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The generic placement of the enigmatic and extinct Logania depressa from New Zealand has been uncertain due to the paucity of available plant material. This diminutive plant has only been collected once from the central North Island, New Zealand, by William Colenso on 22 February 1847. Logania depressa is dioecious and the single collection comprises only male flowers and does not include female flowers or fruit that feature generic diagnostic characters. Previously its relationship to Geniostoma has been considered and its affinities to Orianthera are unknown. Orianthera has been recently recognised as a segregate of Logania. Using leaf material from a small fragment of L. depressa held in Allan Herbarium (CHR) we recovered 9,368 bp of plastid sequence data that mapped to Mitreola yangchuensis, with Mitreola being the closest generic relative of Logania for which whole genome data was available. Available genetic data for Loganiaceae is limited to several chloroplast markers, including the rps16 intron, petD intron, and petD–petB intergenic spacer. From the novel plastid sequence data for Logania depressa, 48 bp of the rps16 intron, 45 bp of the petD intron and 49 bp of the petD–petB intergenic spacer could be recovered to compare with available Loganiaceae sequences. Phylogenetic analysis of these sequences confirmed L. depressa as the only New Zealand member of Logania sens. str., but its relationships to Australian species are unresolved. [ABSTRACT FROM AUTHOR]

Penguins (Sphenisciformes) are an iconic order of flightless, diving seabirds distributed across a large latitudinal range in the Southern Hemisphere. The extensive area over which penguins are endemic is likely to have fostered variation in pathogen pressure, which in turn will have imposed differential selective pressures on the penguin immune system. At the front line of pathogen detection and response, the Toll-like receptors (TLRs) provide insight into host evolution in the face of microbial challenge. TLRs respond to conserved pathogen-associated molecular patterns and are frequently found to be under positive selection, despite retaining specificity for defined agonist classes. We undertook a comparative immunogenetics analysis of TLRs for all penguin species and found evidence of adaptive evolution that was largely restricted to the cell surface-expressed TLRs, with evidence of positive selection at, or near, key agonist-binding sites in TLR1B , TLR4 , and TLR5. Intriguingly, TLR15 , which is activated by fungal products, appeared to have been pseudogenized multiple times in the Eudyptes spp. but a full-length form was present as a rare haplotype at the population level. However, in vitro analysis revealed that even the full-length form of Eudyptes TLR15 was nonfunctional, indicating an ancestral cryptic pseudogenization prior to its eventual disruption multiple times in the Eudyptes lineage. This unusual pseudogenization event could provide an insight into immune adaptation to fungal pathogens such as Aspergillus , which is responsible for significant mortality in wild and captive bird populations. [ABSTRACT FROM AUTHOR]

We describe a new species of Polynesian sandpiper from Henderson Island, Prosobonia sauli sp. nov. , based on multiple Holocene fossil bones collected during the Sir Peter Scott Commemorative Expedition to the Pitcairn Islands (1991–92). Prosobonia sauli is the only species of Prosobonia to be described from bone accumulations and extends the record of known extinct Polynesian sandpipers to four. It is readily differentiated from the extant Tuamotu Sandpiper P. parvirostris in several features of the legs and bill, implying ecological adaptations to different environments. The geographically nearest Prosobonia populations to Henderson Island were found on Mangareva, where it is now extinct. A previous record of a species of Prosobonia from Tubuai, Austral Islands, is here shown to belong to the Sanderling Calidris alba. Our analyses of newly sequenced genetic data, which include the mitochondrial genomes of P. parvirostris and the extinct Tahiti Sandpiper P. leucoptera , confidently resolve the position of Prosobonia as sister-taxon to turnstones and calidrine sandpipers. We present a hypothesis for the timing of divergence between species of Prosobonia and other scolopacid lineages. Our results further provide a framework to interpret the evolution of sedentary lineages within the normally highly migratory Scolopacidae. [ABSTRACT FROM AUTHOR]

Globally, wetlands are in decline due to anthropogenic modification and climate change. Knowledge about the spatial distribution of biodiversity and biological processes within wetlands provides essential baseline data for predicting and mitigating the effects of present and future environmental change on these critical ecosystems. To explore the potential for environmental DNA (eDNA) to provide such insights, we used 16S rRNA metabarcoding to characterise prokaryote communities and predict the distribution of prokaryote metabolic pathways in peats and sediments up to 4m below the surface across seven New Zealand wetlands. Our results reveal distinct vertical structuring of prokaryote communities and metabolic pathways in these wetlands. We also find evidence for differences in the relative abundance of certain metabolic pathways that may correspond to the degree of anthropogenic modification the wetlands have experienced. These patterns, specifically those for pathways related to aerobic respiration and the carbon cycle, can be explained predominantly by the expected effects of wetland drainage. Our study demonstrates that eDNA has the potential to be an important new tool for the assessment and monitoring of wetland health. [ABSTRACT FROM AUTHOR]

Speciation through homoploid hybridization (HHS) is considered extremely rare in animals. This is mainly because the establishment of reproductive isolation as a product of hybridization is uncommon. Additionally, many traits are underpinned by polygeny and/or incomplete dominance, where the hybrid phenotype is an additive blend of parental characteristics. Phenotypically intermediate hybrids are usually at a fitness disadvantage compared with parental species and tend to vanish through backcrossing with parental population(s). It is therefore unknown whether the additive nature of hybrid traits in itself could lead successfully to HHS. Using a multi-marker genetic data set and a meta-analysis of diet and morphology, we investigated a potential case of HHS in the prions (Pachyptila spp.), seabirds distinguished by their bills, prey choice, and timing of breeding. Using approximate Bayesian computation, we show that the medium-billed Salvin's prion (Pachyptila salvini) could be a hybrid between the narrow-billed Antarctic prion (Pachyptila desolata) and broad-billed prion (Pachyptila vittata). Remarkably, P. salvini' s intermediate bill width has given it a feeding advantage with respect to the other Pachyptila species, allowing it to consume a broader range of prey, potentially increasing its fitness. Available metadata showed that P. salvini is also intermediate in breeding phenology and, with no overlap in breeding times, it is effectively reproductively isolated from either parental species through allochrony. These results provide evidence for a case of HHS in nature, and show for the first time that additivity of divergent parental traits alone can lead directly to increased hybrid fitness and reproductive isolation. [ABSTRACT FROM AUTHOR]

The arrival of humans in New Zealand around 750 years ago resulted in widespread faunal extinctions including the endemic Waitaha penguin (Megadyptes waitaha). Previously thought to have only bred on coastal South Island and Stewart Island, recent genetic reanalysis of prehistoric large penguin bones from the lower North Island indicates that the Waitaha penguin may have been a common resident. Here we synthesise previous studies and present new palaeontological and archaeological evidence to suggest that the Waitaha penguin was probably breeding in the lower North Island at the time of human arrival, and did not represent vagrant individuals from more southerly breeding colonies. The elimination of breeding Megadyptes from the North Island would add to the already significant avifaunal losses from New Zealand, of which the North Island suffered the greatest biodiversity loss after the arrival of humans. [ABSTRACT FROM AUTHOR]

Comprehending ecological dynamics requires not only knowledge of modern communities but also detailed reconstructions of ecosystem history. Ancient DNA (aDNA) metabarcoding allows biodiversity responses to major climatic change to be explored at different spatial and temporal scales. We extracted aDNA preserved in fossil rodent middens to reconstruct late Quaternary vegetation dynamics in the hyperarid Atacama Desert. By comparing our paleo‐informed millennial record with contemporary observations of interannual variations in diversity, we show local plant communities behave differentially at different timescales. In the interannual (years to decades) time frame, only annual herbaceous expand and contract their distributional ranges (emerging from persistent seed banks) in response to precipitation, whereas perennials distribution appears to be extraordinarily resilient. In contrast, at longer timescales (thousands of years) many perennial species were displaced up to 1,000 m downslope during pluvial events. Given ongoing and future natural and anthropogenically induced climate change, our results not only provide baselines for vegetation in the Atacama Desert, but also help to inform how these and other high mountain plant communities may respond to fluctuations of climate in the future. [ABSTRACT FROM AUTHOR]

The emergence of islands has been linked to spectacular radiations of diverse organisms. Although penguins spend much of their lives at sea, they rely on land for nesting, and a high proportion of extant species are endemic to geologically young islands. Islands may thus have been crucial to the evolutionary diversification of penguins. We test this hypothesis using a fossil-calibrated phylogeny of mitochondrial genomes (mitogenomes) from all extant and recently extinct penguin taxa. Our temporal analysis demonstrates that numerous recent island-endemic penguin taxa diverged following the formation of their islands during the Plio-Pleistocene, including the Galápagos (Galápagos Islands), northern rockhopper (Gough Island), erect-crested (Antipodes Islands), Snares crested (Snares) and royal (Macquarie Island) penguins. Our analysis also reveals two new recently extinct island-endemic penguin taxa from New Zealand's Chatham Islands: Eudyptes warhami sp. nov. and a dwarf subspecies of the yellow-eyed penguin, Megadyptes antipodes richdalei ssp. nov. Eudyptes warhami diverged from the Antipodes Islands erect-crested penguin between 1.1 and 2.5 Ma, shortly after the emergence of the Chatham Islands (∼3 Ma). This new finding of recently evolved taxa on this young archipelago provides further evidence that the radiation of penguins over the last 5 Ma has been linked to island emergence. Mitogenomic analyses of all penguin species, and the discovery of two new extinct penguin taxa, highlight the importance of island formation in the diversification of penguins, as well as the extent to which anthropogenic extinctions have affected island-endemic taxa across the Southern Hemisphere's isolated archipelagos. [ABSTRACT FROM AUTHOR]

In the 25 years since the first DNA sequences were obtained from the extinct moa, ancient DNA analyses have significantly advanced our understanding of New Zealand's unique fauna. Here, we review how DNA extracted from ancient faunal remains has provided new insights into the evolutionary histories and phylogenetic relationships of New Zealand animals, and the impacts of human activities upon their populations. Moreover, we review how ancient DNA has played a key role in improving our ability to taxonomically identify fragmentary animal remains, determine biological function within extinct species, reconstruct past faunas and communities based on DNA preserved in sediments, resolve aspects of the ecology of extinct animals and characterising prehistoric parasite faunas. As ancient DNA analyses continue to become increasingly applied, and sequencing technologies continue to improve, the next 25 years promises to provide many more exciting new insights and discoveries about New Zealand's unique fauna. [ABSTRACT FROM AUTHOR]

The penguin species Tasidyptes hunteri van Tets & O'Connor, 1983, the sole representative of an extinct penguin genus, was described on the basis of four bones excavated from a prehistoric midden on Tasmania's Hunter Island. Several authors have since questioned the validity of T. hunteri, citing the fragmentary nature of the remains and the similarity of some elements (coracoid and tarsometatarsus) to those of extant crested penguin (Eudyptes) species. We designed four overlapping primer pairs to amplify a 499 bp region of mitochondrial cytochrome c oxidase 1 (COI) in penguins and used these to amplify and sequence COI from all known bones attributed to T. hunteri. The T. hunteri COI sequences were assessed within a phylogenetic framework against COI sequences for all extant penguin species. Our results reveal that the T. hunteri bones are an assemblage of remains from three extant penguin species (Eudyptes pachyrhynchus, E. robustus, Eudyptula novaehollandiae), and we find no molecular support for any of these bones representing an extinct penguin lineage. [ABSTRACT FROM AUTHOR]

Microsatellite loci are ideal for testing hypotheses relating to genetic segregation at fine spatio-temporal scales. They are also conserved among closely related species, making them potentially useful for clarifying interspecific relationships between recently diverged taxa. However, mutations at primer binding sites may lead to increased nonamplification, or disruptions that may result in decreased polymorphism in nontarget species. Furthermore, high mutation rates and constraints on allele size may also with evolutionary time, promote an increase in convergently evolved allele size classes, biasing measures of interspecific genetic differentiation. Here, we used next-generation sequencing to develop microsatellite markers from a shotgun genome sequence of the sub-Antarctic seabird, the thin-billed prion ( Pachyptila belcheri), that we tested for cross-species amplification in other Pachyptila and related sub-Antarctic species. We found that heterozygosity decreased and the proportion of nonamplifying loci increased with phylogenetic distance from the target species. Surprisingly, we found that species trees estimated from interspecific FST provided better approximations of mt DNA relationships among the studied species than those estimated using DC, even though FST was more affected by null alleles. We observed a significantly nonlinear second order polynomial relationship between microsatellite and mt DNA distances. We propose that the loss of linearity with increasing mt DNA distance stems from an increasing proportion of homoplastic allele size classes that are identical in state, but not identical by descent. Therefore, despite high cross-species amplification success and high polymorphism among the closely related Pachyptila species, we caution against the use of microsatellites in phylogenetic inference among distantly related taxa. [ABSTRACT FROM AUTHOR]

Eastern Rockhopper penguins from Marion Island in the sub-Antarctic region. The cover image relates to the Research Article https://doi.org/10.1111/ddi.13399 "Taxonomy based on limited genomic markers may underestimate species diversity of rockhopper penguins and threaten their conservation" by Frugone et al. [Extracted from the article]

The generic relationships of the extinct Trilepidea adamsii (Cheeseman) Tiegh. from New Zealand have been uncertain due to the paucity and age of available plant material. Last seen nearly seventy years ago in 1954, fresh material has not been available for comparative studies. Trilepidea adamsii has morphological affinities to Alepis flavida (Hook.f.) Tiegh., Peraxilla colensoi (Hook.f.) Tiegh. and P. tetrapetala (L.f.) Tiegh. with all taxa being placed in subtribe Elytranthinae, but precise phylogenetic relationships have not been determined. Using leaf material of Trilepidea adamsii from a specimen in Allan Herbarium (CHR) collected in 1920 from near Thames, Coromandel Peninsula, North Island, we recovered approximately 93% of the plastid genome by mapping Illumina sequence reads to a plastid genome sequence of Elytranthe albida (Blume) Blume, with Elytranthe being another genus of Loranthaceae. We also sequenced plastid genomes of Alepis flavida, Peraxilla colensoi and Peraxilla tetrapetala and conducted a phylogenetic analysis using other Loranthaceae plastid genome sequences from GenBank. Phylogenetic analyses of the plastid genome sequences confirmed T. adamsii as sister to a clade comprising Alepis and Peraxilla. While the level of sequence divergence is low, we do not consider that the generic boundaries need to be reassessed. We suggest re-examination of anatomical and morphological traits is warranted to better understand evolution in this lineage of four endemic mistletoe species. [ABSTRACT FROM AUTHOR]

We sought to determine mercury (Hg) and other trace metal concentrations in Adélie (Pygoscelis adeliae) and emperor penguin (Aptenodytes forsteri) breast feathers from the Ross Sea, Antarctica, and relate those concentrations to the trophic position and the habitats in which each of these species forage. Adélie penguin feathers from the southern Ross Sea colonies were higher in Hg than those sampled further north in the Ross Sea, potentially due to greater exposure to local sources, such as volcanism. Female Adélie penguins had lower feather total Hg concentrations than males. This may reflect female penguin's capacity to eliminate Hg through the egg development and laying process, or the larger and/or older prey items that male birds can consume, reflected by their higher trophic position. Emperor penguins have higher Hg concentrations than Adélie penguins which is also partially explained by Adélie penguins feeding at lower trophic levels than emperor penguins. • Hg in Adélie and emperor penguins from the Ross Sea lower than other penguin species • Female Adélie penguins from Cape Bird had lower Hg concentrations than males. • Hg was greater in Adélie penguins breeding at higher latitudes • Hg was higher in emperor penguin than Adélie penguins. • Cd, Cu and Zn were higher in Adélie penguins compared with emperor penguins. • δ15N in emperor penguins was higher than that for Adélie penguins. [ABSTRACT FROM AUTHOR]

Background Penguins (Sphenisciformes) are a remarkable order of flightless wing-propelled diving seabirds distributed widely across the southern hemisphere. They share a volant common ancestor with Procellariiformes close to the Cretaceous-Paleogene boundary (66 million years ago) and subsequently lost the ability to fly but enhanced their diving capabilities. With ∼20 species among 6 genera, penguins range from the tropical Galápagos Islands to the oceanic temperate forests of New Zealand, the rocky coastlines of the sub-Antarctic islands, and the sea ice around Antarctica. To inhabit such diverse and extreme environments, penguins evolved many physiological and morphological adaptations. However, they are also highly sensitive to climate change. Therefore, penguins provide an exciting target system for understanding the evolutionary processes of speciation, adaptation, and demography. Genomic data are an emerging resource for addressing questions about such processes. Results Here we present a novel dataset of 19 high-coverage genomes that, together with 2 previously published genomes, encompass all extant penguin species. We also present a well-supported phylogeny to clarify the relationships among penguins. In contrast to recent studies, our results demonstrate that the genus Aptenodytes is basal and sister to all other extant penguin genera, providing intriguing new insights into the adaptation of penguins to Antarctica. As such, our dataset provides a novel resource for understanding the evolutionary history of penguins as a clade, as well as the fine-scale relationships of individual penguin lineages. Against this background, we introduce a major consortium of international scientists dedicated to studying these genomes. Moreover, we highlight emerging issues regarding ensuring legal and respectful indigenous consultation, particularly for genomic data originating from New Zealand Taonga species. Conclusions We believe that our dataset and project will be important for understanding evolution, increasing cultural heritage and guiding the conservation of this iconic southern hemisphere species assemblage. [ABSTRACT FROM AUTHOR]

• Scarce genetic differentiation between Royal and macaroni penguins. • Population differentiation associated to distance between colonies and temperatures. • Macaroni penguins from Antarctic and sub-Antarctic exhibited genetic differentiation. The study of systematics in wide-ranging seabirds can be challenging due to the vast geographic scales involved, as well as the possible discordance between molecular, morphological and behavioral data. In the Southern Ocean, macaroni penguins (Eudyptes chrysolophus) are distributed over a circumpolar range including populations in Antarctic and sub-Antarctic areas. Macquarie Island, in its relative isolation, is home to a closely related endemic taxon — the royal penguin (Eudyptes schlegeli), which is distinguishable from E. chrysolophus mainly by facial coloration. Although these sister taxa are widely accepted as representing distinct species based on morphological grounds, the extent of their genome-wide differentiation remains uncertain. In this study, we use genome-wide Single Nucleotide Polymorphisms to test genetic differentiation between these geographically isolated taxa and evaluate the main drivers of population structure among breeding colonies of macaroni/royal penguins. Genetic similarity observed between macaroni and royal penguins suggests they constitute a single evolutionary unit. Nevertheless, royal penguins exhibited a tendency to cluster only with macaroni individuals from Kerguelen Island, suggesting that dispersal occurs mainly between these neighboring colonies. A stepping stone model of differentiation of macaroni/royal populations was further supported by a strong pattern of isolation by distance detected across its whole distribution range, possibly driven by large geographic distances between colonies as well as natal philopatry. However, we also detected intraspecific genomic differentiation between Antarctic and sub-Antarctic populations of macaroni penguins, highlighting the role of environmental factors together with geographic distance in the processes of genetic differentiation between Antarctic and sub-Antarctic waters. [ABSTRACT FROM AUTHOR]