Genetic bottlenecks in time and space: reconstructing invasions from contemporary and historical collections

Herbarium accession data offer a useful historical botanical perspective and have been used to track the spread of plant invasions through time and space. Nevertheless, few studies have utilised this resource for genetic analysis to reconstruct a more complete picture of historical invasion dynamics, including the occurrence of separate introduction events. In this study, we combined nuclear and chloroplast microsatellite analyses of contemporary and historical collections of Senecio madagascariensis, a globally invasive weed first introduced to Australia c. 1918 from its native South Africa. Analysis of nuclear microsatellites, together with temporal spread data and simulations of herbarium voucher sampling, revealed distinct introductions to south-eastern Australia and mid-eastern Australia. Genetic diversity of the south-eastern invasive population was lower than in the native range, but higher than in the mid-eastern invasion. In the invasive range, despite its low resolution, our chloroplast microsatellite data revealed the occurrence of new haplotypes over time, probably as the result of subsequent introduction(s) to Australia from the native range during the latter half of the 20th century. Our work demonstrates how molecular studies of contemporary and historical field collections can be combined to reconstruct a more complete picture of the invasion history of introduced taxa. Further, our study indicates that a survey of contemporary samples only (as undertaken for the majority of invasive species studies) would be insufficient to identify potential source populations and occurrence of multiple introductions.Eleanor E. Dormontt, Michael G. Gardner, Martin F. Breed, James G. Rodger, Peter J. Prentis, Andrew J. Low

Opportunities for improved transparency in the timber trade through scientific verification

Published: 09 November 2016In May 2014, the Member States of the United Nations adopted Resolution 23/1 on “strengthening a targeted crime prevention and criminal justice response to combat illicit trafficking in forest products, including timber.” The resolution promotes the development of tools and technologies that can be used to combat the illicit trafficking of timber. Stopping illegal logging worldwide could substantially increase revenue from the legal trade in timber and halt the associated environmental degradation, but law enforcement and timber traders themselves are hampered by the lack of available tools to verify timber legality. Here, we outline how scientific methods can be used to verify global timber supply chains. We advocate that scientific methods are capable of supporting both enforcement and compliance with respect to timber laws but that work is required to expand the applicability of these methods and provide the certification, policy, and enforcement frameworks needed for effective routine implementation.Andrew J. Lowe, Eleanor E. Dormontt, Matthew J. Bowie, Bernd Degen, Shelley Gardner, Darren Thomas, Caitlin Clarke, Anto Rimbawanto, Alex Wiedenhoeft, Yafang Yin, and Nophea Sasak

Advancing DNA barcoding and metabarcoding applications for plants requires systematic analysis of herbarium collections-an Australian perspective

Building DNA barcode databases for plants has historically been ad hoc, and often with a relatively narrow taxonomic focus. To realize the full potential of DNA barcoding for plants, and particularly its application to metabarcoding for mixed-species environmental samples, systematic sequencing of reference collections is required using an augmented set of DNA barcode loci, applied according to agreed data generation and analysis standards. The largest and most complete reference collections of plants are held in herbaria. Australia has a globally significant flora that is well sampled and expertly curated by its herbaria, coordinated through the Council of Heads of Australasian Herbaria. There exists a tremendous opportunity to provide a comprehensive and taxonomically robust reference database for plant DNA barcoding applications by undertaking coordinated and systematic sequencing of the entire flora of Australia utilizing existing herbarium material. In this paper, we review the development of DNA barcoding and metabarcoding and consider the requirements for a robust and comprehensive system. We analyzed the current availability of DNA barcode reference data for Australian plants, recommend priority taxa for database inclusion, and highlight future applications of a comprehensive metabarcoding system. We urge that large-scale and coordinated analysis of herbarium collections be undertaken to realize the promise of DNA barcoding and metabarcoding, and propose that the generation and curation of reference data should become a national investment priority

Is rapid adaptive evolution important in successful invasions?

Eleanor E. Dormontt, Andrew J. Lowe and Peter J. Prenti

Testing putative African tropical forest refugia using chloroplast and nuclear DNA phylogeography

The location and definition of Pleistocene refugia for tropical forest assemblages remains controversial. Phylogeographic methods have been used successfully in temperate ecosystems to locate past forest refugia using genetic data that coincide with pollen core evidence, and in some cases provide the sole basis for their location. Here we present molecular phylogeographic data from nuclear and chloroplast loci for the forest tree Irvingia gabonensis, across the majority of its natural range, in Nigeria, Cameroon and Gabon. It is the first detailed phylogeographic study to posit the location of tropical forest refugia across this region of Africa. Using the same method of restriction fragment length polymorphism screening, 17 alleles were identified across five anonymous nuclear loci and two haplotypes at a single chloroplast locus. Analysis based on nuclear variation identified two genetically diverse, differentiated allelic clusters within the species range, one in southern Nigeria/western Cameroon and the other in southwestern Cameroon. Molecular data are consistent with a historical genetic contraction and bottleneck into these regions in the Pleistocene and/or Holocene, which has been followed by subsequent expansion. Both genetic refugia are located within areas previously suggested as forest refugia from biogeographic studies, supported by available pollen core data, and occur either side of the Sanaga River, a notable biogeographic divide for mammals (particularly primates). Other putative refugia in Gabon do not appear to have acted as genetic refugia for I. gabonensis, and Gabon was most likely recolonised from the SW Cameroon refugial source. In this study, nuclear loci were able to highlight significant phylogeographic structure across the range of a tropical African tree, whereas chloroplast analysis gave a much more limited picture. With the increased availability of sequence data for non-model species, the de novo development and further application of nuclear loci is strongly recommended for phylogeographic studies of plants.Andrew J. Lowe, David Harris, Eleanor Dormontt and Ian K. Dawso

Occasional hybridization between a native and invasive Senecio species in Australia is unlikely to contribute to invasive success

Hybridization between native and invasive species can facilitate introgression of native genes that increase invasive potential by providing exotic species with pre-adapted genes suitable for new environments. In this study we assessed the outcome of hybridization between native Senecio pinnatifolius var. pinnatifolius A.Rich. (dune ecotype) and invasive Senecio madagascariensis Poir. to investigate the potential for introgression of adaptive genes to have facilitated S. madagascariensis spread in Australia. We used amplified fragment length polymorphisms (141 loci) and nuclear microsatellites (2 loci) to genotype a total of 118 adults and 223 seeds from S. pinnatifolius var.pinnatifolius and S. madagascariensis at one allopatric and two shared sites. We used model based clustering and assignment methods to establish whether hybrid seed set and mature hybrids occur in the field. We detected no adult hybrids in any population. Low incidence of hybrid seed set was found at Lennox Head where the contact zone overlapped for 20 m (6% and 22% of total seeds sampled for S. pinnatifolius var. pinnatifolius and S. madagascariensis respectively). One hybrid seed was detected at Ballina where a gap of approximately 150 m was present between species (2% of total seeds sampled for S. madagascariensis). We found no evidence of adult hybrid plants at two shared sites. Hybrid seed set from both species was identified at low levels. Based on these findings we conclude that introgression of adaptive genes from S. pinnatifolius var. pinnatifolius is unlikely to have facilitated S. madagascariensis invasions in Australia. Revisitation of one site after two years could find no remaining S. pinnatifolius var. pinnatifolius, suggesting that contact zones between these species are dynamic and that S. pinnatifolius var. pinnatifolius may be at risk of displacement by S. madagascariensis in coastal areas.Eleanor E. Dormontt, Peter J. Prentis, Michael G. Gardner and Andrew J. Low

Biogeographic concepts define invasion biology

Copyright © 2009 Elsevier Ltd. All rights reserved.John R.U. Wilson, Eleanor E. Dormontt, Peter J. Prentis, Andrew J. Lowe and David M. Richardso

Something in the way you move: dispersal pathways affect invasion success

Copyright © 2009 Elsevier B.V. All rights reserved. ScienceDirect® is a registered trademark of Elsevier B.V.Biological invasions are caused by human-mediated extra-range dispersal and, unlike natural extra-range dispersal, are often the result of multiple introductions from multiple sources to multiple locations. The processes and opportunities that result in propagules moving from one area to another can be used more broadly to differentiate all types of extra-range dispersal. By examining key properties of dispersal pathways (notably propagule pressure, genetic diversity and the potential for simultaneous movement of coevolved species), the establishment and evolutionary trajectories of extra-range dispersal can be better understood. Moreover, elucidation of the mechanistic properties of dispersal pathways is crucial for scientists and managers who wish to assist, minimise or prevent future movements of organisms.John R.U. Wilson, Eleanor E. Dormontt, Peter J. Prentis, Andrew J. Lowe and David M. Richardso

No consistent association between changes in genetic diversity and adaptive responses of Australian acacias in novel ranges

Common garden studies comparing trait differences of exotic species between native and introduced ranges rarely incorporate an analysis of genetic variation, but simply infer that trait shifts between ranges are genetically determined. We compared four growth-related traits (total biomass, relative growth rate RGR, specific leaf area SLA, and root to shoot ratio R:S) of five invasive Fabaceae species (Acacia cyclops, A. longifolia, A. melanoxylon, A. saligna, Paraserianthes lophantha), grown in a common garden experiment using seeds from introduced and native ranges across Australia. Chloroplast microsatellite loci were used to compare genetic diversity of native and introduced populations to determine standing genetic diversity and infer introduction history. We asked whether shifts in traits associated with faster growth due to enemy release in the introduced range were associated with levels of genetic diversity associated with introduction history. We found differences in traits between ranges, although these traits varied among the species. Compared to native-range populations, introduced-range Acacia longifolia had greater biomass and larger SLA; A. cyclops had greater RGR; and A. melanoxylon displayed lower R:S. Genetic diversity in the introduced range was lower for one of those species, A. longifolia, and two others that did not show differences in traits, A. saligna and P. lophantha. Diversity was higher in the introduced range for A. melanoxylon and did not differ among ranges for A. cyclops. These patterns of genetic diversity suggest that a genetic bottleneck may have occurred following the introduction of A. longifolia, A. saligna and P. lophantha. In contrast greater or comparable genetic diversity in the introduced range for A. melanoxylon and A. cyclops suggests introductions from multiple sources. This study has shown that a reduction in genetic diversity in the introduced range is not necessarily associated with a reduced capacity for adaptive responses or invasion potential in the novel range.Carla J. Harris, Eleanor E. Dormontt, Johannes J. Le Roux, Andrew Lowe, Michelle R. Leishma

A set of 204 SNP and INDEL markers for Bigleaf maple (Acer macrophyllum Pursch)

Novel single nucleotide polymorphisms (SNPs) and insertion/deletions (INDELs) were identified for the Bigleaf maple (Acer macrophyllum Pursch) using a combined next generation sequencing approach on the Ion Torrent PGM system with genotyping on the MassARRAY® iPLEX™ platform. Five hundred and ninety-eight putative loci were identified through sequencing of DNA fragments following a double restriction enzyme digest method. Two hundred and four polymorphic loci (199 SNPs and five INDELs) were successfully amplified across 65 individuals from seven populations across the native range of the species. Twenty-nine loci showed evidence of deviation from Hardy–Weinberg Equilibrium, and 85 were significantly linked. Expected heterozygosity ranged from 0.015 to 0.472 and FST from 0.011 to 0.359. These genetic resources will prove useful for future studies into the population genetics and phylogeography of this important and iconic timber species.D. I. Jardine, E. E. Dormontt, K.-J. van Dijk, R. R. M. Dixon, B. Dunker, A. J. Low