Evidence of genomic adaptation to climate in
Eucalyptus microcarpa
: Implications for adaptive potential to projected climate change. Mol Ecol 2017; 26:6002-6020. [DOI: 10.1111/mec.14341] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2017] [Revised: 08/07/2017] [Accepted: 08/14/2017] [Indexed: 12/30/2022]
Affiliation(s)
- Rebecca Jordan
- Bio21 Institute School of BioSciences University of Melbourne Parkville Vic Australia
| | - Ary A. Hoffmann
- Bio21 Institute School of BioSciences University of Melbourne Parkville Vic Australia
| | | | | |
Collapse
|
18
|
Caddy-Retalic S, Andersen AN, Aspinwall MJ, Breed MF, Byrne M, Christmas MJ, Dong N, Evans BJ, Fordham DA, Guerin GR, Hoffmann AA, Hughes AC, van Leeuwen SJ, McInerney FA, Prober SM, Rossetto M, Rymer PD, Steane DA, Wardle GM, Lowe AJ. Bioclimatic transect networks: Powerful observatories of ecological change. Ecol Evol 2017; 7:4607-4619. [PMID: 28690791 PMCID: PMC5496522 DOI: 10.1002/ece3.2995] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2016] [Accepted: 03/21/2017] [Indexed: 01/02/2023] Open
Abstract
Transects that traverse substantial climate gradients are important tools for climate change research and allow questions on the extent to which phenotypic variation associates with climate, the link between climate and species distributions, and variation in sensitivity to climate change among biomes to be addressed. However, the potential limitations of individual transect studies have recently been highlighted. Here, we argue that replicating and networking transects, along with the introduction of experimental treatments, addresses these concerns. Transect networks provide cost‐effective and robust insights into ecological and evolutionary adaptation and improve forecasting of ecosystem change. We draw on the experience and research facilitated by the Australian Transect Network to demonstrate our case, with examples, to clarify how population‐ and community‐level studies can be integrated with observations from multiple transects, manipulative experiments, genomics, and ecological modeling to gain novel insights into how species and systems respond to climate change. This integration can provide a spatiotemporal understanding of past and future climate‐induced changes, which will inform effective management actions for promoting biodiversity resilience.
Collapse
Affiliation(s)
- Stefan Caddy-Retalic
- Australian Transect Network Terrestrial Ecosystem Research Network (TERN) Adelaide SA Australia.,School of Biological Sciences and Environment InstituteUniversity of Adelaide Adelaide SA Australia
| | - Alan N Andersen
- Australian Transect Network Terrestrial Ecosystem Research Network (TERN) Adelaide SA Australia.,Charles Darwin University Darwin NT Australia
| | - Michael J Aspinwall
- Australian Transect Network Terrestrial Ecosystem Research Network (TERN) Adelaide SA Australia.,Hawkesbury Institute for the Environment Western Sydney University Parramatta NSW Australia
| | - Martin F Breed
- Australian Transect Network Terrestrial Ecosystem Research Network (TERN) Adelaide SA Australia.,School of Biological Sciences and Environment InstituteUniversity of Adelaide Adelaide SA Australia
| | - Margaret Byrne
- Australian Transect Network Terrestrial Ecosystem Research Network (TERN) Adelaide SA Australia.,Science and Conservation Division Western Australian Department of Parks and Wildlife Kensington WA Australia
| | - Matthew J Christmas
- Australian Transect Network Terrestrial Ecosystem Research Network (TERN) Adelaide SA Australia.,School of Biological Sciences and Environment InstituteUniversity of Adelaide Adelaide SA Australia
| | - Ning Dong
- Department of Biological Sciences Macquarie University North Ryde NSW Australia.,Ecosystem Modelling and Scaling Infrastructure Terrestrial Ecosystem Research Network (TERN) Adelaide SA Australia
| | - Bradley J Evans
- Ecosystem Modelling and Scaling Infrastructure Terrestrial Ecosystem Research Network (TERN) Adelaide SA Australia.,School Life and Environmental Sciences University of Sydney Sydney NSW Australia
| | - Damien A Fordham
- Australian Transect Network Terrestrial Ecosystem Research Network (TERN) Adelaide SA Australia.,School of Biological Sciences and Environment InstituteUniversity of Adelaide Adelaide SA Australia
| | - Greg R Guerin
- Australian Transect Network Terrestrial Ecosystem Research Network (TERN) Adelaide SA Australia.,School of Biological Sciences and Environment InstituteUniversity of Adelaide Adelaide SA Australia
| | - Ary A Hoffmann
- Australian Transect Network Terrestrial Ecosystem Research Network (TERN) Adelaide SA Australia.,School of BioSciences, Bio 21 InstituteThe University of Melbourne Parkville VIC Australia
| | - Alice C Hughes
- Centre for Integrative Conservation Xishuangbanna Tropical Botanic Garden Chinese Academy of Sciences Menglun, Mengla County Yunnan China
| | - Stephen J van Leeuwen
- Australian Transect Network Terrestrial Ecosystem Research Network (TERN) Adelaide SA Australia.,Science and Conservation Division Western Australian Department of Parks and Wildlife Kensington WA Australia
| | - Francesca A McInerney
- Sprigg Geobiology Centre and School of Physical Sciences University of Adelaide Adelaide SA Australia
| | - Suzanne M Prober
- Australian Transect Network Terrestrial Ecosystem Research Network (TERN) Adelaide SA Australia.,CSIRO Land and Water Wembley WA Australia
| | - Maurizio Rossetto
- Australian Transect Network Terrestrial Ecosystem Research Network (TERN) Adelaide SA Australia.,National Herbarium of NSW Royal Botanic Gardens and Domain Trust Sydney NSW Australia
| | - Paul D Rymer
- Australian Transect Network Terrestrial Ecosystem Research Network (TERN) Adelaide SA Australia.,Hawkesbury Institute for the Environment Western Sydney University Parramatta NSW Australia
| | - Dorothy A Steane
- Australian Transect Network Terrestrial Ecosystem Research Network (TERN) Adelaide SA Australia.,CSIRO Land and Water Wembley WA Australia.,School of Biological Sciences University of Tasmania Private Bag 55 Hobart Tasmania 7001 Australia.,Faculty of Science, Health, Education and Engineering University of the Sunshine Coast Maroochydore QLD Australia
| | - Glenda M Wardle
- School Life and Environmental Sciences University of Sydney Sydney NSW Australia.,Long Term Ecological Research Network Terrestrial Ecosystem Research Network (TERN) Adelaide SA Australia
| | - Andrew J Lowe
- Australian Transect Network Terrestrial Ecosystem Research Network (TERN) Adelaide SA Australia.,School of Biological Sciences and Environment InstituteUniversity of Adelaide Adelaide SA Australia
| |
Collapse
|
19
|
Christmas MJ, Biffin E, Breed MF, Lowe AJ. Targeted capture to assess neutral genomic variation in the narrow-leaf hopbush across a continental biodiversity refugium. Sci Rep 2017; 7:41367. [PMID: 28145488 PMCID: PMC5286450 DOI: 10.1038/srep41367] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2016] [Accepted: 12/20/2016] [Indexed: 11/09/2022] Open
Abstract
The Adelaide geosyncline, a mountainous region in central southern Australia, is purported to be an important continental refugium for Mediterranean and semi-arid Australian biota, yet few population genetic studies have been conducted to test this theory. Here, we focus on a plant species distributed widely throughout the region, the narrow-leaf hopbush, Dodonaea viscosa ssp. angustissima, and examine its genetic diversity and population structure. We used a hybrid-capture target enrichment technique to selectively sequence over 700 genes from 89 individuals across 17 sampling locations. We compared 815 single nucleotide polymorphisms among individuals and populations to investigate population genetic structure. Three distinct genetic clusters were identified; a Flinders/Gammon ranges cluster, an Eastern cluster, and a Kangaroo Island cluster. Higher genetic diversity was identified in the Flinders/Gammon Ranges cluster, indicating that this area is likely to have acted as a refugium during past climate oscillations. We discuss these findings and consider the historical range dynamics of these populations. We also provide methodological considerations for population genomics studies that aim to use novel genomic approaches (such as target capture methods) on non-model systems. The application of our findings to restoration of this species across the region are also considered.
Collapse
Affiliation(s)
- Matthew J. Christmas
- Environment Institute and School of Biological Sciences, The University of Adelaide, North Terrace, SA 5005, Australia
| | - Ed Biffin
- State Herbarium of South Australia, Hackney Road, Adelaide, SA 5000, Australia
| | - Martin F. Breed
- Environment Institute and School of Biological Sciences, The University of Adelaide, North Terrace, SA 5005, Australia
| | - Andrew J. Lowe
- Environment Institute and School of Biological Sciences, The University of Adelaide, North Terrace, SA 5005, Australia
| |
Collapse
|
20
|
Baruch Z, Christmas MJ, Breed MF, Guerin GR, Caddy‐Retalic S, McDonald J, Jardine DI, Leitch E, Gellie N, Hill K, McCallum K, Lowe AJ. Leaf trait associations with environmental variation in the wide‐ranging shrub
Dodonaea viscosa
subsp.
angustissima
(Sapindaceae). AUSTRAL ECOL 2016. [DOI: 10.1111/aec.12474] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- Zdravko Baruch
- School of Biological Sciences University of Adelaide North Terrace Adelaide South Australia 5005 Australia
| | - Matthew J. Christmas
- School of Biological Sciences University of Adelaide North Terrace Adelaide South Australia 5005 Australia
| | - Martin F. Breed
- School of Biological Sciences University of Adelaide North Terrace Adelaide South Australia 5005 Australia
| | - Greg R. Guerin
- School of Biological Sciences University of Adelaide North Terrace Adelaide South Australia 5005 Australia
| | - Stefan Caddy‐Retalic
- School of Biological Sciences University of Adelaide North Terrace Adelaide South Australia 5005 Australia
| | - John McDonald
- School of Biological Sciences University of Adelaide North Terrace Adelaide South Australia 5005 Australia
| | - Duncan I. Jardine
- School of Biological Sciences University of Adelaide North Terrace Adelaide South Australia 5005 Australia
| | - Emrys Leitch
- School of Biological Sciences University of Adelaide North Terrace Adelaide South Australia 5005 Australia
| | - Nick Gellie
- School of Biological Sciences University of Adelaide North Terrace Adelaide South Australia 5005 Australia
| | - Kathryn Hill
- School of Biological Sciences University of Adelaide North Terrace Adelaide South Australia 5005 Australia
| | - Kimberly McCallum
- School of Biological Sciences University of Adelaide North Terrace Adelaide South Australia 5005 Australia
| | - Andrew J. Lowe
- School of Biological Sciences University of Adelaide North Terrace Adelaide South Australia 5005 Australia
| |
Collapse
|