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Byrne M, Ramalho CE, Tapper S, Coates DJ. Topographic Complexity Facilitates Persistence Compared to Signals of Contraction and Expansion in the Adjacent Subdued Landscape. FRONTIERS IN CONSERVATION SCIENCE 2022. [DOI: 10.3389/fcosc.2022.833766] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Topographically heterogeneous areas are likely to act as refugia for species because they facilitate survival during regional climatic stress due to availability of a range of microenvironments. The Stirling Ranges are a topographically complex area in the generally subdued and ancient landscape of south-western Australia. We investigated the influence of these landscape features on the evolutionary history of the rare woody shrub, Banksia brownii through a combined approach using phylogeographic analysis of sequence data from three chloroplast sequences, the trnV–ndhC, trnQ–rps16, and rpl32–ndhF intergenic spacer regions, and species distribution modeling. The Stirling Ranges showed high genetic diversity and differentiation among populations consistent with localized persistence and maintenance of large populations in an area that species distribution modeling identified as providing habitat stability at the Last Glacial Maximum as well as under warmer conditions. In contrast, populations in the adjacent subdued lowlands showed signals of low diversity, suggesting contraction, and subsequent expansion from localized refugia in the west. Cool summers are an important climatic variable for the species and species distribution modeling showed suitable habitat identified at the LGM suggesting expansion at this time following likely contraction during earlier warmer climatic oscillations. The isolated, coastal population at Vancouver Peninsula showed low diversity but no differentiation and it may have been established in more recent historical times, possibly through Aboriginal movement of seed. Our analysis of B. brownii highlights the complex evolutionary history of the species and the influence of topographic complexity and habitat heterogeneity in this global biodiversity hotspot.
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Binks RM, Steane DA, Byrne M. Genomic divergence in sympatry indicates strong reproductive barriers and cryptic species within Eucalyptus salubris. Ecol Evol 2021; 11:5096-5110. [PMID: 34025994 PMCID: PMC8131811 DOI: 10.1002/ece3.7403] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Revised: 02/05/2021] [Accepted: 02/09/2021] [Indexed: 12/26/2022] Open
Abstract
Genetic studies are increasingly detecting cryptic taxa that likely represent a significant component of global biodiversity. However, cryptic taxa are often criticized because they are typically detected serendipitously and may not receive the follow-up study required to verify their geographic or evolutionary limits. Here, we follow-up a study of Eucalyptus salubris that unexpectedly detected two divergent lineages but was not sampled sufficiently to make clear interpretations. We undertook comprehensive sampling for an independent genomic analysis (3,605 SNPs) to investigate whether the two purported lineages remain discrete genetic entities or if they intergrade throughout the species' range. We also assessed morphological and ecological traits, and sequenced chloroplast DNA. SNP results showed strong genome-wide divergence (F ST = 0.252) between two discrete lineages: one dominated the north and one the southern regions of the species' range. Within lineages, gene flow was high, with low differentiation (mean F ST = 0.056) spanning hundreds of kilometers. In the central region, the lineages were interspersed but maintained their genomic distinctiveness: an indirect demonstration of reproductive isolation. Populations of the southern lineage exhibited significantly lower specific leaf area and occurred on soils with lower phosphorus relative to the northern lineage. Finally, two major chloroplast haplotypes were associated with each lineage but were shared between lineages in the central distribution. Together, these results suggest that these lineages have non-contemporary origins and that ecotypic adaptive processes strengthened their divergence more recently. We conclude that these lineages warrant taxonomic recognition as separate species and provide fascinating insight into eucalypt speciation.
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Affiliation(s)
- Rachel M. Binks
- Biodiversity and Conservation ScienceDepartment of Biodiversity, Conservation and AttractionsBentley Delivery CentreBentleyWAAustralia
| | - Dorothy A. Steane
- School of Natural Sciences and ARC Training Centre for Forest ValueUniversity of TasmaniaHobartTasmaniaAustralia
- CSIRO Land and WaterSandy BayTasmaniaAustralia
| | - Margaret Byrne
- Biodiversity and Conservation ScienceDepartment of Biodiversity, Conservation and AttractionsBentley Delivery CentreBentleyWAAustralia
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Gosper CR, Kinloch J, Coates DJ, Byrne M, Pitt G, Yates CJ. Differential exposure and susceptibility to threats based on evolutionary history: how OCBIL theory informs flora conservation. Biol J Linn Soc Lond 2020. [DOI: 10.1093/biolinnean/blaa170] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Abstract
Optimal conservation approaches have been proposed to differ for biota with contrasting evolutionary histories. Natural selection filters the distribution of plant traits over evolutionary time, with the current expression of traits mediating susceptibility to contemporary and often novel threats. We use old, climatically buffered, infertile landscape (OCBIL) theory to compile predictions regarding differences in exposure and susceptibility to key threats between OCBIL and young, often disturbed, fertile landscape (YODFEL) flora. Based on literature and existing data from the Southwest Australian Floristic Region (SWAFR), we evaluate evidence in support of our predictions, finding strong theoretical and empirical support for the proposition that exposure and/or impact of many threats differs between OCBILs and YODFELs. OCBILs have more exposure to land clearance from mining, whereas many YODFELs have greater exposure to land clearance from agriculture, and urban and industrial land uses, and greater overall levels of habitat loss and fragmentation. OCBIL flora are more susceptible to pathogens and extremes of fire interval than YODFEL flora, but conversely may have a greater capacity to persist in smaller populations if small populations featured in the evolutionary history of the species prior to anthropogenic fragmentation, and have substantial resistance to weed invasion. We argue that consideration of evolutionary history has an important role in informing conservation management.
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Affiliation(s)
- Carl R Gosper
- Biodiversity and Conservation Science, Department of Biodiversity, Conservation and Attractions, Bentley Delivery Centre, WA, Australia
| | - Janine Kinloch
- Biodiversity and Conservation Science, Department of Biodiversity, Conservation and Attractions, Bentley Delivery Centre, WA, Australia
| | - David J Coates
- Biodiversity and Conservation Science, Department of Biodiversity, Conservation and Attractions, Bentley Delivery Centre, WA, Australia
| | - Margaret Byrne
- Biodiversity and Conservation Science, Department of Biodiversity, Conservation and Attractions, Bentley Delivery Centre, WA, Australia
| | - Georgie Pitt
- Biodiversity and Conservation Science, Department of Biodiversity, Conservation and Attractions, Bentley Delivery Centre, WA, Australia
| | - Colin J Yates
- Biodiversity and Conservation Science, Department of Biodiversity, Conservation and Attractions, Bentley Delivery Centre, WA, Australia
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Abdelsalam NR, Ali HM, Salem MZM, El-Wakil HE. Quantitative and Qualitative Genetic Studies of Some Acacia Species Grown in Egypt. PLANTS (BASEL, SWITZERLAND) 2020; 9:E243. [PMID: 32069993 PMCID: PMC7076689 DOI: 10.3390/plants9020243] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Revised: 02/07/2020] [Accepted: 02/11/2020] [Indexed: 11/17/2022]
Abstract
The objective of the current work is to study the genetic differentiation between Acacia species growing in Egypt as plant genetic resources based on morphological, biochemical, and molecular markers. The 20 replicates of Acacia tree collected from four localities from Egypt were A. tortilis ssp. raddiana and A. farnesiana (Siwa Oasis and Borg El-Arab City), A. stenophylla, A. sclerosperma (Marsa Matroh City), and A. saligna (Abis Station Farm, Alexandria). The results based on the previous markers indicated highly significant differences between Acacia species, confirming the hypothesis of the possibility of using morphological, biochemical, and molecular parameters in species identification. Qualitative characteristics results indicated some similarities and differences that are taxonomically important for comparing taxonomical grouping with morphological data for the genetic description of Acacia species. The activities of antioxidant enzymes have been studied intensively and the results provide strong similarities between the Acacia species (69%), between A. raddiana (Siwa and Borg Al-Arab) and A. saligna, followed by all Acacia species (50%). Finally, the molecular studies showed that a total of 563 amplification fragments, 190 fragments were monomorphic, and 373 fragments were polymorphic. The highest number of amplification fragments (21) was detected with OPB-20 primer, while OPA-20 showed seven amplification fragments; the average number was 13.09. The results indicated that Acacia species exhibit high genetic differentiation, helpful in the future for genetic improvement programs. The novelty of the current study is highlighting the importance of plant genetic resources in Egypt and using different techniques to measure the differentiation between these species.
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Affiliation(s)
- Nader R. Abdelsalam
- Agricultural Botany Department, Faculty of Agriculture (Saba Basha), Alexandria University, Alexandria 21531, Egypt;
| | - Hayssam M. Ali
- Botany and Microbiology Department, College of Science, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia;
- Timber Trees Research Department, Sabahia Horticulture Research Station, Horticulture Research Institute, Agriculture Research Center, Alexandria 21526, Egypt
| | - Mohamed Z. M. Salem
- Forestry and Wood Technology Department, Faculty of Agriculture (EL-Shatby), Alexandria University, Alexandria 21545, Egypt
| | - Hosam E. El-Wakil
- Agricultural Botany Department, Faculty of Agriculture (Saba Basha), Alexandria University, Alexandria 21531, Egypt;
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Monks L, Barrett S, Beecham B, Byrne M, Chant A, Coates D, Cochrane JA, Crawford A, Dillon R, Yates C. Recovery of threatened plant species and their habitats in the biodiversity hotspot of the Southwest Australian Floristic Region. PLANT DIVERSITY 2019; 41:59-74. [PMID: 31193161 PMCID: PMC6520493 DOI: 10.1016/j.pld.2018.09.006] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2018] [Revised: 09/19/2018] [Accepted: 09/19/2018] [Indexed: 05/22/2023]
Abstract
The Southwest Australian Floristic Region (SWAFR) is a global biodiversity hotspot with high plant diversity and endemism and a broad range of threatening processes. An outcome of this is a high proportion of rare and threatened plant species. Ongoing discovery and taxonomic description of new species, many of which are rare, increases the challenges for recovery of threatened species and prioritisation of conservation actions. Current conservation of this diverse flora is based on integrated and scientific evidence-based management. Here we present an overview of current approaches to the conservation of threatened flora in the SWAFR with a focus on active management through recovery and restoration that is integrated with targeted research. Key threats include disease, fragmentation, invasive weeds, altered fire regimes, grazing, altered hydro-ecology and climate change. We highlight the integrated approach to management of threats and recovery of species with four case studies of threatened flora recovery projects that illustrate the breadth of interventions ranging from In situ management to conservation reintroductions and restoration of threatened species habitats. Our review and case studies emphasise that despite the scale of the challenge, a scientific understanding of threats and their impacts enables effective conservation actions to arrest decline and enhance recovery of threatened species and habitats.
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Affiliation(s)
- Leonie Monks
- Biodiversity and Conservation Science, Department of Biodiversity, Conservation and Attractions, Locked Bag 104, Bentley Delivery Centre, Bentley, Western Australia, 6983, Australia
- Corresponding author.
| | - Sarah Barrett
- Parks and Wildlife Service, Department of Biodiversity, Conservation and Attractions. 120 Albany Highway, Albany, Western Australia, 6330, Australia
| | - Brett Beecham
- Parks and Wildlife Service, Department of Biodiversity, Conservation and Attractions. P.O. Box 100, Narrogin, Western Australia, 6312, Australia
| | - Margaret Byrne
- Biodiversity and Conservation Science, Department of Biodiversity, Conservation and Attractions, Locked Bag 104, Bentley Delivery Centre, Bentley, Western Australia, 6983, Australia
| | - Alanna Chant
- Parks and Wildlife Service, Department of Biodiversity, Conservation and Attractions. P.O. Box 72, Geraldton, Western Australia, 6531, Australia
| | - David Coates
- Biodiversity and Conservation Science, Department of Biodiversity, Conservation and Attractions, Locked Bag 104, Bentley Delivery Centre, Bentley, Western Australia, 6983, Australia
| | - J. Anne Cochrane
- Biodiversity and Conservation Science, Department of Biodiversity, Conservation and Attractions, Locked Bag 104, Bentley Delivery Centre, Bentley, Western Australia, 6983, Australia
| | - Andrew Crawford
- Biodiversity and Conservation Science, Department of Biodiversity, Conservation and Attractions, Locked Bag 104, Bentley Delivery Centre, Bentley, Western Australia, 6983, Australia
| | - Rebecca Dillon
- Biodiversity and Conservation Science, Department of Biodiversity, Conservation and Attractions, Locked Bag 104, Bentley Delivery Centre, Bentley, Western Australia, 6983, Australia
| | - Colin Yates
- Biodiversity and Conservation Science, Department of Biodiversity, Conservation and Attractions, Locked Bag 104, Bentley Delivery Centre, Bentley, Western Australia, 6983, Australia
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6
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Rix MG, Edwards DL, Byrne M, Harvey MS, Joseph L, Roberts JD. Biogeography and speciation of terrestrial fauna in the south-western Australian biodiversity hotspot. Biol Rev Camb Philos Soc 2014; 90:762-93. [PMID: 25125282 DOI: 10.1111/brv.12132] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2013] [Revised: 06/28/2014] [Accepted: 07/02/2014] [Indexed: 01/21/2023]
Abstract
The south-western land division of Western Australia (SWWA), bordering the temperate Southern and Indian Oceans, is the only global biodiversity hotspot recognised in Australia. Renowned for its extraordinary diversity of endemic plants, and for some of the largest and most botanically significant temperate heathlands and woodlands on Earth, SWWA has long fascinated biogeographers. Its flat, highly weathered topography and the apparent absence of major geographic factors usually implicated in biotic diversification have challenged attempts to explain patterns of biogeography and mechanisms of speciation in the region. Botanical studies have always been central to understanding the biodiversity values of SWWA, although surprisingly few quantitative botanical analyses have allowed for an understanding of historical biogeographic processes in both space and time. Faunistic studies, by contrast, have played little or no role in defining hotspot concepts, despite several decades of accumulating quantitative research on the phylogeny and phylogeography of multiple lineages. In this review we critically analyse datasets with explicit supporting phylogenetic data and estimates of the time since divergence for all available elements of the terrestrial fauna, and compare these datasets to those available for plants. In situ speciation has played more of a role in shaping the south-western Australian fauna than has long been supposed, and has occurred in numerous endemic lineages of freshwater fish, frogs, reptiles, snails and less-vagile arthropods. By contrast, relatively low levels of endemism are found in birds, mammals and highly dispersive insects, and in situ speciation has played a negligible role in generating local endemism in birds and mammals. Quantitative studies provide evidence for at least four mechanisms driving patterns of endemism in south-western Australian animals, including: (i) relictualism of ancient Gondwanan or Pangaean taxa in the High Rainfall Province; (ii) vicariant isolation of lineages west of the Nullarbor divide; (iii) in situ speciation; and (iv) recent population subdivision. From dated quantitative studies we derive four testable models of historical biogeography for animal taxa in SWWA, each explicit in providing a spatial, temporal and topological perspective on patterns of speciation or divergence. For each model we also propose candidate lineages that may be worthy of further study, given what we know of their taxonomy, distributions or relationships. These models formalise four of the strongest patterns seen in many animal taxa from SWWA, although other models are clearly required to explain particular, idiosyncratic patterns. Generating numerous new datasets for suites of co-occurring lineages in SWWA will help refine our understanding of the historical biogeography of the region, highlight gaps in our knowledge, and allow us to derive general postulates from quantitative (rather than qualitative) results. For animals, this process has now begun in earnest, as has the process of taxonomically documenting many of the more diverse invertebrate lineages. The latter remains central to any attempt to appreciate holistically biogeographic patterns and processes in SWWA, and molecular phylogenetic studies should - where possible - also lead to tangible taxonomic outcomes.
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Affiliation(s)
- Michael G Rix
- Australian Centre for Evolutionary Biology and Biodiversity, School of Earth and Environmental Sciences, The University of Adelaide, North Terrace, Adelaide, South Australia 5005, Australia.,Department of Terrestrial Zoology, Western Australian Museum, Locked Bag 49, Welshpool DC, Western Australia 6986, Australia
| | - Danielle L Edwards
- Department of Ecology and Evolutionary Biology, Yale University, 21 Sachem Street, New Haven, CT 06520, U.S.A
| | - Margaret Byrne
- Science Division, Department of Parks and Wildlife, Locked Bag 104, Bentley DC, Western Australia 6983, Australia
| | - Mark S Harvey
- Department of Terrestrial Zoology, Western Australian Museum, Locked Bag 49, Welshpool DC, Western Australia 6986, Australia.,School of Animal Biology, Centre for Evolutionary Biology, University of Western Australia, 35 Stirling Highway, Crawley, Western Australia 6009, Australia
| | - Leo Joseph
- Australian National Wildlife Collection, CSIRO National Facilities and Collections, GPO Box 1700, Canberra, Australian Capital Territory 2601, Australia
| | - J Dale Roberts
- Department of Terrestrial Zoology, Western Australian Museum, Locked Bag 49, Welshpool DC, Western Australia 6986, Australia.,School of Animal Biology, Centre for Evolutionary Biology, University of Western Australia, 35 Stirling Highway, Crawley, Western Australia 6009, Australia.,Centre of Excellence in Natural Resource Management, University of Western Australia, PO Box 5771, Albany, Western Australia 6332, Australia
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7
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Nistelberger H, Gibson N, Macdonald B, Tapper SL, Byrne M. Phylogeographic evidence for two mesic refugia in a biodiversity hotspot. Heredity (Edinb) 2014; 113:454-63. [PMID: 24984607 DOI: 10.1038/hdy.2014.46] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2014] [Accepted: 04/03/2014] [Indexed: 11/09/2022] Open
Abstract
Phylogeographic studies of flora in species-rich south-western Australia point to complex evolutionary histories, reflecting patterns of persistence and resilience to climatic changes during the Pleistocene. We asked whether coastal areas of the mid-west and south, as well as granite outcrops and inland ranges, have acted as major refugia within this region during Pleistocene climatic fluctuations by analysing phylogeographic patterns in the shrub Calothamnus quadrifidus R.Br. (Myrtaceae). We determined variation in chloroplast DNA data for 41 populations across the geographic range. Relationships and major clades were resolved using parsimony and Bayesian analyses. We tested for demographic and spatial expansion of the major clades and estimated clade divergence dates using an uncorrelated, lognormal relaxed clock based on two conservative chloroplast mutation rates. Two distinct phylogeographic clades were identified showing divergence during the Pleistocene, consistent with other phylogeographic studies of south-west Australian flora, emphasising the impact of climatic oscillations in driving divergence in this landscape. The southern clade was more diverse, having higher haplotype diversity and greater genetic structure, while the northern clade showed evidence of fluctuation in population size. Regions of high haplotype diversity with adjacent areas of low diversity observed in each clade indicated the locations of two coastal refugia: one on the south coast and another along the mid-west coast. This is the first evidence for major Pleistocene refugia using chloroplast genetic data in a common, widespread species from this region.
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Affiliation(s)
- H Nistelberger
- Science and Conservation Division, Department of Parks and Wildlife, Bentley , Western Australia, Australia
| | - N Gibson
- Science and Conservation Division, Department of Parks and Wildlife, Bentley , Western Australia, Australia
| | - B Macdonald
- Science and Conservation Division, Department of Parks and Wildlife, Bentley , Western Australia, Australia
| | - S-L Tapper
- Science and Conservation Division, Department of Parks and Wildlife, Bentley , Western Australia, Australia
| | - M Byrne
- Science and Conservation Division, Department of Parks and Wildlife, Bentley , Western Australia, Australia
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Tapper SL, Byrne M, Yates CJ, Keppel G, Hopper SD, Van Niel K, Schut AGT, Mucina L, Wardell-Johnson GW. Isolated with persistence or dynamically connected? Genetic patterns in a common granite outcrop endemic. DIVERS DISTRIB 2014. [DOI: 10.1111/ddi.12185] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Affiliation(s)
- S.-L. Tapper
- Science and Conservation Division; Department of Parks and Wildlife; Locked Bag 104, Bentley Delivery Centre; WA 6983 Australia
| | - M. Byrne
- Science and Conservation Division; Department of Parks and Wildlife; Locked Bag 104, Bentley Delivery Centre; WA 6983 Australia
- School of Plant Biology; The University of Western Australia; 35 Stirling Highway Crawley WA 6009 Australia
| | - C. J. Yates
- Science and Conservation Division; Department of Parks and Wildlife; Locked Bag 104, Bentley Delivery Centre; WA 6983 Australia
| | - G. Keppel
- Curtin Institute for Biodiversity and Climate; Curtin University; GPO Box U1987 Perth WA 6845 Australia
- School of Natural and Built Environments and Barbara Hardy Institute; University of South Australia; GPO Box 2471 Adelaide SA 5001 Australia
| | - S. D. Hopper
- Centre of Excellence in Natural Resource Management and School of Plant Biology; The University of Western Australia; Foreshore House, Proudlove Parade Albany WA 6330 Australia
| | - K. Van Niel
- School of Earth and Environment; The University of Western Australia; 35 Stirling Highway Crawley WA 6009 Australia
| | - A. G. T. Schut
- Curtin Institute for Biodiversity and Climate; Curtin University; GPO Box U1987 Perth WA 6845 Australia
| | - L. Mucina
- School of Plant Biology; The University of Western Australia; 35 Stirling Highway Crawley WA 6009 Australia
- Curtin Institute for Biodiversity and Climate; Curtin University; GPO Box U1987 Perth WA 6845 Australia
| | - G. W. Wardell-Johnson
- Curtin Institute for Biodiversity and Climate; Curtin University; GPO Box U1987 Perth WA 6845 Australia
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Richards ZT, Miller DJ, Wallace CC. Molecular phylogenetics of geographically restricted Acropora species: implications for threatened species conservation. Mol Phylogenet Evol 2013; 69:837-51. [PMID: 23850500 DOI: 10.1016/j.ympev.2013.06.020] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2012] [Revised: 06/18/2013] [Accepted: 06/27/2013] [Indexed: 10/26/2022]
Abstract
To better understand the underlying causes of rarity and extinction risk in Acropora (staghorn coral), we contrast the minimum divergence ages and nucleotide diversity of an array of species with different range sizes and levels of threat. Time-calibrated Bayesian analyses based upon concatenated nuclear and mitochondrial sequence data implied contemporary range size and vulnerability are linked to species age. However, contrary to previous hypotheses that suggest geographically restricted Acropora species evolved in the Plio-Pleistocene, the molecular phylogeny depicts some Indo-Australian species have greater antiquity, diverging in the Miocene. Species age is not related to range size as a simple positive linear function and interpreting the precise tempo of evolution in this genus is greatly complicated by morphological homoplasy and a sparse fossil record. Our phylogenetic reconstructions provide new examples of how morphology conceals cryptic evolutionary relationships in this keystone genus, and offers limited support for the species groupings currently used in Acropora systematics. We hypothesize that in addition to age, other mechanisms (such as a reticulate ancestry) delimit the contemporary range of some Acropora species, as evidenced by the complex patterns of allele sharing and paraphyly we uncover. Overall, both new and ancient evolutionary information may be lost if geographically restricted and threatened Acropora species are forced to extinction. In order to protect coral biodiversity and resolve the evolutionary history of staghorn coral, further analyses based on comprehensive and heterogeneous morphological and molecular data utilizing reticulate models of evolution are needed.
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Affiliation(s)
- Z T Richards
- Aquatic Zoology, Western Australian Museum, 49 Kew Street, Welshpool, WA 6106, Australia.
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Steven G N, Subramanyam R. Testing plant barcoding in a sister species complex of pantropical Acacia (Mimosoideae, Fabaceae). Mol Ecol Resour 2013; 9 Suppl s1:172-80. [PMID: 21564976 DOI: 10.1111/j.1755-0998.2009.02642.x] [Citation(s) in RCA: 114] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Acacia species are quite difficult to differentiate using morphological characters. Routine identification of Acacia samples is important in order to distinguish invasive species from rare species or those of economic importance, particularly in the forest industry. The genus Acacia is quite abundant and diverse comprising approximately 1355 species, which is currently divided into three subgenera: subg. Acacia (c. 161 species), subg. Aculiferum (c. 235 species), and subg. Phyllodineae (c. 960 species). It would be prudent to utilize DNA barcoding in the accurate and efficient identification of acacias. The objective of this research is to test barcoding in discriminating multiple populations among a sister-species complex in pantropical Acacia subg. Acacia, across three continents. Based on previous research, we chose three cpDNA regions (rbcL, trnH-psbA and matK). Our results show that all three regions (rbcL, matK and trnH-psbA) can distinguish and support the newly proposed genera of Vachellia Wight & Arn. from Acacia Mill., discriminate sister species within either genera and differentiate biogeographical patterns among populations from India, Africa and Australia. A morphometric analysis confirmed the cryptic nature of these sister species and the limitations of a classification based on phenetic data. These results support the claim that DNA barcoding is a powerful tool for taxonomy and biogeography with utility for identifying cryptic species, biogeograhic patterns and resolving classifications at the rank of genera and species.
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Affiliation(s)
- Newmaster Steven G
- Floristic Diversity Research Group, Biodiversity Institute of Ontario Herbarium (OAC), University of Guelph, Guelph, Ontario, Canada N1G 2W1
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11
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Duckett PE, Stow AJ. Higher genetic diversity is associated with stable water refugia for a gecko with a wide distribution in arid
A
ustralia. DIVERS DISTRIB 2013. [DOI: 10.1111/ddi.12089] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Affiliation(s)
- Paul E. Duckett
- Department of Biological Sciences Macquarie University Sydney NSW 2109 Australia
| | - Adam J. Stow
- Department of Biological Sciences Macquarie University Sydney NSW 2109 Australia
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12
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Le Roux JJ, Brown GK, Byrne M, Ndlovu J, Richardson DM, Thompson GD, Wilson JRU. Phylogeographic consequences of different introduction histories of invasive Australian Acacia species and Paraserianthes lophantha (Fabaceae) in South Africa. DIVERS DISTRIB 2011. [DOI: 10.1111/j.1472-4642.2011.00784.x] [Citation(s) in RCA: 69] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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13
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Byrne M, Yeates DK, Joseph L, Kearney M, Bowler J, Williams MAJ, Cooper S, Donnellan SC, Keogh JS, Leys R, Melville J, Murphy DJ, Porch N, Wyrwoll KH. Birth of a biome: insights into the assembly and maintenance of the Australian arid zone biota. Mol Ecol 2008; 17:4398-417. [PMID: 18761619 DOI: 10.1111/j.1365-294x.2008.03899.x] [Citation(s) in RCA: 321] [Impact Index Per Article: 20.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
The integration of phylogenetics, phylogeography and palaeoenvironmental studies is providing major insights into the historical forces that have shaped the Earth's biomes. Yet our present view is biased towards arctic and temperate/tropical forest regions, with very little focus on the extensive arid regions of the planet. The Australian arid zone is one of the largest desert landform systems in the world, with a unique, diverse and relatively well-studied biota. With foci on palaeoenvironmental and molecular data, we here review what is known about the assembly and maintenance of this biome in the context of its physical history, and in comparison with other mesic biomes. Aridification of Australia began in the Mid-Miocene, around 15 million years, but fully arid landforms in central Australia appeared much later, around 1-4 million years. Dated molecular phylogenies of diverse taxa show the deepest divergences of arid-adapted taxa from the Mid-Miocene, consistent with the onset of desiccation. There is evidence of arid-adapted taxa evolving from mesic-adapted ancestors, and also of speciation within the arid zone. There is no evidence for an increase in speciation rate during the Pleistocene, and most arid-zone species lineages date to the Pliocene or earlier. The last 0.8 million years have seen major fluctuations of the arid zone, with large areas covered by mobile sand dunes during glacial maxima. Some large, vagile taxa show patterns of recent expansion and migration throughout the arid zone, in parallel with the ice sheet-imposed range shifts in Northern Hemisphere taxa. Yet other taxa show high lineage diversity and strong phylogeographical structure, indicating persistence in multiple localised refugia over several glacial maxima. Similar to the Northern Hemisphere, Pleistocene range shifts have produced suture zones, creating the opportunity for diversification and speciation through hybridisation, polyploidy and parthenogenesis. This review highlights the opportunities that development of arid conditions provides for rapid and diverse evolutionary radiations, and re-enforces the emerging view that Pleistocene environmental change can have diverse impacts on genetic structure and diversity in different biomes. There is a clear need for more detailed and targeted phylogeographical studies of Australia's arid biota and we suggest a framework and a set of a priori hypotheses by which to proceed.
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Affiliation(s)
- M Byrne
- Science Division, Department of Environment and Conservation, Locked Bag 104, Bentley Delivery Centre, WA 6983, Australia.
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BYRNE MARGARET, HOPPER STEPHEND. Granite outcrops as ancient islands in old landscapes: evidence from the phylogeography and population genetics of Eucalyptus caesia (Myrtaceae) in Western Australia. Biol J Linn Soc Lond 2007. [DOI: 10.1111/j.1095-8312.2007.00946.x] [Citation(s) in RCA: 86] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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15
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Genetic variation and the mating system in the rare Acacia sciophanes compared with its common sister species Acacia anfractuosa (Mimosaceae). CONSERV GENET 2006. [DOI: 10.1007/s10592-006-9136-7] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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16
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Pharmawati M, Yan G, Sedgley R, Finnegan PM. Chloroplast DNA inheritance and variation in Leucadendron species (Proteaceae) as revealed by PCR-RFLP. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2004; 109:1694-1701. [PMID: 15365629 DOI: 10.1007/s00122-004-1800-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2004] [Accepted: 08/17/2004] [Indexed: 05/24/2023]
Abstract
The inheritance of chloroplast DNA (cpDNA) in Leucadendron species was studied by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) analysis. A total of 100 progeny from five interspecific crosses involving seven parental species were tested, and all progeny exhibited the cpDNA restriction fragment pattern of the female parent, indicating that cpDNA in Leucadendron is maternally inherited. PCR-RFLP was also employed to study cpDNA variation among 21 Leucadendron species. Parsimony analysis using a heuristic search resulted in a phylogenetic tree that showed limited agreement to the taxonomic classification of Leucadendron species, based on morphological characteristics. The incongruence between cpDNA phylogenetic and taxonomic groupings in Leucadendron may be due to reticulate evolution involving a combination of hybridization and introgression, convergent evolution and/or lineage sorting at the interspecific, intersubsectional and intersectional levels.
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Affiliation(s)
- M Pharmawati
- School of Plant Biology, Faculty of Natural and Agricultural Sciences, The University of Western Australia, 35 Stirling Highway, Crawley, WA, 6009, Australia.
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Byrne M, Macdonald B, Brand J. Phylogeography and divergence in the chloroplast genome of Western Australian Sandalwood (Santalum spicatum). Heredity (Edinb) 2004; 91:389-95. [PMID: 14512954 DOI: 10.1038/sj.hdy.6800346] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Western Australian sandalwood (Santalum spicatum) is widespread throughout Western Australia across the semiarid and arid regions. The diversity and phylogeographic patterns within the chloroplast genome of S. spicatum were investigated using restriction fragment length polymorphism analysis of 23 populations. The chloroplast diversity was structured into two main clades that were geographically separated, one centred in the southern (semiarid region) and the other in the northern (arid) region. Fragmentation due to climatic instability was identified as the most likely influence on the differentiation of the lineages. The lineage in the arid region showed a greater level of differentiation than that in the southern region, suggesting a higher level of gene flow or a more recent range expansion of sandalwood in the southern region. The phylogeographic pattern in the chloroplast genome is congruent with that detected in the nuclear genome, which identified different genetic influences between the regions and also suggested a more recent expansion of sandalwood in the southern region.
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Affiliation(s)
- M Byrne
- Science Division, Department of Conservation and Land Management, Locked Bag 104, Bentley Delivery Centre, WA 6983, Australia.
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Yates CJ, Ladd PG. Breeding system, pollination and demography in the rare granite endemic shrub Verticordia staminosa ssp. staminosa in south-west Western Australia. AUSTRAL ECOL 2004. [DOI: 10.1111/j.1442-9993.2004.01336.x] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Abstract
Phylogenetics has a valuable role in the conservation of the flora of Western Australia particularly in the south-west where the complex evolutionary history has resulted in a diverse flora with both relictual and recently evolved components. Phylogenetic analysis contributes to conservation of plants through clarification of taxonomic status, identification of unique evolutionary lineages, determination of relictual and recently derived species, determination of phylogenetic value for conservation priority setting, and identifying phylogenetically independent comparisons between rare and widespread species. The contribution of phylogenetic analysis to these aspects of effective conservation management are discussed with examples from various species in Western Australia.
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Affiliation(s)
- Margaret Byrne
- Science Division, Department of Conservation and Land Management, Locked Bag 104, Bentley Delivery Centre, WA 6983, Australia.
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Byrne M, MacDonald B, Coates D. Phylogeographical patterns in chloroplast DNA variation within the Acacia acuminata (Leguminosae: Mimosoideae) complex in Western Australia. J Evol Biol 2002. [DOI: 10.1046/j.1420-9101.2002.00429.x] [Citation(s) in RCA: 56] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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