James DoreyUniversity of Wollongong | UOW
James Dorey
Doctor of Philosophy
About
59
Publications
12,204
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299
Citations
Introduction
My research interests include evolutionary biology, phylogenetics, island biogeography, ecology, zoology and more.
I am also a professional macro photographer specialising in focus stacking. I focus on native bee diversity but shoot anything that interests me. See more here jamesdoreyphotography.com.au
Additional affiliations
April 2023 - present
October 2018 - August 2021
Position
- Information Officer
Description
- Working to educate the public in the museum's Discovery Centre and working at the front of house.
February 2019 - May 2021
Position
- Project supervisor
Description
- Helping to supervise summer research and honours students at Flinders University, particularly Ellie Powell and Patricia Slattery
Education
February 2018 - January 2022
February 2017 - November 2017
February 2013 - November 2015
Publications
Publications (59)
Bees are the darlings of the insect world. It is a joy to see these insects hard at work, peacefully buzzing from flower to flower. Many people recognise the worth of bees, as well as that they face multiple threats. But very few know about the diversity and importance of our native bee species. There are an estimated 2000 to 3000 bee species in Au...
Island biogeography explores how biodiversity in island ecosystems arises and is maintained. The topographical complexity of islands can drive speciation by providing a diversity of niches that promote adaptive radiation and speciation. However, recent studies have argued that phylogenetic niche conservatism, combined with topographical complexity...
Low-light adapted bees are substantially understudied components of the bee fauna, particularly in Aus-tralia. Whilst several species in Australia are thought to be adapted to low-light conditions, explicit records of these taxa actually foraging at twilight or night are absent from the scientific literature. We present the first observations of Au...
There is substantial debate about the relative roles of climate change and human activities on biodiversity and species demographies over the Holocene. In some cases, these two factors can be resolved using fossil data, but for many taxa such data are not available. Inferring historical demographies of taxa has become common, but the methodologies...
The 2019–2020 Australian Black Summer wildfires demonstrated that single events can have widespread and catastrophic impacts on biodiversity, causing a sudden and marked reduction in population size for many species. In such circumstances, there is a need for conservation managers to respond rapidly to implement priority remedial management actions...
Coadaptation of mitochondrial and nuclear genes is essential for proper cellular function. When populations become isolated, theory predicts that they should maintain mito‐nuclear coadaptation in each population, even as they diverge in genotype. Mito‐nuclear incompatibilities may therefore arise when individuals from populations with divergent co‐...
Insects have a complex coevolutionary history with bacterial symbionts, among which Wolbachia pipientis stands out for its prevalence and role in reproductive manipulation. Wolbachia can induce cytoplasmic incompatibility, feminisation, male killing, and parthenogenesis, greatly influence the population genetics of their hosts and are potential dri...
Our knowledge of biodiversity hinges on sufficient data, reliable methods, and realistic models. Without an accurate assessment of species distributions, we cannot effectively target and stem biodiversity loss. Species range maps are the foundation of such efforts, but countless studies have failed to account for the most basic assumptions of relia...
Determining the ecological and evolutionary mechanisms that underpin patterns of species richness across elevational gradients is a key question in evolutionary ecology, and can help to understand species extinction risk under changing climates. In the tropical montane islands of Fiji, there are 28 species of endemic bee in the subgenus Lasioglossu...
Large parts of the Pacific were thought to host low bee diversity. In Fiji alone, our recent estimates of native bee diversity have rapidly increased by a factor of five (from 4 to >22). Here, we show how including sampling of the forest canopy has quickly uncovered a new radiation of Hylaeus (Hymenoptera: Colletidae) bees in Fiji. We also show tha...
Species occurrence data are foundational for research, conservation, and science communication, but the limited availability and accessibility of reliable data represents a major obstacle, particularly for insects, which face mounting pressures. We present BeeBDC, a new R package, and a global bee occurrence dataset to address this issue. We combin...
Reflecting the state of invertebrate taxonomy globally, many bee taxa in Australia are in need of revision, and this includes the most species-rich endemic subfamily, the Euryglossinae. In addition to undescribed species, many euryglossine species have been described from only a single sex. Over 30 taxonomic papers on euryglossines have been publis...
Our knowledge of biodiversity hinges on sufficient data, reliable methods, and realistic models. Without an accurate assessment of species distributions, we cannot effectively target and stem biodiversity loss. Species range maps are the foundation of such efforts, but countless studies have failed to account for the most basic assumptions of relia...
NOTE: This manuscript and the package behind it are still undergoing tests and development. Once these are complete and a final version is accepted we will update the input data, package versions, and rerun all queries (values will change). Please contact James for further queries of collaborations in the meantime.
Abstract: Species occurrence da...
The challenges of bee research in Asia are unique and severe, reflecting different cultures, landscapes, and faunas. Strategies and frameworks developed in North America or Europe may not prove applicable. Virtually none of these species have been assessed by the IUCN and there is a paucity of public data on even the basics of bee distribution. If...
Although the importance of natural habitats to pollinator diversity is widely recognized, the value of forests to pollinating insects has been largely overlooked in many parts of the world. In this review, we (i) establish the importance of forests to global pollinator diversity, (ii) explore the relationship between forest cover and pollinator div...
Mitochondrial heteroplasmy is the occurrence of more than one type of mitochondrial DNA within a single individual. Although generally reported to occur in a small subset of individuals within a species, there are some instances of widespread heteroplasmy across entire populations. Amphylaeus morosus is an Australian native bee species in the diver...
Bees are a diverse group of insects that are ecologically and agriculturally crucial. Despite this, the taxonomy and biology of most bee species are poorly understood. Such knowledge is foundational for higher level questions and its paucity limits research and conservation of bee species. In this thesis, my first three chapters focus on a relative...
The rapid decline of bee populations over the last decade is thought to be driven by a combination of environmental change, habitat loss, invasive species, co-introduced disease, and chemical use in agriculture. Native bee species, managed honey bees (Apis mellifera), and other introduced bee species in Fiji provide great economic value by assistin...
The Australian endemic bee, Pharohylaeus lactiferus (Colletidae: Hylaeinae) is a rare species that requires conservation assessment. Prior to this study, the last published record of this bee species was from 1923 in Queensland, and nothing was known of its biology. Hence, I aimed to locate extant populations, provide biological information and und...
Anthropogenic climate change and invasive species are two of the greatest threats to biodiversity, affecting the survival, fitness and distribution of many species around the globe. Invasive species are often expected to have broad thermal tolerances, be highly plastic, or have high adaptive potential when faced with novel environments. Tropical is...
The halictine bee genus Homalictus (Apoidea: Halictidae) is distrib- uted broadly across south east Asia, Indonesia, Australia and the archipelagos of the Pacific. The group is well represented in the bee faunas of Australia and Papua New Guinea, but Homalictus is parti- cularly important in the Pacific where it plays a keystone pollination role as...
The species in the subgenus Amegilla (Asaropoda) are revised. Species delineation was decided based on diagnostic morphological characters as well as an incomplete phylogeny based on mitochondrial cytochrome oxidase 1 sequence data. Strong support was obtained for separating the Australian species of Amegilla into the three subgenera previously pro...
The genus Homalictus Cockerell has not been taxonomically reviewed in the Fijian archipelago for 40 years. Here we redescribe the four known species and describe nine new ones, bringing the number of endemic Homalictus in Fiji to 13 species. We provide identifications keys to all species. Most of the species diversity (11 species) have their distri...
Twenty six new species of Australian Leioproctus (subgenusColletellus) (Hymenoptera, Colletidae) are described: aberrans Leijs, sp. n. , alatus Leijs, sp. n. , albipilosus Leijs, sp. n. , albiscopis Leijs, sp. n. , aliceafontanus Leijs, sp. n. , altispinosus Leijs, sp. n. , aratus Leijs, sp. n. , auricorneus Leijs, sp. n. , bidentatus Leijs, sp. n....
The Cambrian explosion is widely seen as evolution's 'big bang', generating a vast diversity of animals in a geological blink of an eye. Two new studies, however, caution against overestimating its magnitude.
The theory of island biogeography remains an active area of research that has been used to explore how biodiversity arises and is maintained in a variety of insular systems. An important parameter of island biogeography is topographic complexity, which is thought to increase available ecological niches that can be exploited through adaptive radiati...
Background
The Mantispidae are a distinctive group of Neuroptera known for the adults’ possession of raptorial forelegs. There are four recognised, extant subfamilies of Mantispidae: the Mantispinae, Symphrasinae, Calomantispinae and Drepanicinae. The life history and larval behaviour of the subfamily Mantispinae is best known: the immatures are sp...
Questions
Questions (4)
Hi all,
I've always wanted to try harvesting and analysing data from NCBI, but I've just never really known the best way forward. I know that I can easily download a whole bunch of data from NCBI by just searching for a group on the website, Geneious, or any other number of programs/scripts. But, I end up with a big mess of data that seems difficult to sort through and actually use.
So, for those who routinely download NCBI sequences — particularly using R — can you point me in the right direction of packages or tutorials to make it easier to:
- Summarise the available data (say by species within a particular genus) on the online databases. Perhaps with an output table showing the number of sequences available for genes X, Y, and Z by taxon A, B, and C.
- Choose the genes (i.e., several commonly used phylogenetics genes) and the species you want and download them into an alignment.
- Follow up question — It doesn't look like these databases store a specimen identifiers. So, do I need to trawl through each paper's tables to then link different genes from a single specimen together. Or, do people usually just link genes together from the same species to get a full compliment (this seems dodgy and prone to author error in identification).
Perhaps there is already a document or paper that really summarises these issues and the best-practice nicely, but my search queries haven't found it yet.
Many thanks in advance!
James
Hi all,
I have been wondering for a while about getting a mobile device to collect data and send it to my mobile while I collect flying insects so that I have these data for collection events. I have started poking around and there are a few devices that look alright (e.g. https://www.pasco.com/products/sensors/wireless/ps-3209#specs-panel – but, I don't know how much it costs without a quote 😢). But, I thought that I should ask to see if anyone else has been on the same quest before me and if they have any recommendations.
Thanks in advance,
James
I'm hoping that someone might have already overcome this issue... I am trying to figure out some fragmentation metrics as part of a large loop in R (version 3.6.2) on a Mac. I'm having a problem with running out of memory when running through some particularly large input files. I feel like this issue might be able to be solved by having those files saved to my temp directory as this works well for the raster package - e.g. below:
> rasterOptions(tmpdir=file.path(TempDir_Home, LoopSp_FileName))
I have tried to make the landscapemetrics package do this in a variety of ways, e.g.:
> rasterOptions(tmpdir=file.path(TempDir_Home,LoopSp_FileName), todisk = TRUE)
or
> options(to_disk = TRUE)
or
> options_landscapemetrics(to_disk = NULL)
But none of these seem to fix the issue! So, I'm hoping that there's a work around or something!
My system is running MacOS Catalina with a 2.4 GHz 8-Core Intel Core i9 and 64 GB 2667 MHz DDR4 of RAM. At points my activity monitor suggests that my r session can be using > 200GB of memory while using calculate_lsm() and sometimes it runs out of memory before even getting to the progress output for the metrics.
Error Output now:
Error: vector memory exhausted (limit reached?)
In addition: Warning messages:
1: 'return_raster = TRUE' or 'to_disk = TRUE' not able for matrix input.
2: 'return_raster = TRUE' or 'to_disk = TRUE' not able for matrix input.
3: 'return_raster = TRUE' or 'to_disk = TRUE' not able for matrix input.
4: 'return_raster = TRUE' or 'to_disk = TRUE' not able for matrix input.
5: 'return_raster = TRUE' or 'to_disk = TRUE' not able for matrix input.
>
Raster info:
class : RasterLayer
dimensions : 37949, 40101, 1521792849 (nrow, ncol, ncell)
resolution : 100, 100 (x, y)
extent : -1888000, 2122100, -4798800, -1003900 (xmin, xmax, ymin, ymax)
crs : +proj=aea +lat_1=-18 +lat_2=-36 +lat_0=0 +lon_0=132 +x_0=0 +y_0=0 +ellps=GRS80 +towgs84=0,0,0,0,0,0,0 +units=m +no_defs
source : /Users/.../Temp_Files/Braunsapis_unicolor/PresAbsRaster_loopBraunsapis_unicolor.grd
names : presence
values : 1, 1 (min, max)
NOTE: the values show presence data, with all other values being NA
Hi all,
I am trying to run a stairway plot analysis (from here - https://sites.google.com/site/jpopgen/stairway-plot using version 2) and I can get right to the end, before getting rebuffed while trying to get the results (using Stairway_output_summary_plot2.class). I wonder if anyone has much experience with this program (or java) and might be able to help. My input and the output error are both below.
Many thanks in advance,
James
Code input:
java -Xmx1g -cp stairway_plot_es/:stairway_plot_es/gral-core-0.11.jar:stairway_plot_es/VectorGraphics2D-0.9.3.jar Stairway_output_summary_plot2 two-epoch_fold.blueprint rand9/
Error:
(base) jamesdorey@Jamess-MacBook-Pro-4:~/Desktop/Uni/My_papers/Fijiensis_paper/Analyses/Stairway_plots/stairway_plot_v2/TEST$ java -Xmx1g -cp stairway_plot_es/:stairway_plot_es/gral-core-0.11.jar:stairway_plot_es/VectorGraphics2D-0.9.3.jar Stairway_output_summary_plot2 two-epoch_fold.blueprint rand9/
Exception in thread "main" java.util.NoSuchElementException
at java.util.StringTokenizer.nextToken(StringTokenizer.java:332)
at Stairway_output_summary_plot2.main(Stairway_output_summary_plot2.java:238)
