Microsatellites are widely used in population genetics, but their evolutionary dynamics remain poorly understood. It is unclear whether microsatellite loci drift in length over time. This is important because the mutation processes that underlie these important genetic markers are central to the evolutionary models that employ microsatellites. We identify more than 27 million microsatellites using a novel and unique dataset of modern and ancient Adelie penguin genomes along with data from 63 published chordate genomes. We investigate microsatellite evolutionary dynamics over 2 timescales: one based on Adelie penguin samples dating to similar to 46.5 ka and the other dating to the diversification of chordates aged more than 500 Ma. We show that the process of microsatellite allele length evolution is at dynamic equilibrium; while there is length polymorphism among individuals, the length distribution for a given locus remains stable. Many microsatellites persist over very long timescales, particularly in exons and regulatory sequences. These often retain length variability, suggesting that they may play a role in maintaining phenotypic variation within populations.

X-cells were first described as an unknown cell type in northern hemisphere flatfish in 1969. Almost a decade later they were described in an Antarctic fish, the bald notothen Trematomus borchgrevinki , thus demonstrating their global distribution. Since this time, X-cells from various northern hemisphere fish species and from three other Antarctic fishes, the emerald notothen Trematomus bernacchii , the crowned notothen Trematomus scotti , and the painted notothen Nototheniops larseni have been identified as perkinsozoan parasites of the Family Xcellidae. Currently there are seven X-cell species described within this family. Here we report the morphology of X-cells isolated from the gill filaments of the bald notothen and include details of some of its division forms. Using short-read high-throughput DNA sequencing technology we have sequenced, assembled, and verified a 5347-bp region of the X-cell rRNA repeat unit that includes the complete 18S gene. In all cases, phylogenetic analyses identified this sequence as a distinct taxon and placed it among the perkinsozoan alveolates alongside other previously identified species in the X-cell family. Using a combination of morphological and genetic evidence we now describe a new X-cell genus and species, Cryoxcellia borchgrevinki gen. nov., sp. nov., from McMurdo Sound, Antarctica.

Long-term changes in the life history and behaviour of seabirds during the non-breeding season can reflect shifts in environmental conditions. However, long-term marine studies are scarce, particularly on southern hemisphere seabirds. Here, we used moult scores from 86 Brown Skuas (Stercorarius antarcticus lonnbergi), a large predatory seabird breeding on the Chatham Islands, Aotearoa/New Zealand to model both the timing and duration of primary feather moult. In addition, we analysed stable isotope values (delta C-13 and delta N-15) from 62 modern (2014-16) and ten museum tail feathers. These data provide insights into the non-breeding behaviour of Brown Skua. Interestingly, our results show that the primary feather moult occurred prior to birds departing the colony, starting on average on 2 January +/- 5 days (SE). The average start of primary feather moult occurred five days prior to the end of breeding (7 January +/- 10 days (SD)) and 42 days before the birds departed the colony (13 February +/- 11 days (SD)). The average duration of primary feather moult was 189 +/- 14 days (SE). Importantly, low delta C-13 values in four females suggested that tail feather moult might also occur while skuas are at the colony. There was no difference in tail feather delta C-13 and delta N-15 values between any pairwise comparison of modern and museum years. However, values of delta N-15 from tail feathers sampled in 2014 were different from those sampled in 2015 and 2016. This large annual variation in delta N-15 values from tail feathers over such a short period makes long-term comparisons difficult to interpret, particularly between years with low sample sizes. While the stable isotope analyses of tail feathers are informative, we recommend future studies of skuas sample the primary coverts rather than tail feathers.

Next-generation sequencing has transformed the fields of ecological and evolutionary genetics by allowing for cost-effective identification of genome-wide variation. Single nucleotide polymorphism (SNP) arrays, or "SNP chips", enable very large numbers of individuals to be consistently genotyped at a selected set of these identified markers, and also offer the advantage of being able to analyse samples of variable DNA quality. We used reduced representation restriction-aided digest sequencing (RAD-seq) of 31 birds of the threatened hihi (Notiomystis cincta; stitchbird) and low-coverage whole genome sequencing (WGS) of 10 of these birds to develop an Affymetrix 50 K SNP chip. We overcame the limitations of having no hihi reference genome and a low quantity of sequence data by separate and pooled de novo assembly of each of the 10 WGS birds. Reads from all individuals were mapped back to these de novo assemblies to identify SNPs. A subset of RAD-seq and WGS SNPs were selected for inclusion on the chip, prioritising SNPs with the highest quality scores whose flanking sequence uniquely aligned to the zebra finch (Taeniopygia guttata) genome. Of the 58,466 SNPs manufactured on the chip, 72% passed filtering metrics and were polymorphic. By genotyping 1,536 hihi on the array, we found that SNPs detected in multiple assemblies were more likely to successfully genotype, representing a cost-effective approach to identify SNPs for genotyping. Here, we demonstrate the utility of the SNP chip by describing the high rates of linkage disequilibrium in the hihi genome, reflecting the history of population bottlenecks in the species.

Many Antarctic notothenioid fishes have major rearrangements in their mitochondrial (mt) genomes. Here, we report the complete mt genomes of 3 trematomin notothenioids: the bald notothen (Trematomus (Pagothenia) borchgrevinki), the spotted notothen (T. nicolai), and the emerald notothen (T. bernacchii). The 3 mt genomes were sequenced using next-generation Illumina technology, and the assemblies verified by Sanger sequencing. When compared with the canonical mt gene order of the Antarctic silverfish (Pleuragramma antarctica), we found a large gene inversion in the 3 trematomin mt genomes that included tRNAIle, ND1, tRNALeu2, 16S, tRNAVal, 12S, tRNAPhe, and the control region. The trematomin mt genomes contained 3 intergenic spacers, which are thought to be the remnants of previous gene and control region duplications. All control regions included the characteristic conserved regulatory sequence motifs. Although short-read next-generation DNA sequencing technology has allowed the rapid and cost-effective sequencing of a large number of complete mt genomes, it is essential in all cases to verify the assembly in order to prevent the publication and use of erroneous data.

1. Urbanisation and anthropogenic alteration of ecosystems has led to conflict between humans and wildlife. Such conflict is often observed in apex predators. Although human-wildlife conflict has been extensively studied, male/female differences in behaviour are rarely considered. 2. We investigated male/female differences in foraging behaviour of the predatory/scavenging brown skua Catharacta antarctica lonnbergi breeding on a New Zealand island nature reserve in proximity to farmland. These skuas are subject to culling, when perceived as a threat to livestock. 3. As part of a long-term ecological study, we used high-resolution Global Positioning System (GPS) devices to characterise the space-use of foraging brown skuas. We also analysed stable isotopes of carbon (delta C-13) and nitrogen (delta N-15) from modern and archived blood samples to investigate possible changes in diet over the past similar to 30 years. 4. Analysis of 100 GPS tracks collected from 2014 to 2016 demonstrated that males and females consistently visited different habitats. Males spent most of their time close to their breeding territory on the island nature reserve and females frequently visited a farmed island approximately two kilometres away. Consistent with this finding, we show that male and female skuas also differed markedly in their diets: males specialised on burrow-nesting white-faced storm petrels Pelagodroma marina (80%) with only a small proportion of sheep remains Ovis aries (<6%) contributing to their diet. In contrast, female diet comprised 27% white-faced storm petrels, other seabirds (18%) and a relatively large proportion of sheep remains (47%). Further, our data (186 blood samples from 122 individuals) show that this male/female difference in diet has persisted at least since 1987. 5. Because females fed disproportionally on sheep remains, they may be more vulnerable to being culled by farmers. Importantly, our case study suggests that intersexual differences in diet and foraging patterns can have major implications for the reproduction and survival of apex predators that interact with farming. We strongly suggest that intersexual differences in behaviour should be considered when investigating human-wildlife conflicts.

Territorial protandry, or early season male-biased settlement at breeding sites, is a widespread phenomenon in a range of animal breeding systems. While protandry is common across several avian lineages and has been linked with increased reproductive success of earlier breeding males in terrestrial species, the selective advantage of breeding protandry has only rarely been studied in seabirds. We assessed the seasonal changes in the sex ratio at the breeding site and sex-specific correlates of arrival date with reproductive success during 2 breeding seasons of a colonial seabird, the Australasian Gannet (Moms serrator), at Cape Kidnappers, New Zealand. We found no biases in overall sex ratios of adults and fledglings but detected a male sex bias during nest site establishment, and a significantly higher probability of reproductive success for earlier-settling males. In contrast, the reproductive success of females did not correlate with the timing of arrival. Our findings provide an assessment of the sex differences in reproductive correlates of the timing of breeding settlement in gannets and are consistent with selective advantages as suggested by indirect selection hypotheses. This study contributes to our understanding of the fitness benefits of protandry, and its linkages with sex differences in breeding philopatry and mate fidelity, in a long-lived seabird species with obligate and extended biparental care.

Allen and O'Connell published “A different paradigm for the initial colonisation of Sahul” in the first number of Archaeology in Oceania this year (55: 1–14). We invited comments from several scholars and a riposte from the authors.

Genomics and ancient DNA methods have revolutionized many areas of biology, including human evolution. Recently we have seen significant advances in archaeogenetics including the use of large-scale genomic datasets to track human movements globally. In addition, advances in ancient and modern genomics have enabled researchers to resolve a range of issues of importance to indigenous people. Most notable among these is the repatriation of ancient remains to their kin i.e. to what Aboriginal Australians refer to as their `Place and Country'. From an historical perspective, new fields of science can be characterized as moving through three stages beginning with description, followed by a focus on mechanisms/functions and finally the formulation of experiments and hypothesis testing. The new science of archaeogenetics is currently in the descriptive stage. It involves large-scale genome sequencing and the use of explanatory narratives. Our analysis suggests that a mature formulation lies in the future.

The ancient catacombs of Egypt harbor millions of well-preserved mummified Sacred Ibis ( Threskiornis aethiopicus ) dating from ∼600BC. Although it is known that a very large number of these ‘votive’ mummies were sacrificed to the Egyptian God Thoth, how the ancient Egyptians obtained millions of these birds for mummification remains unresolved. Ancient Egyptian textual evidences suggest they may have been raised in dedicated large-scale farms. To investigate the most likely method used by the priests to secure birds for mummification, we report the first study of complete mitochondrial genomes of 14 Sacred Ibis mummies interred ∼2500 years ago. We analysed and compared the mitogenomic diversity among Sacred Ibis mummies to that found in modern Sacred Ibis populations from throughout Africa. The ancient birds show a high level of genetic variation comparable to that identified in modern African populations, contrary to the suggestion in ancient hieroglyphics (or ancient writings) of centralized industrial scale farming of sacrificial birds. This suggests a sustained short-term taming of the wild Sacred Ibis for the ritual yearly demand.

BACKGROUND:DNA barcoding utilises a standardised region of the cytochrome c oxidase I (COI) gene to identify specimens to the species level. It has proven to be an effective tool for identification of avian samples. The unique island avifauna of New Zealand is taxonomically and evolutionarily distinct. We analysed COI sequence data in order to determine if DNA barcoding could accurately identify New Zealand birds.RESULTS:We sequenced 928 specimens from 180 species. Additional Genbank sequences expanded the dataset to 1416 sequences from 211 of the estimated 236 New Zealand species. Furthermore, to improve the assessment of genetic variation in non-endemic species, and to assess the overall accuracy of our approach, sequences from 404 specimens collected outside of New Zealand were also included in our analyses. Of the 191 species represented by multiple sequences, 88.5% could be successfully identified by their DNA barcodes. This is likely a conservative estimate of the power of DNA barcoding in New Zealand, given our extensive geographic sampling. The majority of the 13 groups that could not be distinguished contain recently diverged taxa, indicating incomplete lineage sorting and in some cases hybridisation. In contrast, 16 species showed evidence of distinct intra-species lineages, some of these corresponding to recognised subspecies. For species identification purposes a character-based method was more successful than distance and phylogenetic tree-based methods.CONCLUSIONS:DNA barcodes accurately identify most New Zealand bird species. However, low levels of COI sequence divergence in some recently diverged taxa limit the identification power of DNA barcoding. A small number of currently recognised species would benefit from further systematic investigations. The reference database and analysis presented will provide valuable insights into the evolution, systematics and conservation of New Zealand birds.

For Māori of Aotearoa / New Zealand, feathers from native birds hold spiritual significance and were used in various forms of adornment including kites (manu tukutuku), cloaks (kakahu) and feathered bags (kete). Kiwi (Apteryx spp.) are nocturnal birds endemic to New Zealand and were placed by Māori under the special protection of Tane Mahuta, god of the forest. There are currently hundreds of kete (bags) adorned with kiwi feathers (kete kiwi) that are held in museums and private collections worldwide. However, the unique way each bag was made, the composite materials used, and their provenance are largely unknown. We show here that analyses of partial mitochondrial sequences recovered from kete kiwi can provide important insights into sources of materials and ancient construction techniques employed to make these treasured items (taonga).

In 1798, Napoleon Bonaparte’s army invaded Egypt, returning with many treasures including large numbers of Sacred Ibis mummies. The ancient Egyptians revered the ibis and mummified literally millions of them. The French naturalist Georges Cuvier used these mummies to challenge an emerging idea of the time, namely Jean-Baptiste Lamarck’s theory of evolution. Cuvier detected no measurable differences between mummified Sacred Ibis and contemporary specimens of the same species. Consequently, he argued that this was evidence for the “fixity of species.” The “Sacred Ibis debate” predates the so-called “Great Debate” between Cuvier and Geoffroy Saint-Hilaire and the publication of Darwin’s On the Origin of Species five decades later. Cuvier’s views and his study had a profound influence on the scientific and public perception of evolution, setting back the acceptance of evolutionary theory in Europe for decades.

Marine top predators forage in environments that show potentially extreme temporal and spatial variation in prey availability, with reproductive success being crucially linked to food supply. Multiple factors of interannual and sexual variation, as well as variation across breeding stages, can shape patterns of spatial use in foraging seabirds, yet studies that address all of these variables simultaneously are rare. We present spatial assessment of foraging patterns by µGPS tracking of a sexually size monomorphic, long-lived species, the Australasian gannet ( Morus serrator ). The study spanned the incubation and chick-rearing stages in three consecutive breeding seasons. Our findings revealed high interannual variability in foraging distances and trip durations, but no consistent differences between birds across different breeding stages or the sexes. The exception was that core foraging areas were different for female and male Australasian gannets, although trip durations or distances were similar for both sexes. Our results also indicate bimodality in foraging distance and trip duration in this species, while highlighting interannual variability in the extent of bimodality. These findings contribute to a scarcely documented type of foraging behaviour in the seabird family of the Sulidae. Overall, these spatial use patterns provide a baseline for understanding the evolution of sex-specific foraging differences in biparental seabirds, and the extent to which these differences might help in securing breeding success across years of variable food availability.

Pleurobranchaea maculata is a rarely studied species of the Heterobranchia found throughout the south and western Pacific-and recently recorded in Argentina-whose population genetic structure is unknown. Interest in the species was sparked in New Zealand following a series of dog deaths caused by ingestions of slugs containing high levels of the neurotoxin tetrodotoxin. Here we describe the genetic structure and demographic history of P. maculata populations from five principle locations in New Zealand based on extensive analyses of 12 microsatellite loci and the COI and CytB regions of mitochondrial DNA (mtDNA). Microsatellite data showed significant differentiation between northern and southern populations with population structure being associated with previously described regional variations in tetrodotoxin concentrations. However, mtDNA sequence data did not support such structure, revealing a star-shaped haplotype network with estimates of expansion time suggesting a population expansion in the Pleistocene era. Inclusion of publicly available mtDNA sequence sea slugs from Argentina did not alter the star-shaped network. We interpret our data as indicative of a single founding population that fragmented following geographical changes that brought about the present day north-south divide in New Zealand waters. Lack of evidence of cryptic species supports data indicating that differences in toxicity of individuals among regions are a consequence of differences in diet.

We studied genetic similarity between adults and nestlings in putative social families (i.e., 2 adults and a chick) of a seabird that provides obligate biparental care, the Australasian Gannet (Morus serrator), in New Zealand. We detected DNA fingerprint mismatches in 12% of 26 nests between the chick and 1 of the 2 attending adults sampled. No parent-offspring genetic mismatch was detected in nests with 4-week-old or younger and sedentary nestlings, whereas adult-nestling mismatches were detected only in nests with 5-week or older and more mobile young sampled. We conclude that the genetic mating system of this sulid species is predominantly monogamous.

After European colonization, the ancestral remains of Indigenous people were often collected for scientific research or display in museum collections. For many decades, Indigenous people, including Native Americans and Aboriginal Australians, have fought for their return. However, many of these remains have no recorded provenance, making their repatriation very difficult or impossible. To determine whether DNA-based methods could resolve this important problem, we sequenced 10 nuclear genomes and 27 mitogenomes from ancient pre-European Aboriginal Australians (up to 1540 years before the present) of known provenance and compared them to 100 high-coverage contemporary Aboriginal Australian genomes, also of known provenance. We report substantial ancient population structure showing strong genetic affinities between ancient and contemporary Aboriginal Australian individuals from the same geographic location. Our findings demonstrate the feasibility of successfully identifying the origins of unprovenanced ancestral remains using genomic methods.

Brown skuas Catharacta antarctica lonnbergi breed across a broad latitudinal range from the Antarctic to temperate regions. While information on the non-breeding distribution and behaviour for Antarctic and subantarctic populations is known, no data exist for populations breeding at temperate latitudes. We combined geolocation sensing and stable isotope analysis of feather tissue to study the non-breeding behaviour of brown skuas from the temperate Chatham Islands, a population that was historically thought to be resident year-round. Analysis of 27 non-breeding tracks across 2 winters revealed that skuas left the colony for a mean duration of 146 d, which is 64% of the duration reported for Antarctic and subantarctic populations from King George Island, South Shetland Islands, and Bird Island, South Georgia. Consistent with populations of brown skuas from Antarctica and the Subantarctic, the distribution was throughout mixed subtropical-subantarctic and shelf waters. Stable isotope analysis of 72 feathers suggests that moulting takes place over mixed subtropical-subantarctic and subtropical shelf waters. We conclude that brown skuas from the Chatham Islands are migratory, but the year-round mild environmental conditions may reduce the necessity to leave their territories for extended periods.

Sex differences in foraging behavior are typically studied in size-dimorphic taxa. Data on sex-specific behavior in monomorphic taxa are needed to test theories of reproductive investment. It has 'been suggested that in seabirds foraging niche separation may be related to decreased intersexual competition for food between cooperating pair-bonded individuals. Alternatively, sex differences in foraging niches may be driven by different nutritional requirements of females associated with the reproductive costs of egg production and oviposition. To assess these possibilities, we studied a size-monomorphic colonial seabird, the Australasian Gannet (Mortis serrator) at the Cape Kidnappers gannetry, New Zealand. We recorded maximum dive depths, and distinct diet composition of incubating females as indicated by stable isotopic signatures. Results suggested greater female foraging effort during early times of incubation, indicated by significantly deeper maximum dives. Sex-specific foraging patterns across other breeding stages were more variable. Nitrogen stable isotopic values showed that incubating females occupied a different trophic position compared to males at the same breeding stage, and also from those of gannets of both sexes at later stages of parental care. Overall, the data are consistent with cost-ofoviposition compensation in females necessitating male-bias in parental care in biparental breeders. Further research is needed to unravel the implications of nutritional needs for the evolution of sex differences in behavior in this and other monomorphic taxa.