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On the origin of animals and placental mammals: a critique of literalist readings of the fossil record.

The fossil record is incomplete, as evidenced by the pervasive presence of ghost lineages throughout the Tree of Life. For example, across placental mammals, at least 720 Myr of basal lineages are ghost lineages, that is, lineages that have left no fossil evidence of their past history. In contrast, some studies have suggested that the fossil record is a faithful temporal archive of evolutionary history and thus the times of diversification of clades must be close to the ages of their oldest fossils. Such literalist interpretations have been contradicted by analysis of molecular datasets which, in many cases, indicate that groups including placental mammals and animals may have originated at times substantially older than their fossil records. Some of those studies have further argued that, in the case of animals and placental mammals, molecular clocks are uninformative, suffer from characteristic pathologies, and thus cannot distinguish between recent and ancient hypotheses of diversification. Here, we reexamine these two cases and show, using Bayesian model selection theory, that the explosive diversification models previously proposed for animals and placental mammals have a posterior probability of ∼0. We show the characteristic pathologies purportedly discovered do not exist, highlight errors in previous analyses, and provide advice on best practice for molecular-clock dating analysis.

Animals

Parting ways: Pan-Homo divergence revisited.

The timing of divergence between hominins and the bonobo-chimpanzee clade has been at the core of palaeoanthropological debate for over a century. The earliest molecular studies indicated divergence times ranging from 5 Ma to as recently as 1.3 Ma. This study critically reviews the trends of time estimates published between 1967 and 2023, and analyses how these are supported or rejected by the current molecular and fossil records. We compiled 202 divergence estimates and defined three distinct thresholds based on fossil evidence at 4.4 Ma (Australopithecus anamensis and Ardipithecus ramidus), 6.2 Ma (Orrorin tugenensis and Ardipithecus kadabba), and 7.2 Ma (Sahelanthropus tchadensis). We then used these thresholds to filter out molecular estimates that are too young to fit the fossil record. Overall, the data suggests a divergence event within the late Miocene, with each threshold pushing it further back, 8.63-6.38, 10.33-7.81, and 10.95-8.81 Ma, respectively. We use a quadratic regression to demonstrate that estimates have been slowly shifting from ~ 6 Ma to ~ 8.5 Ma over the past 56 years. A Bayesian meta-analysis of genomic estimates filtered by our most consensual threshold (i.e., assuming Australopithecus belongs to Hominini) indicates that the split must have occurred early in the late Miocene, most likely before 7 Ma (~ 99.5% posterior probability) with a pooled effect of 8.69-7.28 Ma. We conclude that, despite an initial bias towards younger estimates, the molecular timing for the last common ancestor (LCA) of Pan-Homo has been progressively approaching the intervals suggested by the current fossil record.

Animals

Genome Report: De novo genome assembly of the greater Bermuda land snail, Poecilozonites bermudensis (Mollusca: Gastropoda), confirms ancestral genome duplication.

Poecilozonites bermudensis, the greater Bermuda land snail, is a critically endangered species and one of only two extant members in its genus. These snails are one of Bermuda's few endemic animal clades and their rich fossil record was the basis for the punctuated equilibria model of speciation. Once thought extinct, recent conservation efforts have focused on the recovery of the species, yet no genomic information or other molecular sequences have been available to inform these initiatives. We present a high-quality, annotated genome for P. bermudensis generated using PacBio long read and Omni-C short read sequencing. The resulting assembly is approximately 1.36 Gb with a scaffold N50 of 44.t Mb and 31 chromosome-length scaffolds. Nearly 43 percent of the genome was identified as repeat content. This assembly will serve as a resource for the conservation and study of P. bermudensis, and its only close extant and also critically endangered relative, P. circumfirmatus. Additionally, this genome adds to the growing body of data needed for a more complete understanding of gastropod evolution and for evolutionary processes in general.

Annotation

Paleogenomic sex inference of mammoth remains sheds light on the anthropogenic nature of bone accumulations.

Whether large accumulations of woolly mammoth (Mammuthus primigenius) bones reflect natural mortality or deliberate human resource exploitation has long been debated, with major implications for understanding Late Pleistocene human-megafaunal interactions.1,2,3,4,5 Here, we use ancient DNA to investigate site-formation hypotheses by comparing genetic sex ratios from mammoth remains recovered in putative anthropogenic bone accumulations and from geographically dispersed, non-anthropogenic contexts. We studied genome-wide data from 521 woolly mammoths-including 100 mammoths from bone accumulation sites and 421 mammoths from natural depositional settings across Eurasia and North America-of which 448 are newly generated. Genetic sex determination reveals a striking contrast between contexts: mammoths from dispersed sites show a male bias (∼66.5%), which is consistent with the heightened vulnerability of solitary males to hazards such as natural traps, where bones are more likely to be preserved, whereas mammoths from anthropogenic bone accumulations are predominantly female (∼70%). This female bias is pervasive across multiple sites, indicating an anthropogenic origin for these accumulations as a result of Upper Paleolithic hunters preferentially exploiting female mammoths, possibly derived from herd contexts. Together, these results provide population-scale genetic evidence that highlights the central role of mammoths in the subsistence and material economies of some Paleolithic communities.

Animals

Denisovans from southwestern China and their subsistence strategies.

Growing fossil and genomic evidence has substantially advanced our understanding of Denisovans' evolutionary history1-9, yet their technological behaviours and subsistence strategies remain poorly documented. Here we present a comprehensive analysis of hominin fossils and associated archaeological remains from Bianfu Cave, Yunnan Province, southwestern China. The hominin fossils are dated to about 167-134 thousand years ago (ka), whereas the cultural sequence spanned from about 190 ka to 70 ka, representing one of the longest cultural records most parsimoniously attributed to Denisovans-identified through enamel-dentine junction morphology and palaeoproteomic analyses10. The new fossils include four teeth that expand the known dental variation of this group, two cranial fragments and a radius. Faunal and pollen records indicate a conifer-dominated forest or forest-steppe environment across Marine Isotope Stages 6 to 4. The inhabitants of Bianfu Cave practised specialized hunting of medium- to large-bodied prey and used a technological strategy characterized by expedient core reduction and tool production, alongside pervasive use of unmodified bones. This pattern suggests an adaptive system prioritizing the exploitation of object affordance over intensive tool manufacture. Bianfu Cave provides unprecedented insights into Denisovan biology, behaviour and ecology in eastern Asia and points to a substantial genetic and cultural legacy in later populations in Southeast Asia and Oceania.

Journal Article

The Continuity Trap in Data Science Health Research.

Secondary use is now the ordinary condition of data science health research rather than an exception to it. Electronic health records collected for clinical care become prediction tools and inputs for generative AI; imaging archives become foundation-model corpora; genomic datasets become resources for polygenic risk scores; and legacy biospecimens become renewable, indefinitely distributable cell lines. Governance has responded by emphasizing verifiable instruments such as provenance logs, repository approvals, broad-consent forms, data-use agreements, model cards, records of processing, and locality-preserving architectures. These instruments are necessary, and they answer real questions about lineage, privacy, institutional responsibility, and accountability, but they are not sufficient to establish that a present use remains ethically justified. We define ethical continuity as the persistence of normatively relevant relationships between the original conditions of data generation or material collection and subsequent downstream uses, such that current uses remain justifiable in light of the expectations, permissions, meanings, and relational obligations present at entrustment. We then define the Continuity Trap as a review-stage governance error in which a salient signal of continuity in one domain is treated as sufficient evidence of ethical continuity overall, causing inquiry into the remaining domains to close prematurely. The trap is not ordinary noncompliance, ethics creep, or a demand for universal rereview; it is a cross-domain inference error that can arise even in careful, good-faith review. We distinguish it from proxy closure, of which it is a continuity-specific subtype, and from Goodhart's and Campbell's laws, which describe how measures degrade once they become targets. We operationalize ethical continuity across 4 domains: provenance, semantics, authorization, and relational standing, developed in our Representational Veracity framework, and we show that these domains can diverge as data are linked, transformed, modeled, and redeployed. We identify the institutional mechanisms-provenance privilege, descriptor sedimentation, authorization fossilization, and community effacement-that cause auditable signals to be overread, and we examine how the US Health Insurance Portability and Accountability Act (HIPAA) of 1996, the General Data Protection Regulation, the European Health Data Space, US Food and Drug Administration guidance, the US National Institute of Standards and Technology (NIST) AI Risk Management Framework, and federated-learning governance can reduce risk while still inducing continuity traps. We apply the framework to consent and nonconsent settings, including public health, immunization, syndromic, and wastewater surveillance, polygenic risk scores, induced pluripotent stem cells, federated learning, and health-related large language models. The policy implication is trigger-based continuity review: rather than rereviewing every reuse, investigators and reviewers should identify the weakest continuity domain at the present data stage and impose a domain-matched safeguard, recorded in a short continuity statement. This reframing is intended for the committees, repositories, funders, and governance bodies that decide whether reuse may proceed, and it matters most in cross-border and low-resource settings. Provenance should begin ethical review; it should not end it.

Data Science

Advancing responsible genomic analyses of ancient mollusc shells.

The analysis of the DNA entrapped in ancient shells of molluscs has the potential to shed light on the evolution and ecology of this very diverse phylum. Ancient genomics could help reconstruct the responses of molluscs to past climate change, pollution, and human subsistence practices at unprecedented temporal resolutions. Applications are however still in their infancy, partly due to our limited knowledge of DNA preservation in calcium carbonate shells and the need for optimized methods for responsible genomic data generation. To improve ancient shell genomic analyses, we applied high-throughput DNA sequencing to 27 Mytilus mussel shells dated to ~111-6500 years Before Present, and investigated the impact, on DNA recovery, of shell imaging, DNA extraction protocols and shell sub-sampling strategies. First, we detected no quantitative or qualitative deleterious effect of micro-computed tomography for recording shell 3D morphological information prior to sub-sampling. Then, we showed that double-digestion and bleach treatment of shell powder prior to silica-based DNA extraction improves shell DNA recovery, also suggesting that DNA is protected in preservation niches within ancient shells. Finally, all layers that compose Mytilus shells, i.e., the nacreous (aragonite) and prismatic (calcite) carbonate layers, with or without the outer organic layer (periostracum) proved to be valuable DNA reservoirs, with aragonite appearing as the best substrate for genomic analyses. Our work contributes to the understanding of long-term molecular preservation in biominerals and we anticipate that resulting recommendations will be helpful for future efficient and responsible genomic analyses of ancient mollusc shells.

Animals