13 Works

Regarding the F-word: the effects of data Filtering on inferred genotype-environment associations

Collin Ahrens, Rebecca Jordan, Jason Bragg, Peter Harrison, Tara Hopley, Helen Bothwell, Kevin Murray, Dorothy Steane, John Whale, Margaret Byrne, Rose Andrew & Paul Rymer
Genotype-environment association (GEA) methods have become part of the standard landscape genomics toolkit, yet, we know little about how to best filter genotype-by-sequencing data to provide robust inferences for environmental adaptation. In many cases, default filtering thresholds for minor allele frequency and missing data are applied regardless of sample size, having unknown impacts on the results. These effects could be amplified in downstream predictions, including management strategies. Here, we investigate the effects of filtering on...

Plant collections for conservation and restoration: can they be adapted and adaptable?

Jason Bragg, Marlien Van Der Merwe, Jia-Yee Yap, Justin Borevitz & Maurizio Rossetto
Plant collections are important for the conservation of threatened species, and as a source of 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,...

Evolutionary processes in an undescribed eucalypt: implications for the translocation of a critically endangered species

Susan Rutherford, Trevor C Wilson, Jia-Yee Samantha Yap, Enhua Lee, Graeme Errington & Maurizio Rossetto
Background and Aims Knowledge of the evolutionary processes responsible for the distribution of threatened and highly localised 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 km 2 area of Sydney, Australia and is threatened by increased urbanisation. Eucalyptus sp....

Data from: Managing the risk of genetic swamping of a rare and restricted tree

Susan Rutherford, Marlien Van Der Merwe, Peter G. Wilson, Robert M. Kooyman & Maurizio Rossetto
Hybridisation is a complex process that has important evolutionary consequences. In the case of rare species, a comprehensive understanding of inter-specific hybridisation can be critical for their conservation and management. Eucalyptus tetrapleura is a rare species of ironbark that is restricted to a 40 km × 100 km area around Grafton on the North Coast of New South Wales (Australia), and is distinctive in that it has four ribs on the sides of its buds...

Tspe_v1 (Telopea speciosissima) genome supplementary files for: Chromosome-level de novo genome assembly of Telopea speciosissima (New South Wales waratah) using long-reads, linked-reads and Hi-C

Stephanie Chen, Maurizio Rossetto, Marlien Van Der Merwe, Patricia Lu-Irving, Jia-Yee Yap, Hervé Sauquet, Greg Bourke, Timothy Amos, Jason Bragg & Richard Edwards
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 %...

Data from: Speciation in the presence of gene flow: population genomics of closely related and diverging Eucalyptus species

Susan Rutherford, Maurizio Rossetto, Jason G. Bragg, Hannah McPherson, Doug Benson, Stephen P. Bonser & Peter G. Wilson
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...

Data from: Conserving the genetic diversity of condemned populations: optimizing collections and translocation

Jason Bragg, Jia-Yee Yap, Trevor Wilson, Enhua Lee & Maurizio Rossetto
We generated SNP genotype data from two endangered plant species, Pimelea spicata and Eucalyptus sp. Cattai. For each, we genotyped plants from a population that was 'condemned,' or that would soon be destoyed. We used the genotype data to design ex situ germplasm collections that preserved the diversity in the condemned populations, in ways that were optimized. Here, we provide an archive of these SNP genotype data, and the code that was used to analyse...

Data from: Whole-chloroplast analysis as an approach for fine-tuning the preservation of a highly charismatic but critically endangered species, Wollemia nobilis (Araucariaceae)

Abigail Greenfield, Hannah McPherson, Tony Auld, Sven Delaney, Catherine A. Offord, Marlien Van Der Merwe, Jia-Yee S. Yap & Maurizio Rossetto
The critically endangered Wollemia nobilis W.G. Jones, K.D. Hill & J.M. Allen is endemic to Wollemi National Park north of Sydney (Australia). All known wild individuals are restricted to four sites in a single canyon system. W. nobilis can reproduce sexually but at all sites individual clumps can be multi-stemmed from a common base. In the first genetic study of this species, no genetic variation was found across multiple genetic marker types representing hundreds of...

Spatial, climate and ploidy factors drive genomic diversity and resilience in the widespread grass Themeda triandra

Collin Ahrens, Elizabeth A. James, Adam D. Miller, Ferguson Scott, Nicola C. Aitken, Ashley W. Jones, Patricia Lu‐Irving, Justin O. Borevitz, David J. Cantrill & Paul D. Rymer
This data set was used to assess the climate resilience of Themeda triandra, a foundational species and the most widespread plant in Australia, by assessing the relative contributions of spatial, environmental, and ploidy factors to contemporary genomic variation. Reduced-representation genome sequencing on 472 samples from 52 locations was used to test how the distribution of genomic variation, including ploidy polymorphism, supports adaptation to hotter and drier climates.

Temperature predicts the rate of molecular evolution in Australian Eugongylinae skinks

Jeremias Ivan, Craig Moritz, Sally Potter, Jason Bragg, Rust Turakulov & Xia Hua
Temperature differences over time and space has been hypothesized to cause variation in the rate of molecular evolution of species, but empirical evidence is mixed. To further test this hypothesis, we utilized a large exon-capture sequence data of Australian Eugongylinae skinks, exemplifying a radiation of temperature-sensitive ectotherms spanning a large latitudinal gradient. The association between temperature (and other species traits) and long-term substitution rate was assessed based on 1268 sequenced exons of 44 species pairs...

Looks can be deceiving: speciation dynamics of co-distributed Angophora (Myrtaceae) species in a varying landscape

Susan Rutherford, Justin Wan, Joel Cohen, Doug Benson & Maurizio Rossetto
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...

Data from: Assemblage Accumulation Curves: A framework for resolving species accumulation in biological communities using chloroplast genome sequences

Marlien Van Der Merwe, Samantha Yap, Jason G. Bragg, Caroline Cristofolini, Charles S. P. Foster, Simon Y. W. Ho & Maurizio Rossetto
The timing and tempo of the processes involved in community assembly are of substantial concern to community ecologists and conservation managers. The fossil record is a valuable source of data for studying past changes in community composition, but it is not always detailed enough to allow the process of community assembly to be resolved at regional or site scales while tracing the trajectories of known species with associated known traits. We present a three‐step framework...

Data from: An expanded plastid phylogeny of Marsilea with emphasis on North American species

W. Mark Whitten, Colette C. Jacono & Nathalie S. Nagalingum
Ferns of the genus Marsilea (water clover) are potentially invasive aquatic and wetland plants. They are difficult to identify to species because of subtle diagnostic characters, the sterile condition of many specimens, and unresolved taxonomic problems. We sequenced four plastid regions (rbcL, rps4, rps4-trnS spacer, and trnL-F spacer) from 223 accessions across ca. 38 species. Our goals were to: 1) attempt to identify problematic Marsilea specimens from the southeastern U.S., and 2) assess species delimitation...

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