Search for: All records

The field of ichnology has been a branch of paleontology since the mid 19th century. Vertebrate tracks are a vast dataset compared to vertebrate body fossils: an individual organism will leave only one body, but will leave many tracks and only one body to potentially be preserved. Tracks are direct records of organismal behavior and can be used as proxies for biodiversity and paleoecology. The use of anatomy-consistent morphology in ichnotaxonomy incorporates trackmaker identity by correlating the morphology of the track with that of available track-maker(s). Standard practice is to interpret ichnotaxa to a family level for trackmakers, but the Linnaean rank and cladistic status of trackmaker taxa actually varies greatly. Our work aims to harmonize the ichnological and body fossil records of early Carboniferous tetrapods to better ground trackmaker inferences. For example, the Pennsylvanian-Permian ichnogenus Limnopus is referred to eryopid temnospondyls. However, large ichnospecies (e.g., L. littoralis, L. waynesburgensis) are 200% larger than small ichnospecies (e.g., L. vagus). It has been suggested that the different ichnospecies of Limnopus represent distinct ontogenetic stages of the trackmaker, including the similar but smaller ichnogenus Batrachichnus. Of the few Carboniferous temnospondyls for which the manus and pes are both known in detail, the morphology of the large Limnopus morph is consistent with that of Eryops, but edopid trackmakers cannot be discounted. This has minimal implications for reconstructing ecosystems, given the similarities between eryopids and edopids. However, this uncertainty in the identity of the trackmaker makes the use of Limnopus as a biostratigraphic appearance datum for Eryopidae problematic. The recent consolidation of Limnopus species into the type (L. heterodactylopus) ensures greater ichnotaxonomic consistency, but weakens the track-trackmaker link. Interpretation of Carboniferous pentadactyl tracks must account for the presence of pentadactyly among multiple stem tetrapod families by the late Mississippian. Trackways and skeletal remains — specifically autopodia — are scant in the earlier Mississippian, but both hint at a reduction of pedal digit number to five by this time. The timing of manual digit reduction remains uncertain, but coexistence of a probably hexadactyl manus (Pederpes, Whatcheeriidae) with pendatactyl and tetradactyl manual prints highlights the earliest Carboniferous as a time of diversity and dynamism in early tetrapod morphology. 

Metagenomes encode an enormous diversity of proteins, reflecting a multiplicity of functions and activities. Exploration of this vast sequence space has been limited to a comparative analysis against reference microbial genomes and protein families derived from those genomes. Here, to examine the scale of yet untapped functional diversity beyond what is currently possible through the lens of reference genomes, we develop a computational approach to generate reference-free protein families from the sequence space in metagenomes. We analyze 26,931 metagenomes and identify 1.17 billion protein sequences longer than 35 amino acids with no similarity to any sequences from 102,491 reference genomes or the Pfam database. Using massively parallel graph-based clustering, we group these proteins into 106,198 novel sequence clusters with more than 100 members, doubling the number of protein families obtained from the reference genomes clustered using the same approach. We annotate these families on the basis of their taxonomic, habitat, geographical, and gene neighborhood distributions and, where sufficient sequence diversity is available, predict protein three-dimensional models, revealing novel structures. Overall, our results uncover an enormously diverse functional space, highlighting the importance of further exploring the microbial functional dark matter. 

Abstract The assembly of single-amplified genomes (SAGs) and metagenome-assembled genomes (MAGs) has led to a surge in genome-based discoveries of members affiliated with Archaea and Bacteria, bringing with it a need to develop guidelines for nomenclature of uncultivated microorganisms. The International Code of Nomenclature of Prokaryotes (ICNP) only recognizes cultures as ‘type material’, thereby preventing the naming of uncultivated organisms. In this Consensus Statement, we propose two potential paths to solve this nomenclatural conundrum. One option is the adoption of previously proposed modifications to the ICNP to recognize DNA sequences as acceptable type material; the other option creates a nomenclatural code for uncultivated Archaea and Bacteria that could eventually be merged with the ICNP in the future. Regardless of the path taken, we believe that action is needed now within the scientific community to develop consistent rules for nomenclature of uncultivated taxa in order to provide clarity and stability, and to effectively communicate microbial diversity. 

Abstract The calving of A‐68, the 5,800‐km², 1‐trillion‐ton iceberg shed from the Larsen C Ice Shelf in July 2017, is one of over 10 significant ice‐shelf loss events in the past few decades resulting from rapid warming around the Antarctic Peninsula. The rapid thinning, retreat, and collapse of ice shelves along the Antarctic Peninsula are harbingers of warming effects around the entire continent. Ice shelves cover more than 1.5 million km²and fringe 75% of Antarctica's coastline, delineating the primary connections between the Antarctic continent, the continental ice, and the Southern Ocean. Changes in Antarctic ice shelves bring dramatic and large‐scale modifications to Southern Ocean ecosystems and continental ice movements, with global‐scale implications. The thinning and rate of future ice‐shelf demise is notoriously unpredictable, but models suggest increased shelf‐melt and calving will become more common. To date, little is known about sub‐ice‐shelf ecosystems, and our understanding of ecosystem change following collapse and calving is predominantly based on responsive science once collapses have occurred. In this review, we outline what is known about (a) ice‐shelf melt, volume loss, retreat, and calving, (b) ice‐shelf‐associated ecosystems through sub‐ice, sediment‐core, and pre‐collapse and post‐collapse studies, and (c) ecological responses in pelagic, sympagic, and benthic ecosystems. We then discuss major knowledge gaps and how science might address these gaps. This article is categorized under:Climate, Ecology, and Conservation > Modeling Species and Community Interactions