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Ever since Alfred Russel Wallace's nineteenth-century observation that related terrestrial species are often separated on opposing riverbanks, major Amazonian rivers have been recognized as key drivers of speciation. However, rivers are dynamic entities whose widths and courses may vary through time. It thus remains unknown how effective rivers are at reducing gene flow and promoting speciation over long timescales. We fit demographic models to genomic sequences to reconstruct the history of gene flow in three pairs of avian taxa fully separated by different Amazonian rivers, and whose geographic ranges do not make contact in headwater regions where rivers may cease to be barriers. Models with gene flow were best fit but still supported an initial period without any gene flow, which ranged from 187 000 to over 959 000 years, suggesting that rivers are capable of initiating speciation through long stretches of allopatric divergence. Allopatry was followed by either bursts or prolonged episodes of gene flow that retarded genomic differentiation but did not fully homogenize populations. Our results support Amazonian rivers as key barriers that promoted speciation and the build-up of species richness, but they also suggest that river barriers are often leaky, with genomic divergence accumulating slowly owing to episodes of substantial gene flow.

The diversity of cephalic morphologies in mandibulates (myriapods and pancrustaceans) was key to their evolutionary success. A group of Cambrian bivalved arthropods called hymenocarines exhibit diagnostic mandibulate traits that illustrate this diversity, but many forms are still poorly known. These include the odaraiids, typified by Odaraia alata from the Burgess Shale (Wuliuan), characterized by its unique tubular carapace and rudder-like tail fan, and one of the largest Cambrian euarthropods at nearly 20 cm in length. Unfortunately, odaraiid cephalic anatomy has been largely unknown, limiting evolutionary scenarios and putting their mandibulate affinities into question. Here, we reinvestigate Odaraia based on new specimens from the Burgess Shale and describe exquisitely preserved mandibles with teeth and adjacent structures: a hypostome, maxillae and potential paragnaths. These structures can be homologized with those of Cambrian fuxianhuiids and extant mandibulates, and suggest that the ancestral mandibulate head could have had a limbless segment but retained its plasticity, allowing for limb re-expression within Pancrustacea. Furthermore, we show the presence of limbs with spinose endites which created a suspension-feeding structure. This discovery provides morphological evidence for suspension feeding among large Cambrian euarthropods and evinces the increasing exploitation of planktonic resources in Cambrian pelagic food webs.

Cnidarians are regarded as one of the earliest-diverging animal phyla. One of the hallmarks of the cnidarian body plan is the evolution of a free-swimming medusa in some medusozoan classes, but the origin of this innovation remains poorly constrained by the fossil record and molecular data. Previously described macrofossils, putatively representing medusa stages of crown-group medusozoans from the Cambrian of Utah and South China, are here reinterpreted as ctenophore-grade organisms. Other putative Ediacaran to Cambrian medusozoan fossils consist mainly of microfossils and tubular forms. Here we describe Burgessomedusa phasmiformis gen. et sp. nov., the oldest unequivocal macroscopic free-swimming medusa in the fossil record. Our study is based on 182 exceptionally preserved body fossils from the middle Cambrian Burgess Shale (Raymond Quarry, British Columbia, Canada). Burgessomedusa possesses a cuboidal umbrella up to 20 cm high and over 90 short, finger-like tentacles. Phylogenetic analysis supports a medusozoan affinity, most likely as a stem group to Cubozoa or Acraspeda (a group including Staurozoa, Cubozoa and Scyphozoa). Burgessomedusa demonstrates an ancient origin for the free-swimming medusa life stage and supports a growing number of studies showing an early evolutionary diversification of Medusozoa, including of the crown group, during the late Precambrian-Cambrian transition.

Avian skeletal morphology is associated with locomotor function, including flight style, swimming and terrestrial locomotion, and permits informed inferences on locomotion in extinct taxa. The fossil taxon Ichthyornis (Avialae: Ornithurae) has long been regarded as highly aerial, with flight similar to terns or gulls (Laridae), and skeletal features resembling foot-propelled diving adaptations. However, rigorous testing of locomotor hypotheses has yet to be performed on Ichthyornis , despite its notable phylogenetic position as one of the most crownward stem birds. We analysed separate datasets of three-dimensional sternal shape (geometric morphometrics) and skeletal proportions (linear measurements across the skeleton), to examine how well these data types predict locomotor traits in Neornithes. We then used this information to infer locomotor capabilities of Ichthyornis. We find strong support for both soaring and foot-propelled swimming capabilities in Ichthyornis. Further, sternal shape and skeletal proportions provide complementary information on avian locomotion: skeletal proportions allow better predictions of the capacity for flight, whereas sternal shape predicts variation in more specific locomotor abilities such as soaring, foot-propelled swimming and escape burst flight. These results have important implications for future studies of extinct avialan ecology and underscore the importance of closely considering sternum morphology in investigations of fossil bird locomotion.

Small and fragmented populations may become rapidly differentiated due to genetic drift, making it difficult to distinguish whether neutral genetic structure is a signature of recent demographic events, or of long-term evolutionary processes that could have allowed populations to adaptively diverge. We sequenced 52 whole genomes to examine Holocene demographic history and patterns of adaptation in kiwi ( Apteryx ), and recovered 11 strongly differentiated genetic clusters corresponding to previously recognized lineages. Demographic models suggest that all 11 lineages experienced dramatic population crashes relative to early- or mid-Holocene levels. Small population size is associated with low genetic diversity and elevated genetic differentiation ( F ST ), suggesting that population declines have strengthened genetic structure and led to the loss of genetic diversity. However, population size is not correlated with inbreeding rates. Eight lineages show signatures of lineage-specific selective sweeps (284 sweeps total) that are unlikely to have been caused by demographic stochasticity. Overall, these results suggest that despite strong genetic drift associated with recent bottlenecks, most kiwi lineages possess unique adaptations and should be recognized as separate adaptive units in conservation contexts. Our work highlights how whole-genome datasets can address longstanding uncertainty about the evolutionary and conservation significance of small and fragmented populations of threatened species.

The in situ preservation of animal behaviour in the fossil record is exceedingly rare, but can lead to unique macroecological and macroevolutionary insights, especially regarding early representatives of major animal clades. We describe a new complex ecological relationship from the middle Cambrian Burgess Shale (Raymond Quarry, Canada). More than 30 organic tubes were recorded with multiple enteropneust and polychaete worms preserved within them. Based on the tubicolous nature of fossil enteropneusts, we suggest that they were the tube builders while the co-preserved polychaetes were commensals. These findings mark, to our knowledge, the first record of commensalism within Annelida and Hemichordata in the entire fossil record. The finding of multiple enteropneusts sharing common tubes suggests that either the tubes represent reproductive structures built by larger adults, and the enteropneusts commonly preserved within are juveniles, or these enteropneusts were living as a pseudo-colony without obligate attachment to each other, and the tube was built collaboratively. While neither hypothesis can be ruled out, gregarious behaviour was clearly an early trait of both hemichordates and annelids. Further, commensal symbioses in the Cambrian may be more common than currently recognized.

Radiodonts, a clade of Cambro-Devonian stem group euarthropods, have classically been regarded as nektonic apex predators. However, many aspects of radiodont morphology and ecology have remained unclear because of the typically fragmentary nature of fossil material. Here, we describe a new hurdiid radiodont based on abundant and exceptionally well-preserved fossils from the Burgess Shale (Marble Canyon area, British Columbia, Canada). Cambroraster falcatus gen. et sp. nov. is characterized by an extra-large horseshoe-shaped head carapace, bearing conspicuous posterolateral spinous processes, and partially covering a short trunk with eight pairs of lateral flaps. Each of the pair of frontal appendages possess five mesially curving rake-like endites equipped with a series of anteriorly directed hooked spines, altogether surrounding the oral cone. This feeding apparatus suggests a micro to macrophagous sediment-sifting feeding ecology. Cambroraster illuminates the evolution of Hurdiidae and evinces the exploitation of the diversifying infauna by these large and specialized nektobenthic carnivores in the aftermath of the Cambrian explosion.

Agnostids (agnostinids and eodiscinids) are a widespread and biostratigraphically important group of Cambro-Ordovician euarthropods whose evolutionary affinities have been highly controversial. Their dumbbell-shaped calcified tergum was traditionally suggested to unite them with trilobites, but agnostinids have alternatively been interpreted as stem-crustaceans, based on Orsten larval material from the Cambrian of Sweden. We describe exceptionally preserved soft tissues from mature individuals of the agnostinids Peronopsis and Ptychagnostus from the middle Cambrian (Wuliuan Stage) Burgess Shale (Walcott Quarry and Marble Canyon, British Columbia, Canada), facilitating the testing of alternative hypotheses. The digestive tract includes conspicuous ramifying cephalic diverticulae. The cephalon carries one pair of elongate spinous antennules projecting to the front, two pairs of appendages with distally setose, oar-like exopods, and three pairs of presumably biramous appendages with endopods sporting club-shaped exites. The trunk bears five appendage pairs, at least the first two of which are similar to the posteriormost cephalic pairs. The combined evidence supports a nektobenthic and detritivorous lifestyle for agnostinids. A head with six appendiferous segments contrasts strikingly with the four known in trilobites and five typical of mandibulates. Agnostinids are retrieved as the sister group to polymeroid trilobites in our phylogeny, implying that crustacean-like morphologies evolved homoplastically. This result highlights the variability in segmental composition of the artiopodan head. Finally, our study emphasizes the continued role of Burgess Shale-type fossils in resolving the affinities of problematic biomineralizing taxa.

Bats represent one of the largest and most striking nocturnal mammalian radiations, exhibiting many visual system specializations for performance in light-limited environments. Despite representing the greatest ecological diversity and species richness in Chiroptera, Neotropical lineages have been undersampled in molecular studies, limiting the potential for identifying signatures of selection on visual genes associated with differences in bat ecology. Here, we investigated how diverse ecological pressures mediate long-term shifts in selection upon long-wavelength ( Lws ) and short-wavelength ( Sws1 ) opsins, photosensitive cone pigments that form the basis of colour vision in most mammals, including bats. We used codon-based likelihood clade models to test whether ecological variables associated with reliance on visual information (e.g. echolocation ability and diet) or exposure to varying light environments (e.g. roosting behaviour and foraging habitat) mediated shifts in evolutionary rates in bat cone opsin genes. Using additional cone opsin sequences from newly sequenced eye transcriptomes of six Neotropical bat species, we found significant evidence for different ecological pressures influencing the evolution of the cone opsins. While Lws is evolving under significantly lower constraint in highly specialized high-duty cycle echolocating lineages, which have enhanced sonar ability to detect and track targets, variation in Sws1 constraint was significantly associated with foraging habitat, exhibiting elevated rates of evolution in species that forage among vegetation. This suggests that increased reliance on echolocation as well as the spectral environment experienced by foraging bats may differentially influence the evolution of different cone opsins. Our study demonstrates that different ecological variables may underlie contrasting evolutionary patterns in bat visual opsins, and highlights the suitability of clade models for testing ecological hypotheses of visual evolution., (© 2018 The Author(s).)

Weaponry, for the purpose of intraspecific combat or predator defence, is one of the most widespread animal adaptations, yet the selective pressures and constraints governing its phenotypic diversity and skeletal regionalization are not well understood. Here, we investigate the evolution of tail weaponry in amniotes, a rare form of weaponry that nonetheless evolved independently among a broad spectrum of life including mammals, turtles and dinosaurs. Using phylogenetic comparative methods, we test for links between morphology, ecology and behaviour in extant amniotes known to use the tail as a weapon, and in extinct taxa bearing osseous tail armaments. We find robust ecological and morphological correlates of both tail lashing behaviour and bony tail weaponry, including large body size, body armour and herbivory, suggesting these life-history parameters factor into the evolution of antipredator behaviours and tail armaments. We suggest that the evolution of tail weaponry is rare because large, armoured herbivores are uncommon in extant terrestrial faunas, as they have been throughout evolutionary history., (© 2018 The Author(s).)

Adaptive radiations have been hypothesized to contribute broadly to the diversity of organisms. Models of adaptive radiation predict that ecological opportunity and ecological release, the availability of empty ecological niches and the response by adapting lineages to occupy them, respectively, drive patterns of phenotypic and lineage diversification. Adaptive radiations driven by 'ecological opportunity' are well established in island systems; it is less clear if ecological opportunity influences continent-wide diversification. We use Neotropical cichlid fishes to test if variation in rates of functional evolution is consistent with changing ecological opportunity. Across a functional morphological axis associated with ram-suction feeding traits, evolutionary rates declined through time as lineages diversified in South America. Evolutionary rates of ram-suction functional morphology also appear to have accelerated as cichlids colonized Central America and encountered renewed opportunity. Our results suggest that ecological opportunity may play an important role in shaping patterns of morphological diversity of even broadly distributed lineages like Neotropical cichlids., (© 2016 The Author(s).)

Amniotes, tetrapods that evolved the cleidoic egg and thus independence from aquatic larval stages, appeared ca 314 Ma during the Coal Age. The rapid diversification of amniotes and other tetrapods over the course of the Late Carboniferous period was recently attributed to the fragmentation of coal-swamp rainforests ca 307 Ma. However, the amniote fossil record during the Carboniferous is relatively sparse, with ca 33% of the diversity represented by single specimens for each species. We describe here a new species of reptilian amniote that was collected from uppermost Carboniferous rocks of Prince Edward Island, Canada. Erpetonyx arsenaultorum gen. et sp. nov. is a new parareptile distinguished by 29 presacral vertebrae and autapomorphies of the carpus. Phylogenetic analyses of parareptiles reveal E. arsenaultorum as the closest relative of bolosaurids. Stratigraphic calibration of our results indicates that parareptiles began their evolutionary radiation before the close of the Carboniferous Period, and that the diversity of end-Carboniferous reptiles is 80% greater than suggested by previous work. Latest Carboniferous reptiles were still half as diverse as synapsid amniotes, a disparity that may be attributable to preservational biases, to collecting biases, to the origin of herbivory in tetrapods or any combination of these factors., (© 2015 The Author(s) Published by the Royal Society. All rights reserved.)

Hibernating mammals need to be insensitive to acid in order to cope with conditions of high CO2; however, the molecular basis of acid tolerance remains largely unknown. The African naked mole-rat (Heterocephalus glaber) and hibernating mammals share similar environments and physiological features. In the naked mole-rat, acid insensitivity has been shown to be conferred by the functional motif of the sodium ion channel NaV1.7. There is now an opportunity to evaluate acid insensitivity in other taxa. In this study, we tested for functional convergence of NaV1.7 in 71 species of mammals, including 22 species that hibernate. Our analyses revealed a functional convergence of amino acid sequences, which occurred at least six times independently in mammals that hibernate. Evolutionary analyses determined that the convergence results from both parallel and divergent evolution of residues in the functional motif. Our findings not only identify the functional molecules responsible for acid insensitivity in hibernating mammals, but also open new avenues to elucidate the molecular underpinnings of acid insensitivity in mammals.

Burgess Shale-type deposits are renowned for their exquisite preservation of soft-bodied organisms, representing a range of animal body plans that evolved during the Cambrian 'explosion'. However, the rarity of these fossil deposits makes it difficult to reconstruct the broader-scale distributions of their constituent organisms. By contrast, microscopic skeletal elements represent an extensive chronicle of early animal evolution--but are difficult to interpret in the absence of corresponding whole-body fossils. Here, we provide new observations on the dorsal spines of the Cambrian lobopodian (panarthropod) worm Hallucigenia sparsa from the Burgess Shale (Cambrian Series 3, Stage 5). These exhibit a distinctive scaly microstructure and layered (cone-in-cone) construction that together identify a hitherto enigmatic suite of carbonaceous and phosphatic Cambrian microfossils--including material attributed to Mongolitubulus, Rushtonites and Rhombocorniculum--as spines of Hallucigenia-type lobopodians. Hallucigeniids are thus revealed as an important and widespread component of disparate Cambrian communities from late in the Terreneuvian (Cambrian Stage 2) through the 'middle' Cambrian (Series 3); their apparent decline in the latest Cambrian may be partly taphonomic. The cone-in-cone construction of hallucigeniid sclerites is shared with the sclerotized cuticular structures (jaws and claws) in modern onychophorans. More generally, our results emphasize the reciprocal importance and complementary roles of Burgess Shale-type fossils and isolated microfossils in documenting early animal evolution.

The origin and timing of the diversification of modern birds remains controversial, primarily because phylogenetic relationships are incompletely resolved and uncertainty persists in molecular estimates of lineage ages. Here, we present a species tree for the major palaeognath lineages using 27 nuclear genes and 27 archaic retroposon insertions. We show that rheas are sister to the kiwis, emu and cassowaries, and confirm ratite paraphyly because tinamous are sister to moas. Divergence dating using 10 genes with broader taxon sampling, including emu, cassowary, ostrich, five kiwis, two rheas, three tinamous, three extinct moas and 15 neognath lineages, suggests that three vicariant events and possibly two dispersals are required to explain their historical biogeography. The age of crown group birds was estimated at 131 Ma (95% highest posterior density 122-138 Ma), similar to previous molecular estimates. Problems associated with gene tree discordance and incomplete lineage sorting in birds will require much larger gene sets to increase species tree accuracy and improve error in divergence times. The relatively rapid branching within neoaves pre-dates the extinction of dinosaurs, suggesting that the genesis of the radiation within this diverse clade of birds was not in response to the Cretaceous-Paleogene extinction event.

Classic problems in historical biogeography are where did penguins originate, and why are such mobile birds restricted to the Southern Hemisphere? Competing hypotheses posit they arose in tropical-warm temperate waters, species-diverse cool temperate regions, or in Gondwanaland approximately 100 mya when it was further north. To test these hypotheses we constructed a strongly supported phylogeny of extant penguins from 5851 bp of mitochondrial and nuclear DNA. Using Bayesian inference of ancestral areas we show that an Antarctic origin of extant taxa is highly likely, and that more derived taxa occur in lower latitudes. Molecular dating estimated penguins originated about 71 million years ago in Gondwanaland when it was further south and cooler. Moreover, extant taxa are inferred to have originated in the Eocene, coincident with the extinction of the larger-bodied fossil taxa as global climate cooled. We hypothesize that, as Antarctica became ice-encrusted, modern penguins expanded via the circumpolar current to oceanic islands within the Antarctic Convergence, and later to the southern continents. Thus, global cooling has had a major impact on penguin evolution, as it has on vertebrates generally. Penguins only reached cooler tropical waters in the Galapagos about 4 mya, and have not crossed the equatorial thermal barrier.

Most populations of migrant shorebirds around the world are in serious decline, suggesting that vital condition-dependent rates such as fecundity and annual survival are being affected globally. A striking example is the red knot (Calidris canutus rufa) population wintering in Tierra del Fuego, which undertakes marathon 30,000 km hemispheric migrations annually. In spring, migrant birds forage voraciously on horseshoe crab eggs in Delaware Bay in the eastern USA before departing to breed in Arctic polar deserts. From 1997 to 2002 an increasing proportion of knots failed to reach threshold departure masses of 180-200 g, possibly because of later arrival in the Bay and food shortage from concurrent over-harvesting of crabs. Reduced nutrient storage, especially in late-arriving birds, possibly combined with reduced sizes of intestine and liver during refuelling, had severe fitness consequences for adult survival and recruitment of young in 2000-2002. From 1997 to 2002 known survivors in Delaware Bay were heavier at initial capture than birds never seen again, annual survival of adults decreased by 37% between May 2000 and May 2001, and the number of second-year birds in wintering flocks declined by 47%. Population size in Tierra del Fuego declined alarmingly from 51,000 to 27,000 in 2000-2002, seriously threatening the viability of this subspecies. Demographic modelling predicts imminent endangerment and an increased risk of extinction of the subspecies without urgent risk-averse management.

To test the hypothesis put forward by Feduccia of the origin of modern birds from transitional birds, we sequenced the first two complete mitochondrial genomes of shorebirds (ruddy turnstone and blackish oystercatcher) and compared their sequences with those of already published avian genomes. When corrected for rate heterogeneity across sites and non-homogeneous nucleotide compositions among lineages in maximum likelihood (ML), the optimal tree places palaeognath birds as sister to the neognaths including shorebirds. This optimal topology is a re-rooting of recently published ordinal-level avian trees derived from mitochondrial sequences. Using a penalized likelihood (PL) rate-smoothing process in conjunction with dates estimated from fossils, we show that the basal splits in the bird tree are much older than the Cretaceous-Tertiary (K-T) boundary, reinforcing previous molecular studies that rejected the derivation of modern birds from transitional shorebirds. Our mean estimate for the origin of modern birds at about 123 million years ago (Myr ago) is quite close to recent estimates using both nuclear and mitochondrial genes, and supports theories of continental break-up as a driving force in avian diversification. Not only did many modern orders of birds originate well before the K-T boundary, but the radiation of major clades occurred over an extended period of at least 40 Myr ago, thus also falsifying Feduccia's rapid radiation scenario following a K-T bottleneck.

A reptile specimen from the Lystrosaurus Assemblage Zone of the Beaufort Group, lowermost Triassic of South Africa, represents a new procolophonoid parareptile. Sauropareion anoplus gen. et sp. nov. is identified as the sister taxon of Procolophonidae in a phylogenetic analysis of procolophonoids. Stratigraphic calibration of the most parsimonious tree reveals that four of the six procolophonoid lineages originating in the Permian Period extended into the succeeding Triassic Period. This relatively high taxic survivorship (67%) across the Permo-Triassic boundary strongly suggests that procolophonoids were little if at all affected by the mass extinction event that punctuated the end of the Palaeozoic Era (ca. 251 million years ago).

The ratites have stimulated much debate as to how such large flightless birds came to be distributed across the southern continents, and whether they are a monophyletic group or are composed of unrelated lineages that independently lost the power of flight. Hypotheses regarding the relationships among taxa differ for morphological and molecular data sets, thus hindering attempts to test whether plate tectonic events can explain ratite biogeography. Here, we present the complete mitochondrial DNA genomes of two extinct moas from New Zealand, along with those of five extant ratites (the lesser rhea, the ostrich, the great spotted kiwi, the emu and the southern cassowary and two tinamous from different genera. The non-stationary base composition in these sequences violates the assumptions of most tree-building methods. When this bias is corrected using neighbour-joining with log-determinant distances and non-homogeneous maximum likelihood, the ratites are found to be monophlyletic, with moas basal, as in morphological trees. The avian sequences also violate a molecular clock, so we applied a non-parametric rate smoothing algorithm, which minimizes ancestor-descendant local rate changes, to date nodes in the tree. Using this method, most of the major ratite lineages fit the vicariance biogeography hypothesis, the exceptions being the ostrich and the kiwi, which require dispersal to explain their present distribution.