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Whole-genome sequencing projects are increasingly populating the tree of life and characterizing biodiversity1–4. Sparse taxon sampling has previously been proposed to confound phylogenetic inference5, and captures only a fraction of the genomic diversity. Here we report a substantial step towards the dense representation of avian phylogenetic and molecular diversity, by analysing 363 genomes from 92.4% of bird families—including 267 newly sequenced genomes produced for phase II of the Bird 10,000 Genomes (B10K) Project. We use this comparative genome dataset in combination with a pipeline that leverages a reference-free whole-genome alignment to identify orthologous regions in greater numbers than has previously been possible and to recognize genomic novelties in particular bird lineages. The densely sampled alignment provides a single-base-pair map of selection, has more than doubled the fraction of bases that are confdently predicted to be under conservation and reveals extensive patterns of weak selection in predominantly non-coding DNA. Our results demonstrate that increasing the diversity of genomes used in comparative studies can reveal more shared and lineage-specifc variation, and improve the investigation of genomic characteristics. We anticipate that this genomic resource will ofer new perspectives on evolutionary processes in cross-species comparative analyses and assist in eforts to conserve species.

Network optimality has been described in genes, proteins and human communicative networks. In the latter, optimality leads to the efficient transmission of information with a minimum number of connections. Whilst studies show that differences in centrality exist in animal networks with central individuals having higher fitness, network efficiency has never been studied in animal groups. Here we studied 78 groups of primates (24 species). We found that group size and neocortex ratio were correlated with network efficiency. Centralisation (whether several individuals are central in the group) and modularity (how a group is clustered) had opposing effects on network efficiency, showing that tolerant species have more efficient networks. Such network properties affecting individual fitness could be shaped by natural selection. Our results are in accordance with the social brain and cultural intelligence hypotheses, which suggest that the importance of network efficiency and information flow through social learning relates to cognitive abilities.

Modern nautilids ( Nautilus and Allonautilus ) have often been studied by paleontologists to better understand the anatomy and ecology of fossil relatives. Because direct observations of these animals are difficult, the analysis of light stable isotopes (C, O) preserved in their shells has been employed to reveal their habitat and life history. We aim to (1) reconstruct the habitat depth of Nautilus macromphalus and (2) decipher the fraction of metabolic carbon in its shell by analyzing oxygen and carbon isotopes (δ 18 O, δ 13 C) in the septa of two specimens in combination with analyses of water samples from the area. Additionally, we investigate whether morphological changes during ontogeny are reflected in the isotopic values of the shells. Results reveal that the patterns of change of δ 18 O and δ 13 C in the septa of N . macromphalus pre- and post-hatching are consistent with previous studies. Values of δ 18 O water range from 0.7 to 1.4‰ (VSMOW), with a maximum value coincident with a salinity maximum at ~150 m. We use the temperature and δ 18 O water profiles to calculate equilibrium values of δ 18 O aragonite with depth. Comparing these values with the measured δ 18 O of the septa shows that the habitat depth of N . macromphalus is ~140 m pre-hatching and ~370 m post-hatching. Using δ 13 C of shell carbonate and published data on metabolic carbon, the fraction of metabolic carbon is reconstructed as ~21% and 14% pre- and post-hatching, respectively. The reconstructed depth pre-hatching is slightly shallower than in N . pompilius from the Philippines and Fiji, but the post-hatching depth is similar. However, it is important to emphasize that these estimates represent average over time and space because nautilus is a mobile animal. Lastly, the changes in morphological parameters and the changes in δ 13 C and δ 18 O during ontogeny do not coincide except at hatching and at the onset of maturity.

Lice are socially-transmitted ectoparasites. Transmission depends upon their host’s degree of contact with conspecifics. While grooming facilitates ectoparasite transmission via body contact, it also constrains their spread through parasite removal. We investigated relations between parasite burden and sociality in female Japanese macaques following two opposing predictions: i) central females in contact/grooming networks harbour more lice, related to their numerous contacts; ii) central females harbour fewer lice, related to receiving more grooming. We estimated lice load non-invasively using the conspicuous louse egg-picking behaviour performed by macaques during grooming. We tested for covariation in several centrality measures and lice load, controlling for season, female reproductive state and dominance rank. Results show that the interaction between degree centrality (number of partners) and seasonality predicted lice load: females interacting with more partners had fewer lice than those interacting with fewer partners in winter and summer, whereas there was no relationship between lice load and centrality in spring and fall. This is counter to the prediction that increased contact leads to greater louse burden but fits the prediction that social grooming limits louse burden. Interactions between environmental seasonality and both parasite and host biology appeared to mediate the role of social processes in louse burden.

Ichthyopterygia is a major clade of reptiles that colonized the ocean after the end-Permian mass extinction, with the oldest fossil records found in early Spathian substage (late Olenekian, late Early Triassic) strata in the western USA. Here, we describe reptilian remains found in situ in the early Spathian Neocolumbites insignis ammonoid zone of South Primorye in the Russian Far East. Specimen NSM PV 23854 comprises fragmentary axial elements exhibiting a combination of morphological characteristics typical of Ichthyopterygia. The cylindrical centra suggest that the specimen represents a basal ichthyopterygian, and its size is comparable to that of Utatsusaurus . Specimen NSM PV 24995 is represented by a single limb bone, which is tentatively identified as an ichthyopterygian humerus. With a body length of approximately 5 m estimated from the humeral length, NSM PV 24995 represents one of the largest specimens of early Spathian marine reptiles known to date. Such size variation among the earliest ichthyopterygians might suggest an explosive diversification in size immediately after the end-Permian mass extinction. Both vertebrae and humerus specimens exhibit an extremely cancellous inner structure, suggesting a high degree of aquatic adaptation in ichthyopterygians, despite their short history of evolution in the ocean.

Seabirds are considered to be useful and practical indicators of the state of marine ecosystems because they integrate across changes in the lower trophic levels and the physical environment. Signals from this key group of species can indicate broad scale impacts or response to environmental change. Recent studies of penguin populations, the most commonly abundant Antarctic seabirds in the west Antarctic Peninsula and western Ross Sea, have demonstrated that physical changes in Antarctic marine environments have profound effects on biota at high trophic levels. Large populations of the circumpolar-breeding Adélie penguin occur in East Antarctica, but direct, standardized population data across much of this vast coastline have been more limited than in other Antarctic regions. We combine extensive new population survey data, new population estimation methods, and re-interpreted historical survey data to assess decadal-scale change in East Antarctic Adélie penguin breeding populations. We show that, in contrast to the west Antarctic Peninsula and western Ross Sea where breeding populations have decreased or shown variable trends over the last 30 years, East Antarctic regional populations have almost doubled in abundance since the 1980's and have been increasing since the earliest counts in the 1960's. The population changes are associated with five-year lagged changes in the physical environment, suggesting that the changing environment impacts primarily on the pre-breeding age classes. East Antarctic marine ecosystems have been subject to a number of changes over the last 50 years which may have influenced Adélie penguin population growth, including decadal-scale climate variation, an inferred mid-20th century sea-ice contraction, and early-to-mid 20th century exploitation of fish and whale populations.

Recently, research on domestic mammals’ sociocognitive skills toward humans has been prolific, allowing us to better understand the human–animal relationship. For example, horses have been shown to distinguish human beings on the basis of photographs and voices and to have cross-modal mental representations of individual humans and human emotions. This leads to questions such as the extent to which horses can differentiate human attributes such as age. Here, we tested whether horses discriminate human adults from children. In a cross-modal paradigm, we presented 31 female horses with two simultaneous muted videos of a child and an adult saying the same neutral sentence, accompanied by the sound of an adult’s or child’s voice speaking the sentence. The horses looked significantly longer at the videos that were incongruent with the heard voice than at the congruent videos. We conclude that horses can match adults’ and children’s faces and voices cross-modally. Moreover, their heart rates increased during children’s vocalizations but not during adults’. This suggests that in addition to having mental representations of adults and children, horses have a stronger emotional response to children’s voices than adults’ voices.

Sentinel species, like Adélie penguins, have been used to assess the impact of environmental changes, and their link with sea ice has eceived considerable attention. Here, we tested if foraging Adélie penguins from 2 colonies in East Antarctica target the distant sea-ice edge or take advantage of closer open waters that are readily available near their colony. We examined the foraging behaviour of penguins during the incubation trips of females in 2016 and males in 2017, using GPS tracking and diet data in view of daily sea-ice data and bathymetry. In 2016−2017, sea-ice cover was extensive during females’ trips but flaw leads and polynyas were close to both study sites. Sea ice receded rapidly during males’ trips in 2017−2018. Despite close open water near both colonies in both years, females and males preferentially targeted the continental slope and the sea-ice edge to forage. In addition, there was no difference in the diet of penguins from both colonies: all penguins fed mostly on Antarctic krill and males also foraged on Antarctic silverfish. Our results highlight the importance of the sea-ice edge for penguins, an area where food abundance is predictable. It is likely that resource availability was not sufficient in closer open water areas at such an early stage in the breeding season. The behaviours displayed by the penguins from both colonies were similar, suggesting a common behaviour across colonies in Terre Adélie, although additional sites would be necessary to confirm this hypothesis.

Forkhead Box L2 (FOXL2) is a member of the FOXL class of transcription factors, which are essential for ovarian differentiation and function. In the endometrium, FOXL2 is also thought to be important in cattle; however, it is not clear how its expression is regulated. The maternal recognition of pregnancy signal in cattle, interferon-Tau, does not regulate FOXL2 expression. Therefore, in the present study, we examined whether the ovarian steroid hormones that orchestrate implantation regulate FOXL2 gene expression in ruminants. In sheep, we confirmed that FOXL2 mRNA and protein was expressed in the endometrium across the oestrous cycle (day 4 to day 15 post-oestrus). Similar to the bovine endometrium, ovine FOXL2 endometrial expression was low during the luteal phase of the oestrous cycle (4 to 12 days post-oestrus) and at implantation (15 days post-oestrus) while mRNA and protein expression significantly increased during the luteolytic phase (day 15 post-oestrus in cycle). In pregnant ewes, inhibition of progesterone production by trilostane during the day 5 to 16 period prevented the rise in progesterone concentrations and led to a significant increase of FOXL2 expression in caruncles compared with the control group (1.4-fold, p < 0.05). Ovariectomized ewes or cows that were supplemented with exogenous progesterone for 12 days or 6 days, respectively, had lower endometrial FOXL2 expression compared with control ovariectomized females (sheep, mRNA, 1.8-fold; protein, 2.4-fold; cattle; mRNA, 2.2-fold; p < 0.05). Exogenous oestradiol treatments for 12 days in sheep or 2 days in cattle did not affect FOXL2 endometrial expression compared with control ovariectomized females, except at the protein level in both endometrial areas in the sheep. Moreover, treating bovine endometrial explants with exogenous progesterone for 48h reduced FOXL2 expression. Using in vitro assays with COS7 cells we also demonstrated that progesterone regulates the FOXL2 promoter activity through the progesterone receptor. Collectively, our findings imply that endometrial FOXL2 is, as a direct target of progesterone, involved in early pregnancy and implantation.

In fishes, sonic abilities for communication purpose usually involve a single mechanism. We describe here the sonic mechanism and sounds in two species of boxfish, the spotted trunkfish Ostracion meleagris and the yellow boxfish Ostracion cubicus . The sonic mechanism utilizes a T-shaped swimbladder with a swimbladder fenestra and two separate sonic muscle pairs. Extrinsic vertical muscles attach to the vertebral column and the swimbladder. Perpendicularly and below these muscles, longitudinal intrinsic muscles cover the swimbladder fenestra. Sounds are exceptional since they are made of two distinct types produced in a sequence. In both species, humming sounds consist of long series (up to 45 s) of hundreds of regular low-amplitude pulses. Hums are often interspersed with irregular click sounds with an amplitude that is ten times greater in O. meleagris and forty times greater in O. cubicus . There is no relationship between fish size and many acoustic characteristics because muscle contraction rate dictates the fundamental frequency. We suggest that hums and clicks are produced by either separate muscles or by a combination of the two. The mechanism complexity supports an investment of boxfish in this communication channel and underline sounds as having important functions in their way of life.