Simon Y. W. Ho’s research while affiliated with UNSW Sydney and other places

Koalas are an iconic, endangered, Australian marsupial. Disease, habitat destruction, and catastrophic mega‐fires have reduced koalas to remnant patches of their former range. With increased likelihood of extreme weather events and ongoing habitat clearing across Australia, koala populations are vulnerable to further declines and isolation. Small, isolated populations are considered at risk when there is increased inbreeding, erosion of genomic diversity, and loss of adaptive potential, all of which reduce their ability to respond to prevailing threats. Here, we characterized the current genomic landscape of koalas using data from The Koala Genome Survey, a joint initiative between the Australian Federal and New South Wales Governments that aimed to provide a future‐proofed baseline genomic dataset across the koala's range in eastern Australia. We identified several regions of the continent where koalas have low genomic diversity and high inbreeding, as measured by runs of homozygosity. These populations included coastal sites along southeast Queensland and northern and mid‐coast New South Wales, as well as southern New South Wales and Victoria. Analysis of genomic vulnerability to future climates revealed that northern koala populations were more at risk due to the extreme expected changes in this region, but that the adaptation required was minimal compared with other species. Our genomic analyses indicate that continued development, particularly linear infrastructure along coastal sites, and resultant habitat destruction are causing isolation and subsequent genomic erosion across many koala populations. Habitat protection and the formation of corridors must be employed for all koala populations to maintain current levels of diversity. For highly isolated koala populations, active management may be the only way to improve genomic diversity in the short term. If koalas are to be conserved for future generations, reversing their genomic isolation must be a priority in conservation planning.

The Southern Ocean is warming more rapidly than other parts of our planet. How this region’s endemic biodiversity will respond to such changes can be illuminated by studying past events, through genetic analyses of time-series data sets including historic and fossil remains. Archaeological and subfossil remains show that the southern elephant seal ( Mirounga leonina ) was common along the coasts of Australia and New Zealand in the recent past. This species is now mostly confined to sub-Antarctic islands and the southern tip of South America. We analysed ancient seal samples from Australia (Tasmania), New Zealand, and the Antarctic mainland to examine how southern elephant seals have responded to a changing climate and anthropogenic pressures during the Holocene. Our analyses show that these seals formed part of a broader Australasian lineage, comprising seals from all sampled locations from the south Pacific sector of the Southern Ocean. Our study demonstrates that southern elephant seal populations have dynamically altered both range and population sizes under climatic and human pressures, over surprisingly short evolutionary timeframes for such a large, long-lived mammal. Significance Statement Genetic data, alongside historic, archaeological, and subfossil remains show that Australasian populations of the southern elephant seal have been shaped by range expansions and contractions following the Last Glacial Maximum, with subsequent contractions during the late Holocene. These expansion and contraction events are likely to have been a direct result of climate change-induced habitat expansion and contraction, along with Indigenous and European sealing. Prehistoric climate change and more recent human pressures have substantially altered the geographic distribution and population size of southern elephant seals over short evolutionary timescales.

Studies of biogeographic processes have often centred islands as model systems, yet questions remain about the role of Pleistocene sea-level fluctuations in shaping islands' biodiversity. One novel, potentially informative model system is the Lord Howe Island Group of Australia. Despite the World Heritage status of this archipelago, almost nothing is known of the biogeographic origins, evolutionary distinctiveness or genetic diversity of the ecological communities across its 28 islands. In this study, we focused on the cockroach Panesthia lata , an ecologically specialized invertebrate with one of the broadest recorded distributions of any LHIG species. To investigate the influence of Pleistocene sea-level fluctuations on LHIG fauna, we explored the phylogeography of P. lata using single-nucleotide polymorphisms and complete mitochondrial genomes. Our analyses reveal that the lineage on the permanently isolated islet Ball's Pyramid is highly divergent from the remaining populations, while those on the episodically connected Lord Howe, Roach and Blackburn Islands experienced gene flow during the last glacial period. These results offer the first evidence that Pleistocene land bridges allowed for overland migration across the archipelago. Further, although P. lata was believed to have been locally extirpated by rodents on Lord Howe Island, we discovered two surviving, relict populations. We also detected high levels of inbreeding in all populations, emphasizing the need for ongoing conservation management. Finally, the combination of shallow genetic structure and low diversity suggests that genetic rescue from another island may be a viable strategy to conserve the Lord Howe Island population of P. lata , as well as other species that have been similarly impacted by rodents.

The progressive aridification of the Australian continent, and coincident decline of mesic forest, has been a powerful driver of allopatric and environmental speciation in native species. The relictual mesic forests of the eastern seaboard now harbour a diverse group of endemic fauna, including the wood‐feeding cockroaches of the genus Panesthia , which reached the continent via two separate invasions from Melanesia. The more recent of these colonization events gave rise to a group of five recognized species, occurring in mainland woodlands, sclerophylls and rainforests, as well as the forests and grasslands of the Lord Howe Island Group. Due to limited sampling in molecular studies and doubt regarding the standing taxonomy, there is little certainty about relationships among the species and poor understanding of the effects of ancient climatic change upon their evolution. We undertook a comprehensive phylogenetic analysis of the clade, using complete mitogenomes and nuclear ribosomal markers from nearly all known morphospecies and populations. Our time‐calibrated phylogenetic analyses reveal an additional six unrecognized, highly divergent lineages and suggest that these have arisen primarily through vicariance as rainforests fragmented during Plio‐Pleistocene glacial cycles (2–5 million years ago). Ancestral niche estimations also evidence a tropical rainforest origin for the group, followed by at least three niche transitions into drier forest, including one associated with the singular colonization of the Lord Howe Island Group. Finally, we find evidence of frequent, parallel wing reduction, in potential association with the contraction of forest habitats into small refugia. Our results reiterate the far‐reaching role of ancient aridification in driving speciation, niche expansion and morphological evolution in Australian fauna.

Wu et al. (1) conducted a phylogenomic analysis resulting in a new time frame for the diversification of modern birds, concluding that the rapid radiation of Neoaves occurred well before the Cretaceous–Paleogene (K–Pg) extinction event and that this catastrophic event did not affect their diversification dynamics. Here, we show that the divergence times obtained by Wu et al. were compromised by problems with their choices of fossils and calibration strategy.

Plants carry genetic material in three compartments, the nuclear, mitochondrial, and chloroplast genomes. These genomes interact with each other to various degrees and are subject to shared evolutionary drivers exerted by their host organisms. However, it is not clear whether the three plant genomes display covarying evolutionary signals. We tested for correlated evolutionary rates between nuclear and organellar genomes using extensive data sets from the major clades of land plants (Embryophyta), including mosses, ferns, gymnosperms, and angiosperms. To examine the evolutionary dynamics in parasitic angiosperms, which are under distinctive selective pressures, we analysed data sets from mistletoes, broomrapes, sandalwoods, and rafflesias. Evolutionary rates of nuclear and organellar genomes were positively linked in land plants, except in the parasitic angiosperms. We also found similar positive correlations for rates of nonsynonymous and synonymous change between nuclear and organellar genomes. Our results also reveal extensive evolutionary rate variation across land plant taxa. Overall, we find that nuclear, mitochondrial, and chloroplast genomes in land plants share similar drivers of mutaNon rates, despite considerable variaNon in life history, morphology, and genome sizes among clades. Our findings lay the foundaNon for further exploraNon of the impact of co-evoluNonary interacNons on shared evoluNonary rates between genomes.

Aim To date a vicariant event through the mutualistic relationship of a hylid frog and its bromeliad host found across two isolated mountain ranges as part of an island–continental split and to use this information to calibrate a molecular dating analysis of hylids. Location South America. Time Period Pliocene. Major Taxa Studied Treefrogs, Arboranae. Methods Pliocene tectonic movements sank a portion of a mountain range that connected present‐day Trinidad (island) and northern Venezuela, eventually isolating populations of the golden tree frog Phytotriades auratus and its host bromeliad Glomeropitcairnia erectiflora on both sides of a saltwater barrier. We estimated the submersion rate timing of the vicariant event, then employed ecological niche modelling to establish the distribution of the frog and its host to the Pliocene. We generated nucleotide sequence data for the hylid on each side of the marine barrier and proposed a biogeographic calibration for the split between populations. Using Bayesian phylogenetic analysis, we evaluated the impact of incorporating this biogeographic calibration on estimates of treefrog divergence times. Results A relatively continuous, high‐elevation mountain range existed before the Pliocene and the opening of the Gulf of Paria (4.45 ± 0.85 Ma). Phytotriades auratus and G. erectiflora would have been distributed across the Paria and Northern Range mountains as a single population since the Pliocene. Divergence times among treefrogs (Arboranae) were older than those inferred using fossil calibrations alone, with mean age estimates for subfamilies and genera being ~2 and ~1.2 million years older, respectively. Main Conclusions Our study presents a biogeographic calibration based on a vicariant model that connects the evolution of the populations of a hylid through geology and ecological data. The implementation of this date as a molecular clock calibration reduces the uncertainty in date estimates for the shallower nodes in the phylogeny of Arboranae.

Ninu (greater bilby, Macrotis lagotis ) are desert-dwelling, culturally and ecologically important marsupials. In collaboration with Indigenous rangers and conservation managers, we generated the Ninu chromosome-level genome assembly (3.66 Gbp) and genome sequences for the extinct Yallara (lesser bilby, Macrotis leucura ). We developed and tested a scat single-nucleotide polymorphism panel to inform current and future conservation actions, undertake ecological assessments and improve our understanding of Ninu genetic diversity in managed and wild populations. We also assessed the beneficial impact of translocations in the metapopulation ( N = 363 Ninu). Resequenced genomes (temperate Ninu, 6; semi-arid Ninu, 6; and Yallara, 4) revealed two major population crashes during global cooling events for both species and differences in Ninu genes involved in anatomical and metabolic pathways. Despite their 45-year captive history, Ninu have fewer long runs of homozygosity than other larger mammals, which may be attributable to their boom–bust life history. Here we investigated the unique Ninu biology using 12 tissue transcriptomes revealing expression of all 115 conserved eutherian chorioallantoic placentation genes in the uterus, an XY 1 Y 2 sex chromosome system and olfactory receptor gene expansions. Together, we demonstrate the holistic value of genomics in improving key conservation actions, understanding unique biological traits and developing tools for Indigenous rangers to monitor remote wild populations.

The progressive aridification of the Australian continent, and coincident decline of mesic forest, has been a powerful driver of allopatric and environmental speciation in native species. The relictual mesic forests of the eastern seaboard now harbor a diverse group of endemic fauna, including the wood-feeding cockroaches of the genus Panesthia, which reached the continent via two separate invasions from Melanesia. The more recent of these colonization events gave rise to a group of five recognized species, occurring in mainland woodlands, sclerophylls and rainforests, as well as the forests and grasslands of the Lord Howe Island Group. Due to limited sampling in molecular studies and doubt regarding the standing taxonomy, there is little certainty about relationships among the species and poor understanding of the effects of ancient climatic changes upon their evolution. We undertook a comprehensive phylogenetic analysis of the clade, using complete mitogenomes and nuclear ribosomal markers from nearly all known morphospecies and populations. Our time–calibrated phylogenetic analyses reveal six unrecognized, highly divergent lineages, and suggest that these have arisen primarily through vicariance as rainforests fragmented during Plio-Pleistocene glacial cycles (2–5 million years ago). Ancestral niche reconstructions also evidence a tropical rainforest origin for the group, followed by at least three niche transitions into drier forest, including one associated with the singular colonization of the Lord Howe Island Group. Finally, we find evidence of frequent, parallel wing reduction, in potential association with the contraction of forest habitats into small refugia. Our results reiterate the far–reaching role of ancient aridification in driving speciation, niche expansion and morphological evolution in Australian fauna.