Benchmarking Taxonomic and Genetic Diversity After the Fact: Lessons Learned From the Catastrophic 2019–2020 Australian Bushfires

Environmental catastrophes are increasing in frequency and severity under climate change, and they substantially impact biodiversity. Recovery actions after catastrophes depend on prior benchmarking of biodiversity and that in turn minimally requires critical assessment of taxonomy and species-level diversity. Long-term recovery of species also requires an understanding of within-species diversity. Australia’s 2019–2020 bushfires were unprecedented in their extent and severity and impacted large portions of habitats that are not adapted to fire. Assessments of the fires’ impacts on vertebrates identified 114 species that were a high priority for management. In response, we compiled explicit information on taxonomic diversity and genetic diversity within fire-impacted vertebrates to provide to government agencies undertaking rapid conservation assessments. Here we discuss what we learned from our effort to benchmark pre-fire taxonomic and genetic diversity after the event. We identified a significant number of candidate species (genetic units that may be undescribed species), particularly in frogs and mammals. Reptiles and mammals also had high levels of intraspecific genetic structure relevant to conservation management. The first challenge was making published genetic data fit for purpose because original publications often focussed on a different question and did not provide raw sequence read data. Gaining access to analytical files and compiling appropriate individual metadata was also time-consuming. For many species, significant unpublished data was held by researchers. Identifying which data existed was challenging. For both published and unpublished data, substantial sampling gaps prevented areas of a species’ distribution being assigned to a conservation unit. Summarising sampling gaps across species revealed that many areas were poorly sampled across taxonomic groups. To resolve these issues and prepare responses to future catastrophes, we recommend that researchers embrace open data principles including providing detailed metadata. Governments need to invest in a skilled taxonomic workforce to document and describe biodiversity before an event and to assess its impacts afterward. Natural history collections should also target increasing their DNA collections based on sampling gaps and revise their collection strategies to increasingly take population-scale DNA samples in order to document within-species genetic diversity.Funding for this project was provided by the National Environmental Science Programme Threatened Species Recovery Hub, Theme 8: Post bushfire recovery support, and the Centre for Biodiversity Analysis (https://biology.anu.edu.au/research/centres-units/centre-biodiv ersity-analysis)

Chromosomics: Bridging the Gap between Genomes and Chromosomes

The recent advances in DNA sequencing technology are enabling a rapid increase in the number of genomes being sequenced. However, many fundamental questions in genome biology remain unanswered, because sequence data alone is unable to provide insight into how the genome is organised into chromosomes, the position and interaction of those chromosomes in the cell, and how chromosomes and their interactions with each other change in response to environmental stimuli or over time. The intimate relationship between DNA sequence and chromosome structure and function highlights the need to integrate genomic and cytogenetic data to more comprehensively understand the role genome architecture plays in genome plasticity. We propose adoption of the term ‘chromosomics’ as an approach encompassing genome sequencing, cytogenetics and cell biology, and present examples of where chromosomics has already led to novel discoveries, such as the sex-determining gene in eutherian mammals. More importantly, we look to the future and the questions that could be answered as we enter into the chromosomics revolution, such as the role of chromosome rearrangements in speciation and the role more rapidly evolving regions of the genome, like centromeres, play in genome plasticity. However, for chromosomics to reach its full potential, we need to address several challenges, particularly the training of a new generation of cytogeneticists, and the commitment to a closer union among the research areas of genomics, cytogenetics, cell biology and bioinformatics. Overcoming these challenges will lead to ground-breaking discoveries in understanding genome evolution and functio

A pragmatic approach for integrating molecular tools into biodiversity conservation

DATA AVAILABILITY STATEMENT : The data availability statement does not apply for this article.SUPPLEMENTARY MATERIAL : TABLE S1. Case studies in which genetic data are being used to inform conservation.Molecular tools are increasingly applied for assessing and monitoring biodiversity and informing conservation action. While recent developments in genetic and genomic methods provide greater sensitivity in analysis and the capacity to address new questions, they are not equally available to all practitioners: There is considerable bias across institutions and countries in access to technologies, funding, and training. Consequently, in many cases, more accessible traditional genetic data (e.g., microsatellites) are still utilized for making conservation decisions. Conservation approaches need to be pragmatic by tackling clearly defined management questions and using the most appropriate methods available, while maximizing the use of limited resources. Here we present some key questions to consider when applying the molecular toolbox for accessible and actionable conservation management. Finally, we highlight a number of important steps to be addressed in a collaborative way, which can facilitate the broad integration of molecular data into conservation.Open Access funding enabled and organized by Projekt DEAL.http://wileyonlinelibrary.com/journal/csp2hj2024BiochemistryGeneticsMicrobiology and Plant PathologySDG-15:Life on lan

Taxonomy of rock-wallabies, Petrogale (Marsupialia : Macropodidae). V. A description of two new subspecies of the black-footed rock-wallaby (Petrogale lateralis)

The black-footed rock-wallaby (Petrogale lateralis) is the most widespread member of the endemic Australian macropodid genus Petrogale. Considerable morphological and genetic diversity within this species has long been recognised and P. lateralis is currently divided into three described subspecies (P. lateralis lateralis, P. l. pearsoni, P. l. hacketti) and two undescribed forms (MacDonnell Ranges race, West Kimberley race). Chromosomal, morphological, genic and genomic studies have demonstrated that these five taxa are closely related but distinguishable. Here, we formally name the MacDonnell Ranges race and the West Kimberley race as subspecies of P. lateralis

Gene flow despite complex Robertsonian fusions among rock-wallaby (Petrogale) species

Complex Robertsonian rearrangements, with shared arms in different fusions, are expected to prevent gene flow between hybrids through missegregation during meiosis. Here, we estimate gene flow between recently diverged and chromosomally diverse rock-wallabies (Petrogale) to test for this form of chromosomal speciation. Contrary to expectations, we observe relatively high admixture among species with complex fusions. Our results reinforce the need to consider alternative roles of chromosome change, together with genic divergence, in driving speciation

Understanding Historical Demographic Processes to Inform Contemporary Conservation of an Arid zone Specialist: The Yellow-Footed Rock-Wallaby

Little genetic research has been undertaken on mammals across the vast expanse of the arid biome in Australia, despite continuing species decline and need for conservation management. Here, we evaluate the contemporary and historical genetic connectivity of the yellow-footed rock-wallaby, Petrogale xanthopus xanthopus, a threatened macropodid which inhabits rocky outcrops across the disconnected mountain range systems of the southern arid biome. We use 17 microsatellite loci together with mitochondrial control region data to determine the genetic diversity of populations and the evolutionary processes shaping contemporary population dynamics on which to base conservation recommendations. Our results indicate the highly fragmented populations have reduced diversity and limited contemporary gene flow, with most populations having been through population bottlenecks. Despite limited contemporary gene flow, the phylogeographic relationships of the mitochondrial control region indicate a lack of structure and suggests greater historical connectivity. This is an emerging outcome for mammals across this arid region. On the basis of our results, we recommend augmentation of populations of P. x. xanthopus, mixing populations from disjunct mountain range systems to reduce the chance of continued diversity loss and inbreeding depression, and therefore maximize the potential for populations to adapt and survive into the future.This research was funded by the South Australian Department of Environment and Natural Resources

A rapid PCR-RFLP diagnostic test for distinguishing sympatric bandicoot species (Marsupialia: Peramelidae) in southeastern Australia

The southern brown bandicoot (Isoodon obesulus) has a fragmented coastal distribution in Australia. It is found on Cape York Peninsula in north Queensland (QLD), in southeastern New South Wales (NSW), Victoria (VIC), Tasmania, southeastern South Australia (SA) and in southwest Western Australia. Although I. obesulus was originally widespread along the southeast coast of NSW (Strahan 1995), the species has declined since the European settlement of Australia and is now restricted to two small populations, located on the northern outskirts of Sydney\ud and the far southeast corner of the state. As a result, I. obesulus is listed as an endangered species (Schedule 1) of the Threatened Species Act 1995 (NSW)

Looking back to go forward: genetics informs future management of captive and reintroduced populations of the black-footed rock-wallaby Petrogale lateralis

Active management is essential to the survival of many threatened species globally. Captive breeding programmes can play an important role in facilitating the supplementation, translocation and reintroduction of wild populations. However, understanding the genetic dynamics within and among wild and captive populations is crucial to the planning and implementation of ex situ management, as adaptive potential is, in part, driven by genetic diversity. Here, we use 14 microsatellite loci and mitochondrial Control Region sequence to examine the population genetics of both wild populations and captive colonies of the endangered warru (the MacDonnell Ranges race of the black-footed rock-wallaby Petrogale lateralis) in central Australia, to understand how historical evolutionary processes have shaped current diversity and ensure effective ex situ management. Whilst microsatellite data reveal significant contemporary differentiation amongst remnant warru populations, evidence of contemporary dispersal and relatively weak isolation by distance, as well as a lack of phylogeographic structure suggests historical connectivity. Genetic diversity within current captive populations is lower than in the wild source populations. Based on our genetic data and ecological observations, we predict outbreeding depression is unlikely and hence make the recommendation that captive populations be managed as one genetic group. This will increase genetic diversity within the captive population and as a result increase the adaptive potential of reintroduced populations. We also identify a new site in the Musgrave Ranges which contains unique alleles but also connectivity with a population 6 km away. This novel genetic diversity could be used as a future source for supplementation