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The total-evidence approach to divergence time dating uses molecular and morphological data from extant and fossil species to infer phylogenetic relationships, species divergence times, and macroevolutionary parameters in a single coherent framework. Current model-based implementations of this approach lack an appropriate model for the tree describing the diversification and fossilization process and can produce estimates that lead to erroneous conclusions. We address this shortcoming by providing a total-evidence method implemented in a Bayesian framework. This approach uses a mechanistic tree prior to describe the underlying diversification process that generated the tree of extant and fossil taxa. Previous attempts to apply the total-evidence approach have used tree priors that do not account for the possibility that fossil samples may be direct ancestors of other samples, that is, ancestors of fossil or extant species or of clades. The fossilized birth–death (FBD) process explicitly models the diversification, fossilization, and sampling processes and naturally allows for sampled ancestors. This model was recently applied to estimate divergence times based on molecular data and fossil occurrence dates. We incorporate the FBD model and a model of morphological trait evolution into a Bayesian total-evidence approach to dating species phylogenies. We apply this method to extant and fossil penguins and show that the modern penguins radiated much more recently than has been previously estimated, with the basal divergence in the crown clade occurring at ∼12.7 Ma and most splits leading to extant species occurring in the last 2 myr. Our results demonstrate that including stem-fossil diversity can greatly improve the estimates of the divergence times of crown taxa. The method is available in BEAST2 (version 2.4) software www.beast2.org with packages SA (version at least 1.1.4) and morph-models (version at least 1.0.4) installed.

Penguins are the only extant family of flightless diving birds. They currently comprise at least 18 species, distributed from polar to tropical environments in the Southern Hemisphere. The history of their diversification and adaptation to these diverse environments remains controversial. We used 22 new genomes from 18 penguin species to reconstruct the order, timing, and location of their diversification, to track changes in their thermal niches through time, and to test for associated adaptation across the genome. Our results indicate that the penguin crown-group originated during the Miocene in New Zealand and Australia, not in Antarctica as previously thought, and that Aptenodytes is the sister group to all other extant penguin species. We show that lineage diversification in penguins was largely driven by changing climatic conditions and by the opening of the Drake Passage and associated intensification of the Antarctic Circumpolar Current (ACC). Penguin species have introgressed throughout much of their evolutionary history, following the direction of the ACC, which might have promoted dispersal and admixture. Changes in thermal niches were accompanied by adaptations in genes that govern thermoregulation and oxygen metabolism. Estimates of ancestral effective population sizes (Nₑ) confirm that penguins are sensitive to climate shifts, as represented by three different demographic trajectories in deeper time, themost common (in 11 of 18 penguin species) being an increased Nₑ between 40 and 70 kya, followed by a precipitous decline during the Last Glacial Maximum. The latter effect is most likely a consequence of the overall decline in marine productivity following the last glaciation.

The development of an organism involves the formation of patterns from initially homogeneous surfaces in a reproducible manner. Simulations of various theoretical models recapitulate final states of natural patterns, yet drawing testable hypotheses from those often remains difficult. Consequently, little is known about pattern-forming events. Here, we surveyed plumage patterns and their emergence in Galliformes, ratites, passerines, and penguins, together representing the three major taxa of the avian phylogeny, and built a unified model that not only reproduces final patterns but also intrinsically generates shared and varying directionality, sequence, and duration of patterning. We used in vivo and ex vivo experiments to test its parameter-based predictions. We showed that directional and sequential pattern progression depends on a species-specific prepattern: an initial break in surface symmetry launches a travelling front of sharply defined, oriented domains with self-organising capacity. This front propagates through the timely transfer of increased cell density mediated by cell proliferation, which controls overall patterning duration. These results show that universal mechanisms combining prepatterning and self-organisation govern the timely emergence of the plumage pattern in birds.

The gastrointestinal tract microbiota is known to play very important roles in the well being of animals. It is a complex community composed by hundreds of microbial species interacting closely among them and with their host, that is, a microbial ecosystem. The development of high throughput sequencing techniques allows studying the diversity of such communities in a realistic way and considerable work has been carried out in mammals and some birds such as chickens. Wild birds have received less attention and in particular, in the case of penguins, only a few individuals of five species have been examined with molecular techniques. We collected cloacal samples from Chinstrap penguins in the Vapour Col rookery in Deception Island, Antarctica, and carried out pyrosequencing of the V1-V3 region of the 16S rDNA in samples from 53 individuals, 27 adults and 26 chicks. This provided the first description of the Chinstrap penguin gastrointestinal tract microbiota and the most extensive in any penguin species. Firmicutes, Bacteoridetes, Proteobacteria, Fusobacteria, Actinobacteria, and Tenericutes were the main components. There were large differences between chicks and adults. The former had more Firmicutes and the latter more Bacteroidetes and Proteobacteria. In addition, adults had richer and more diverse bacterial communities than chicks. These differences were also observed between parents and their offspring. On the other hand, nests explained differences in bacterial communities only among chicks. We suggest that environmental factors have a higher importance than genetic factors in the microbiota composition of chicks. The results also showed surprisingly large differences in community composition with other Antarctic penguins including the congeneric Adélie and Gentoo penguins.

We report 156 sediment metagenomes from Adélie penguin ( Pygoscelis adeliae ) colonies dating back 6000 years along the Ross Sea coast, Antarctica, and identify marine and terrestrial eukaryotes, including locally occurring bird and seal species. The data reveal spatiotemporal patterns of Adélie penguin diet, including spatial patterns in consumption of cnidarians, a historically overlooked component of Adélie penguin diets. Relative proportions of Adélie penguin mitochondrial lineages detected at each colony are comparable to those previously reported from bones. Elevated levels of Adélie penguin mitochondrial nucleotide diversity in upper stratigraphic samples of several active colonies are consistent with recent population growth. Moreover, the highest levels of Adélie penguin mitochondrial nucleotide diversity recovered from surface sediment layers are from the two largest colonies, indicating that seda DNA could provide estimates for the former size of abandoned colonies. Seda DNA also reveals prior occupation of the Cape Hallett Adélie penguin colony site by southern elephant seal ( Mirounga leonina ), demonstrating how terrestrial seda DNA can detect faunal turnover events in Antarctica driven by past climate or sea ice conditions. Low rates of cytosine deamination indicate exceptional seda DNA preservation within the region, suggesting there is high potential for recovering much older seda DNA records from local Pleistocene terrestrial sediments. Seda DNA can facilitate reconstruction of past species distributions. Here, the authors generate metagenomes from 156 stratigraphically-sampled sediments and use them to reconstruct the history of 10 Adélie penguin colonies, including penguin diet and diversity, spanning 6000 years.

Purifying selection is the most pervasive type of selection, as it constantly removes deleterious mutations arising in populations, directly scaling with population size. Highly expressed genes appear to accumulate fewer nonsynonymous mutations between divergent species' lineages (known as E–R anticorrelation), pointing toward gene expression as an additional component modulating the selection coefficient of protein-coding mutations. However, estimates of the effect of gene expression on segregating deleterious variants in natural populations are scarce, as is an understanding of the relative contribution of population size and gene expression to purifying selection. Here, we analyze genomic and transcriptomic data from two natural populations of closely related sister species with different demographic histories, the Emperor penguin (Aptenodytes forsteri) and the King penguin (Aptenodytes patagonicus), and show that purifying selection at the population level depends on gene expression rate, resulting in very high selection coefficients at highly expressed genes. Leveraging realistic forward simulations, we estimate that the top 10% of the most highly expressed genes in a genome experience a selection pressure corresponding to an average selection coefficient of −0.1, which decreases to a selection coefficient of −0.01 for the top 50%. Gene expression rate can be regarded as a fundamental parameter of protein evolution in natural populations, maintaining selection effective even at small population size. We suggest gene expression could be considered as a major component of gene-specific selection coefficients, which are notoriously difficult to derive in nonmodel species under real-world conditions.

The main motivation for this study was to determine the occurrence of Toxoplasma gondii, a cosmopolitan widespread zoonotic parasite distribution that can infect a wide variety of mammals and birds, in Magellanic penguins (Spheniscus magellanicus) in Brazil. In recent decades there has been a significant increase in the number of penguins originating from Argentinian and Chilean Patagonia, where these birds are born, that arrive on the Brazilian coast, where many of them are stranded and rescued. Tissue samples were collected from 330 individuals surveyed from 2012-2015 at the Institute for Marine Animal Research and Rehabilitation (IPRAM) located in Cariacica, state of Espirito Santo, Brazil. Serum were collected from 145 animals surveyed in 2015 for the detection of anti-T. gondii antibodies using the Modified Agglutination Test (MAT ≥20) and 18 birds were positive, with titers of 20 (7 birds), 40 (9 birds) and 80 (2 birds). Mouse bioassay for the isolation of T. gondii was performed using tissues from 54 penguins that were also surveyed in 2015, but no isolates were obtained. DNA from tissue samples of 330 individuals was PCR amplified and sequenced to detect tissue cyst forming coccidians by using pan sarcocystids-directed primers (based on 18S rDNA). These samples were from animals surveyed in 2015 and from frozen stocked tissues from animals surveyed in the years 2012 and 2013. The positives were PCR amplified and sequenced with genus Sarcocystis-specific primers (based on internal transcribed spacer 1, RNA polymerase beta subunit coding gene, and cytochrome B coding gene) and with Sarcocystis falcatula/Sarcocystis neurona- specific primers (based on surface antigens SAG2, SAG3 and SAG4). Sixteen (3.0%) of pectoral muscle samples were positive by all the seven molecular markers and all the samples were identical to each other. Organisms close related to Sarcocystis falcatula were confirmed in all cases. This is the first report on molecular detection of infection by S. falcatula-related organisms and the first report of seropositivity for T. gondii in free-living Magellanic penguins in Brazil. Felids and didephid opossums are definitive hosts of T. gondii and S. falcatula, respectively. Where the penguins acquire the infective forms of the parasites shed by the terrestrial mammals remains to be elucidated.

Despite its isolation and extreme climate, Antarctica is home to diverse fauna and associated microorganisms. It has been proposed that the most iconic Antarctic animal, the penguin, experiences low pathogen pressure, accounting for their disease susceptibility in foreign environments. There is, however, a limited understanding of virome diversity in Antarctic species, the extent of in situ virus evolution, or how it relates to that in other geographic regions. To assess whether penguins have limited microbial diversity we determined the RNA viromes of three species of penguins and their ticks sampled on the Antarctic peninsula. Using total RNA sequencing we identified 107 viral species, comprising likely penguin associated viruses ( n  = 13), penguin diet and microbiome associated viruses ( n  = 82), and tick viruses ( n  = 8), two of which may have the potential to infect penguins. Notably, the level of virome diversity revealed in penguins is comparable to that seen in Australian waterbirds, including many of the same viral families. These data run counter to the idea that penguins are subject to lower pathogen pressure. The repeated detection of specific viruses in Antarctic penguins also suggests that rather than being simply spill-over hosts, these animals may act as key virus reservoirs.

Identifying contemporary population structure and genetic connectivity among seabird populations is essential for developing conservation plans for threatened species, especially as factors like philopatry, non-breeding behavior, and oceanographic features might limit gene flow between isolated populations and influence changes in genetic diversity over time. Here, we characterize the population structure of three closely related crested penguin species in New Zealand: Tawaki ( Eudyptes pachyrhynchus ; Fiordland penguins), erect-crested penguins/tawaki nana hī ( Eudyptes sclateri ), and eastern rockhopper penguins/tawaki piki toka ( Eudyptes filholi ). Whereas tawaki populations appear to be stable, the erect-crested and eastern rockhopper penguin populations have seen dramatic declines in the recent historical record. To understand the genetic implications of these differences in population trajectories, we assessed genetic connectivity among multiple colonies using thousands of nuclear autosomal loci. Our results indicate that tawaki are a single, genetically diverse population without colony-based structure, which is consistent with the currently observed stable or increasing population of tawaki. However, conservation efforts should continue to prioritize protecting marine habitats to safeguard this species. In contrast, we identified two genetically distinct populations of erect-crested penguins corresponding to the Antipodes Islands and the Bounty Islands groups. The Antipodes Islands eastern rockhopper population exhibited high levels of coancestry and low genetic diversity, consistent with population decline and limited immigration. The lack of gene flow and genetic diversity in both erect-crested and eastern rockhopper penguins on the Antipodes Islands raises concerns and highlights the need for continued research to identify the causes of declines to inform conservation efforts of these penguins.

Climate change is a major threat to global biodiversity. Antarctic ecosystems are no exception. Investigating past species responses to climatic events can distinguish natural from anthropogenic impacts. Climate change produces ‘winners’, species that benefit from these events and ‘losers’, species that decline or become extinct. Using molecular techniques, we assess the demographic history and population structure of Pygoscelis penguins in the Scotia Arc related to climate warming after the Last Glacial Maximum (LGM). All three pygoscelid penguins responded positively to post-LGM warming by expanding from glacial refugia, with those breeding at higher latitudes expanding most. Northern ( Pygoscelis papua papua ) and Southern ( Pygoscelis papua ellsworthii ) gentoo sub-species likely diverged during the LGM. Comparing historical responses with the literature on current trends, we see Southern gentoo penguins are responding to current warming as they did during post-LGM warming, expanding their range southwards. Conversely, Adélie and chinstrap penguins are experiencing a ‘reversal of fortunes’ as they are now declining in the Antarctic Peninsula, the opposite of their response to post-LGM warming. This suggests current climate warming has decoupled historic population responses in the Antarctic Peninsula, favoring generalist gentoo penguins as climate change ‘winners’, while Adélie and chinstrap penguins have become climate change ‘losers’.