Inferring Taxonomic Affinities and Genetic Distances Using Morphological Features Extracted from Specimen Images: A Case Study with a Bivalve Data Set.

Reconstructing the tree of life and understanding the relationships of taxa are core questions in evolutionary and systematic biology. The main advances in this field in the last decades were derived from molecular phylogenetics; however, for most species, molecular data are not available. Here, we explore the applicability of 2 deep learning methods-supervised classification approaches and unsupervised similarity learning-to infer organism relationships from specimen images.

Early Oligocene kelp holdfasts and stepwise evolution of the kelp ecosystem in the North Pacific.

Kelp forests are highly productive and economically important ecosystems worldwide, especially in the North Pacific Ocean. However, current hypotheses for their evolutionary origins are reliant on a scant fossil record. Here, we report fossil hapteral kelp holdfasts from western Washington State, USA, indicating that kelp has existed in the northeastern Pacific Ocean since the earliest Oligocene.

Resource partitioning among brachiopods and bivalves at ancient hydrocarbon seeps: A hypothesis.

Brachiopods were thought to have dominated deep-sea hydrothermal vents and hydrocarbon seeps for most of the Paleozoic and Mesozoic, and were believed to have been outcompeted and replaced by chemosymbiotic bivalves during the Late Cretaceous. But recent findings of bivalve-rich seep deposits of Paleozoic and Mesozoic age have questioned this paradigm. By tabulating the generic diversity of the dominant brachiopod and bivalve clades-dimerelloid brachiopods and chemosymbiotic bivalves-from hydrocarbon seeps through the Phanerozoic, we show that their evolutionary trajectories are largely unrelated to one another, indicating that they have not been competing for the same resources.

A biogeographic network reveals evolutionary links between deep-sea hydrothermal vent and methane seep faunas.

Deep-sea hydrothermal vents and methane seeps are inhabited by members of the same higher taxa but share few species, thus scientists have long sought habitats or regions of intermediate character that would facilitate connectivity among these habitats. Here, a network analysis of 79 vent, seep, and whale-fall communities with 121 genus-level taxa identified sedimented vents as a main intermediate link between the two types of ecosystems. Sedimented vents share hot, metal-rich fluids with mid-ocean ridge-type vents and soft sediment with seeps.

Effects of sample storage and shell orientation on LA-ICPMS trace element measurements on deep-sea mussels.

Geochemical markers are being increasingly applied to fundamental questions in population and community ecology in marine habitats because they allow inferences on individuals dispersal, but vital effects, small sample size and instrumental limitation are still challenging particularly in deep-sea studies. Here we use shells of the deep-sea bivalve Idas modiolaeformis to assess potential effects of sample storage, mineralogy, and valve orientation on LA-ICPMS measurements. Trace element concentrations of (24)Mg, (43)Ca, (88)Sr, (137)Ba, (208)Pb, and (238)U are not affected by the two most commonly used storage methods of biologic deep-sea samples (frozen at -20°C and fixed in 95% ethanol); thus combined analysis of differently preserved specimens is possible when the number of individuals is insufficient and distinct sample fixation is needed for multiple purposes.

Cenozoic Methane-Seep Faunas of the Caribbean Region.

We report new examples of Cenozoic cold-seep communities from Colombia, Cuba, the Dominican Republic, Trinidad, and Venezuela, and attempt to improve the stratigraphic dating of Cenozoic Caribbean seep communities using strontium isotope stratigraphy. Two seep faunas are distinguished in Barbados: the late Eocene mudstone-hosted 'Joes River fauna' consists mainly of large lucinid bivalves and tall abyssochrysoid gastropods, and the early Miocene carbonate-hosted 'Bath Cliffs fauna' containing the vesicomyid Pleurophopsis, the mytilid Bathymodiolus and small gastropods. Two new Oligocene seep communities from the Sinú River basin in Colombia consist of lucinid bivalves including Elongatolucina, thyasirid and solemyid bivalves, and Pleurophopsis.

Did shifting seawater sulfate concentrations drive the evolution of deep-sea methane-seep ecosystems?

The origin and evolution of the faunas inhabiting deep-sea hydrothermal vents and methane seeps have been debated for decades. These faunas rely on a local source of sulfide and other reduced chemicals for nutrition, which spawned the hypothesis that their evolutionary history is independent from that of photosynthesis-based food chains and instead driven by extinction events caused by deep-sea anoxia. Here I use the fossil record of seep molluscs to show that trends in body size, relative abundance and epifaunal/infaunal ratios track current estimates of seawater sulfate concentrations through the last 150 Myr.

The paleoecology, habitats, and stratigraphic range of the enigmatic cretaceous brachiopod peregrinella.

Modern and Cenozoic deep-sea hydrothermal-vent and methane-seep communities are dominated by large tubeworms, bivalves and gastropods. In contrast, many Early Cretaceous seep communities were dominated by the largest Mesozoic rhynchonellid brachiopod, the dimerelloid Peregrinella, the paleoecologic and evolutionary traits of which are still poorly understood. We investigated the nature of Peregrinella based on 11 occurrences world wide and a literature survey.

Mollusks from late Mesozoic seep deposits, chiefly in California.

Twenty-nine mollusk species from Late Jurassic to Eocene hydrocarbon seep deposits from California (USA), Japan, New Zealand, and Barbados are described and illustrated. Twenty species belong to Gastropoda and nine to Bivalvia. Seven new species, three new genera, and one new family are introduced.

First glimpse into Lower Jurassic deep-sea biodiversity: in situ diversification and resilience against extinction.

Owing to the assumed lack of deep-sea macrofossils older than the Late Cretaceous, very little is known about the geological history of deep-sea communities, and most inference-based hypotheses argue for repeated recolonizations of the deep sea from shelf habitats following major palaeoceanographic perturbations. We present a fossil deep-sea assemblage of echinoderms, gastropods, brachiopods and ostracods, from the Early Jurassic of the Glasenbach Gorge, Austria, which includes the oldest known representatives of a number of extant deep-sea groups, and thus implies that in situ diversification, in contrast to immigration from shelf habitats, played a much greater role in shaping modern deep-sea biodiversity than previously thought. A comparison with coeval shelf assemblages reveals that, at least in some of the analysed groups, significantly more extant families/superfamilies have endured in the deep sea since the Early Jurassic than in the shelf seas, which suggests that deep-sea biota are more resilient against extinction than shallow-water ones.

Adaptive radiation of chemosymbiotic deep-sea mussels.

Adaptive radiations present fascinating opportunities for studying the evolutionary process. Most cases come from isolated lakes or islands, where unoccupied ecological space is filled through novel adaptations. Here, we describe an unusual example of an adaptive radiation: symbiotic mussels that colonized island-like chemosynthetic environments such as hydrothermal vents, cold seeps and sunken organic substrates on the vast deep-sea floor.

Osedax borings in fossil marine bird bones.

The bone-eating marine annelid Osedax consumes mainly whale bones on the deep-sea floor, but recent colonization experiments with cow bones and molecular age estimates suggesting a possible Cretaceous origin of Osedax indicate that this worm might be able grow on a wider range of substrates. The suggested Cretaceous origin was thought to imply that Osedax could colonize marine reptile or fish bones, but there is currently no evidence that Osedax consumes bones other than those of mammals. We provide the first evidence that Osedax was, and most likely still is, able to consume non-mammalian bones, namely bird bones.

Fossil traces of the bone-eating worm Osedax in early Oligocene whale bones.

Osedax is a recently discovered group of siboglinid annelids that consume bones on the seafloor and whose evolutionary origins have been linked with Cretaceous marine reptiles or to the post-Cretaceous rise of whales. Here we present whale bones from early Oligocene bathyal sediments exposed in Washington State, which show traces similar to those made by Osedax today. The geologic age of these trace fossils ( approximately 30 million years) coincides with the first major radiation of whales, consistent with the hypothesis of an evolutionary link between Osedax and its main food source, although older fossils should certainly be studied.

Deep-sea food bonanzas: early Cenozoic whale-fall communities resemble wood-fall rather than seep communities.

The evolutionary history of invertebrate communities utilizing whale carcasses and sunken wood in the deep-sea is explored using fossil evidence. Compared to modern whale-fall communities, the Eo-Oligocene examples lack those vent-type taxa that most heavily rely on sulphide produced by anaerobic breakdown of bone lipids, but are very similar in their trophic structure to contemporaneous wood-falls. This sheds doubt on the hypothesis that whale-falls were evolutionary stepping stones for taxa that now inhabit hydrothermal vents and seeps.

Cold-seep mollusks are older than the general marine mollusk fauna.

The origin and possible antiquity of faunas at deep-sea hydrothermal vents and seeps have been debated since their discovery. We used the fossil record of seep mollusks to show that the living seep genera have significantly longer geologic ranges than the marine mollusks in general, but have ranges similar to those of deep-sea taxa, suggesting that seep faunas may be shaped by the factors that drive the evolution of life in the deep sea in general. Our data indicate that deep-sea anoxic/dysoxic events did not affect seep faunas, casting doubt on the suggested anoxic nature and/or global extent of these events.