National Herbarium of NSW

Sydney, Australia

National Herbarium of NSW

Sydney, Australia
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Van der Merwe M.,National Herbarium of NSW | Van der Merwe M.,University of Adelaide | Mcpherson H.,National Herbarium of NSW | Mcpherson H.,University of Adelaide | And 2 more authors.
Molecular Ecology Resources | Year: 2014

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. © 2013 John Wiley & Sons Ltd.

Mellick R.,National Herbarium of NSW | Mellick R.,University of Adelaide | Lowe A.,University of Adelaide | Rossetto M.,National Herbarium of NSW
Australian Journal of Botany | Year: 2011

The east Australian rainforests provide a unique system with which to study historic climate-driven habitat fragmentation. The long life span of rainforest conifers and consequent lag effects on genetic variation, offer insights into demographic stochasticity in small populations and persistence in increasingly fragmented systems. Microsatellite markers were used to investigate the genetic diversity and structure of Podocarpus elatus (Podocarpaceae), a long-lived rainforest conifer endemic to Australia. Twenty-seven populations throughout the east Australian rainforests were screened and two divergent regions separated by the dry Clarence River valley (New South Wales) were discovered. This biogeographic barrier may be referred to as the Clarence River Corridor. Niche modelling techniques were employed to verify the incidence of habitat divergence between the two regions. Significantly high inbreeding was detected throughout the species range with no evidence of recent bottlenecks. Most of the diversity in the species resides between individuals within populations, which suggest the species would be sensitive to the adverse effects of inbreeding, yet evidence suggests that these populations have been small for several generations. Slightly higher diversity estimates were found in the southern region, but it is likely that the species survived historic population contraction in dispersed refugia within each of these genetically differentiated regions. © 2011 CSIRO.

Li X.,University of Macau | Yang Y.,University of Macau | Henry R.J.,University of Queensland | Rossetto M.,National Herbarium of NSW | And 2 more authors.
Biological Reviews | Year: 2014

DNA barcoding is currently a widely used and effective tool that enables rapid and accurate identification of plant species; however, none of the available loci work across all species. Because single-locus DNA barcodes lack adequate variations in closely related taxa, recent barcoding studies have placed high emphasis on the use of whole-chloroplast genome sequences which are now more readily available as a consequence of improving sequencing technologies. While chloroplast genome sequencing can already deliver a reliable barcode for accurate plant identification it is not yet resource-effective and does not yet offer the speed of analysis provided by single-locus barcodes to unspecialized laboratory facilities. Here, we review the development of candidate barcodes and discuss the feasibility of using the chloroplast genome as a super-barcode. We advocate a new approach for DNA barcoding that, for selected groups of taxa, combines the best use of single-locus barcodes and super-barcodes for efficient plant identification. Specific barcodes might enhance our ability to distinguish closely related plants at the species and population levels. © 2014 Cambridge Philosophical Society.

Mellick R.,National Herbarium of NSW | Mellick R.,University of Adelaide | Lowe A.,University of Adelaide | Allen C.,National Herbarium of NSW | And 2 more authors.
Journal of Biogeography | Year: 2012

Aim We examine the range expansion/contraction dynamics during the last glacial cycle of the late-successional tropical rain forest conifer Podocarpus elatus using a combination of modelling and molecular marker analyses. Specifically, we test whether distributional changes predicted by environmental niche modelling are in agreement with (1) the glacial maximum contractions inferred from the southern fossil record, and (2) population genetic-based estimates of range disjunctions and demographic dynamics. In addition, we test whether northern and southern ranges are likely to have experienced similar expansion/contraction dynamics. Location Eastern Australian tropical and subtropical rain forests. Methods Environmental niche modelling was completed for three time periods during the last glacial cycle and was interpreted in light of the known palynology. We collected 109 samples from 32 populations across the entire range of P. elatus. Six microsatellite loci and Bayesian coalescence analysis were used to infer population expansion/contraction dynamics, and five sequenced loci (one plastid and four nuclear) were used to quantify genetic structure/diversity. Results Environmental niche modelling suggested that the northern and southern ranges of P. elatus experienced different expansion/contraction dynamics. In the northern range, the habitat suitable for P. elatus persisted in a small refugial area during the Last Glacial Maximum (LGM, 21ka) and then expanded during the post-glacial period. Conversely, in the south suitable habitat was widespread during the LGM but subsequently contracted. These differential dynamics were supported by Bayesian analyses of the population genetic data (northern dispersal) and are consistent with the greater genetic diversity in the south compared with the north. A contact zone between the two genetically divergent groups (corresponding to the Macleay Overlap Zone) was supported by environmental niche modelling and molecular analyses. Main conclusions The climatic fluctuations of the Quaternary have differentially impacted the northern and southern ranges of a broadly distributed rain forest tree in Australia. Recurrent contraction/expansion cycles contributed to the genetic distinction between northern and southern distributions of P. elatus. By combining molecular and environmental niche modelling evidence, this unique study undermines the general assumption that broadly distributed species respond in a uniform way to climate change. © 2012 Blackwell Publishing Ltd.

Mellick R.,National Herbarium of NSW | Wilson P.D.,Macquarie University | Rossetto M.,National Herbarium of NSW
Diversity | Year: 2013

Here we investigate the interaction between ecology and climate concerning the distribution of rainforest species differentially distributed along altitudinal gradients of eastern Australia. The potential distributions of the two species closely associated with different rainforest types were modelled to infer the potential contribution of post-glacial warming on spatial distribution and altitudinal range shift. Nothofagus moorei is an integral element of cool temperate rainforest, including cloud forests at high elevation. This distinct climatic envelope is at increased risk with future global warming. Elaeocarpus grandis on the other hand is a lowland species and typical element of subtropical rainforest occupying a climatic envelope that may shift upwards into areas currently occupied by N. moorei. Climate envelope models wereused to infer range shift differences between the two species in the past (21 thousand years ago), current and future (2050) scenarios, and to provide a framework to explain observed genetic diversity/structure of both species. The models suggest continuing contraction of the highland cool temperate climatic envelope and expansion of the lowland warm subtropical envelope, with both showing a core average increase in elevation in response to post-glacial warming. Spatial and altitudinal overlap between the species climatic envelopes was at a maximum during the last glacial maximum and is predicted to be a minimum at 2050. © 2013 by the authors; licensee MDPI, Basel, Switzerland.

Milner M.L.,Australian National University | Rossetto M.,National Herbarium of NSW | Crisp M.D.,Australian National University | Weston P.H.,National Herbarium of NSW
American Journal of Botany | Year: 2012

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. © 2012 Botanical Society of America.

Rossetto M.,National Herbarium of NSW | Thurlby K.A.G.,National Herbarium of NSW | Offord C.A.,Mount Annan Botanic Garden | Allen C.B.,National Herbarium of NSW | Weston P.H.,National Herbarium of NSW
BMC Evolutionary Biology | Year: 2011

Background: Inter-population distance and differences in breeding times are barriers to reproduction that can contribute to genotypic differentiation between populations. Temporal changes in environmental conditions and local selective processes can further contribute to the establishment of reproductive barriers. Telopea speciosissima (Proteaceae) is an excellent subject for studying the effect of geographic, edaphic and phenological heterogeneity on genotypic differentiation because previous studies show that these factors are correlated with morphological variation. Molecular, morphological and environmental datasets were combined to characterise the relative influence of these factors on inter-population differentiation, and Bayesian analyses were used to investigate current levels of admixture between differentiated genomes. Results: A landscape genetic approach involving molecular and morphological analyses identified three endpoints of differentiated population groups: coastal, upland and southern. The southern populations, isolated from the other populations by an edaphic barrier, show low migration and no evidence of admixture with other populations. Amongst the northern populations, coastal and upland populations are connected along a skewed altitudinal gradient by genetically intermediate populations. The strong association between temperature and flowering time in Telopea speciosissima was shown to maintain a temporally unstable reproductive barrier between coastal and upland populations. Conclusions: Substrate-mediated allopatry appears to be responsible for long-term genetic isolation of the southern populations. However, the temperature-dependent reproductive barrier between upland and coastal populations bears the genetic signature of temporal adjustments. The extreme climatic events of the last glacial maximum are likely to have caused more complete allochronic isolation between upland and coastal populations, as well as exerting increased selective pressure upon local genomes. However, at intermediate altitudes, current climatic conditions allow for the incorporation of alleles from previously distinct genomes, generating new, intermediate genomic assemblages and possibly increasing overall adaptive potential. © 2011 Rossetto et al; licensee BioMed Central Ltd.

Milner M.L.,Australian National University | Weston P.H.,National Herbarium of NSW | Rossetto M.,National Herbarium of NSW | Crisp M.D.,Australian National University
Journal of Biogeography | Year: 2015

Aim: We tested whether the divergence of South American and Australian Lomatia was the result of the breakup of Gondwana, and assessed the date of divergence between Tasmania and mainland Australia, and across the Hunter River Valley. Location: South America (Chile and Argentina) and eastern Australia (Tasmania, Victoria, New South Wales and Queensland). Methods: We sequenced one chloroplast (psbA-trnH intergenic spacer) and two nuclear (PHYA and ITS) markers across all 12 species of Lomatia, five species of Telopea and Embothrium coccineum, and included sequences from GenBank for the rest of the tribe Embothrieae. Species relationships were inferred using Bayesian and maximum likelihood analyses, then divergence times estimated using the random local clock in beast. Results: The chronogram is congruent with geological events: SAm (SAm (SAm (Tas (NEQld (SEAus north of the Hunter + SEAus south of the Hunter))))). South American and Australian species of Lomatia diverged between 35 and 64 Ma. Tasmanian species of Lomatia diverged from mainland Australian taxa c. 32 Ma. Mainland Australian species of Lomatia are mostly not corroborated as monophyletic but show a divergence either side of the Hunter River Valley, dated at 17 Ma. Main conclusions: The divergence date between South American Lomatia ferruginea and Australian species cannot exclude Gondwanan vicariance; however, divergences within South America occurred prior to separation of South America and Australia from Antarctica. Tasmanian species diverged from mainland Australia in the early Oligocene. Mainland Australian species of Lomatia are not resolved but form two clades representing populations north and south of the Hunter River Valley, confirming the Hunter River Valley as a significant barrier to gene flow for plants. We suggest that drying events that divided northern and southern floras at the Hunter River Valley occurred at the same time as those that divided eastern and western floras. © 2015 John Wiley & Sons Ltd.

Rossetto M.,National Herbarium of NSW | Allen C.B.,National Herbarium of NSW | Thurlby K.A.G.,National Herbarium of NSW | Weston P.H.,National Herbarium of NSW | And 2 more authors.
BMC Evolutionary Biology | Year: 2012

Background: Four of the five species of Telopea (Proteaceae) are distributed in a latitudinal replacement pattern on the south-eastern Australian mainland. In similar circumstances, a simple allopatric speciation model that identifies the origins of genetic isolation within temporal geographic separation is considered as the default model. However, secondary contact between differentiated lineages can result in similar distributional patterns to those arising from a process of parapatric speciation (where gene flow between lineages remains uninterrupted during differentiation). Our aim was to use the characteristic distributional patterns in Telopea to test whether it reflected the evolutionary models of allopatric or parapatric speciation. Using a combination of genetic evidence and environmental niche modelling, we focused on three main questions: do currently described geographic borders coincide with genetic and environmental boundaries; are there hybrid zones in areas of secondary contact between closely related species; did species distributions contract during the last glacial maximum resulting in distributional gaps even where overlap and hybridisation currently occur?. Results: Total genomic DNA was extracted from 619 individuals sampled from 36 populations representing the four species. Seven nuclear microsatellites (nSSR) and six chloroplast microsatellites (cpSSR) were amplified across all populations. Genetic structure and the signature of admixture in overlap zones was described using the Bayesian clustering methods implemented in STUCTURE and NewHybrids respectively. Relationships between chlorotypes were reconstructed as a median-joining network. Environmental niche models were produced for all species using environmental parameters from both the present day and the last glacial maximum (LGM).The nSSR loci amplified a total of 154 alleles, while data for the cpSSR loci produced a network of six chlorotypes. STRUCTURE revealed an optimum number of five clusters corresponding to the four recognised species with the additional division of T. speciosissima into populations north and south of the Shoalhaven River valley. Unexpectedly, the northern disjunct population of T. oreades grouped with T. mongaensis and was identified as a hybrid swarm by the Bayesian assignment test implemented in NewHybrids. Present day and LGM environmental niche models differed dramatically, suggesting that distributions of all species had repeatedly expanded and contracted in response to Pleistocene climatic oscillations and confirming strongly marked historical distributional gaps among taxes. Conclusions: Genetic structure and bio-climatic modeling results are more consistent with a history of allopatric speciation followed by repeated episodes of secondary contact and localised hybridisation, rather than with parapatric speciation. This study on Telopea shows that the evidence for temporal exclusion of gene flow can be found even outside obvious geographical contexts, and that it is possible to make significant progress towards excluding parapatric speciation as a contributing evolutionary process. © 2012 Rossetto et al.; licensee BioMed Central Ltd.

Gallagher R.V.,Macquarie University | Makinson R.O.,National Herbarium of NSW | Hancock N.,Macquarie University
Austral Ecology | Year: 2015

Assisted colonization is a form of conservation translocation which introduces species at risk from extinction to new habitats, beyond their current range, in anticipation of more suitable conditions. Identifying which species, communities and ecosystems may benefit most from assisted colonization in coming decades is a key goal for conservation. Climate change is expected to lead to the loss or movement of suitable habitat for a range of species and anticipating which can be effectively conserved through assisted colonization is critical. Here, we identify a series of scenarios that may predispose terrestrial species to the need for assisted colonization in order to reduce extinction risk resulting from anthropogenic climate change and assemble a list of traits commonly associated with at-risk species. These traits may help to provide broad-scale guidance on how to select species to target for assisted colonization as a conservation management response to climate change. We also identify six key themes associated with successful conservation translocations including recipient site selection and preparation, a clear understanding of species biology and ecology, and taking lessons from invasive species research. © 2014 Ecological Society of Australia.

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