Population genomics of decline and local extinction in the endangered Australian Pookila

Burns, Phoebe A.; Rowe, Kevin C.; Parrott, Marissa L.; Roycroft, Emily

doi:10.1016/j.biocon.2023.110183

Cited by 5 publications

(10 citation statements)

References 71 publications

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“…Island populations of P. delicatulus typically showed significantly lower heterozygosity compared to mainland populations (Figure 2); however, individuals from the larger Melville Island and Groote Eylandt both had heterozygosity values comparable to their respective mainland relatives. Consistent with a population genomic study on P. novaehollandiae (Burns et al., 2023), we found high geographic structuring between the northern and southern ESUs, and very low diversity in the threatened southern ESU (Figure 2). Based on estimates from a data‐complete alignment, all populations except for the southern ESU of P. novaehollandiae showed significantly negative Tajima's D value, suggesting recent population expansion in all other species, although, in contrast, estimates when sites with missing data were included were not significant (Table S2).…”

Section: Resultssupporting

confidence: 91%

“…bolami. Despite contraction during the Holocene, the LGM habitat for P. novaehollandiae was similarly distributed to the present day, consistent with substantial divergence between the northern and southern ESUs (estimated at 200 kya, Burns et al, 2023). Where there are gaps in present-day species distributions, palaeo-SDMs indicate that these areas could have been previously inhabited (Figure 5).…”

Section: Present Species Distributions Map Biome Boundariesmentioning

confidence: 56%

“…Molecular species delimitation analysis in BPP supports these three lineages of P. delicatulus as distinct species with 100% posterior probability. As a point of comparison, BPP did not support the delimitation of the two geographically isolated, phylogeographic lineages of P. novaehollandiae as species (northern and southern ESU; Burns et al., 2023). Hereafter and in figures, the northern delicate mouse lineage is referred to as P. delicatulus [Gould 1842], the eastern lineage as P. mimulus Thomas 1926, and the western lineage as P. pilbarensis sp.…”

Section: Resultsmentioning

confidence: 89%

“…In 5). Genetic rescue within the southern ESU seeks to increase the adaptive capacity of the species in Victoria (Burns et al, 2023).…”

Section: A Suture Zone In the Mesic Biomementioning

confidence: 99%

“…lineages of P. novaehollandiae as species (northern and southern ESU;Burns et al, 2023). Hereafter and in figures, the northern delicate mouse lineage is referred to as P. delicatulus [Gould 1842], the eastern lineage as P. mimulus Thomas 1926, and the western lineage as P. pilbarensis sp.…”

mentioning

confidence: 99%

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Speciation across biomes: Rapid diversification with reproductive isolation in the Australian delicate mice

Roycroft,

Ford,

Ramm

et al. 2024

Molecular Ecology

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Phylogeographic studies of continental clades, especially when combined with palaeoclimate modelling, provide powerful insight into how environment drives speciation across climatic contexts. Australia, a continent characterized by disparate modern biomes and dynamic climate change, provides diverse opportunity to reconstruct the impact of past and present environments on diversification. Here, we use genomic‐scale data (1310 exons and whole mitogenomes from 111 samples) to investigate Pleistocene diversification, cryptic diversity, and secondary contact in the Australian delicate mice (Hydromyini: Pseudomys), a recent radiation spanning almost all Australian environments. Across northern Australia, we find no evidence for introgression between cryptic lineages within Pseudomys delicatulus sensu lato, with palaeoclimate models supporting contraction and expansion of suitable habitat since the last glacial maximum. Despite multiple contact zones, we also find little evidence of introgression at a continental scale, with the exception of a potential hybrid zone in the mesic biome. In the arid zone, combined insights from genetic data and palaeomodels support a recent expansion in the arid specialist P. hermannsburgensis and contraction in the semi‐arid P. bolami. In the face of repeated secondary contact, differences in sperm morphology and chromosomal rearrangements are potential mechanisms that maintain species boundaries in these recently diverged species. Additionally, we describe the western delicate mouse as a new species and recommend taxonomic reinstatement of the eastern delicate mouse. Overall, we show that speciation in an evolutionarily young and widespread clade has been driven by environmental change, and potentially maintained by divergence in reproductive morphology and chromosome rearrangements.

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Section: Resultssupporting

confidence: 91%

Section: Present Species Distributions Map Biome Boundariesmentioning

confidence: 56%

Section: Resultsmentioning

confidence: 89%

“…In 5). Genetic rescue within the southern ESU seeks to increase the adaptive capacity of the species in Victoria (Burns et al, 2023).…”

Section: A Suture Zone In the Mesic Biomementioning

confidence: 99%

mentioning

confidence: 99%

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Speciation across biomes: Rapid diversification with reproductive isolation in the Australian delicate mice

Roycroft,

Ford,

Ramm

et al. 2024

Molecular Ecology

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Building meaningful collaboration in conservation genetics and genomics

Shaw,

Brockett,

Pierson

et al. 2024

Conserv Genet

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Genetic diversity is the foundation of biodiversity, and preserving it is therefore fundamental to conservation practice. However, global conservation efforts face significant challenges integrating genetic and genomic approaches into applied management and policy. As collaborative partnerships are increasingly recognized as key components of successful conservation efforts, we explore their role and relevance in the Australian context, by engaging with key entities from across the conservation sector, including academia, botanic gardens, herbaria, seed banks, governmental/non-governmental organisations, private industry, museums, Traditional Owners, Indigenous rangers, and zoos and aquaria. By combining perspectives from these entities with comprehensive literature review, we identified five guiding principles for conservation genetic and genomic research and explored the different elements of, and approaches to, collaboration. Our reflections suggest that there is a substantial overlap in research interests across the Australian conservation sector, and our findings show that collaboration is increasing. We discuss approaches to building collaborative partnerships, the reciprocal benefits of collaborating, and some remaining challenges associated with data generation, data collection, and cross-cultural considerations. We emphasise the need for long-term national resourcing for sample and data storage and consistency in collecting, generating and reporting genetic data. While informed by the Australian experience, our goal is to support researchers and practitioners to foster meaningful collaborations that achieve measurable management outcomes in conservation genetics and genomics, both in Australia and globally.

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The threatened Pookila (Pseudomys novaehollandiae) hosts a diverse macrobiome of arthropods at varying risks of co-extinction

Kwak,

Burns,

Hastriter

et al. 2024

J Insect Conserv

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Population genomics of decline and local extinction in the endangered Australian Pookila

Cited by 5 publications

References 71 publications

Speciation across biomes: Rapid diversification with reproductive isolation in the Australian delicate mice

Speciation across biomes: Rapid diversification with reproductive isolation in the Australian delicate mice

Building meaningful collaboration in conservation genetics and genomics

The threatened Pookila (Pseudomys novaehollandiae) hosts a diverse macrobiome of arthropods at varying risks of co-extinction

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