James Raymond Peter Worth

James Raymond Peter Worth
Forestry and Forest Products Research Institute | FFPRI · Department of Forest Genetics

PhD

About

125
Publications
13,127
Reads
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655
Citations
Citations since 2016
57 Research Items
532 Citations
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2016201720182019202020212022020406080100
2016201720182019202020212022020406080100
Introduction
My major motivation is to help to conserve biodiversity and ecosystem function into the future. The world’s biodiversity is under unprecedented pressure from habitat loss and climate change of a magnitude that has not occurred for millennia. My current focus is to improve predictions of the impacts of environmental change on forest biomes by undertaking multidisciplinary research integrating information from genetics, ecology, paleobotany and species distribution modelling.
Additional affiliations
October 2012 - March 2015
University of Tasmania
Position
  • PostDoc Position
October 2010 - September 2012
Kyoto University
Position
  • PostDoc Position

Publications

Publications (125)
Article
The Japanese archipelago exhibits a notable difference in snow depth in winter, deep snow on the Sea of Japan side and low snow cover on the Pacific Ocean side. This contrasting pattern has shaped the distribution of infraspecific taxon pairs in a range of woody plants, with taxa found on the Sea of Japan side typically exhibiting a stunted shrub f...
Article
While clonal growth is important in the East Asian Fagus subgenus Engleriana and the North American Fagus grandifolia (subgenus Fagus), for other subge- nus Fagus species the vast majority of regeneration involves sexual reproduc- tion with clonal growth only rarely observed. Here we aim to confirm using nuclear microsatellite markers whether clona...
Article
Full-text available
Rear-edge populations are of significant scientific interest because they can contain allelic variation not found in core-range populations. However, such populations can differ in their level of genetic diversity and divergence reflecting variation in life-history traits, demographic histories and human impacts. Using 13 EST-microsatellites, we in...
Article
Warm-edge populations, that is, those usually small and isolated populations at the boundary of species maximum temperature tolerance, are of particular scientific and conservation interest. This is especially the case for those that have long been geographically isolated, potentially through multiple glaciations, which can have a disproportionate...
Data
Details about reasoning for using HTS data, sampling, 5S-IGS identification, pre-processing, amplicon length/GC content diversity within each sample/major type, and description of most prominent length-polymorphic patterns. Includes three supplement tables, 15 supplementary figures and two appendices: Appendix A gives a summary of Data S2; Append...
Data
This file is part of the figshare data collection associated to the main paper. When using these data, please cite: Simeone, Cardoni et al. (2021): High-Throughput Sequencing of 5S-IGS in Fagus L. - Updated. figshare. Online resource. https://doi.org/10.6084/m9.figshare.16803481.v1
Data
Basic information about samples, obtained HTS reads, and completely annotated lists for the 4,693 variants with an abundance of ≥ 4, as-is and summarised as Pivot tables. Uses auto-filter, auto-generating and auto-formatting functionality; up-to-date version of EXCEL® is recommended to properly view the file. This file is part of the figshare data...
Data
Details about downstream in-depth analysis of 38 selected variants, including selection process and a fully annotated alignment in tabulated, graphically enhanced form. This file is part of the figshare data collection associated to the main paper. When using these data, please cite: Simeone, Cardoni et al. (2021): High-Throughput Sequencing of 5S...
Data
Tabulation and characterization of gene incongruence seen in, and phylogenetic information that can be extracted from, the 28-gene data of Jiang et al. (2021); including tree inference, bootstrapping and gene-wise model statistics. The file makes extensive use of colouring and auto-filter functionality not available in pre-view mode. Up-to-date ve...
Preprint
Full-text available
DNA barcode databases are increasingly available for a range of organisms facilitating the wide application of DNA barcode –based pursuits. Here we announce the development of a comprehensive DNA barcode database of the Japanese woody flora representing 43 orders, 99 families, 303 genera and 834 species and comprising 77.3% of genera and 72.2% of s...
Article
Full-text available
Standard models of plant speciation assume strictly dichotomous genealogies in which a species, the ancestor, is replaced by two offspring species. The reality in wind‐pollinated trees with long evolutionary histories is more complex: species evolve from other species through isolation when genetic drift exceeds gene flow; lineage mixing can give r...
Article
Full-text available
Glacial relict plants are often endangered because extant populations can be small, geographically isolated and persist in suboptimal environments, leading to increased clonality and reduced genetic diversity putting their survival at further risk. This study examines how restriction to interglacial refugia has impacted the genetic diversity and st...
Preprint
Full-text available
Standard models of speciation assume strictly dichotomous genealogies in which a species, the ancestor, is replaced by two offspring species. The reality is more complex: plant species can evolve from other species via isolation when genetic drift exceeds gene flow; lineage mixing can give rise to new species (hybrid taxa such as nothospecies and a...
Article
Full-text available
Inventories of species recently extinct or threatened with extinction may be found in global databases. However, despite the large number of published fossil based-studies, specific databases on the vulnerability of species in the past are not available. We compiled a worldwide database of published fossil records of plant range losses over the las...
Article
Tuber himalayense is a species of edible Asiatic black truffle which is sister to Tuber indicum. Local populations contribute significantly to the reproduction of truffles, but fundamental data of fine-scale genetic structure is lacking in Asiatic truffle species. In this study, we provide the first report on the genotypic diversity and spatial fru...
Article
Full-text available
Thuja sutchuenensis Franch. is an extremely endangered conifer (Cupressaceae) species that is endemic to southwestern China. It was once considered extinct in the wild and was rediscovered after 100 years later in October 1999. Due to the habitat destruction from nature and humans, the population has decreased sharply and the distribution range is...
Article
Full-text available
Nuclear Expressed Sequence Tag (EST) microsatellite markers were developed for the Tasmanian palaeoendemic conifer Lagarostrobos franklinii (Hook.-f.) Quinn for genetic studies. RNAseq data was mined for EST microsatellites, and primer pairs were synthesised from 70 contigs with 50 producing amplification products. Of these 50, 10 reliably amplifie...
Article
Full-text available
Glyptostrobus pensilis (Staunt.) Koch is a relict species in the Cupressaceae that previously had a global distribution but is now restricted to Southern China and two disjunct populations along the Annamite ranges in Laos and Vietnam. Using nuclear and chloroplast microsatellite markers (cpSSR and nSSR, respectively), we investigated the genetic d...
Article
Full-text available
Objective: Design polymorphic microsatellite loci that will be useful for studies of the genetic diversity, gene-flow and reproduction in the Japanese endemic conifer Thuja standishii and test the transferability of these loci to the two other East Asian species, T. sutchuenensis and T. koraiensis. Results: Fifteen loci were developed which disp...
Preprint
Full-text available
Objective: Design polymorphic microsatellite loci that will be useful for studies of the genetic diversity, structure and reproduction in the Japanese endemic conifer Thuja standishii and test the transferability of these loci to the two other East Asian species, T. sutchuenensis and T. koraiensis . Results: Fifteen loci were developed which displa...
Article
Full-text available
Premise: Glyptostrobus pensilis (Cupressaceae) is a critically endangered conifer native to China, Laos, and Vietnam, with only a few populations remaining in the wild. Methods and results: Using a complete chloroplast genome sequence, we designed 70 cpSSR loci and tested them for amplification success and polymorphism in 16 samples. Ten loci we...
Article
Full-text available
This study reports the whole chloroplast genome of Fagus crenata (subgenus Fagus), a foundation tree species of Japanese temperate forests. The genome has a total of 158,227 bp containing 111 genes, including 76 protein-coding genes, 31 tRNA genes and 4 ribosomal RNA genes. Comparison with the only other published Fagus chloroplast genome, F. engel...
Preprint
Full-text available
This study reports the whole chloroplast genome of Fagus crenata (subgenus Fagus ), a foundation tree species of Japanese temperate forests. The genome was a total of 158,247 bp in length containing 111 genes. Comparison with the only other published Fagu s chloroplast genome, F. engeleriana (subgenus Engleriana ) shows that the genomes are relativ...
Preprint
This study reports the whole chloroplast genome of Fagus crenata (subgenus Fagus ), a foundation tree species of Japanese temperate forests. The genome was a total of 158,247 bp in length containing 111 genes. Comparison with the only other published Fagu s chloroplast genome, F. engeleriana (subgenus Engleriana ) shows that the genomes are relativ...
Article
Phylogeography infers patterns of migration, demography and historical relationships from genetic data. Such studies have been particularly useful in understanding vicariance and colonization processes in pest species. Using a low-density SNP data set we investigated the range-wide phylogeography of mountain pine beetle in North America using Appro...
Article
Full-text available
Phylogeography infers patterns of migration, demography, and historical relationships from genetic data. Such studies have been particularly useful in understanding vicariance and colonization processes in pest species. Using a low-density single-nucleotide polymorphism (SNP) data set we investigated the range-wide phylogeography of mountain pine b...
Article
Full-text available
Tsuga diversifolia (Pinaceae) is a dominant tree of the subalpine forests of Japan distributed from northern Honshu to Shikoku island (Aizawa, 2005). The only other Tsuga species in Japan, the temperate forest dominant T. sieboldii sometimes abuts the range of T. diversifolia at the edge of the subalpine zone, where distinguishing the species can b...
Article
Full-text available
The eastern Australian temperate biota harbours many plants with fragmented geographic ranges distributed over 1000s of kilometres, yet the spatial genetic structure of their populations remains largely unstudied. In this study, we investigated genetic variation of the nuclear internal transcribed spacer (ITS) and chloroplast DNA sequences to disen...
Article
Full-text available
1 The often patchy distribution of serpentine geology can lead to abrupt changes in soil and microclimates. Thus, serpentine areas provide an ideal natural setting to understand how divergent selection drives the process of local adaptation in edaphically specialized plants. When the serpentine ecotype is surrounded by a related non‐serpentine ecot...
Article
Full-text available
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,...
Article
Full-text available
Nuclear microsatellite markers were developed for the two Tsuga species native to the Japanese Archipelago, Tsuga diversifolia and T. sieboldii, and a population with genetic affinities to T. diversifolia on Ulleung Island, Korea. Tsuga diversifolia and T. sieboldii are widespread dominant trees of temperate and subalpine forests in Japan but to da...
Article
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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...
Data
Phylogenetic tree reconstruction of 12 taxa of Fagales using maximum likelihood (ML) based on the 69 shared protein-coding genes sequences.
Data
The distribution and presence of simple sequence repeats (SSRs) in the cp genome of M.rubra-FJZS (A) and M. rubra-YNML (B).
Article
Full-text available
Morella rubra (Myricaceae), also known as Chinese bayberry, is an economically important, subtropical, evergreen fruit tree. The phylogenetic placement of Myricaceae within Fagales and the origin of Chinese bayberry’s domestication are still unresolved. In this study, we report the chloroplast (cp) genome of M. rubra and take advantage of several p...
Article
Full-text available
The impacts of Holocene fires on the genetic architecture of fire-intolerant species have largely been overlooked. Here, we investigate the relative impacts of the last glacial climate versus Holocene fires on the genetic diversity of two co-occurring, fire-intolerant conifers using a comparative population genetic study. The palaeoendemic plant-ri...
Article
Full-text available
Global increases in fire frequency driven by anthropogenic greenhouse emissions and land use change could threaten unique and ancient species by creeping into long-term fire refugia. The perhumid and mountainous western half of Tasmania is a globally important refugium for palaeo-endemic, fire intolerant lineages, especially conifers. Reproductive...
Research
Full-text available
This manuscript is the English version of a chapter recently published in Japanese describing the genetic diversity of the relictual conifer Japanese umbrella pine.
Article
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Premise of the study: Homoploid hybrid speciation is receiving growing attention due the increasing recognition of its role in speciation. We investigate if individuals intermediate in morphology between the two species of the conifer genus Athrotaxis represent a homoploid hybrid species, A. laxifolia, or are spontaneous F1 hybrids. Methods: A t...
Article
AimPalaeoendemics are clades that are ancient but geographically restricted, often because they have been selected against in other areas. Ecological similarities among palaeoendemics may be indicators of ancient environments. We determine the environmental ranges of the remarkable palaeoendemic plants of Tasmania to deduce whether they indicate th...
Article
Full-text available
Nothofagus cunninghamii is a long-lived, wind-pollinated tree species that dominates the cool temperate rainforests of southeastern Australia. The species' distribution is more or less continuous in western Tasmania but is fragmented elsewhere. However, it is unknown whether this fragmentation has affected the species' genetic architecture. Thus, w...