Katherine L. Moon

Reconstructions of evolutionary history can be restricted by a lack of high-quality reference genomes. To date, only four of the eight species of bears (family Ursidae) have chromosome-level genome assemblies. Here, we present assemblies for three additional species—the sun, sloth, and Andean bears—and use a whole-genome alignment of all bear species and other carnivores to reconstruct the evolution of Ursidae. Multiple divergence dating approaches suggest that the six Ursine bears likely diversified in the last 5 Ma, but that divergence times within Ursinae are significantly impacted by gene tree heterogeneity. Consistent with this, we observe that nearly 50% of gene trees conflict with our highly supported species tree, a pattern driven by a significant early hybridization event within Ursinae. We also find that the karyotype of Ursinae is largely similar to the ancestral karyotype of all bears twenty million years prior. In contrast to this conservation of structure, dozens of chromosomal fissions and fusions associated with LINE/L1 retrotransposons dramatically restructured the genomes of the giant panda and Andean bear. Finally, we leverage these genomes to identify species-specific evidence for positive selection on genes associated with color, diet, and metabolism. One of these genes, TCPN2, has a role in pigmentation and shows a series of amino acid mutations in the polar bear over the last 0.5 Ma. Collectively, these new genomic resources enable improved reconstruction of the complex evolutionary history of bears and clarify how this enigmatic group diversified.

The majority of islands surrounding the Antarctic continent are poorly characterized in terms of microbial macroecology due to their remote locations, geographical isolation and access difficulties. The 2016/2017 Antarctic Circumnavigation Expedition (ACE) provided unprecedented access to a number of these islands. In the present study we use metagenomic methods to investigate the microbial ecology of soil samples recovered from 11 circum‐Antarctic islands as part of ACE, and to investigate the functional potential of their soil microbial communities. Comparisons of the prokaryote and lower eukaryote phylogenetic compositions of the soil communities indicated that the various islands harbored spatially distinct microbiomes with limited overlap. In particular, we identified a high prevalence of lichen‐associated fungal taxa in the soils, suggesting that terrestrial lichens may be one of the key drivers of soil microbial ecology on these islands. Differential abundance and redundancy analyses suggested that these soil microbial communities are also strongly shaped by multiple abiotic factors, including soil pH and average annual temperatures. Most importantly, we demonstrate that the islands sampled in this study can be clustered into three distinct large‐scale biogeographical regions in a conservation context, the sub‐, Maritime and Continental Antarctic, which are distinct in both environmental conditions and microbial ecology, but are consistent with the widely‐used regionalization applied to multicellular Antarctic terrestrial organisms. Functional profiling of the island soil metagenomes from these three broad biogeographical regions also suggested a degree of functional differentiation, reflecting their distinct microbial ecologies. Taken together, these results represent the most extensive characterization of the microbial ecology of Antarctic island soils to date.

We reconstruct the phenotype of Balto, the heroic sled dog renowned for transporting diphtheria antitoxin to Nome, Alaska, in 1925, using evolutionary constraint estimates from the Zoonomia alignment of 240 mammals and 682 genomes from dogs and wolves of the 21st century. Balto shares just part of his diverse ancestry with the eponymous Siberian husky breed. Balto’s genotype predicts a combination of coat features atypical for modern sled dog breeds, and a slightly smaller stature. He had enhanced starch digestion compared with Greenland sled dogs and a compendium of derived homozygous coding variants at constrained positions in genes connected to bone and skin development. We propose that Balto’s population of origin, which was less inbred and genetically healthier than that of modern breeds, was adapted to the extreme environment of 1920s Alaska.

A mammoth’s life: Fossils have long given us glimpses of the life that came before us, but these glimpses are generally static. They tell us a bit about species that lived, but not much about how they lived. Evolving techniques are deepening our viewpoint. Wooller et al . examined isotopes collected from the tusk of a 17,000-year-old mammoth to elucidate his movements from birth to death. This included his time—likely with a herd—as an infant and juvenile, then as a prime age adult, and then a declining senior over his approximately 28-year life span. —SNV

Advances in high throughput genomic approaches are enabling the accurate appraisal of movements of diverse species, previously considered intractable. The impact of long-distance dispersal and distribution changes on species interactions (such as host-parasite interactions) is of particular importance as attempts are made to project how ecosystems will shift under environmental change. The sub-Antarctic region, comprising isolated islands separated by hundreds to thousands of kilometres of open ocean, presents an ideal model system for studying long-distance dispersal, distribution, and ecosystem change. Here we used genomic methods to determine the extent of movement of penguin ticks (Ixodes uriae) among different host species, and among penguin colonies at small (within an island) and large (among islands separated by >6000 km) scales, in the sub-Antarctic region. Our results suggest that I. uriae ticks may be readily shared between distantly related penguin species with similar phenology, but indicate that – as inferred by previous research – ticks are less likely to be shared between flighted and non-flighted sea- birds. We also find evidence for small-scale movements of penguin ticks with their hosts, but no evidence for movements between islands separated by thousands of kilometers of open ocean. These inferred limitations to penguin tick movement could be the result of restricted host movements or the inability of penguin ticks to survive extended trips at sea. Our findings help elucidate parasite-host dynamics, with implications for host health and persistence in a region experiencing rapid environmental change.

Aim: Organisms with poor intrinsic dispersal capacity, such as parasites, often rely entirely on transport with host species that have a greater dispersal capacity. Penguins, for example, are exploited by terrestrial ectoparasites when they come ashore to breed. Recent research indicates that Little Penguin (Eudyptula minor and E. novaehollandiae) hard ticks (Ixodes eudyptidis and I. kohlsi) may be capable of surviving short periods (days) at sea with their hosts, but their capacity to survive longer voyages (weeks) is not known. We here aimed to assess whether phylogeographical patterns in Little Penguins and their ticks indicate that the terrestrial ectoparasites are able to disperse long distances at sea with their swimming hosts.Location: Southern Australia and New Zealand.Taxon: Ixodes eudyptidis and I. kohlsi ticks.Methods: We conducted a broad‐scale genomic assessment of Little Penguin ticks from across their hosts’ ranges in Australia and New Zealand. Using genotyping by sequencing, we generated SNP data sets from ticks from 14 penguin colonies, and analysed phylogeographical structure. We included ticks from some sympatric flighted seabirds to verify host specificity.Results: We resolved two distinct lineages of Ixodes from Little Penguins, with one restricted to Australia, and the other found throughout New Zealand and in low numbers at some eastern Australian sites. Both lineages exhibited phylogeographical structure consistent with patterns observed in their hosts, with some evidence of occasional oceanic dispersal, including across the Tasman Sea between Australia and New Zealand. Ticks from sympatric short‐tailed shearwaters (Ardenna tenuirostris), which disperse aerially, were genetically distinct from those collected from Little Penguins, supporting prior evidence of host specificity in seabird ticks.Main conclusions: The most parsimonious explanation for our results is that ticks can travel at sea with Little Penguins. We infer that some terrestrial ectoparasites associated with aquatically dispersing hosts have evolved the capacity to survive oceanic voyages.

One of the most extreme examples of parasite adaptation comes from terrestrial ectoparasites exploiting marine hosts. Despite the ubiquity of such ectoparasitism and its ecological and evolutionary importance, investigations of the responses of ectoparasites to conditions encountered on their hosts are rare. In the case of penguins and their ticks, current understanding suggests that ticks freely parasitize their hosts on land but are incapable of surviving extended oceanic journeys. We examined this conjecture by assessing the physiological capacity of little penguin ticks to endure at-sea foraging and dispersal events of their hosts. Survival in penguins ticks was not significantly compromised by exposure to depths commonly associated with host dives (40 and 60 m), repeated seawater exposure relevant to the most common (30 s) and longest (120 s) recorded host dives, or extended (48 h) exposure to seawater. Mean (±SD) closed-phase durations in adult and nymphal ticks exhibiting discontinuous gas exchange ( 339±237 and 240±295 s, respectively) exceeded that of the maximum recorded host dive duration (120 s). Normoxic-anoxic-normoxic respirometry also confirmed spiracle closure. Mean metabolic rates ( 0.354±0.220 and 4.853±4.930 μL/h at 25°C for unfed and fed adult females, respectively) were significantly influenced by temperature; optimal and LT50 temperatures for adult ticks and fed nymphal ticks were typically higher than swimming penguin body temperatures. These findings suggest that marine host dispersal is unlikely to present an insurmountable barrier to long-distance tick dispersal. Such dispersal has important implications for evolutionary theory, conservation, and epidemiology.

Parasite population structure can be used to infer fine-scale movement in host species. Many penguin species form large social colonies, and are highly philopatric, returning to the same nest or burrow, along the same route, after each trip to sea. Within a colony, however, the local abundance, physical similarity, and nocturnal habits of penguins hinder the observation of fine-scale movements. To determine the extent of movement and interaction of penguins within colonies, a genotyping by sequencing (GBS) approach was used to study the fine-scale structure of ticks—which depend on host movements for dispersal—exploiting the largest Little Penguin (Eudyptula novaehollandiae) colony in Australia (Phillip Island, Victoria). No barriers to tick gene flow were identified, and we infer that extensive penguin movement occurs throughout the colony. Our findings support the hypothesis that some penguin species are highly gregarious, socializing widely within colonies despite strong nest-site philopatry. La structure des populations de parasites peut être utilisée pour inférer les déplacements à fine échelle des espèces hôtes. Plusieurs espèces de manchots forment de grandes colonies sociales et sont fortement philopatriques, retournant au même nid ou terrier le long du même trajet, après chaque voyage vers la mer. Dans une colonie, cependant, l'abondance locale, la similarité physique et les habitudes nocturnes des manchots entravent l'observation des déplacements à fine échelle. Afin de déterminer l'étendue des déplacements et des interactions entre manchots au sein des colonies, une approche de génotypage par séquençage (GBS) a été utilisée pour étudier la structure à fine échelle des tiques – lesquelles dépendent des déplacements des hôtes pour se disperser – qui parasitent la plus grande colonie d'Eudyptula novaehollandiae en Australie (Phillip Island, dans l'État de Victoria). Aucun obstacle au flux génétique des tiques n'a été identifié. Nous déduisons que des déplacements importants se produisent dans la colonie. Nos résultats appuient l'hypothèse que certaines espèces de manchots sont très grégaires et socialisent beaucoup au sein des colonies malgré une grande philopatrie au site de nidification. Mots-clés: tique, génomique, polymorphismes mononucléotidiques (SNP), déplacement des hôtes, génotypage par séquençage (GBS)

Extreme and remote environments provide useful settings to test ideas about the ecological and evolutionary drivers of biological diversity. In the sub‐Antarctic, isolation by geographic, geological and glaciological processes has long been thought to underpin patterns in the region's terrestrial and marine diversity. Molecular studies using increasingly high‐resolution data are, however, challenging this perspective, demonstrating that many taxa disperse among distant sub‐Antarctic landmasses. Here, we reconsider connectivity in the sub‐Antarctic region, identifying which taxa are relatively isolated, which are well connected, and the scales across which this connectivity occurs in both terrestrial and marine systems. Although many organisms show evidence of occasional long‐distance, trans‐oceanic dispersal, these events are often insufficient to maintain gene flow across the region. Species that do show evidence of connectivity across large distances include both active dispersers and more sedentary species. Overall, connectivity patterns in the sub‐Antarctic at intra‐ and inter‐island scales are highly complex, influenced by life‐history traits and local dynamics such as relative dispersal capacity and propagule pressure, natal philopatry, feeding associations, the extent of human exploitation, past climate cycles, contemporary climate, and physical barriers to movement. An increasing use of molecular data – particularly genomic data sets that can reveal fine‐scale patterns – and more effective international collaboration and communication that facilitates integration of data from across the sub‐Antarctic, are providing fresh insights into the processes driving patterns of diversity in the region. These insights offer a platform for assessing the ways in which changing dispersal mechanisms, such as through increasing human activity and changes to wind and ocean circulation, may alter sub‐Antarctic biodiversity patterns in the future.