1
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Rutherford S, Rossetto M, Bragg JG, Wan JSH. Where to draw the boundaries? Using landscape genomics to disentangle the scribbly gum species complex. Am J Bot 2023; 110:e16245. [PMID: 37747108 DOI: 10.1002/ajb2.16245] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Revised: 09/18/2023] [Accepted: 09/18/2023] [Indexed: 09/26/2023]
Abstract
PREMISE Species delimitation is an integral part of evolution and ecology and is vital in conservation science. However, in some groups, species delimitation is difficult, especially where ancestral relationships inferred from morphological or genetic characters are discordant, possibly due to a complicated demographic history (e.g., recent divergences between lineages). Modern genetic techniques can take into account complex histories to distinguish species at a reasonable cost and are increasingly used in numerous applications. We focus on the scribbly gums, a group of up to five closely related and morphologically similar "species" within the eucalypts. METHODS Multiple populations of each recognized scribbly gum species were sampled over a wide region across climates, and genomewide scans were used to resolve species boundaries. RESULTS None of the taxa were completely divergent, and there were two genetically distinct entities: the inland distributed Eucalyptus rossii and a coastal conglomerate consisting of four species forming three discernible, but highly admixed groups. Divergence among taxa was likely driven by temporal vicariant processes resulting in partial separation across biogeographic barriers. High interspecific gene flow indicated separated taxa reconnected at different points in time, blurring species boundaries. CONCLUSIONS Our results highlight the need for genetic screening when dealing with closely related taxonomic entities, particularly those with modest morphological differences. We show that high-throughput sequencing can be effective at identifying species groupings and processes driving divergence, even in the most taxonomically complex groups, and be used as a standard practice for disentangling species complexes.
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Affiliation(s)
- Susan Rutherford
- Department of Environmental Science, College of Science, Mathematics and Technology, Wenzhou-Kean University, Wenzhou, Zhejiang Province, China
- Department of Environmental and Sustainability Sciences, The Dorothy and George Hennings College of Science, Mathematics and Technology, Kean University, Union, NJ, USA
- School of Environment and Safety Engineering, Jiangsu University, Zhenjiang, Jiangsu Province, China
- Research Centre for Ecosystem Resilience, Australian Institute of Botanic Science, Royal Botanic Garden Sydney, Mrs Macquaries Road, Sydney, New South Wales, Australia
- Zhejiang Bioinformatics International Science and Technology Cooperation Center, Wenzhou, Zhejiang Province, China
| | - Maurizio Rossetto
- Research Centre for Ecosystem Resilience, Australian Institute of Botanic Science, Royal Botanic Garden Sydney, Mrs Macquaries Road, Sydney, New South Wales, Australia
| | - Jason G Bragg
- Research Centre for Ecosystem Resilience, Australian Institute of Botanic Science, Royal Botanic Garden Sydney, Mrs Macquaries Road, Sydney, New South Wales, Australia
| | - Justin S H Wan
- School of Environment and Safety Engineering, Jiangsu University, Zhenjiang, Jiangsu Province, China
- Research Centre for Ecosystem Resilience, Australian Institute of Botanic Science, Royal Botanic Garden Sydney, Mrs Macquaries Road, Sydney, New South Wales, Australia
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2
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Ens EJ, Rossetto M, Costello O. Recognising Indigenous plant-use histories for inclusive biocultural restoration. Trends Ecol Evol 2023; 38:896-898. [PMID: 37573174 DOI: 10.1016/j.tree.2023.06.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 06/28/2023] [Accepted: 06/30/2023] [Indexed: 08/14/2023]
Abstract
Indigenous Peoples have manipulated environments and species for millennia. However, restoration science often overlooks ancient human plant dispersal, niche construction, and selection pressures that may have resulted in plant 'cultural traits'. Concerted efforts to acknowledge Indigenous plant-use histories in restoration could help to abate the coextinction of species and cultures.
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Affiliation(s)
- Emilie J Ens
- School of Natural Sciences, University Road, Macquarie University, NSW 2109, Australia.
| | - Maurizio Rossetto
- The Royal Botanic Garden Sydney, Mrs Macquarie's Road, Sydney, NSW 2000, Australia
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3
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Tridello A, Boursier Niutta C, Rossetto M, Berto F, Paolino DS. Experimental scatter of the fatigue response of additively manufactured components: a statistical method based on the Profile Likelihood. Sci Rep 2023; 13:15335. [PMID: 37714874 PMCID: PMC10504310 DOI: 10.1038/s41598-023-40249-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Accepted: 08/07/2023] [Indexed: 09/17/2023] Open
Abstract
The fatigue response of additively manufactured (AM) specimens is mainly driven by manufacturing defects, like pores and lack of fusion defects, which are mainly responsible for the large variability of fatigue data in the S-N plot. The analysis of the results of AM tests can be therefore complex: for example, the influence of a specific factor, e.g. the building direction, can be concealed by the experimental variability. Accordingly, appropriate statistical methodologies should be employed to safely and properly analyze the results of fatigue tests on AM specimens. In the present paper, a statistical methodology for the analysis of the AM fatigue test results is proposed. The approach is based on shifting the experimental failures to a reference number of cycles starting from the estimated P-S-N curves. The experimental variability of the fatigue strength at the reference number of cycles is also considered by estimating the profile likelihood function. This methodology has been validated with literature datasets and has proven its effectiveness in dealing with the experimental scatter typical of AM fatigue test results.
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Affiliation(s)
- A Tridello
- Department of Mechanical and Aerospace Engineering, Politecnico di Torino, C.so Duca degli Abruzzi 24, 10129, Turin, Italy.
| | - C Boursier Niutta
- Department of Mechanical and Aerospace Engineering, Politecnico di Torino, C.so Duca degli Abruzzi 24, 10129, Turin, Italy
| | - M Rossetto
- Department of Mechanical and Aerospace Engineering, Politecnico di Torino, C.so Duca degli Abruzzi 24, 10129, Turin, Italy
| | - F Berto
- Department of Chemical Engineering, Materials and Environment, Università La Sapienza, 00185, Rome, Italy
| | - D S Paolino
- Department of Mechanical and Aerospace Engineering, Politecnico di Torino, C.so Duca degli Abruzzi 24, 10129, Turin, Italy
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4
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Stevenson DW, Ramakrishnan S, de Santis Alves C, Coelho LA, Kramer M, Goodwin S, Ramos OM, Eshel G, Sondervan VM, Frangos S, Zumajo-Cardona C, Jenike K, Ou S, Wang X, Lee YP, Loke S, Rossetto M, McPherson H, Nigris S, Moschin S, Little DP, Katari MS, Varala K, Kolokotronis SO, Ambrose B, Croft LJ, Coruzzi GM, Schatz M, McCombie WR, Martienssen RA. The genome of the Wollemi pine, a critically endangered "living fossil" unchanged since the Cretaceous, reveals extensive ancient transposon activity. bioRxiv 2023:2023.08.24.554647. [PMID: 37662366 PMCID: PMC10473749 DOI: 10.1101/2023.08.24.554647] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/05/2023]
Abstract
We present the genome of the living fossil, Wollemia nobilis, a southern hemisphere conifer morphologically unchanged since the Cretaceous. Presumed extinct until rediscovery in 1994, the Wollemi pine is critically endangered with less than 60 wild adults threatened by intensifying bushfires in the Blue Mountains of Australia. The 12 Gb genome is among the most contiguous large plant genomes assembled, with extremely low heterozygosity and unusual abundance of DNA transposons. Reduced representation and genome re-sequencing of individuals confirms a relictual population since the last major glacial/drying period in Australia, 120 ky BP. Small RNA and methylome sequencing reveal conservation of ancient silencing mechanisms despite the presence of thousands of active and abundant transposons, including some transferred horizontally to conifers from arthropods in the Jurassic. A retrotransposon burst 8-6 my BP coincided with population decline, possibly as an adaptation enhancing epigenetic diversity. Wollemia, like other conifers, is susceptible to Phytophthora, and a suite of defense genes, similar to those in loblolly pine, are targeted for silencing by sRNAs in leaves. The genome provides insight into the earliest seed plants, while enabling conservation efforts.
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Affiliation(s)
| | | | - Cristiane de Santis Alves
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA
- Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Laís Araujo Coelho
- Department of Epidemiology and Biostatistics, School of Public Health; Institute for Genomics in Health; Division of Infectious Diseases, Department of Medicine, and Department of Cell Biology, College of Medicine, SUNY Downstate Health Sciences University, Brooklyn, NY 11203-2098, USA
| | - Melissa Kramer
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA
| | - Sara Goodwin
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA
| | | | - Gil Eshel
- Center for Genomics & Systems Biology, New York University, New York, NY 10003, USA
| | | | - Samantha Frangos
- Center for Genomics & Systems Biology, New York University, New York, NY 10003, USA
| | | | - Katherine Jenike
- Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA
| | - Shujun Ou
- Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA
- Department of Molecular Genetics, The Ohio State University, Columbus, OH 43210, USA
| | - Xiaojin Wang
- Purdue University, 610 Purdue Mall, West Lafayette, IN 47907, USA
| | - Yin Peng Lee
- Charles River Laboratories Australia, 17-19 Hi-Tech Ct, Kilsyth VIC 3137, Australia
| | - Stella Loke
- Charles River Laboratories Australia, 17-19 Hi-Tech Ct, Kilsyth VIC 3137, Australia
| | - Maurizio Rossetto
- Research Centre for Ecosystem Resilience, Royal Botanic Garden Sydney, Sydney, NSW 2000, Australia
| | - Hannah McPherson
- National Herbarium of New South Wales, Australian Botanic Garden, Mount Annan, NSW 2567, Australia
| | - Sebastiano Nigris
- Dipartimento di Biologia, Università degli studi di Padova, via U. Bassi 58/B, 35131 Padova, Italy; and Botanical Garden, Università degli studi di Padova, via Orto Botanico 15, 35123 Padova, Italy
| | - Silvia Moschin
- Dipartimento di Biologia, Università degli studi di Padova, via U. Bassi 58/B, 35131 Padova, Italy; and Botanical Garden, Università degli studi di Padova, via Orto Botanico 15, 35123 Padova, Italy
| | - Damon P. Little
- The New York Botanical Garden, 2900 Southern Boulevard, Bronx, NY 10458, USA
| | - Manpreet S. Katari
- Center for Genomics & Systems Biology, New York University, New York, NY 10003, USA
| | - Kranthi Varala
- Purdue University, 610 Purdue Mall, West Lafayette, IN 47907, USA
| | - Sergios-Orestis Kolokotronis
- Department of Epidemiology and Biostatistics, School of Public Health; Institute for Genomics in Health; Division of Infectious Diseases, Department of Medicine, and Department of Cell Biology, College of Medicine, SUNY Downstate Health Sciences University, Brooklyn, NY 11203-2098, USA
| | - Barbara Ambrose
- The New York Botanical Garden, 2900 Southern Boulevard, Bronx, NY 10458, USA
| | - Larry J. Croft
- School of Medicine, Deakin University, Waurn Ponds, Victoria 3216, Australia
| | - Gloria M. Coruzzi
- Center for Genomics & Systems Biology, New York University, New York, NY 10003, USA
| | - Michael Schatz
- Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA
| | | | - Robert A. Martienssen
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA
- Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
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Doyle CAT, Yap JS, Bragg J, Rossetto M, Orme A, Ooi MJK. Reproductive characteristics, population genetics, and pairwise kinship inform strategic recovery of a plant species in a fragmented landscape. Conservat Sci and Prac 2023. [DOI: 10.1111/csp2.12910] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/25/2023] Open
Affiliation(s)
- Chantelle A. T. Doyle
- Centre for Ecosystem Science, School of Biological Earth and Environmental Sciences University of New South Wales Sydney New South Wales Australia
| | - Jia‐Yee Samantha Yap
- Research Centre for Ecosystem Resilience, The Royal Botanic Garden Sydney Sydney New South Wales Australia
| | - Jason Bragg
- Research Centre for Ecosystem Resilience, The Royal Botanic Garden Sydney Sydney New South Wales Australia
| | - Maurizio Rossetto
- Research Centre for Ecosystem Resilience, The Royal Botanic Garden Sydney Sydney New South Wales Australia
| | - Andrew Orme
- National Herbarium of New South Wales, Australian Institute of Botanical Science Royal Botanic Garden Sydney New South Wales Australia
| | - Mark J. K. Ooi
- Centre for Ecosystem Science, School of Biological Earth and Environmental Sciences University of New South Wales Sydney New South Wales Australia
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Lu-Irving P, Bragg JG, Rossetto M, King K, O’Brien M, van der Merwe MM. Capturing Genetic Diversity in Seed Collections: An Empirical Study of Two Congeners with Contrasting Mating Systems. Plants (Basel) 2023; 12:522. [PMID: 36771606 PMCID: PMC9921034 DOI: 10.3390/plants12030522] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Revised: 01/10/2023] [Accepted: 01/13/2023] [Indexed: 06/18/2023]
Abstract
Plant mating systems shape patterns of genetic diversity and impact the long-term success of populations. As such, they are relevant to the design of seed collections aiming to maximise genetic diversity (e.g., germplasm conservation, ecological restoration). However, for most species, little is known empirically about how variation in mating systems and genetic diversity is distributed. We investigated the relationship between genetic diversity and mating systems in two functionally similar, co-occurring species of Hakea (Proteaceae), and evaluated the extent to which genetic diversity was captured in seeds. We genotyped hundreds of seedlings and mother plants via DArTseq, and developed novel implementations of two approaches to inferring the mating system from SNP data. A striking contrast in patterns of genetic diversity between H. sericea and H. teretifolia was revealed, consistent with a contrast in their mating systems. While both species had mixed mating systems, H. sericea was found to be habitually selfing, while H. teretifolia more evenly employed both selfing and outcrossing. In both species, seed collection schemes maximised genetic diversity by increasing the number of maternal lines and sites sampled, but twice as many sites were needed for the selfing species to capture equivalent levels of genetic variation at a regional scale.
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Affiliation(s)
- Patricia Lu-Irving
- Research Centre for Ecosystem Resilience, Australian Institute of Botanical Science, Royal Botanic Gardens Sydney, Mrs Macquaries Rd., Sydney, NSW 2000, Australia
| | - Jason G. Bragg
- Research Centre for Ecosystem Resilience, Australian Institute of Botanical Science, Royal Botanic Gardens Sydney, Mrs Macquaries Rd., Sydney, NSW 2000, Australia
| | - Maurizio Rossetto
- Research Centre for Ecosystem Resilience, Australian Institute of Botanical Science, Royal Botanic Gardens Sydney, Mrs Macquaries Rd., Sydney, NSW 2000, Australia
| | - Kit King
- Research Centre for Ecosystem Resilience, Australian Institute of Botanical Science, Royal Botanic Gardens Sydney, Mrs Macquaries Rd., Sydney, NSW 2000, Australia
| | - Mitchell O’Brien
- Research Centre for Ecosystem Resilience, Australian Institute of Botanical Science, Royal Botanic Gardens Sydney, Mrs Macquaries Rd., Sydney, NSW 2000, Australia
- Commonwealth Scientific and Industrial Research Organisation (CSIRO), Innovation Quarter Westmead, Level 3, East Tower, 158-164 Hawkesbury Rd., Westmead, NSW 2145, Australia
| | - Marlien M. van der Merwe
- Research Centre for Ecosystem Resilience, Australian Institute of Botanical Science, Royal Botanic Gardens Sydney, Mrs Macquaries Rd., Sydney, NSW 2000, Australia
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7
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Wilson TC, Rossetto M, Bain D, Yap JS, Wilson PD, Stimpson ML, Weston PH, Croft L. A turn in species conservation for hairpin banksias: demonstration of oversplitting leads to better management of diversity. Am J Bot 2022; 109:1652-1671. [PMID: 36164832 PMCID: PMC9828017 DOI: 10.1002/ajb2.16074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Revised: 08/29/2022] [Accepted: 08/30/2022] [Indexed: 06/16/2023]
Abstract
PREMISE Understanding evolutionary history and classifying discrete units of organisms remain overwhelming tasks, and lags in this workload concomitantly impede an accurate documentation of biodiversity and conservation management. Rapid advances and improved accessibility of sensitive high-throughput sequencing tools are fortunately quickening the resolution of morphological complexes and thereby improving the estimation of species diversity. The recently described and critically endangered Banksia vincentia is morphologically similar to the hairpin banksia complex (B. spinulosa s.l.), a group of eastern Australian flowering shrubs whose continuum of morphological diversity has been responsible for taxonomic controversy and possibly questionable conservation initiatives. METHODS To assist conservation while testing the current taxonomy of this group, we used high-throughput sequencing to infer a population-scale evolutionary scenario for a sample set that is comprehensive in its representation of morphological diversity and a 2500-km distribution. RESULTS Banksia spinulosa s.l. represents two clades, each with an internal genetic structure shaped through historical separation by biogeographic barriers. This structure conflicts with the existing taxonomy for the group. Corroboration between phylogeny and population statistics aligns with the hypothesis that B. collina, B. neoanglica, and B. vincentia should not be classified as species. CONCLUSIONS The pattern here supports how morphological diversity can be indicative of a locally expressed suite of traits rather than relationship. Oversplitting in the hairpin banksias is atypical since genomic analyses often reveal that species diversity is underestimated. However, we show that erring on overestimation can yield negative consequences, such as the disproportionate prioritization of a geographically anomalous population.
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Affiliation(s)
- Trevor C. Wilson
- Plant Discovery and Evolution, Australian Institute of Botanical ScienceRoyal Botanic Gardens and Domain TrustSydneyAustralia
- Research Centre for Ecosystem Resilience, Australian Institute of Botanical ScienceThe Royal Botanic Garden SydneyAustralia
| | - Maurizio Rossetto
- Research Centre for Ecosystem Resilience, Australian Institute of Botanical ScienceThe Royal Botanic Garden SydneyAustralia
| | - David Bain
- Ecosystems and Threatened Species, Biodiversity Conservation and ScienceNSW Department of Planning and EnvironmentWollongongAustralia
| | - Jia‐Yee S. Yap
- Research Centre for Ecosystem Resilience, Australian Institute of Botanical ScienceThe Royal Botanic Garden SydneyAustralia
| | - Peter D. Wilson
- Research Centre for Ecosystem Resilience, Australian Institute of Botanical ScienceThe Royal Botanic Garden SydneyAustralia
| | - Margaret L. Stimpson
- Botany, School of Environmental and Rural ScienceUniversity of New EnglandArmidaleNSW2351Australia
| | - Peter H. Weston
- Plant Discovery and Evolution, Australian Institute of Botanical ScienceRoyal Botanic Gardens and Domain TrustSydneyAustralia
| | - Larry Croft
- Centre of Integrative Ecology, School of Life and Environmental SciencesDeakin UniversityGeelong3125VictoriaAustralia
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8
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Wilson TC, Rossetto M, Bain D, Yap JYS, Wilson PD, Stimpson ML, Weston PH, Croft L. A turn in species conservation for hairpin banksias: demonstration of oversplitting leads to better management of diversity. Am J Bot 2022. [PMID: 36164832 DOI: 10.5061/dryad.69p8cz94x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
PREMISE Understanding evolutionary history and classifying discrete units of organisms remain overwhelming tasks, and lags in this workload concomitantly impede an accurate documentation of biodiversity and conservation management. Rapid advances and improved accessibility of sensitive high-throughput sequencing tools are fortunately quickening the resolution of morphological complexes and thereby improving the estimation of species diversity. The recently described and critically endangered Banksia vincentia is morphologically similar to the hairpin banksia complex (B. spinulosa s.l.), a group of eastern Australian flowering shrubs whose continuum of morphological diversity has been responsible for taxonomic controversy and possibly questionable conservation initiatives. METHODS To assist conservation while testing the current taxonomy of this group, we used high-throughput sequencing to infer a population-scale evolutionary scenario for a sample set that is comprehensive in its representation of morphological diversity and a 2500-km distribution. RESULTS Banksia spinulosa s.l. represents two clades, each with an internal genetic structure shaped through historical separation by biogeographic barriers. This structure conflicts with the existing taxonomy for the group. Corroboration between phylogeny and population statistics aligns with the hypothesis that B. collina, B. neoanglica, and B. vincentia should not be classified as species. CONCLUSIONS The pattern here supports how morphological diversity can be indicative of a locally expressed suite of traits rather than relationship. Oversplitting in the hairpin banksias is atypical since genomic analyses often reveal that species diversity is underestimated. However, we show that erring on overestimation can yield negative consequences, such as the disproportionate prioritization of a geographically anomalous population.
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Affiliation(s)
- Trevor C Wilson
- Plant Discovery and Evolution, Australian Institute of Botanical Science, Royal Botanic Gardens and Domain Trust, Sydney, Australia
- Research Centre for Ecosystem Resilience, Australian Institute of Botanical Science, The Royal Botanic Garden Sydney, Australia
| | - Maurizio Rossetto
- Research Centre for Ecosystem Resilience, Australian Institute of Botanical Science, The Royal Botanic Garden Sydney, Australia
| | - David Bain
- Ecosystems and Threatened Species, Biodiversity Conservation and Science, NSW Department of Planning and Environment, Wollongong, Australia
| | - Jia-Yee S Yap
- Research Centre for Ecosystem Resilience, Australian Institute of Botanical Science, The Royal Botanic Garden Sydney, Australia
| | - Peter D Wilson
- Research Centre for Ecosystem Resilience, Australian Institute of Botanical Science, The Royal Botanic Garden Sydney, Australia
| | - Margaret L Stimpson
- Botany, School of Environmental and Rural Science, University of New England, Armidale, NSW, 2351, Australia
| | - Peter H Weston
- Plant Discovery and Evolution, Australian Institute of Botanical Science, Royal Botanic Gardens and Domain Trust, Sydney, Australia
| | - Larry Croft
- Centre of Integrative Ecology, School of Life and Environmental Sciences, Deakin University, Geelong, 3125, Victoria, Australia
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9
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Rutherford S, Wilson TC, Yap JYS, Lee E, Errington G, Rossetto M. Evolutionary processes in an undescribed eucalypt: implications for the translocation of a critically endangered species. Ann Bot 2022; 130:491-508. [PMID: 35802354 PMCID: PMC9510949 DOI: 10.1093/aob/mcac091] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Accepted: 07/07/2022] [Indexed: 06/15/2023]
Abstract
BACKGROUND AND AIMS Knowledge of the evolutionary processes responsible for the distribution of threatened and highly localized species is important for their conservation. Population genomics can provide insights into evolutionary processes to inform management practices, including the translocation of threatened plant species. In this study, we focus on a critically endangered eucalypt, Eucalyptus sp. Cattai, which is restricted to a 40-km2 area of Sydney, Australia, and is threatened by increased urbanization. Eucalyptus sp. Cattai has yet to be formally described in part due to its suspected hybrid origin. Here, we examined evolutionary processes and species boundaries in E. sp. Cattai to determine whether translocation was warranted. METHODS We used genome-wide scans to investigate the evolutionary relationships of E. sp. Cattai with related species, and to assess levels of genetic health and admixture. Morphological trait and genomic data were obtained from seedlings of E. sp. Cattai propagated in a common garden to assess their genetic provenance and hybrid status. KEY RESULTS All analyses revealed that E. sp. Cattai was strongly supported as a distinct species. Genetic diversity varied across populations, and clonality was unexpectedly high. Interspecific hybridization was detected, and was more prevalent in seedlings compared to in situ adult plants, indicating that post-zygotic barriers may restrict the establishment of hybrids. CONCLUSIONS Multiple evolutionary processes (e.g. hybridization and clonality) can operate within one rare and restricted species. Insights regarding evolutionary processes from our study were used to assist with the translocation of genetically 'pure' and healthy ex situ seedlings to nearby suitable habitat. Our findings demonstrate that it is vital to provide an understanding of evolutionary relationships and processes with an examination of population genomics in the design and implementation of an effective translocation strategy.
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Affiliation(s)
| | - Trevor C Wilson
- Research Centre for Ecosystem Resilience, Australian Institute of Botanic Science, Royal Botanic Garden Sydney, Sydney, Australia
| | - Jia-Yee Samantha Yap
- Research Centre for Ecosystem Resilience, Australian Institute of Botanic Science, Royal Botanic Garden Sydney, Sydney, Australia
| | - Enhua Lee
- Biodiversity and Conservation Division, New South Wales Department of Planning and Environment, Sydney, Australia
| | - Graeme Errington
- Australian PlantBank, Australian Institute of Botanical Science, Australian Botanic Garden, Mount Annan, New South Wales, Australia
| | - Maurizio Rossetto
- Research Centre for Ecosystem Resilience, Australian Institute of Botanic Science, Royal Botanic Garden Sydney, Sydney, Australia
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10
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Yap JYS, Rossetto M, Das S, Wilson PD, Beaumont LJ, Henry RJ. Tracking habitat or testing its suitability? Similar distributional patterns can hide very different histories of persistence versus nonequilibrium dynamics. Evolution 2022; 76:1209-1228. [PMID: 35304742 DOI: 10.1111/evo.14460] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 12/20/2021] [Accepted: 12/29/2021] [Indexed: 01/21/2023]
Abstract
The expansions and contractions of a species' range in response to temporal changes in selective filters leave genetic signatures that can inform a more accurate reconstruction of their evolutionary history across the landscape. After a long period of continental decline, Australian rainforests settled into localized patterns of contraction or expansion during the climatic fluctuations of the Quaternary. The environmental impacts of recurring glacial and interglacial periods also intensified the arrival of new lineages from the Sunda shelf, and it can be expected that immigrant versus locally persistent taxa responded to environmental challenges in quantifiably different manner. To investigate how such differences impact on species' distribution, we contrast landscape genomic patterns and changes in habitat availability between a species with a long continental history on Doryphora sassafras and a Sunda-derived species (Toona ciliata), across a distributional overlap. Extensive landscape-level homogeneity across chloroplast and nuclear genomes for the Sunda-derived T. ciliata, characterize the genetic signature of a very recent invasion and a rapid southern "exploratory" expansion that had not been previously recorded in the Australian flora (i.e., of Gondwanan origin or Sahul-derived). In contrast, D. sassafras is consistent with other Sahul-derived species characterized by strong geographical divergence and regional differentiation. Interestingly, our findings suggest that admixture between genetically divergent populations during expansion events might be a contributing factor to the successful colonization of novel habitats. Overall, this study identifies some of the mechanisms regulating the rearrangements in species distributions and assemblage composition that follow major environmental shifts, and reminds us how a species' current range might not necessarily define species' habitat preference, with the consequence that estimates of past or future range might not always be reliable.
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Affiliation(s)
- Jia-Yee Samantha Yap
- Research Centre for Ecosystem Resilience, Australian Institute of Botanical Science, The Royal Botanic Garden, Sydney, New South Wales, Australia.,Queensland Alliance of Agriculture and Food Innovation, University of Queensland, Brisbane, Queensland, Australia
| | - Maurizio Rossetto
- Research Centre for Ecosystem Resilience, Australian Institute of Botanical Science, The Royal Botanic Garden, Sydney, New South Wales, Australia.,Queensland Alliance of Agriculture and Food Innovation, University of Queensland, Brisbane, Queensland, Australia
| | - Sourav Das
- Department of Biological Sciences, Macquarie University, Brisbane, New South Wales, Australia.,Department of Forestry and Environmental Science, Shahjalal University of Science and Technology, Sylhet, Bangladesh
| | - Peter D Wilson
- Research Centre for Ecosystem Resilience, Australian Institute of Botanical Science, The Royal Botanic Garden, Sydney, New South Wales, Australia.,Department of Biological Sciences, Macquarie University, Brisbane, New South Wales, Australia
| | - Linda J Beaumont
- Department of Biological Sciences, Macquarie University, Brisbane, New South Wales, Australia
| | - Robert J Henry
- Queensland Alliance of Agriculture and Food Innovation, University of Queensland, Brisbane, Queensland, Australia
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11
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Sentinella AT, Moles AT, Bragg JG, Rossetto M, Sherwin WB. Detecting steps in spatial genetic data: Which diversity measures are best? PLoS One 2022; 17:e0265110. [PMID: 35287164 PMCID: PMC8920294 DOI: 10.1371/journal.pone.0265110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Accepted: 02/23/2022] [Indexed: 12/05/2022] Open
Abstract
Accurately detecting sudden changes, or steps, in genetic diversity across landscapes is important for locating barriers to gene flow, identifying selectively important loci, and defining management units. However, there are many metrics that researchers could use to detect steps and little information on which might be the most robust. Our study aimed to determine the best measure/s for genetic step detection along linear gradients using biallelic single nucleotide polymorphism (SNP) data. We tested the ability to differentiate between linear and step-like gradients in genetic diversity, using a range of diversity measures derived from the q-profile, including allelic richness, Shannon Information, GST, and Jost-D, as well as Bray-Curtis dissimilarity. To determine the properties of each measure, we repeated simulations of different intensities of step and allele proportion ranges, with varying genome sample size, number of loci, and number of localities. We found that alpha diversity (within-locality) based measures were ineffective at detecting steps. Further, allelic richness-based beta (between-locality) measures (e.g., Jaccard and Sørensen dissimilarity) were not reliable for detecting steps, but instead detected departures from fixation. The beta diversity measures best able to detect steps were: Shannon Information based measures, GST based measures, a Jost-D related measure, and Bray-Curtis dissimilarity. No one measure was best overall, with a trade-off between those measures with high step detection sensitivity (GST and Bray-Curtis) and those that minimised false positives (a variant of Shannon Information). Therefore, when detecting steps, we recommend understanding the differences between measures and using a combination of approaches.
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Affiliation(s)
- Alexander T. Sentinella
- Evolution & Ecology Research Centre, School of Biological, Earth and Environmental Sciences, UNSW Sydney, Sydney, NSW, Australia
- * E-mail:
| | - Angela T. Moles
- Evolution & Ecology Research Centre, School of Biological, Earth and Environmental Sciences, UNSW Sydney, Sydney, NSW, Australia
| | - Jason G. Bragg
- Evolution & Ecology Research Centre, School of Biological, Earth and Environmental Sciences, UNSW Sydney, Sydney, NSW, Australia
- Research Centre for Ecosystem Resilience, Australian Institute of Botanical Science, The Royal Botanic Garden Sydney, Sydney, NSW, Australia
| | - Maurizio Rossetto
- Research Centre for Ecosystem Resilience, Australian Institute of Botanical Science, The Royal Botanic Garden Sydney, Sydney, NSW, Australia
| | - William B. Sherwin
- Evolution & Ecology Research Centre, School of Biological, Earth and Environmental Sciences, UNSW Sydney, Sydney, NSW, Australia
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12
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Bragg JG, van der Merwe M, Yap JYS, Borevitz J, Rossetto M. Plant collections for conservation and restoration: can they be adapted and adaptable? Mol Ecol Resour 2022; 22:2171-2182. [PMID: 35229464 DOI: 10.1111/1755-0998.13605] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Revised: 02/13/2022] [Accepted: 02/18/2022] [Indexed: 11/29/2022]
Abstract
Plant collections are important for the conservation of threatened species, and can provide material for ecological restoration. Typically we want collections to have high genetic diversity so populations founded from it are adaptable to future challenges. Sometimes, we have additional objectives for collections, such as enrichment for desirable traits controlled by adaptive alleles. We used landscape genomic datasets for two plants, Westringia fruticosa and Wilkiea huegeliana, to design collections that are genetically diverse, and that are adapted to warming climates. We characterized temperature adaptation by: (i) using the mean annual temperature of the sites of origin of the plants, and (ii) using the representation of alleles that are associated with warm temperatures. In Westringia fruticosa, there was a negative correlation, or tradeoff, between designing a collection that was both genetically diverse and adapted to warm temperatures. This tradeoff was weaker in Wilkiea huegeliana. We hypothesized this was because neutral genetic variation was strongly correlated with temperature in Westringia fruticosa, and not in Wilkiea huegeliana. Accordingly, when we shuffled the temperature data, breaking up the covariance between Westringia fruticosa genetic variation and temperature, there was a relaxation of the observed tradeoff. In sum, we explore tradeoffs between promoting genetic diversity and selecting for a specific trait in plant collections, and show that the strength of this tradeoff varies between two species. This represents a useful step towards understanding when selection will have a large cost in genetic diversity, and when it will be possible to design a collection that is both adapted and adaptable.
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Affiliation(s)
- Jason G Bragg
- Research Centre for Ecosystem Resilience, Royal Botanic Gardens and Domain Trust, Mrs Macquaries Rd, Sydney, NSW, 2000, Australia.,School of Biological Earth and Environmental Sciences, University of New South Wales, Sydney, New South Wales, 2052, Australia
| | - Marlien van der Merwe
- Research Centre for Ecosystem Resilience, Royal Botanic Gardens and Domain Trust, Mrs Macquaries Rd, Sydney, NSW, 2000, Australia
| | - Jia-Yee Samantha Yap
- Research Centre for Ecosystem Resilience, Royal Botanic Gardens and Domain Trust, Mrs Macquaries Rd, Sydney, NSW, 2000, Australia
| | - Justin Borevitz
- Research School of Biology, Australian National University, Canberra, Australia
| | - Maurizio Rossetto
- Research Centre for Ecosystem Resilience, Royal Botanic Gardens and Domain Trust, Mrs Macquaries Rd, Sydney, NSW, 2000, Australia
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13
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Cooke P, Fahey M, Ens EJ, Raven M, Clarke PA, Rossetto M, Turpin G. Applying biocultural research protocols in ecology: Insider and outsider experiences from Australia. Eco Management Restoration 2022. [DOI: 10.1111/emr.12545] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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14
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Hogg CJ, Ottewell K, Latch P, Rossetto M, Biggs J, Gilbert A, Richmond S, Belov K. Threatened Species Initiative: Empowering conservation action using genomic resources. Proc Natl Acad Sci U S A 2022; 119:e2115643118. [PMID: 35042806 PMCID: PMC8795520 DOI: 10.1073/pnas.2115643118] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Globally, 15,521 animal species are listed as threatened by the International Union for the Conservation of Nature, and of these less than 3% have genomic resources that can inform conservation management. To combat this, global genome initiatives are developing genomic resources, yet production of a reference genome alone does not conserve a species. The reference genome allows us to develop a suite of tools to understand both genome-wide and functional diversity within and between species. Conservation practitioners can use these tools to inform their decision-making. But, at present there is an implementation gap between the release of genome information and the use of genomic data in applied conservation by conservation practitioners. In May 2020, we launched the Threatened Species Initiative and brought a consortium of genome biologists, population biologists, bioinformaticians, population geneticists, and ecologists together with conservation agencies across Australia, including government, zoos, and nongovernment organizations. Our objective is to create a foundation of genomic data to advance our understanding of key Australian threatened species, and ultimately empower conservation practitioners to access and apply genomic data to their decision-making processes through a web-based portal. Currently, we are developing genomic resources for 61 threatened species from a range of taxa, across Australia, with more than 130 collaborators from government, academia, and conservation organizations. Developed in direct consultation with government threatened-species managers and other conservation practitioners, herein we present our framework for meeting their needs and our systematic approach to integrating genomics into threatened species recovery.
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Affiliation(s)
- Carolyn J Hogg
- School of Life & Environmental Science, University of Sydney, Sydney, NSW 2006, Australia;
| | - Kym Ottewell
- Conservation Science Centre, Department of Biodiversity, Conservation, & Attractions, Kensington, WA 6151, Australia
| | - Peter Latch
- Australian Government Department of Agriculture, Water & Environment, Canberra, ACT 2600, Australia
| | - Maurizio Rossetto
- Research Centre for Ecosystem Resilience, Australian Institute of Botanical Science, The Royal Botanic Garden Sydney, Sydney, NSW 2000, Australia
| | - James Biggs
- Zoo and Aquarium Association Australasia, Mosman, NSW 2088, Australia
| | | | | | - Katherine Belov
- School of Life & Environmental Science, University of Sydney, Sydney, NSW 2006, Australia
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15
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Chen SH, Rossetto M, van der Merwe M, Lu-Irving P, Yap JYS, Sauquet H, Bourke G, Amos TG, Bragg JG, Edwards RJ. Chromosome-level de novo genome assembly of Telopea speciosissima (New South Wales waratah) using long-reads, linked-reads and Hi-C. Mol Ecol Resour 2022; 22:1836-1854. [PMID: 35016262 DOI: 10.1111/1755-0998.13574] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2021] [Revised: 12/03/2021] [Accepted: 12/03/2021] [Indexed: 11/29/2022]
Abstract
Telopea speciosissima, the New South Wales waratah, is an Australian endemic woody shrub in the family Proteaceae. Waratahs have great potential as a model clade to better understand processes of speciation, introgression and adaptation, and are significant from a horticultural perspective. Here, we report the first chromosome-level genome for T. speciosissima. Combining Oxford Nanopore long-reads, 10x Genomics Chromium linked-reads and Hi-C data, the assembly spans 823 Mb (scaffold N50 of 69.0 Mb) with 97.8% of Embryophyta BUSCOs "Complete". We present a new method in Diploidocus (https://github.com/slimsuite/diploidocus) for classifying, curating and QC-filtering scaffolds, which combines read depths, k-mer frequencies and BUSCO predictions. We also present a new tool, DepthSizer (https://github.com/slimsuite/depthsizer), for genome size estimation from the read depth of single-copy orthologues and estimate the genome size to be approximately 900 Mb. The largest 11 scaffolds contained 94.1% of the assembly, conforming to the expected number of chromosomes (2n = 22). Genome annotation predicted 40,158 protein-coding genes, 351 rRNAs and 728 tRNAs. We investigated CYCLOIDEA (CYC) genes, which have a role in determination of floral symmetry, and confirm the presence of two copies in the genome. Read depth analysis of 180 "Duplicated" BUSCO genes using a new tool, DepthKopy (https://github.com/slimsuite/depthkopy), suggests almost all are real duplications, increasing confidence in the annotation and highlighting a possible need to revise the BUSCO set for this lineage. The chromosome-level T. speciosissima reference genome (Tspe_v1) provides an important new genomic resource of Proteaceae to support the conservation of flora in Australia and further afield.
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Affiliation(s)
- Stephanie H Chen
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, Kensington, New South Wales, Australia.,Research Centre for Ecosystem Resilience, Australian Institute of Botanical Science, The Royal Botanic Garden Sydney, Sydney, New South Wales, Australia
| | - Maurizio Rossetto
- Research Centre for Ecosystem Resilience, Australian Institute of Botanical Science, The Royal Botanic Garden Sydney, Sydney, New South Wales, Australia.,Queensland Alliance of Agriculture and Food Innovation, University of Queensland, St Lucia, Queensland, Australia
| | - Marlien van der Merwe
- Research Centre for Ecosystem Resilience, Australian Institute of Botanical Science, The Royal Botanic Garden Sydney, Sydney, New South Wales, Australia
| | - Patricia Lu-Irving
- Research Centre for Ecosystem Resilience, Australian Institute of Botanical Science, The Royal Botanic Garden Sydney, Sydney, New South Wales, Australia
| | - Jia-Yee S Yap
- Research Centre for Ecosystem Resilience, Australian Institute of Botanical Science, The Royal Botanic Garden Sydney, Sydney, New South Wales, Australia.,Queensland Alliance of Agriculture and Food Innovation, University of Queensland, St Lucia, Queensland, Australia
| | - Hervé Sauquet
- National Herbarium of New South Wales, Royal Botanic Gardens and Domain Trust, Sydney, New South Wales, Australia.,School of Biological, Earth and Environmental Sciences, UNSW Sydney, New South Wales, Australia
| | - Greg Bourke
- Blue Mountains Botanic Garden, Mount Tomah, New South Wales, Australia
| | - Timothy G Amos
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, Kensington, New South Wales, Australia
| | - Jason G Bragg
- Research Centre for Ecosystem Resilience, Australian Institute of Botanical Science, The Royal Botanic Garden Sydney, Sydney, New South Wales, Australia.,School of Biological, Earth and Environmental Sciences, UNSW Sydney, New South Wales, Australia
| | - Richard J Edwards
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, Kensington, New South Wales, Australia
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16
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Falster D, Gallagher R, Wenk EH, Wright IJ, Indiarto D, Andrew SC, Baxter C, Lawson J, Allen S, Fuchs A, Monro A, Kar F, Adams MA, Ahrens CW, Alfonzetti M, Angevin T, Apgaua DMG, Arndt S, Atkin OK, Atkinson J, Auld T, Baker A, von Balthazar M, Bean A, Blackman CJ, Bloomfield K, Bowman DMJS, Bragg J, Brodribb TJ, Buckton G, Burrows G, Caldwell E, Camac J, Carpenter R, Catford JA, Cawthray GR, Cernusak LA, Chandler G, Chapman AR, Cheal D, Cheesman AW, Chen SC, Choat B, Clinton B, Clode PL, Coleman H, Cornwell WK, Cosgrove M, Crisp M, Cross E, Crous KY, Cunningham S, Curran T, Curtis E, Daws MI, DeGabriel JL, Denton MD, Dong N, Du P, Duan H, Duncan DH, Duncan RP, Duretto M, Dwyer JM, Edwards C, Esperon-Rodriguez M, Evans JR, Everingham SE, Farrell C, Firn J, Fonseca CR, French BJ, Frood D, Funk JL, Geange SR, Ghannoum O, Gleason SM, Gosper CR, Gray E, Groom PK, Grootemaat S, Gross C, Guerin G, Guja L, Hahs AK, Harrison MT, Hayes PE, Henery M, Hochuli D, Howell J, Huang G, Hughes L, Huisman J, Ilic J, Jagdish A, Jin D, Jordan G, Jurado E, Kanowski J, Kasel S, Kellermann J, Kenny B, Kohout M, Kooyman RM, Kotowska MM, Lai HR, Laliberté E, Lambers H, Lamont BB, Lanfear R, van Langevelde F, Laughlin DC, Laugier-Kitchener BA, Laurance S, Lehmann CER, Leigh A, Leishman MR, Lenz T, Lepschi B, Lewis JD, Lim F, Liu U, Lord J, Lusk CH, Macinnis-Ng C, McPherson H, Magallón S, Manea A, López-Martinez A, Mayfield M, McCarthy JK, Meers T, van der Merwe M, Metcalfe DJ, Milberg P, Mokany K, Moles AT, Moore BD, Moore N, Morgan JW, Morris W, Muir A, Munroe S, Nicholson Á, Nicolle D, Nicotra AB, Niinemets Ü, North T, O'Reilly-Nugent A, O'Sullivan OS, Oberle B, Onoda Y, Ooi MKJ, Osborne CP, Paczkowska G, Pekin B, Guilherme Pereira C, Pickering C, Pickup M, Pollock LJ, Poot P, Powell JR, Power SA, Prentice IC, Prior L, Prober SM, Read J, Reynolds V, Richards AE, Richardson B, Roderick ML, Rosell JA, Rossetto M, Rye B, Rymer PD, Sams MA, Sanson G, Sauquet H, Schmidt S, Schönenberger J, Schulze ED, Sendall K, Sinclair S, Smith B, Smith R, Soper F, Sparrow B, Standish RJ, Staples TL, Stephens R, Szota C, Taseski G, Tasker E, Thomas F, Tissue DT, Tjoelker MG, Tng DYP, de Tombeur F, Tomlinson K, Turner NC, Veneklaas EJ, Venn S, Vesk P, Vlasveld C, Vorontsova MS, Warren CA, Warwick N, Weerasinghe LK, Wells J, Westoby M, White M, Williams NSG, Wills J, Wilson PG, Yates C, Zanne AE, Zemunik G, Ziemińska K. AusTraits, a curated plant trait database for the Australian flora. Sci Data 2021; 8:254. [PMID: 34593819 PMCID: PMC8484355 DOI: 10.1038/s41597-021-01006-6] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Accepted: 08/05/2021] [Indexed: 02/08/2023] Open
Abstract
We introduce the AusTraits database - a compilation of values of plant traits for taxa in the Australian flora (hereafter AusTraits). AusTraits synthesises data on 448 traits across 28,640 taxa from field campaigns, published literature, taxonomic monographs, and individual taxon descriptions. Traits vary in scope from physiological measures of performance (e.g. photosynthetic gas exchange, water-use efficiency) to morphological attributes (e.g. leaf area, seed mass, plant height) which link to aspects of ecological variation. AusTraits contains curated and harmonised individual- and species-level measurements coupled to, where available, contextual information on site properties and experimental conditions. This article provides information on version 3.0.2 of AusTraits which contains data for 997,808 trait-by-taxon combinations. We envision AusTraits as an ongoing collaborative initiative for easily archiving and sharing trait data, which also provides a template for other national or regional initiatives globally to fill persistent gaps in trait knowledge.
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Affiliation(s)
- Daniel Falster
- Evolution & Ecology Research Centre, School of Biological, Earth, and Environmental Sciences, UNSW Sydney, Sydney, Australia.
| | - Rachael Gallagher
- Department of Biological Sciences, Macquarie University, Sydney, Australia
- Hawkesbury Institute for the Environment, Western Sydney University, Sydney, Australia
| | - Elizabeth H Wenk
- Evolution & Ecology Research Centre, School of Biological, Earth, and Environmental Sciences, UNSW Sydney, Sydney, Australia
| | - Ian J Wright
- Department of Biological Sciences, Macquarie University, Sydney, Australia
| | - Dony Indiarto
- Evolution & Ecology Research Centre, School of Biological, Earth, and Environmental Sciences, UNSW Sydney, Sydney, Australia
| | | | - Caitlan Baxter
- Evolution & Ecology Research Centre, School of Biological, Earth, and Environmental Sciences, UNSW Sydney, Sydney, Australia
| | - James Lawson
- NSW Department of Primary Industries, Orange, Australia
| | - Stuart Allen
- Department of Biological Sciences, Macquarie University, Sydney, Australia
| | - Anne Fuchs
- Centre for Australian National Biodiversity Research (a joint venture between Parks Australia and CSIRO), Canberra, ACT, Australia
| | - Anna Monro
- Centre for Australian National Biodiversity Research (a joint venture between Parks Australia and CSIRO), Canberra, ACT, Australia
| | - Fonti Kar
- Evolution & Ecology Research Centre, School of Biological, Earth, and Environmental Sciences, UNSW Sydney, Sydney, Australia
| | - Mark A Adams
- Swinburne University of Technology, Hawthorn, Australia
| | - Collin W Ahrens
- Hawkesbury Institute for the Environment, Western Sydney University, Sydney, Australia
| | - Matthew Alfonzetti
- Department of Biological Sciences, Macquarie University, Sydney, Australia
| | | | - Deborah M G Apgaua
- Centre for Rainforest Studies, School for Field Studies, Yungaburra, Queensland, 4872, Australia
| | | | - Owen K Atkin
- The Australian National University, Canberra, Australia
| | - Joe Atkinson
- Evolution & Ecology Research Centre, School of Biological, Earth, and Environmental Sciences, UNSW Sydney, Sydney, Australia
| | - Tony Auld
- NSW Department of Planning Industry and Environment, Parramatta, Australia
| | | | - Maria von Balthazar
- Department of Botany and Biodiversity Research, University of Vienna, Vienna, Austria
| | | | | | | | | | - Jason Bragg
- Research Centre for Ecosystem Resilience, Australian Institute of Botanical Science, Royal Botanic Gardens and Domain Trust, Sydney, Australia
| | | | | | | | | | - James Camac
- Centre of Excellence for Biosecurity Risk Analysis, The University of Melbourne, Melbourne, Australia
| | | | | | | | - Lucas A Cernusak
- College of Science and Engineering, James Cook University, Cairns, QLD, Australia
| | | | - Alex R Chapman
- Western Australian Herbarium, Keiran McNamara Conservation Science Centre, Department of Biodiversity, Conservation and Attractions, Western Australia, Kensington, Australia
| | - David Cheal
- Centre for Environmental Management, School of Health & Life Sciences, Federation University, Mount Helen, Australia
| | | | - Si-Chong Chen
- Royal Botanic Gardens, Richmond, Kew, United Kingdom
| | - Brendan Choat
- Hawkesbury Institute for the Environment, Western Sydney University, Sydney, Australia
| | - Brook Clinton
- Centre for Australian National Biodiversity Research (a joint venture between Parks Australia and CSIRO), Canberra, ACT, Australia
| | - Peta L Clode
- University of Western Australia, Crawley, Australia
| | - Helen Coleman
- Western Australian Herbarium, Keiran McNamara Conservation Science Centre, Department of Biodiversity, Conservation and Attractions, Western Australia, Kensington, Australia
| | - William K Cornwell
- Evolution & Ecology Research Centre, School of Biological, Earth, and Environmental Sciences, UNSW Sydney, Sydney, Australia
| | | | - Michael Crisp
- The Australian National University, Canberra, Australia
| | - Erika Cross
- Charles Sturt University, Bathurst, Australia
| | - Kristine Y Crous
- Hawkesbury Institute for the Environment, Western Sydney University, Sydney, Australia
| | - Saul Cunningham
- Fenner School of Environment and Society, The Australian National University, Canberra, Australia
| | | | - Ellen Curtis
- University of Technology Sydney, Sydney, Australia
| | - Matthew I Daws
- Environment Department, Alcoa of Australia, Huntly, Western Australia, Australia
| | - Jane L DeGabriel
- School of Marine and Tropical Biology, James Cook University, Douglas, Australia
| | - Matthew D Denton
- School of Agriculture, Food and Wine, University of Adelaide, Adelaide, Australia
| | - Ning Dong
- Department of Biological Sciences, Macquarie University, Sydney, Australia
| | | | - Honglang Duan
- Institute for Forest Resources & Environment of Guizhou, Guizhou University, Guiyang, China
| | | | - Richard P Duncan
- Institute for Applied Ecology, University of Canberra, ACT, 2617, Canberra, Australia
| | - Marco Duretto
- National Herbarium of New South Wales, Australian Institute of Botanical Science, Royal Botanic Gardens and Domain Trust, Sydney, Australia
| | - John M Dwyer
- School of Biological Sciences, The University of Queensland, St Lucia, Australia
| | | | | | - John R Evans
- The Australian National University, Canberra, Australia
| | - Susan E Everingham
- Evolution & Ecology Research Centre, School of Biological, Earth, and Environmental Sciences, UNSW Sydney, Sydney, Australia
| | | | - Jennifer Firn
- Queensland University of Technology, Brisbane, Australia
| | - Carlos Roberto Fonseca
- Departamento de Ecologia, Universidade Federal do Rio Grande do Norte, Natal, Natal - RN, Brazil
| | | | - Doug Frood
- Pathways Bushland and Environment Consultancy, Sydney, Australia
| | - Jennifer L Funk
- Department of Plant Sciences, University of California, Davis, USA
| | | | - Oula Ghannoum
- Hawkesbury Institute for the Environment, Western Sydney University, Sydney, Australia
| | | | - Carl R Gosper
- Biodiversity and Conservation Science, Department of Biodiversity, Conservation and Attractions, Kensington, WA, Australia
| | - Emma Gray
- Department of Biological Sciences, Macquarie University, Sydney, Australia
| | | | - Saskia Grootemaat
- Evolution & Ecology Research Centre, School of Biological, Earth, and Environmental Sciences, UNSW Sydney, Sydney, Australia
| | | | - Greg Guerin
- Terrestrial Ecosystem Research Network, The School of Biological Sciences, The University of Adelaide, Adelaide, SA, 5005, Australia
| | - Lydia Guja
- Centre for Australian National Biodiversity Research (a joint venture between Parks Australia and CSIRO), Canberra, ACT, Australia
| | - Amy K Hahs
- School of Ecosystem and Forest Sciences, The University of Melbourne, Melbourne, Australia
| | | | | | - Martin Henery
- arks Australia, Department of Agriculture, Water and the Environment, Hobart, Australia
| | - Dieter Hochuli
- School of Life and Environmental Sciences, The University of Sydney, Camperdown, Australia
| | | | - Guomin Huang
- Nanchang Institute of Technology, Nanchang, China
| | - Lesley Hughes
- Department of Biological Sciences, Macquarie University, Sydney, Australia
| | - John Huisman
- Western Australian Herbarium, Biodiversity and Conservation Science, Department of Biodiversity, Conservation and Attractions, Kensington, Western Australia, Australia
| | | | - Ashika Jagdish
- Evolution & Ecology Research Centre, School of Biological, Earth, and Environmental Sciences, UNSW Sydney, Sydney, Australia
| | - Daniel Jin
- School of Life and Environmental Sciences, The University of Sydney, Camperdown, Australia
| | | | - Enrique Jurado
- Universidad Autonoma de Nuevo Leon, San Nicolás de los Garza, Mexico
| | | | | | - Jürgen Kellermann
- State Herbarium of South Australia, Botanic Gardens and State Herbarium, Hackney Road, Adelaide, SA, 5000, Australia
| | | | - Michele Kohout
- Department of Environment, Land, Water and Planning, Victoria, Australia
| | - Robert M Kooyman
- Department of Biological Sciences, Macquarie University, Sydney, Australia
| | - Martyna M Kotowska
- Department of Plant Ecology and Ecosystems Research, University of Goettingen, Göttingen, Germany
| | - Hao Ran Lai
- University of Canterbury, Christchurch, New Zealand
| | - Etienne Laliberté
- Institut de recherche en biologie végétale, Université de Montréal, 4101 Sherbrooke Est, Montréal, H1X 2B2, Canada
| | - Hans Lambers
- University of Western Australia, Crawley, Australia
| | | | - Robert Lanfear
- Ecology and Evolution, Research School of Biology, Australian National University, Canberra, Australia
| | - Frank van Langevelde
- Wildlife Ecology & Conservation Group, Wageningen University, Wageningen, The Netherlands
| | - Daniel C Laughlin
- Department of Botany, University of Wyoming, Laramie, WY, 82071, USA
| | | | | | | | - Andrea Leigh
- University of Technology Sydney, Sydney, Australia
| | | | - Tanja Lenz
- Department of Biological Sciences, Macquarie University, Sydney, Australia
| | - Brendan Lepschi
- Centre for Australian National Biodiversity Research (a joint venture between Parks Australia and CSIRO), Canberra, ACT, Australia
| | | | - Felix Lim
- AMAP (Botanique et Modélisation de l'Architecture des Plantes et des Végétations), Université de Montpellier, CIRAD, CNRS, INRA, IRD, Montpellier, France
| | | | | | - Christopher H Lusk
- Environmental Research Institute, University of Waikato, Hamilton, New Zealand
| | | | - Hannah McPherson
- National Herbarium of New South Wales, Australian Institute of Botanical Science, Royal Botanic Gardens and Domain Trust, Sydney, Australia
| | - Susana Magallón
- Laboratorio Nacional de Ciencias de la Sostenibilidad, Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - Anthony Manea
- Department of Biological Sciences, Macquarie University, Sydney, Australia
| | - Andrea López-Martinez
- Laboratorio Nacional de Ciencias de la Sostenibilidad, Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - Margaret Mayfield
- School of Biological Sciences, The University of Queensland, St Lucia, Australia
| | | | | | - Marlien van der Merwe
- Research Centre for Ecosystem Resilience, Australian Institute of Botanical Science, Royal Botanic Gardens and Domain Trust, Sydney, Australia
| | | | | | | | - Angela T Moles
- Evolution & Ecology Research Centre, School of Biological, Earth, and Environmental Sciences, UNSW Sydney, Sydney, Australia
| | - Ben D Moore
- Hawkesbury Institute for the Environment, Western Sydney University, Sydney, Australia
| | | | | | | | - Annette Muir
- Department of Environment, Land, Water and Planning, Victoria, Australia
| | - Samantha Munroe
- Terrestrial Ecosystem Research Network, The School of Biological Sciences, The University of Adelaide, Adelaide, SA, 5005, Australia
| | | | - Dean Nicolle
- Currency Creek Arboretum, Currency Creek, Australia
| | | | - Ülo Niinemets
- Estonian University of Life Sciences, Tartu, Estonia
| | - Tom North
- Centre for Australian National Biodiversity Research (a joint venture between Parks Australia and CSIRO), Canberra, ACT, Australia
| | | | | | - Brad Oberle
- Division of Natural Sciences, New College of Florida, Sarasota, USA
| | - Yusuke Onoda
- Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | - Mark K J Ooi
- Centre for Ecosystem Science, School of Biological, Earth, and Environmental Sciences, UNSW, Sydney, Australia
| | - Colin P Osborne
- University of Sheffield, Department of Animal and Plant Sciences, Sheffield, United Kingdom
| | - Grazyna Paczkowska
- Western Australian Herbarium, Keiran McNamara Conservation Science Centre, Department of Biodiversity, Conservation and Attractions, Western Australia, Kensington, Australia
| | - Burak Pekin
- Istanbul Technical University, Eurasia Institute of Earth Sciences, Istanbul, Turkey
| | - Caio Guilherme Pereira
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, USA
| | | | | | | | - Pieter Poot
- College of Science and Engineering, James Cook University, Cairns, QLD, Australia
| | - Jeff R Powell
- Hawkesbury Institute for the Environment, Western Sydney University, Sydney, Australia
| | - Sally A Power
- Hawkesbury Institute for the Environment, Western Sydney University, Sydney, Australia
| | | | | | | | - Jennifer Read
- School of Biological Sciences, Monash University, Clayton, Australia
| | - Victoria Reynolds
- School of Biological Sciences, The University of Queensland, St Lucia, Australia
| | | | - Ben Richardson
- Western Australian Herbarium, Department of Biodiversity, Conservation and Attractions, Western Australia, Kensington, Australia
| | | | - Julieta A Rosell
- Laboratorio Nacional de Ciencias de la Sostenibilidad, Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - Maurizio Rossetto
- National Herbarium of New South Wales, Australian Institute of Botanical Science, Royal Botanic Gardens and Domain Trust, Sydney, Australia
| | - Barbara Rye
- Western Australian Herbarium, Department of Biodiversity, Conservation and Attractions, Western Australia, Kensington, Australia
| | - Paul D Rymer
- Hawkesbury Institute for the Environment, Western Sydney University, Sydney, Australia
| | - Michael A Sams
- School of Biological Sciences, The University of Queensland, St Lucia, Australia
| | - Gordon Sanson
- School of Biological Sciences, Monash University, Clayton, Australia
| | - Hervé Sauquet
- National Herbarium of New South Wales, Australian Institute of Botanical Science, Royal Botanic Gardens and Domain Trust, Sydney, Australia
| | - Susanne Schmidt
- School of Agriculture and Food Science, University of Queensland, St Lucia, Australia
| | - Jürg Schönenberger
- Department of Botany and Biodiversity Research, University of Vienna, Vienna, Austria
| | | | - Kerrie Sendall
- Rider University, Lawrence Township, Lawrenceville, NJ, USA
| | - Steve Sinclair
- Department of Plant Ecology and Ecosystems Research, University of Goettingen, Göttingen, Germany
| | - Benjamin Smith
- Hawkesbury Institute for the Environment, Western Sydney University, Sydney, Australia
| | - Renee Smith
- Hawkesbury Institute for the Environment, Western Sydney University, Sydney, Australia
| | | | - Ben Sparrow
- Terrestrial Ecosystem Research Network, The School of Biological Sciences, The University of Adelaide, Adelaide, SA, 5005, Australia
| | - Rachel J Standish
- Environmental and Conservation Sciences, Murdoch University, Murdoch, Australia
| | - Timothy L Staples
- School of Biological Sciences, The University of Queensland, St Lucia, Australia
| | - Ruby Stephens
- Department of Biological Sciences, Macquarie University, Sydney, Australia
| | | | - Guy Taseski
- Evolution & Ecology Research Centre, School of Biological, Earth, and Environmental Sciences, UNSW Sydney, Sydney, Australia
| | - Elizabeth Tasker
- NSW Department of Planning Industry and Environment, Parramatta, Australia
| | | | - David T Tissue
- Hawkesbury Institute for the Environment, Western Sydney University, Sydney, Australia
| | - Mark G Tjoelker
- Hawkesbury Institute for the Environment, Western Sydney University, Sydney, Australia
| | - David Yue Phin Tng
- Centre for Rainforest Studies, School for Field Studies, Yungaburra, Queensland, 4872, Australia
| | - Félix de Tombeur
- TERRA Teaching and Research Centre, Gembloux Agro-Bio Tech, University of Liege, Gembloux, Belgium
| | | | | | | | - Susanna Venn
- Centre for Integrative Ecology, School of Life and Environmental Sciences, Deakin University, Burwood, Australia
| | - Peter Vesk
- University of Melbourne, Melbourne, Australia
| | - Carolyn Vlasveld
- School of Biological Sciences, Monash University, Clayton, Australia
| | | | - Charles A Warren
- School of Life and Environmental Sciences, The University of Sydney, Camperdown, Australia
| | | | | | - Jessie Wells
- School of Biological Sciences, The University of Queensland, St Lucia, Australia
| | - Mark Westoby
- Department of Biological Sciences, Macquarie University, Sydney, Australia
| | - Matthew White
- Department of Environment, Land, Water and Planning, Victoria, Australia
| | | | - Jarrah Wills
- School of Life and Environmental Sciences, The University of Sydney, Camperdown, Australia
| | - Peter G Wilson
- National Herbarium of NSW and Royal Botanic Gardens and Domain Trust, Sydney, Australia
| | - Colin Yates
- Biodiversity and Conservation Science, Department of Biodiversity, Conservation and Attractions, Kensington, WA, Australia
| | - Amy E Zanne
- Department of Biological Sciences, George Washington University, Washington, DC, 20052, USA
- Department of Biology, University of Miami, Coral Gables, Florida 33146 USA, George Washington University, Washington, DC, 20052, USA
| | | | - Kasia Ziemińska
- AMAP (Botanique et Modélisation de l'Architecture des Plantes et des Végétations), Université de Montpellier, CIRAD, CNRS, INRA, IRD, Montpellier, France
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17
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Bragg JG, Yap JS, Wilson T, Lee E, Rossetto M. Conserving the genetic diversity of condemned populations: Optimizing collections and translocation. Evol Appl 2021; 14:1225-1238. [PMID: 34025763 PMCID: PMC8127699 DOI: 10.1111/eva.13192] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Accepted: 12/14/2020] [Indexed: 11/28/2022] Open
Abstract
We consider approaches for conserving genetic diversity from plant populations whose destruction is imminent. We do this using SNP genotype data from two endangered species, Pimelea spicata and Eucalyptus sp. Cattai. For both species, we genotyped plants from a 'condemned' population and designed ex situ collections, characterizing how the size and composition of the collection affected the genetic diversity preserved. Consistent with previous observations, populations where genetic diversity was optimized captured more alleles than populations of equal size chosen at random. This benefit of optimization was larger when the propagation population was small. That is, small numbers of individuals (e.g. 20) needed to be selected carefully to capture a comparable proportion of alleles to optimized populations, but larger random populations (e.g. >48) captured almost as many alleles as optimized populations. We then examined strategies for generating translocation populations based on the horticultural constraints presented by each species. In P. spicata, which is readily grown from cuttings, we designed translocation populations of different sizes, using different numbers of ramets from each member of propagation populations. We then performed simulations to predict the loss of alleles from these populations over 10 generations. Large translocation populations were predicted to maintain a greater proportion of source population alleles than smaller translocation populations, but this effect was saturated beyond 200 individuals. In E. sp. Cattai, we examined strategies to promote the diversity of progeny from a conservation planting scenario with 36 individuals. This included the optimization of the spatial arrangement of the planting and supplementing the diversity of the condemned population with individuals from additional sites. In sum, we studied approaches for designing genetically diverse translocations of condemned populations for two species that require contrasting methods of propagation, illustrating the application of approaches that were useful in different circumstances.
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Affiliation(s)
- Jason G. Bragg
- Research Centre for Ecosystem ResilienceAustralian Institute of Botanical Science, The Royal Botanic Garden SydneySydneyNSWAustralia
- School of Biological Earth and Environmental SciencesUniversity of New South WalesSydneyNSWAustralia
| | - Jia‐Yee S. Yap
- Research Centre for Ecosystem ResilienceAustralian Institute of Botanical Science, The Royal Botanic Garden SydneySydneyNSWAustralia
- Queensland Alliance of Agriculture and Food InnovationUniversity of QueenslandSanta LuciaQLDAustralia
| | - Trevor Wilson
- Research Centre for Ecosystem ResilienceAustralian Institute of Botanical Science, The Royal Botanic Garden SydneySydneyNSWAustralia
| | - Enhua Lee
- Biodiversity and Conservation DivisionDepartment of Planning, Industry and EnvironmentParramattaNSWAustralia
| | - Maurizio Rossetto
- Research Centre for Ecosystem ResilienceAustralian Institute of Botanical Science, The Royal Botanic Garden SydneySydneyNSWAustralia
- Queensland Alliance of Agriculture and Food InnovationUniversity of QueenslandSanta LuciaQLDAustralia
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18
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Rossetto M, Yap JYS, Lemmon J, Bain D, Bragg J, Hogbin P, Gallagher R, Rutherford S, Summerell B, Wilson TC. A conservation genomics workflow to guide practical management actions. Glob Ecol Conserv 2021. [DOI: 10.1016/j.gecco.2021.e01492] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
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19
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Rutherford S, Wan JSH, Cohen JM, Benson D, Rossetto M. Looks can be deceiving: speciation dynamics of co-distributed Angophora (Myrtaceae) species in a varying landscape. Evolution 2020; 75:310-329. [PMID: 33325041 DOI: 10.1111/evo.14140] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Revised: 11/05/2020] [Accepted: 11/24/2020] [Indexed: 11/30/2022]
Abstract
Understanding the mechanisms underlying species divergence remains a central goal in evolutionary biology. Landscape genetics can be a powerful tool for examining evolutionary processes. We used genome-wide scans to genotype samples from populations of eight Angophora species. Angophora is a small genus within the eucalypts comprising common and rare species in a heterogeneous landscape, making it an appropriate group to study speciation. We found A. hispida was highly differentiated from the other species. Two subspecies of A. costata (subsp. costata and subsp. euryphylla) formed a group, while the third (subsp. leiocarpa, which is only distinguished by its smooth fruits and provenance) was supported as a distinct pseudocryptic species. Other species that are morphologically distinct could not be genetically differentiated (e.g., A. floribunda and A. subvelutina). Distribution and genetic differentiation within Angophora were strongly influenced by temperature and humidity, as well as biogeographic barriers, particularly rivers and higher elevation regions. While extensive introgression was found between many populations of some species (e.g., A. bakeri and A. floribunda), others only hybridized at certain locations. Overall, our findings suggest multiple mechanisms drove evolutionary diversification in Angophora and highlight how genome-wide analyses of related species in a diverse landscape can provide insights into speciation.
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Affiliation(s)
- Susan Rutherford
- Institute of Environment and Ecology, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang, China.,Research Centre for Ecosystem Resilience, Australian Institute of Botanic Science, Sydney, Australia
| | - Justin S H Wan
- Institute of Environment and Ecology, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang, China.,Research Centre for Ecosystem Resilience, Australian Institute of Botanic Science, Sydney, Australia
| | - Joel M Cohen
- Research Centre for Ecosystem Resilience, Australian Institute of Botanic Science, Sydney, Australia
| | - Doug Benson
- Research Centre for Ecosystem Resilience, Australian Institute of Botanic Science, Sydney, Australia
| | - Maurizio Rossetto
- Research Centre for Ecosystem Resilience, Australian Institute of Botanic Science, Sydney, Australia
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20
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Ribeiro Bizuti M, Eneida de Almeida M, Roberto Barbato P, Savi Geremia D, Inácio Andrioli A, Rossetto M. Support to academic education in view of the consolidation of the universal health system in Brazil. Eur J Public Health 2020. [DOI: 10.1093/eurpub/ckaa166.636] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Abstract
The Federal University of Fronteira Sul (UFFS) is the first higher-level institution in Brazil to emerge from the processes of social and political participation of social movements and networks of civil associations. Its objective is to ensure access to higher education for the entire population of the region named Fronteira Sul, historically excluded, in order to contribute to the resolution of local and regional problems. Its public and popular character is structural, with a historical aspect of a struggle of more than forty years of various social movements for the federal university, in defense of society and its ideas: democracy, equality, respect for diversity, citizenship, right to free public education, sustainability and social justice. The center of political action at UFFS is in direction of universal human rights, equality and the reduction of social inequality, being one of the structuring axes, the strengthening of Policies and Practices for the Promotion of Public Health, since society has presented its demands guided by the concerns with health care in the region. CEBES is a national entity created in 1976, whose historical mission is the struggle for the democratization of society and the defense of social rights, in particular the universal right to health. As a supraparty plural space, it brings together activists, leaders, researchers, teachers, professionals and students, together with other entities in the fight for health. It was responsible for founding the Brazilian Sanitary Reform Movement, by producing and disseminating information, knowledge and critical analyzes aimed at strengthening subjects through the expansion of critical thinking and health awareness, essential elements for political practice and action. The Chapecó nucleus was created to contribute to academic education in the health field by respecting the founding principles of social justice that are in the Federal Constitution of 1988, universality, equity and integrality.
Key messages
Present the Chapecó nucleus created to contribute to academic education in the health field, while respecting the founding principles of social justice and democracy. To present UFFS as an important institution for universal human rights and its commitment to the reduction of social inequality in the strengthening of Public Health Promotion Policies and Practices.
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Affiliation(s)
| | | | | | | | | | - M Rossetto
- Federal University of Fronteira Sul, Chapecó, Brazil
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21
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Affiliation(s)
- Jia‐Yee S. Yap
- National Herbarium of New South Wales Royal Botanic Garden Sydney NSW Australia
- Queensland Alliance of Agriculture and Food Innovation University of Queensland Brisbane Qld Australia
| | - Marlien Merwe
- National Herbarium of New South Wales Royal Botanic Garden Sydney NSW Australia
| | - Andrew J. Ford
- CSIRO, Land and Water Tropical Forest Research Centre Atherton Qld Australia
| | - Robert J. Henry
- Queensland Alliance of Agriculture and Food Innovation University of Queensland Brisbane Qld Australia
| | - Maurizio Rossetto
- National Herbarium of New South Wales Royal Botanic Garden Sydney NSW Australia
- Queensland Alliance of Agriculture and Food Innovation University of Queensland Brisbane Qld Australia
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22
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Gallagher RV, Falster DS, Maitner BS, Salguero-Gómez R, Vandvik V, Pearse WD, Schneider FD, Kattge J, Poelen JH, Madin JS, Ankenbrand MJ, Penone C, Feng X, Adams VM, Alroy J, Andrew SC, Balk MA, Bland LM, Boyle BL, Bravo-Avila CH, Brennan I, Carthey AJR, Catullo R, Cavazos BR, Conde DA, Chown SL, Fadrique B, Gibb H, Halbritter AH, Hammock J, Hogan JA, Holewa H, Hope M, Iversen CM, Jochum M, Kearney M, Keller A, Mabee P, Manning P, McCormack L, Michaletz ST, Park DS, Perez TM, Pineda-Munoz S, Ray CA, Rossetto M, Sauquet H, Sparrow B, Spasojevic MJ, Telford RJ, Tobias JA, Violle C, Walls R, Weiss KCB, Westoby M, Wright IJ, Enquist BJ. Open Science principles for accelerating trait-based science across the Tree of Life. Nat Ecol Evol 2020; 4:294-303. [PMID: 32066887 DOI: 10.1038/s41559-020-1109-6] [Citation(s) in RCA: 73] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2019] [Accepted: 01/10/2020] [Indexed: 01/22/2023]
Abstract
Synthesizing trait observations and knowledge across the Tree of Life remains a grand challenge for biodiversity science. Species traits are widely used in ecological and evolutionary science, and new data and methods have proliferated rapidly. Yet accessing and integrating disparate data sources remains a considerable challenge, slowing progress toward a global synthesis to integrate trait data across organisms. Trait science needs a vision for achieving global integration across all organisms. Here, we outline how the adoption of key Open Science principles-open data, open source and open methods-is transforming trait science, increasing transparency, democratizing access and accelerating global synthesis. To enhance widespread adoption of these principles, we introduce the Open Traits Network (OTN), a global, decentralized community welcoming all researchers and institutions pursuing the collaborative goal of standardizing and integrating trait data across organisms. We demonstrate how adherence to Open Science principles is key to the OTN community and outline five activities that can accelerate the synthesis of trait data across the Tree of Life, thereby facilitating rapid advances to address scientific inquiries and environmental issues. Lessons learned along the path to a global synthesis of trait data will provide a framework for addressing similarly complex data science and informatics challenges.
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Affiliation(s)
- Rachael V Gallagher
- Department of Biological Sciences, Macquarie University, Sydney, New South Wales, Australia.
| | - Daniel S Falster
- Evolution and Ecology Research Centre and School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - Brian S Maitner
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, USA
| | - Roberto Salguero-Gómez
- Department of Zoology, Oxford University, Oxford, UK.,Centre for Biodiversity and Conservation Science, University of Queensland, Brisbane, Queensland, Australia.,Evolutionary Demography Laboratory, Max Plank Institute for Demographic Research, Rostock, Germany
| | - Vigdis Vandvik
- Department of Biological Sciences, University of Bergen, Bergen, Norway.,Bjerknes Centre for Climate Research, University of Bergen, Bergen, Norway
| | - William D Pearse
- Ecology Center and Department of Biology, Utah State University, Logan, UT, USA
| | | | - Jens Kattge
- Max Planck Institute for Biogeochemistry, Jena, Germany.,German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
| | | | - Joshua S Madin
- Hawai'i Institute of Marine Biology, University of Hawai'i at Manoa, Manoa, HI, USA
| | - Markus J Ankenbrand
- Department of Bioinformatics, Biocenter, University of Wuerzburg, Wuerzburg, Germany.,Center for Computational and Theoretical Biology, Biocenter, University of Wuerzburg, Wuerzburg, Germany.,Comprehensive Heart Failure Center, University Hospital Wuerzburg, Wuerzburg, Germany
| | - Caterina Penone
- Institute of Plant Sciences, University of Bern, Bern, Switzerland
| | - Xiao Feng
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, USA
| | - Vanessa M Adams
- Discipline of Geography and Spatial Sciences, University of Tasmania, Hobart, Tasmania, Australia
| | - John Alroy
- Department of Biological Sciences, Macquarie University, Sydney, New South Wales, Australia
| | - Samuel C Andrew
- Commonwealth Scientific and Industrial Research Organisation (CSIRO), Canberra, Australian Capital Territory, Australia
| | - Meghan A Balk
- Bio5 Institute, University of Arizona, Tucson, AZ, USA
| | - Lucie M Bland
- School of Life and Environmental Sciences, Centre for Integrative Ecology, Deakin University, Geelong, Victoria, Australia
| | - Brad L Boyle
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, USA
| | - Catherine H Bravo-Avila
- Department of Biology, University of Miami, Miami, FL, USA.,Fairchild Tropical Botanic Garden, Coral Gables, FL, USA
| | - Ian Brennan
- Research School of Biology, Australian National University, Canberra, Australian Capital Territory, Australia
| | - Alexandra J R Carthey
- Department of Biological Sciences, Macquarie University, Sydney, New South Wales, Australia
| | - Renee Catullo
- Research School of Biology, Australian National University, Canberra, Australian Capital Territory, Australia
| | - Brittany R Cavazos
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA, USA
| | - Dalia A Conde
- Species360 Conservation Science Alliance, Bloomington, MN, USA.,Interdisciplinary Center on Population Dynamics, University of Southern Denmark, Odense, Denmark.,Department of Biology, University of Southern Denmark, Odense, Denmark
| | - Steven L Chown
- School of Biological Sciences, Monash University, Melbourne, Victoria, Australia
| | - Belen Fadrique
- Department of Biology, University of Miami, Miami, FL, USA
| | - Heloise Gibb
- Department of Ecology, Environment and Evolution and Centre for Future Landscapes, La Trobe University, Melbourne, Victoria, Australia
| | - Aud H Halbritter
- Department of Biological Sciences, University of Bergen, Bergen, Norway.,Bjerknes Centre for Climate Research, University of Bergen, Bergen, Norway
| | - Jennifer Hammock
- National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
| | - J Aaron Hogan
- International Center for Tropical Botany, Department of Biological Sciences, Florida International University, Miami, FL, USA
| | - Hamish Holewa
- Commonwealth Scientific and Industrial Research Organisation (CSIRO), Canberra, Australian Capital Territory, Australia
| | - Michael Hope
- Commonwealth Scientific and Industrial Research Organisation (CSIRO), Canberra, Australian Capital Territory, Australia
| | - Colleen M Iversen
- Climate Change Science Institute and Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Malte Jochum
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany.,Institute of Plant Sciences, University of Bern, Bern, Switzerland.,Institute of Biology, Leipzig University, Leipzig, Germany
| | - Michael Kearney
- School of BioSciences, The University of Melbourne, Melbourne, Victoria, Australia
| | - Alexander Keller
- Department of Bioinformatics, Biocenter, University of Wuerzburg, Wuerzburg, Germany.,Center for Computational and Theoretical Biology, Biocenter, University of Wuerzburg, Wuerzburg, Germany
| | - Paula Mabee
- Department of Biology, University of South Dakota, Vermillion, SD, USA
| | - Peter Manning
- Senckenberg Biodiversity and Climate Research Centre (SBiK-F), Frankfurt, Germany
| | - Luke McCormack
- Center for Tree Science, The Morton Arboretum, Lisle, IL, USA
| | - Sean T Michaletz
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada
| | - Daniel S Park
- Department of Organismic and Evolutionary Biology and Harvard University Herbaria, Harvard University, Cambridge, MA, USA
| | - Timothy M Perez
- Department of Biology, University of Miami, Miami, FL, USA.,Fairchild Tropical Botanic Garden, Coral Gables, FL, USA
| | - Silvia Pineda-Munoz
- School of Biological Sciences and School of Earth & Atmospheric Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Courtenay A Ray
- School of Life Sciences, Arizona State University, Tempe, AZ, USA
| | - Maurizio Rossetto
- National Herbarium of New South Wales, Royal Botanic Gardens and Domain Trust, Sydney, New South Wales, Australia.,Queensland Alliance of Agriculture and Food Innovation, University of Queensland, Brisbane, Queensland, Australia
| | - Hervé Sauquet
- Evolution and Ecology Research Centre and School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, New South Wales, Australia.,National Herbarium of New South Wales, Royal Botanic Gardens and Domain Trust, Sydney, New South Wales, Australia.,Ecologie Systématique Evolution, Univ. Paris-Sud, CNRS, AgroParisTech, Universite Paris-Saclay, Orsay, France
| | - Benjamin Sparrow
- TERN / School of Biological Sciences, Faculty of Science, The University of Adelaide, Adelaide, South Australia, Australia
| | - Marko J Spasojevic
- Department of Evolution, Ecology, and Organismal Biology, University of California Riverside, Riverside, CA, USA
| | - Richard J Telford
- Department of Biological Sciences, University of Bergen, Bergen, Norway.,Bjerknes Centre for Climate Research, University of Bergen, Bergen, Norway
| | - Joseph A Tobias
- Department of Life Sciences, Imperial College London, London, UK
| | - Cyrille Violle
- CEFE, CNRS, Univ Montpellier, Université Paul Valéry Montpellier, Montpellier, France
| | | | | | - Mark Westoby
- Department of Biological Sciences, Macquarie University, Sydney, New South Wales, Australia
| | - Ian J Wright
- Department of Biological Sciences, Macquarie University, Sydney, New South Wales, Australia
| | - Brian J Enquist
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, USA.,Santa Fe Institute, Santa Fe, NM, USA
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23
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Bragg JG, Cuneo P, Sherieff A, Rossetto M. Optimizing the genetic composition of a translocation population: Incorporating constraints and conflicting objectives. Mol Ecol Resour 2019; 20:54-65. [DOI: 10.1111/1755-0998.13074] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Revised: 07/18/2019] [Accepted: 07/30/2019] [Indexed: 11/30/2022]
Affiliation(s)
- Jason G. Bragg
- National Herbarium of New South Wales Royal Botanic Gardens and Domain Trust Sydney NSW Australia
| | - Peter Cuneo
- Australian PlantBank Australian Botanic Garden, Mount Annan Royal Botanic Gardens and Domain Trust Sydney NSW Australia
| | - Ahamad Sherieff
- NSW Office of Environment and Heritage Hurstville NSW Australia
| | - Maurizio Rossetto
- National Herbarium of New South Wales Royal Botanic Gardens and Domain Trust Sydney NSW Australia
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24
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Kooyman RM, Morley RJ, Crayn DM, Joyce EM, Rossetto M, Slik JF, Strijk JS, Su T, Yap JYS, Wilf P. Origins and Assembly of Malesian Rainforests. Annu Rev Ecol Evol Syst 2019. [DOI: 10.1146/annurev-ecolsys-110218-024737] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Unraveling the origins of Malesia's once vast, hyperdiverse rainforests is a perennial challenge. Major contributions to rainforest assembly came from floristic elements carried on the Indian Plate and montane elementsfrom the Australian Plate (Sahul). The Sahul component is now understood to include substantial two-way exchanges with Sunda inclusive of lowland taxa. Evidence for the relative contributions of the great Asiatic floristic interchanges (GAFIs) with India and Sahul, respectively, to the flora of Malesia comes from contemporary lineage distributions, the fossil record, time-calibrated phylogenies, functional traits, and the spatial structure of genetic diversity. Functional-trait and biome conservatism are noted features of montane austral lineages from Sahul (e.g., diverse Podocarpaceae), whereas the abundance and diversity of lowland lineages, including Syzygium (Myrtaceae) and the Asian dipterocarps (Dipterocarpoideae), reflect a less well understood combination of dispersal, ecology, and adaptive radiations. Thus, Malesian rainforest assembly has been shaped by sharply contrasting evolutionary origins and biogeographic histories.
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Affiliation(s)
- Robert M. Kooyman
- Department of Biological Sciences, Macquarie University, Sydney, New South Wales 2109, Australia
- National Herbarium of New South Wales, Royal Botanic Gardens and Domain Trust, Sydney, New South Wales 2000, Australia
| | - Robert J. Morley
- Palynova UK, Littleport, Cambridgeshire CB6 1PY, United Kingdom
- Earth Sciences Department, Royal Holloway, University of London, Egham, Surrey TW20 0EX, United Kingdom
| | - Darren M. Crayn
- Australian Tropical Herbarium and Centre for Tropical Environmental Sustainability Science, James Cook University, Smithfield, Queensland 4878, Australia
| | - Elizabeth M. Joyce
- Australian Tropical Herbarium and Centre for Tropical Environmental Sustainability Science, James Cook University, Smithfield, Queensland 4878, Australia
| | - Maurizio Rossetto
- National Herbarium of New South Wales, Royal Botanic Gardens and Domain Trust, Sydney, New South Wales 2000, Australia
| | - J.W. Ferry Slik
- Environmental and Life Sciences, Faculty of Science, Universiti Brunei Darussalam, Gadong BE1410, Brunei Darussalam
| | - Joeri S. Strijk
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Forestry, Guangxi University, Nanning, Guangxi 530005, China
- Alliance for Conservation Tree Genomics, Pha Tad Ke Botanical Garden, 06000 Luang Prabang, Lao PDR
- Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla 666303, China
| | - Tao Su
- Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla 666303, China
- Southeast Asia Biodiversity Research Institute, Chinese Academy of Sciences, Yezin, Nay Pyi Taw 05282, Myanmar
| | - Jia-Yee S. Yap
- National Herbarium of New South Wales, Royal Botanic Gardens and Domain Trust, Sydney, New South Wales 2000, Australia
- Queensland Alliance of Agriculture and Food Innovation, University of Queensland, Brisbane, Queensland 4072, Australia
| | - Peter Wilf
- Department of Geosciences, Pennsylvania State University, University Park, Pennsylvania 16802, USA
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25
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Rutherford S, van der Merwe M, Wilson PG, Kooyman RM, Rossetto M. Managing the risk of genetic swamping of a rare and restricted tree. CONSERV GENET 2019. [DOI: 10.1007/s10592-019-01201-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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26
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Merwe M, Yap JS, Bragg JG, Cristofolini C, Foster CSP, Ho SYW, Rossetto M. Assemblage accumulation curves: A framework for resolving species accumulation in biological communities using DNA sequences. Methods Ecol Evol 2019. [DOI: 10.1111/2041-210x.13181] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Marlien Merwe
- National Herbarium of New South Wales Royal Botanic Garden Sydney Sydney New South Wales Australia
| | - Jia‐Yee S. Yap
- National Herbarium of New South Wales Royal Botanic Garden Sydney Sydney New South Wales Australia
- Queensland Alliance of Agriculture and Food Innovation University of Queensland Brisbane Queensland Australia
| | - Jason G. Bragg
- National Herbarium of New South Wales Royal Botanic Garden Sydney Sydney New South Wales Australia
| | - Caroline Cristofolini
- National Herbarium of New South Wales Royal Botanic Garden Sydney Sydney New South Wales Australia
| | - Charles S. P. Foster
- School of Life and Environmental Sciences University of Sydney Sydney New South Wales Australia
| | - Simon Y. W. Ho
- School of Life and Environmental Sciences University of Sydney Sydney New South Wales Australia
| | - Maurizio Rossetto
- National Herbarium of New South Wales Royal Botanic Garden Sydney Sydney New South Wales Australia
- Queensland Alliance of Agriculture and Food Innovation University of Queensland Brisbane Queensland Australia
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Guerin GR, Andersen AN, Rossetto M, van Leeuwen S, Byrne M, Sparrow B, Rodrigo M, Lowe AJ. Consistent sorting but contrasting transition zones in plant communities along bioclimatic gradients. Acta Oecologica 2019. [DOI: 10.1016/j.actao.2019.01.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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Rossetto M, Bragg J, Kilian A, McPherson H, van der Merwe M, Wilson PD. Restore and Renew: a genomics‐era framework for species provenance delimitation. Restor Ecol 2018. [DOI: 10.1111/rec.12898] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
- Maurizio Rossetto
- National Herbarium of New South WalesRoyal Botanic Garden Sydney Mrs Macquaries Road, Sydney NSW 2000 Australia
| | - Jason Bragg
- National Herbarium of New South WalesRoyal Botanic Garden Sydney Mrs Macquaries Road, Sydney NSW 2000 Australia
| | - Andrzej Kilian
- Diversity Arrays TechnologyUniversity of Canberra Bruce ACT 2617 Australia
| | - Hannah McPherson
- National Herbarium of New South WalesRoyal Botanic Garden Sydney Mrs Macquaries Road, Sydney NSW 2000 Australia
| | - Marlien van der Merwe
- National Herbarium of New South WalesRoyal Botanic Garden Sydney Mrs Macquaries Road, Sydney NSW 2000 Australia
| | - Peter D. Wilson
- National Herbarium of New South WalesRoyal Botanic Garden Sydney Mrs Macquaries Road, Sydney NSW 2000 Australia
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29
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Worth JRP, Marthick JR, Rossetto M, Cohen J, Bourke G, Jordan GJ. Development of 15 nuclear EST microsatellite markers for the paleoendemic conifer Pherosphaera hookeriana (Podocarpaceae). Appl Plant Sci 2018; 6:e01160. [PMID: 30131902 PMCID: PMC6025810 DOI: 10.1002/aps3.1160] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Accepted: 04/10/2018] [Indexed: 05/23/2023]
Abstract
PREMISE OF THE STUDY Nuclear microsatellite markers were developed for population genetic analysis of the threatened paleoendemic conifer Pherosphaera hookeriana (Podocarpaceae). METHODS AND RESULTS Fifteen variable loci were identified showing one to 13 alleles per population, with seven loci displaying at least four alleles in all populations, and the average number of alleles per locus ranging from 4.80 to 5.93 per population. Levels of observed heterozygosity per locus varied from 0.00 to 0.91, while average heterozygosity across all loci varied from 0.54 to 0.63 between populations. All loci also amplified in the endangered congener P. fitzgeraldii, but only five of the loci had more than one allele. CONCLUSIONS These 15 loci are the first microsatellite markers developed in the genus Pherosphaera. These loci will be useful for investigating the species' extant genetic diversity and structure, the impact of past environmental change, and the significance of asexual reproduction.
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Affiliation(s)
- James R. P. Worth
- Department of Forest Molecular Genetics and BiotechnologyForestry and Forest Products Research InstituteMatsunosato 1TsukubaIbaraki305‐8687Japan
| | - James R. Marthick
- Menzies Institute for Medical ResearchUniversity of TasmaniaHobartTasmaniaAustralia
| | - Maurizio Rossetto
- National Herbarium of New South WalesRoyal Botanic Gardens and Domain TrustMrs. Macquaries RoadSydneyNew South Wales2000Australia
| | - Joel Cohen
- National Herbarium of New South WalesRoyal Botanic Gardens and Domain TrustMrs. Macquaries RoadSydneyNew South Wales2000Australia
| | - Greg Bourke
- Blue Mountains Botanic Garden1–17 Tomah DriveMount TomahNew South Wales2758Australia
| | - Gregory J. Jordan
- School of Biological SciencesUniversity of TasmaniaPrivate Bag 55HobartTasmaniaAustralia
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Rutherford S, Rossetto M, Bragg JG, McPherson H, Benson D, Bonser SP, Wilson PG. Speciation in the presence of gene flow: population genomics of closely related and diverging Eucalyptus species. Heredity (Edinb) 2018; 121:126-141. [PMID: 29632325 DOI: 10.1038/s41437-018-0073-2] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2017] [Revised: 03/12/2018] [Accepted: 03/12/2018] [Indexed: 01/22/2023] Open
Abstract
Speciation is a complex process that is fundamental to the origins of biological diversity. While there has been considerable progress in our understanding of speciation, there are still many unanswered questions, especially regarding barriers to gene flow in diverging populations. Eucalyptus is an appropriate system for investigating speciation mechanisms since it comprises species that are rapidly evolving across heterogeneous environments. We examined patterns of genetic variation within and among six closely related Eucalyptus species in subgenus Eucalyptus section Eucalyptus in south-eastern Australia (commonly known as the "green ashes"). We used reduced representation genome sequencing to genotype samples from populations across altitudinal and latitudinal gradients. We found one species, Eucalyptus cunninghamii, to be highly genetically differentiated from the others, and a population of mallees from Mount Banks to be genetically distinct and therefore likely to be a new undescribed species. Only modest levels of differentiation were found between all other species in the study. There was population structure within some species (e.g., E. obstans) corresponding to geographical factors, indicating that vicariance may have played a role in the evolution of the group. Overall, we found that lineages within the green ashes are differentiated to varying extents, from strongly diverged to much earlier stages of the speciation continuum. Furthermore, our results suggest the green ashes represent a group where a range of mechanisms (e.g., reticulate evolution and vicariance) have been operating in concert. These findings not only offer insights into recent speciation mechanisms in Eucalyptus, but also other species complexes.
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Affiliation(s)
- Susan Rutherford
- Evolution and Ecology Research Centre, School of Biological, Earth and Environmental Sciences, UNSW, Kensington, Sydney, Australia. .,National Herbarium of NSW, Royal Botanic Garden Sydney, Sydney, Australia.
| | - Maurizio Rossetto
- National Herbarium of NSW, Royal Botanic Garden Sydney, Sydney, Australia
| | - Jason G Bragg
- National Herbarium of NSW, Royal Botanic Garden Sydney, Sydney, Australia
| | - Hannah McPherson
- National Herbarium of NSW, Royal Botanic Garden Sydney, Sydney, Australia
| | - Doug Benson
- National Herbarium of NSW, Royal Botanic Garden Sydney, Sydney, Australia
| | - Stephen P Bonser
- Evolution and Ecology Research Centre, School of Biological, Earth and Environmental Sciences, UNSW, Kensington, Sydney, Australia
| | - Peter G Wilson
- National Herbarium of NSW, Royal Botanic Garden Sydney, Sydney, Australia
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31
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Mackay K, Gross C, Rossetto M. Small populations of fig trees offer a keystone food resource and conservation benefits for declining insectivorous birds. Glob Ecol Conserv 2018. [DOI: 10.1016/j.gecco.2018.e00403] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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32
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Foster CSP, Sauquet H, van der Merwe M, McPherson H, Rossetto M, Ho SYW. Evaluating the Impact of Genomic Data and Priors on Bayesian Estimates of the Angiosperm Evolutionary Timescale. Syst Biol 2018; 66:338-351. [PMID: 27650175 DOI: 10.1093/sysbio/syw086] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2015] [Accepted: 09/10/2016] [Indexed: 11/14/2022] Open
Abstract
The evolutionary timescale of angiosperms has long been a key question in biology. Molecular estimates of this timescale have shown considerable variation, being influenced by differences in taxon sampling, gene sampling, fossil calibrations, evolutionary models, and choices of priors. Here, we analyze a data set comprising 76 protein-coding genes from the chloroplast genomes of 195 taxa spanning 86 families, including novel genome sequences for 11 taxa, to evaluate the impact of models, priors, and gene sampling on Bayesian estimates of the angiosperm evolutionary timescale. Using a Bayesian relaxed molecular-clock method, with a core set of 35 minimum and two maximum fossil constraints, we estimated that crown angiosperms arose 221 (251-192) Ma during the Triassic. Based on a range of additional sensitivity and subsampling analyses, we found that our date estimates were generally robust to large changes in the parameters of the birth-death tree prior and of the model of rate variation across branches. We found an exception to this when we implemented fossil calibrations in the form of highly informative gamma priors rather than as uniform priors on node ages. Under all other calibration schemes, including trials of seven maximum age constraints, we consistently found that the earliest divergences of angiosperm clades substantially predate the oldest fossils that can be assigned unequivocally to their crown group. Overall, our results and experiments with genome-scale data suggest that reliable estimates of the angiosperm crown age will require increased taxon sampling, significant methodological changes, and new information from the fossil record. [Angiospermae, chloroplast, genome, molecular dating, Triassic.].
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Affiliation(s)
- Charles S P Foster
- School of Life and Environmental Sciences, Edgeworth David Building A11, University of Sydney, Sydney, New South Wales 2006, Australia
| | - Hervê Sauquet
- Laboratoire écologie, Systématique, évolution, Université Paris-Sud, CNRS UMR 8079, bat. 360, Orsay 91405, France
| | - Marlien van der Merwe
- National Herbarium of New South Wales, Royal Botanic Gardens & Domain Trust, Mrs Macquaries Road, Sydney, New South Wales 2000, Australia
| | - Hannah McPherson
- National Herbarium of New South Wales, Royal Botanic Gardens & Domain Trust, Mrs Macquaries Road, Sydney, New South Wales 2000, Australia
| | - Maurizio Rossetto
- National Herbarium of New South Wales, Royal Botanic Gardens & Domain Trust, Mrs Macquaries Road, Sydney, New South Wales 2000, Australia
| | - Simon Y W Ho
- School of Life and Environmental Sciences, Edgeworth David Building A11, University of Sydney, Sydney, New South Wales 2006, Australia
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33
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Rossetto M, Ens EJ, Honings T, Wilson PD, Yap JYS, Costello O, Round ER, Bowern C. From Songlines to genomes: Prehistoric assisted migration of a rain forest tree by Australian Aboriginal people. PLoS One 2017; 12:e0186663. [PMID: 29117184 PMCID: PMC5695580 DOI: 10.1371/journal.pone.0186663] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2017] [Accepted: 10/05/2017] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Prehistoric human activities have contributed to the dispersal of many culturally important plants. The study of these traditional interactions can alter the way we perceive the natural distribution and dynamics of species and communities. Comprehensive research on native crops combining evolutionary and anthropological data is revealing how ancient human populations influenced their distribution. Although traditional diets also included a suite of non-cultivated plants that in some cases necessitated the development of culturally important technical advances such as the treatment of toxic seed, empirical evidence for their deliberate dispersal by prehistoric peoples remains limited. Here we integrate historic and biocultural research involving Aboriginal people, with chloroplast and nuclear genomic data to demonstrate Aboriginal-mediated dispersal of a non-cultivated rainforest tree. RESULTS We assembled new anthropological evidence of use and deliberate dispersal of Castanospermum australe (Fabaceae), a non-cultivated culturally important riparian tree that produces toxic but highly nutritious water-dispersed seed. We validated cultural evidence of recent human-mediated dispersal by revealing genomic homogeneity across extensively dissected habitat, multiple catchments and uneven topography in the southern range of this species. We excluded the potential contribution of other dispersal mechanisms based on the absence of suitable vectors and current distributional patterns at higher elevations and away from water courses, and by analyzing a comparative sample from northern Australia. CONCLUSIONS Innovative studies integrating evolutionary and anthropological data will continue to reveal the unexpected impact that prehistoric people have had on current vegetation patterns. A better understanding of how traditional practices shaped species' distribution and assembly will directly inform cultural heritage management strategies, challenge "natural" species distribution assumptions, and provide innovative baseline data for pro-active biodiversity management.
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Affiliation(s)
- Maurizio Rossetto
- National Herbarium of NSW, Royal Botanic Gardens and Domain Trust, Sydney, New South Wales, Australia
- Queensland Alliance of Agriculture and Food Innovation, University of Queensland, Brisbane, Australia
| | - Emilie J. Ens
- Department of Environmental Sciences, Macquarie University, Sydney, New South Wales, Australia
| | - Thijs Honings
- National Herbarium of NSW, Royal Botanic Gardens and Domain Trust, Sydney, New South Wales, Australia
- Biological Sciences, Leiden University, Sylviusweg, Leiden, the Netherlands
| | - Peter D. Wilson
- National Herbarium of NSW, Royal Botanic Gardens and Domain Trust, Sydney, New South Wales, Australia
| | - Jia-Yee S. Yap
- National Herbarium of NSW, Royal Botanic Gardens and Domain Trust, Sydney, New South Wales, Australia
- Queensland Alliance of Agriculture and Food Innovation, University of Queensland, Brisbane, Australia
| | - Oliver Costello
- Aboriginal Heritage and Joint Management Team, Office of Environment and Heritage, New South Wales, Australia
| | - Erich R. Round
- Ancient Language Lab, School of Languages and Cultures, University of Queensland, Brisbane, Australia
| | - Claire Bowern
- Department of Linguistics, Yale University, New Haven, Connecticut, United States of America
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Lowe AJ, Smyth AK, Atkins K, Avery R, Belbin L, Brown N, Budden AE, Gioia P, Guru S, Hardie M, Hirsch T, Hobern D, La Salle J, Loarie SR, Miles M, Milne D, Nicholls M, Rossetto M, Smits J, Sparrow B, Terrill G, Turner D, Wardle GM. Publish openly but responsibly. Science 2017; 357:141. [PMID: 28706032 DOI: 10.1126/science.aao0054] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Affiliation(s)
- Andrew J Lowe
- Department of Biological Sciences, University of Adelaide, Adelaide, SA 5005, Australia.
| | - Anita K Smyth
- Terrestrial Ecosystem Research Network-Ecoinformatics, University of Adelaide, Adelaide SA 5005, Australia
| | - Ken Atkins
- Department of Parks and Wildlife, Kensington, WA 6151, Australia
| | - Ron Avery
- Office of Environment and Heritage, Sydney South, NSW 1232, Australia
| | - Lee Belbin
- Atlas of Living Australia, Tasmania, Australia
| | - Noleen Brown
- Department of Science, Information Technology and Innovation, Brisbane, QLD 4001, Australia
| | - Amber E Budden
- DataONE, University of New Mexico, Albuquerque, NM 87106, USA
| | - Paul Gioia
- Department of Parks and Wildlife, Kensington, WA 6151, Australia
| | - Siddeswara Guru
- Terrestrial Ecosystem Research Network, The University of Queensland, Queensland, QLD 4072
| | - Mel Hardie
- Department of Environment, Land, Water, and Planning, East Melbourne, VIC 8002, Australia
| | - Tim Hirsch
- Global Biodiversity Information Facility Secretariat, Copenhagen, 2100, Denmark
| | - Donald Hobern
- Global Biodiversity Information Facility Secretariat, Copenhagen, 2100, Denmark
| | - John La Salle
- Atlas of Living Australia, CSIRO National Research Collections Australia, Canberra, ACT 2601, Australia
| | - Scott R Loarie
- iNaturalist.org, California Academy of Sciences, San Francisco, CA 94118, USA
| | - Matt Miles
- Department of Environment, Water, and Natural Resources, Adelaide, SA 5000, Australia
| | - Damian Milne
- Department of Environment and Natural Resources, Palmerston, NT 0830, Australia
| | - Miles Nicholls
- Atlas of Living Australia, CSIRO National Research Collections Australia, Canberra, ACT 2601, Australia
| | - Maurizio Rossetto
- National Herbarium of New South Wales, Royal Botanic Garden and Domain Trust, Sydney, NSW 2000, Australia
| | - Jennifer Smits
- Environment, Planning and Sustainable Development Directorate, Australian Capital Territory Government, Canberra, ACT 2601, Australia
| | - Ben Sparrow
- Terrestrial Ecosystem Research Network-Ecoinformatics, University of Adelaide, Adelaide SA 5005, Australia
| | - Gregston Terrill
- Department of Environment and Energy, Parkes, ACT 2600, Australia
| | - David Turner
- Terrestrial Ecosystem Research Network-Ecoinformatics, University of Adelaide, Adelaide SA 5005, Australia
| | - Glenda M Wardle
- School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW 2006, Australia
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35
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Worth JRP, Holland BR, Beeton NJ, Schönfeld B, Rossetto M, Vaillancourt RE, Jordan GJ. Habitat type and dispersal mode underlie the capacity for plant migration across an intermittent seaway. Ann Bot 2017; 120:539-549. [PMID: 28961707 PMCID: PMC5737502 DOI: 10.1093/aob/mcx086] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2016] [Accepted: 06/06/2017] [Indexed: 06/07/2023]
Abstract
BACKGROUND AND AIMS Investigating species distributions across geographic barriers is a commonly utilized method in biogeography to help understand the functional traits that allow plants to disperse successfully. Here the biogeographic pattern analysis approach is extended by using chloroplast DNA whole-genome 'mining' to examine the functional traits that have impacted the dispersal of widespread temperate forest species across an intermittent seaway, the 200 km wide Bass Strait of south-eastern Australia. METHODS Multiple, co-distributed species of both dry and wet forests were sampled from five regions on either side of the Strait to obtain insights into past dispersal of these biomes via seed. Using a next-generation sequencing-based pool-seq method, the sharing of single nucleotide polymorphisms (SNPs) was estimated between all five regions in the chloroplast genome. KEY RESULTS A total of 3335 SNPs were detected in 20 species. SNP sharing patterns between regions provided evidence for significant seed-mediated gene flow across the study area, including across Bass Strait. A higher proportion of shared SNPs in dry forest species, especially those dispersed by birds, compared with wet forest species suggests that dry forest species have undergone greater seed-mediated gene flow across the study region during past climatic oscillations and sea level changes associated with the interglacial/glacial cycles. CONCLUSIONS This finding is consistent with a greater propensity for long-distance dispersal for species of open habitats and proxy evidence that expansive areas of dry vegetation occurred during times of exposure of Bass Strait during glacials. Overall, this study provides novel genetic evidence that habitat type and its interaction with dispersal traits are major influences on dispersal of plants.
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Affiliation(s)
- J R P Worth
- Forestry and Forest Products Research Institute, Matsunosato 1, Tsukuba, Ibaraki 305-8687, Japan
| | - B R Holland
- School of Physical Sciences, University of Tasmania, Private Bag 37, Hobart, Tasmania 7001, Australia
| | - N J Beeton
- School of Biological Sciences, University of Tasmania, Private Bag 55, Hobart, Tasmania 7001, Australia
| | - B Schönfeld
- School of Biological Sciences, University of Tasmania, Private Bag 55, Hobart, Tasmania 7001, Australia
| | - M Rossetto
- National Herbarium of New South Wales, Royal Botanic Gardens & Domain Trust, Mrs Macquaries Rd, Sydney, NSW, 2000, Australia
| | - R E Vaillancourt
- School of Biological Sciences, University of Tasmania, Private Bag 55, Hobart, Tasmania 7001, Australia
| | - G J Jordan
- School of Biological Sciences, University of Tasmania, Private Bag 55, Hobart, Tasmania 7001, Australia
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36
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Rutherford S, Bonser SP, Wilson PG, Rossetto M. Seedling response to environmental variability: The relationship between phenotypic plasticity and evolutionary history in closely related Eucalyptus species. Am J Bot 2017; 104:840-857. [PMID: 28611071 DOI: 10.3732/ajb.1600439] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2016] [Accepted: 05/01/2017] [Indexed: 06/07/2023]
Abstract
PREMISE OF THE STUDY Phenotypic plasticity is an important means through which organisms cope with environmental variability. We investigated seedling plasticity in the green ash eucalypts within a phylogenetic framework to examine the relationship between plasticity and evolutionary history. The green ashes are a diverse group, which include the tallest flowering plant in the world (Eucalyptus regnans) and a rare mallee less than 1 m tall (E. cunninghamii). METHODS Seedlings of 12 species were exposed to high and low nutrient and water availability in a factorial experiment. Leaf trait and total plant plasticity were evaluated using the phenotypic plasticity index. A phylogeny of the species was estimated using genome-wide scans. KEY RESULTS We found significant differences in functional traits across species, growth forms, and substrates in response to changes in resource availability. Many traits (e.g., leaf width) were highly plastic for most species. Interspecific differences in leaf-level plasticity was significant, however plasticity was not correlated with phylogeny. Species with broader environmental niches had higher leaf-level plasticity than species with narrower environmental ranges. CONCLUSIONS Plastic responses to environmental variability can differ widely among closely related species, and plasticity is therefore likely to be associated with many factors, including habitat and range size, as well as evolutionary history. Our results provided insights for species delimitation in Eucalyptus, which have management implications. Because of the high number of rare species and that other species are commercially important, a more comprehensive understanding of plasticity is essential for predicting their response to changing climates.
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Affiliation(s)
- Susan Rutherford
- Evolution and Ecology Research Centre, School of Biological, Earth and Environmental Sciences, UNSW Australia, Sydney, Australia
- National Herbarium of New South Wales, Royal Botanic Gardens and Domain Trust, Sydney, Australia
| | - Stephen P Bonser
- Evolution and Ecology Research Centre, School of Biological, Earth and Environmental Sciences, UNSW Australia, Sydney, Australia
| | - Peter G Wilson
- National Herbarium of New South Wales, Royal Botanic Gardens and Domain Trust, Sydney, Australia
| | - Maurizio Rossetto
- National Herbarium of New South Wales, Royal Botanic Gardens and Domain Trust, Sydney, Australia
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37
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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] [What about the content of this article? (0)] [Affiliation(s)] [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.
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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
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Rossetto M, Kooyman R, Yap JYS, Laffan SW. From ratites to rats: the size of fleshy fruits shapes species' distributions and continental rainforest assembly. Proc Biol Sci 2017; 282:20151998. [PMID: 26645199 DOI: 10.1098/rspb.2015.1998] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Seed dispersal is a key process in plant spatial dynamics. However, consistently applicable generalizations about dispersal across scales are mostly absent because of the constraints on measuring propagule dispersal distances for many species. Here, we focus on fleshy-fruited taxa, specifically taxa with large fleshy fruits and their dispersers across an entire continental rainforest biome. We compare species-level results of whole-chloroplast DNA analyses in sister taxa with large and small fruits, to regional plot-based samples (310 plots), and whole-continent patterns for the distribution of woody species with either large (more than 30 mm) or smaller fleshy fruits (1093 taxa). The pairwise genomic comparison found higher genetic distances between populations and between regions in the large-fruited species (Endiandra globosa), but higher overall diversity within the small-fruited species (Endiandra discolor). Floristic comparisons among plots confirmed lower numbers of large-fruited species in areas where more extreme rainforest contraction occurred, and re-colonization by small-fruited species readily dispersed by the available fauna. Species' distribution patterns showed that larger-fruited species had smaller geographical ranges than smaller-fruited species and locations with stable refugia (and high endemism) aligned with concentrations of large fleshy-fruited taxa, making them a potentially valuable conservation-planning indicator.
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Affiliation(s)
- Maurizio Rossetto
- National Herbarium of NSW, The Royal Botanic Gardens and Domain Trust, Mrs Macquaries Road, Sydney, New South Wales 2000, Australia QAAFI, The University of Queensland, St Lucia, Queensland 4072, Australia
| | - Robert Kooyman
- National Herbarium of NSW, The Royal Botanic Gardens and Domain Trust, Mrs Macquaries Road, Sydney, New South Wales 2000, Australia Department of Biological Sciences, Macquarie University, Sydney, New South Wales 2109, Australia
| | - Jia-Yee S Yap
- National Herbarium of NSW, The Royal Botanic Gardens and Domain Trust, Mrs Macquaries Road, Sydney, New South Wales 2000, Australia QAAFI, The University of Queensland, St Lucia, Queensland 4072, Australia
| | - Shawn W Laffan
- Centre for Ecosystem Science, School of Biological, Earth and Environmental Science, University of New South Wales, Sydney 2052, Australia
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Broadhurst L, Breed M, Lowe A, Bragg J, Catullo R, Coates D, Encinas-Viso F, Gellie N, James E, Krauss S, Potts B, Rossetto M, Shepherd M, Byrne M. Genetic diversity and structure of the Australian flora. DIVERS DISTRIB 2016. [DOI: 10.1111/ddi.12505] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Affiliation(s)
- Linda Broadhurst
- Centre for Australian National Biodiversity Research; CSIRO National Research Collections Australia; PO Box 1600 Canberra ACT 2601 Australia
| | - Martin Breed
- Environment Institute; School of Biological Sciences; University of Adelaide; North Terrace SA 5005 Australia
| | - Andrew Lowe
- Environment Institute; School of Biological Sciences; University of Adelaide; North Terrace SA 5005 Australia
| | - Jason Bragg
- National Herbarium of NSW; Royal Botanic Gardens & Domain Trust; Mrs Macquaries Road Sydney NSW 2000 Australia
| | - Renee Catullo
- School of Science and Health; Western Sydney University; Sydney NSW 2751 Australia
| | - David Coates
- Science and Conservation Division; Department of Parks and Wildlife; Locked Bag 104 Bentley Delivery Centre Perth WA 6983 Australia
| | - Francisco Encinas-Viso
- Centre for Australian National Biodiversity Research; CSIRO National Research Collections Australia; PO Box 1600 Canberra ACT 2601 Australia
| | - Nick Gellie
- Environment Institute; School of Biological Sciences; University of Adelaide; North Terrace SA 5005 Australia
| | - Elizabeth James
- Royal Botanic Gardens Victoria; Private Bag 2000 Melbourne Vic. 3141 Australia
| | - Siegfried Krauss
- Science Directorate, Botanic Gardens and Parks Authority; Fraser Avenue West Perth WA 6005 Australia
- School of Plant Biology; The University of Western Australia; Crawley WA 6907 Australia
| | - Brad Potts
- School of Biological Sciences; University of Tasmania; Hobart Tas. 7001 Australia
| | - Maurizio Rossetto
- National Herbarium of NSW; Royal Botanic Gardens & Domain Trust; Mrs Macquaries Road Sydney NSW 2000 Australia
| | - Mervyn Shepherd
- Southern Cross Plant Science; Southern Cross University; Lismore NSW 2480 Australia
| | - Margaret Byrne
- Science and Conservation Division; Department of Parks and Wildlife; Locked Bag 104 Bentley Delivery Centre Perth WA 6983 Australia
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Kooyman RM, Wilf P, Barreda VD, Carpenter RJ, Jordan GJ, Sniderman JMK, Allen A, Brodribb TJ, Crayn D, Feild TS, Laffan SW, Lusk CH, Rossetto M, Weston PH. Paleo-Antarctic rainforest into the modern Old World tropics: the rich past and threatened future of the "southern wet forest survivors". Am J Bot 2014; 101:2121-2135. [PMID: 25480709 DOI: 10.3732/ajb.1400340] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
UNLABELLED • PREMISE OF STUDY Have Gondwanan rainforest floral associations survived? Where do they occur today? Have they survived continuously in particular locations? How significant is their living floristic signal? We revisit these classic questions in light of significant recent increases in relevant paleobotanical data.• METHODS We traced the extinction and persistence of lineages and associations through the past across four now separated regions-Australia, New Zealand, Patagonia, and Antarctica-using fossil occurrence data from 63 well-dated Gondwanan rainforest sites and 396 constituent taxa. Fossil sites were allocated to four age groups: Cretaceous, Paleocene-Eocene, Neogene plus Oligocene, and Pleistocene. We compared the modern and ancient distributions of lineages represented in the fossil record to see if dissimilarity increased with time. We quantified similarity-dissimilarity of composition and taxonomic structure among fossil assemblages, and between fossil and modern assemblages.• KEY RESULTS Strong similarities between ancient Patagonia and Australia confirmed shared Gondwanan rainforest history, but more of the lineages persisted in Australia. Samples of ancient Australia grouped with the extant floras of Australia, New Guinea, New Caledonia, Fiji, and Mt. Kinabalu. Decreasing similarity through time among the regional floras of Antarctica, Patagonia, New Zealand, and southern Australia reflects multiple extinction events.• CONCLUSIONS Gondwanan rainforest lineages contribute significantly to modern rainforest community assembly and often co-occur in widely separated assemblages far from their early fossil records. Understanding how and where lineages from ancient Gondwanan assemblages co-occur today has implications for the conservation of global rainforest vegetation, including in the Old World tropics.
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Affiliation(s)
- Robert M Kooyman
- Department of Biological Sciences, Macquarie University, North Ryde 2113, Sydney, Australia National Herbarium of NSW, Royal Botanic Gardens and Domain Trust, Mrs Macquaries Road, Sydney 2000, Australia
| | - Peter Wilf
- Department of Geosciences, Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Viviana D Barreda
- Museo Argentino de Ciencias Naturales, CONICET, División Paleobotánica, Av. Ángel Gallardo 470, C1405DJR Buenos Aires, Argentina
| | - Raymond J Carpenter
- School of Earth and Environmental Sciences, Benham Bldg DX 650 312, University of Adelaide, South Australia, Australia
| | - Gregory J Jordan
- School of Biological Sciences, University of Tasmania, Private Bag 55 Hobart, 7001 Tasmania, Australia
| | - J M Kale Sniderman
- School of Earth Sciences, University of Melbourne, Melbourne 3010, Australia
| | - Andrew Allen
- Department of Biological Sciences, Macquarie University, North Ryde 2113, Sydney, Australia
| | - Timothy J Brodribb
- School of Biological Sciences, University of Tasmania, Private Bag 55 Hobart, 7001 Tasmania, Australia
| | - Darren Crayn
- Australian Tropical Herbarium, School of Marine and Tropical Biology, James Cook University, Cairns, Australia
| | - Taylor S Feild
- Australian Tropical Herbarium, School of Marine and Tropical Biology, James Cook University, Cairns, Australia
| | - Shawn W Laffan
- Centre for Ecosystem Science, School of Biological, Earth and Environmental Sciences, University of New South Wales, Kensington 2052, Sydney, Australia
| | - Christopher H Lusk
- School of Science, University of Waikato, Private Bag 3105, Hamilton, New Zealand
| | - Maurizio Rossetto
- National Herbarium of NSW, Royal Botanic Gardens and Domain Trust, Mrs Macquaries Road, Sydney 2000, Australia
| | - Peter H Weston
- National Herbarium of NSW, Royal Botanic Gardens and Domain Trust, Mrs Macquaries Road, Sydney 2000, Australia
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Rossetto M, Henry RJ. Escape from the laboratory: new horizons for plant genetics. Trends Plant Sci 2014; 19:554-555. [PMID: 25008042 DOI: 10.1016/j.tplants.2014.06.011] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2014] [Revised: 06/23/2014] [Accepted: 06/30/2014] [Indexed: 06/03/2023]
Abstract
Next generation sequencing (NGS) is changing the way biologists work, as large amounts of genetic data can be easily outsourced commercially. Consequently, crucial research efforts in plant genetics can now be found outside the traditional laboratory setting, allowing for novel and more challenging scientific questions to be answered by virtual collaborative networks.
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Affiliation(s)
- Maurizio Rossetto
- National Herbarium of NSW, The Royal Botanic Gardens & Domain Trust, Mrs Macquaries Road, Sydney 2000, NSW Australia.
| | - Robert J Henry
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane 4072, QLD Australia
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Heslewood MM, Lowe AJ, Crayn DM, Rossetto M. Contrasting levels of connectivity and localised persistence characterise the latitudinal distribution of a wind-dispersed rainforest canopy tree. Genetica 2014; 142:251-64. [DOI: 10.1007/s10709-014-9771-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2013] [Accepted: 05/31/2014] [Indexed: 11/29/2022]
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McIntosh EJ, Rossetto M, Weston PH, Wardle GM. Maintenance of strong morphological differentiation despite ongoing natural hybridization between sympatric species of Lomatia (Proteaceae). Ann Bot 2014; 113:861-872. [PMID: 24489011 PMCID: PMC3962242 DOI: 10.1093/aob/mct314] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2013] [Accepted: 12/13/2013] [Indexed: 06/03/2023]
Abstract
BACKGROUND AND AIMS When species cohesion is maintained despite ongoing natural hybridization, many questions are raised about the evolutionary processes operating in the species complex. This study examined the extensive natural hybridization between the Australian native shrubs Lomatia myricoides and L. silaifolia (Proteaceae). These species exhibit striking differences in morphology and ecological preferences, exceeding those found in most studies of hybridization to date. METHODS Nuclear microsatellite markers (nSSRs), genotyping methods and morphometric analyses were used to uncover patterns of hybridization and the role of gene flow in morphological differentiation between sympatric species. KEY RESULTS The complexity of hybridization patterns differed markedly between sites, however, signals of introgression were present at all sites. One site provided evidence of a large hybrid swarm and the likely presence of multiple hybrid generations and backcrosses, another site a handful of early generational hybrids and a third site only traces of admixture from a past hybridization event. The presence of cryptic hybrids and a pattern of morphological bimodality amongst hybrids often disguised the extent of underlying genetic admixture. CONCLUSIONS Distinct parental habitats and phenotypes are expected to form barriers that contribute to the rapid reversion of hybrid populations to their parental character state, due to limited opportunities for hybrid/intermediate advantage. Furthermore, strong genomic filters may facilitate continued gene flow between species without the danger of assimilation. Stochastic fire events facilitate temporal phenological isolation between species and may partly explain the bi-directional and site-specific patterns of hybridization observed. Furthermore, the findings suggest that F1 hybrids are rare, and backcrosses may occur rapidly following these initial hybridization events.
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Affiliation(s)
- Emma J. McIntosh
- The Royal Botanic Gardens and Domain Trust, Sydney, New South Wales, Australia
- School of Biological Sciences, the University of Sydney, Sydney, New South Wales, Australia
| | - Maurizio Rossetto
- The Royal Botanic Gardens and Domain Trust, Sydney, New South Wales, Australia
| | - Peter H. Weston
- The Royal Botanic Gardens and Domain Trust, Sydney, New South Wales, Australia
| | - Glenda M. Wardle
- School of Biological Sciences, the University of Sydney, Sydney, New South Wales, Australia
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Li X, Yang Y, Henry RJ, Rossetto M, Wang Y, Chen S. Plant DNA barcoding: from gene to genome. Biol Rev Camb Philos Soc 2014; 90:157-66. [DOI: 10.1111/brv.12104] [Citation(s) in RCA: 438] [Impact Index Per Article: 43.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2013] [Revised: 02/05/2014] [Accepted: 02/27/2014] [Indexed: 12/01/2022]
Affiliation(s)
- Xiwen Li
- State Key Laboratory of Quality Research in Chinese Medicine; Institute of Chinese Medical Sciences, University of Macau; Macau 999078 China
| | - Yang Yang
- State Key Laboratory of Quality Research in Chinese Medicine; Institute of Chinese Medical Sciences, University of Macau; Macau 999078 China
| | - Robert J. Henry
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland; Brisbane Queensland 4072 Australia
| | - Maurizio Rossetto
- National Herbarium of NSW, The Royal Botanic Gardens and Domain Trust; Mrs Macquaries Road Sydney New South Wales 2000 Australia
| | - Yitao Wang
- State Key Laboratory of Quality Research in Chinese Medicine; Institute of Chinese Medical Sciences, University of Macau; Macau 999078 China
| | - Shilin Chen
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences; Beijing 100700 China
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Kooyman RM, Rossetto M, Sauquet H, Laffan SW. Landscape patterns in rainforest phylogenetic signal: isolated islands of refugia or structured continental distributions? PLoS One 2013; 8:e80685. [PMID: 24312493 PMCID: PMC3846590 DOI: 10.1371/journal.pone.0080685] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2013] [Accepted: 10/04/2013] [Indexed: 11/30/2022] Open
Abstract
Objectives Identify patterns of change in species distributions, diversity, concentrations of evolutionary history, and assembly of Australian rainforests. Methods We used the distribution records of all known rainforest woody species in Australia across their full continental extent. These were analysed using measures of species richness, phylogenetic diversity (PD), phylogenetic endemism (PE) and phylogenetic structure (net relatedness index; NRI). Phylogenetic structure was assessed using both continental and regional species pools. To test the influence of growth-form, freestanding and climbing plants were analysed independently, and in combination. Results Species richness decreased along two generally orthogonal continental axes, corresponding with wet to seasonally dry and tropical to temperate habitats. The PE analyses identified four main areas of substantially restricted phylogenetic diversity, including parts of Cape York, Wet Tropics, Border Ranges, and Tasmania. The continental pool NRI results showed evenness (species less related than expected by chance) in groups of grid cells in coastally aligned areas of species rich tropical and sub-tropical rainforest, and in low diversity moist forest areas in the south-east of the Great Dividing Range and in Tasmania. Monsoon and drier vine forests, and moist forests inland from upland refugia showed phylogenetic clustering, reflecting lower diversity and more relatedness. Signals for evenness in Tasmania and clustering in northern monsoon forests weakened in analyses using regional species pools. For climbing plants, values for NRI by grid cell showed strong spatial structuring, with high diversity and PE concentrated in moist tropical and subtropical regions. Conclusions/Significance Concentrations of rainforest evolutionary history (phylo-diversity) were patchily distributed within a continuum of species distributions. Contrasting with previous concepts of rainforest community distribution, our findings of continuous distributions and continental connectivity have significant implications for interpreting rainforest evolutionary history and current day ecological processes, and for managing rainforest diversity in changing circumstances.
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Affiliation(s)
- Robert M. Kooyman
- Department of Biological Sciences, Macquarie University, Sydney, Australia
- National Herbarium of New South Wales (NSW), Royal Botanic Gardens and Domain Trust, Sydney, Australia
- * E-mail:
| | - Maurizio Rossetto
- National Herbarium of New South Wales (NSW), Royal Botanic Gardens and Domain Trust, Sydney, Australia
| | - Hervé Sauquet
- Laboratoire Ecologie, Systématique, Evolution, Université Paris-Sud, CNRS UMR 8079, Orsay, France
| | - Shawn W. Laffan
- School of Biological, Earth and Environmental Sciences, University of New South Wales, Kensington, Sydney, Australia
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Kooyman RM, Zanne AE, Gallagher RV, Cornwell W, Rossetto M, O'Connor P, Parkes EA, Catterall CF, Laffan SW, Lusk CH. Effects of growth form and functional traits on response of woody plants to clearing and fragmentation of subtropical rainforest. Conserv Biol 2013; 27:1468-1477. [PMID: 23869490 DOI: 10.1111/cobi.12088] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2012] [Accepted: 02/03/2013] [Indexed: 06/02/2023]
Abstract
The conservation implications of large-scale rainforest clearing and fragmentation on the persistence of functional and taxonomic diversity remain poorly understood. If traits represent adaptive strategies of plant species to particular circumstances, the expectation is that the effect of forest clearing and fragmentation will be affected by species functional traits, particularly those related to dispersal. We used species occurrence data for woody plants in 46 rainforest patches across 75,000 ha largely cleared of forest by the early 1900s to determine the combined effects of area reduction, fragmentation, and patch size on the taxonomic structure and functional diversity of subtropical rainforest. We compiled species trait values for leaf area, seed dry mass, wood density, and maximum height and calculated species niche breadths. Taxonomic structure, trait values (means, ranges), and the functional diversity of assemblages of climbing and free-standing plants in remnant patches were quantified. Larger rainforest patches had higher species richness. Species in smaller patches were taxonomically less related than species in larger patches. Free-standing plants had a high percentage of frugivore dispersed seeds; climbers had a high proportion of small wind-dispersed seeds. Connections between the patchy spatial distribution of free-standing species, larger seed sizes, and dispersal syndrome were weak. Assemblages of free-standing plants in patches showed more taxonomic and spatial structuring than climbing plants. Smaller isolated patches retained relatively high functional diversity and similar taxonomic structure to larger tracts of forest despite lower species richness. The response of woody plants to clearing and fragmentation of subtropical rainforest differed between climbers and slow-growing mature-phase forest trees but not between climbers and pioneer trees. Quantifying taxonomic structure and functional diversity provides an improved basis for conservation planning and management by elucidating the effects of forest-area reduction and fragmentation. Efectos de la Forma de Crecimiento y Atributos Funcionales en la Respuesta de Plantas Leñosas al Desmonte y Fragmentación de Bosque Lluvioso Subtropical.
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Affiliation(s)
- R M Kooyman
- National Herbarium of NSW, Royal Botanic Gardens and Domain Trust, Mrs Macquaries Road, Sydney, 2000, Australia; Department of Biological Sciences, Macquarie University, North Ryde 2113, Sydney, Australia
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van der Merwe M, McPherson H, Siow J, Rossetto M. Next-Gen phylogeography of rainforest trees: exploring landscape-level cpDNA variation from whole-genome sequencing. Mol Ecol Resour 2013; 14:199-208. [PMID: 24119022 DOI: 10.1111/1755-0998.12176] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2013] [Revised: 08/29/2013] [Accepted: 09/07/2013] [Indexed: 11/30/2022]
Abstract
Standardized phylogeographic studies across codistributed taxa can identify important refugia and biogeographic barriers, and potentially uncover how changes in adaptive constraints through space and time impact on the distribution of genetic diversity. The combination of next-generation sequencing and methodologies that enable uncomplicated analysis of the full chloroplast genome may provide an invaluable resource for such studies. Here, we assess the potential of a shotgun-based method across twelve nonmodel rainforest trees sampled from two evolutionary distinct regions. Whole genomic shotgun sequencing libraries consisting of pooled individuals were used to assemble species-specific chloroplast references (in silicio). For each species, the pooled libraries allowed for the detection of variation within and between data sets (each representing a geographic region). The potential use of nuclear rDNA as an additional marker from the NGS libraries was investigated by mapping reads against available references. We successfully obtained phylogeographically informative sequence data from a range of previously unstudied rainforest trees. Greater levels of diversity were found in northern refugial rainforests than in southern expansion areas. The genetic signatures of varying evolutionary histories were detected, and interesting associative patterns between functional characteristics and genetic diversity were identified. This approach can suit a wide range of landscape-level studies. As the key laboratory-based steps do not require prior species-specific knowledge and can be easily outsourced, the techniques described here are even suitable for researchers without access to wet-laboratory facilities, making evolutionary ecology questions increasingly accessible to the research community.
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Affiliation(s)
- M van der Merwe
- National Herbarium of NSW, Royal Botanic Gardens & Domain Trust, Mrs Macquaries road, Sydney, NSW, 2000, Australia; School of Earth and Environmental Sciences, The University of Adelaide, Adelaide, SA, 5005, Australia
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McPherson H, van der Merwe M, Delaney SK, Edwards MA, Henry RJ, McIntosh E, Rymer PD, Milner ML, Siow J, Rossetto M. Capturing chloroplast variation for molecular ecology studies: a simple next generation sequencing approach applied to a rainforest tree. BMC Ecol 2013; 13:8. [PMID: 23497206 PMCID: PMC3605380 DOI: 10.1186/1472-6785-13-8] [Citation(s) in RCA: 99] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2012] [Accepted: 03/01/2013] [Indexed: 01/31/2023] Open
Abstract
BACKGROUND With high quantity and quality data production and low cost, next generation sequencing has the potential to provide new opportunities for plant phylogeographic studies on single and multiple species. Here we present an approach for in silicio chloroplast DNA assembly and single nucleotide polymorphism detection from short-read shotgun sequencing. The approach is simple and effective and can be implemented using standard bioinformatic tools. RESULTS The chloroplast genome of Toona ciliata (Meliaceae), 159,514 base pairs long, was assembled from shotgun sequencing on the Illumina platform using de novo assembly of contigs. To evaluate its practicality, value and quality, we compared the short read assembly with an assembly completed using 454 data obtained after chloroplast DNA isolation. Sanger sequence verifications indicated that the Illumina dataset outperformed the longer read 454 data. Pooling of several individuals during preparation of the shotgun library enabled detection of informative chloroplast SNP markers. Following validation, we used the identified SNPs for a preliminary phylogeographic study of T. ciliata in Australia and to confirm low diversity across the distribution. CONCLUSIONS Our approach provides a simple method for construction of whole chloroplast genomes from shotgun sequencing of whole genomic DNA using short-read data and no available closely related reference genome (e.g. from the same species or genus). The high coverage of Illumina sequence data also renders this method appropriate for multiplexing and SNP discovery and therefore a useful approach for landscape level studies of evolutionary ecology.
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Affiliation(s)
- Hannah McPherson
- National Herbarium of NSW, The Royal Botanic Gardens and Domain Trust, Mrs Macquaries Road, 2000, Sydney, NSW, Australia
- Australian Centre for Evolutionary Biology and Biodiversity, School of Earth and Environmental Science, University of Adelaide, Adelaide, SA, Australia
| | - Marlien van der Merwe
- National Herbarium of NSW, The Royal Botanic Gardens and Domain Trust, Mrs Macquaries Road, 2000, Sydney, NSW, Australia
- Australian Centre for Evolutionary Biology and Biodiversity, School of Earth and Environmental Science, University of Adelaide, Adelaide, SA, Australia
| | - Sven K Delaney
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, 2052, Sydney, NSW, Australia
| | - Mark A Edwards
- Southern Cross Plant Science, Southern Cross University, 2480, Lismore, NSW, Australia
| | - Robert J Henry
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, 4072, Brisbane, QLD, Australia
| | - Emma McIntosh
- National Herbarium of NSW, The Royal Botanic Gardens and Domain Trust, Mrs Macquaries Road, 2000, Sydney, NSW, Australia
| | - Paul D Rymer
- National Herbarium of NSW, The Royal Botanic Gardens and Domain Trust, Mrs Macquaries Road, 2000, Sydney, NSW, Australia
- Hawkesbury Institute for the Environment, University of Western Sydney, Hawkesbury Campus, 2753, Richmond, NSW, Australia
| | - Melita L Milner
- National Herbarium of NSW, The Royal Botanic Gardens and Domain Trust, Mrs Macquaries Road, 2000, Sydney, NSW, Australia
| | - Juelian Siow
- National Herbarium of NSW, The Royal Botanic Gardens and Domain Trust, Mrs Macquaries Road, 2000, Sydney, NSW, Australia
| | - Maurizio Rossetto
- National Herbarium of NSW, The Royal Botanic Gardens and Domain Trust, Mrs Macquaries Road, 2000, Sydney, NSW, Australia
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Eliott FG, Connelly C, Rossetto M, Shepherd M, Rice N, Henry RJ. Novel microsatellite markers for the endangered Australian rainforest tree Davidsonia jerseyana (Cunoniaceae) and cross-species amplification in the Davidsonia genus. CONSERV GENET RESOUR 2013. [DOI: 10.1007/s12686-012-9758-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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Milner ML, Rossetto M, Crisp MD, Weston PH. The impact of multiple biogeographic barriers and hybridization on species-level differentiation. Am J Bot 2012; 99:2045-2057. [PMID: 23221499 DOI: 10.3732/ajb.1200327] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
PREMISE OF THE STUDY The glacial cycles of the Quaternary did not impact Australia in the same way as Europe and North America. Here we investigate the history of population isolation, species differentiation, and hybridization in the southeastern Australian landscape, using five species of Lomatia (Proteaceae). We use a chloroplast DNA phylogeography to assess chloroplast haplotype (chlorotype) sharing among these species and whether species with shared distributions have been affected by shared biogeographic barriers. • METHODS We used six chloroplast DNA simple sequence repeats (cpSSR) across five species of Lomatia, sampled across their entire distributional range in southeastern Australia. Resulting size data were combined, presented as a network, and visualized on a map. Biogeographical barriers were tested using AMOVA. To explore hypotheses of chlorotype origin, we converted the network into a cladogram and reconciled with all possible species trees using parsimony-based tree mapping. • KEY RESULTS Some chlorotypes were shared across multiple species of Lomatia in the study, including between morphologically differentiated species. Chlorotypes were either widespread in distribution or geographically restricted to specific regions. Biogeographical structure was identified across the range of Lomatia. The most parsimonious reconciled tree incorporated horizontal transfer of chlorotypes. • CONCLUSIONS Lomatia shows evidence of both incomplete lineage sorting and extensive hybridization between co-occurring species. Although the species in the study appear to have responded to a number of biogeographic barriers to varying degrees, our findings identified the Hunter River Valley as the most important long-term biogeographic barrier for the genus in southeastern Australia.
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Affiliation(s)
- Melita L Milner
- Evolution, Ecology and Genetics, School of Biology, The Australian National University, Building 116 Daley Road, Canberra, ACT 0200, Australia.
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