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At least 19 recordsLinked to original sources

bioRxiv2023

AI in Paleontology

Accumulating data have led to the emergence of data-driven paleontological studies, which reveal an unprecedented picture of evolutionary history. However, the fast-growing quantity and complication of data modalities make data processing laborious and inconsistent, while also lacking clear benchmarks to evaluate data collection and generation, and the performances of different methods on similar tasks. Recently, Artificial Intelligence (AI) is widely practiced across scientific disciplines, but has not become mainstream in paleontology where manual workflows are still typical. In this study, we review more than 70 paleontological AI studies since the 1980s, covering major tasks including micro-and macrofossil classification, image segmentation, and prediction. These studies feature a wide range of techniques such as Knowledge Based Systems (KBS), neural networks, transfer learning, and many other machine learning methods to automate a variety of paleontological research workflows. Here, we discuss their methods, datasets, and performance and compare them with more conventional AI studies. We attribute the recent increase in paleontological AI studies to the lowering bar in training and deployment of AI models rather than real progress. We also present recently developed AI implementations such as diffusion model content generation and Large Language Models (LLMs) to speculate how these approaches may interface with paleontological research. Even though AI has not yet flourished in paleontological research, successful implementation of AI is growing and show promise for transformative effect on the workflow in paleontological research in the years to come. HighlightsO_LIFirst systematic review of AI applications in paleontology. C_LIO_LIThere is a 10 to 20-year gap between AI in paleontology and mainstream studies. C_LIO_LIRecent progress in paleontological AI studies is likely a result of lowering bar in training and deployment. C_LIO_LIFuture direction discussed for interactions between paleontology and AI. C_LI

paleontology↗

bioRxiv2020

Modern, archaeological, and paleontological DNA analysis of a human-harvested marine gastropod (Strombus pugilis) from Caribbean Panama

Although protocols exist for the recovery of ancient DNA from land snail and marine bivalve shells, marine conch shells have yet to be studied from a paleogenomic perspective. We first present reference assemblies for both a 623.7 Mbp nuclear genome and a 15.4 kbp mitochondrial genome for Strombus pugilis, the West Indian fighting conch. We next detail a method to extract and sequence DNA from conch shells and apply it to conch from Bocas del Toro, Panama across three time periods: recently-eaten and discarded (n=3), Late Holocene (984-1258 BP) archaeological midden (n=5), and a mid-Holocene (5711-7187 BP) paleontological fossil coral reef (n=5). These results are compared to control DNA extracted from live-caught tissue and fresh shells (n=5). Using high-throughput sequencing, we were able to obtain S. pugilis nuclear sequence reads from shells across all age periods: up to 92.5 thousand filtered reads per sample in live-caught shell material, 4.57 thousand for modern discarded shells, 12.1 thousand reads for archaeological shells, and 114 reads in paleontological shells. We confirmed authenticity of the ancient DNA recovered from the archaeological and paleontological shells based on 5.7x higher average frequency of deamination-driven misincorporations and 15% shorter average read lengths compared to the modern shells. Reads also mapped to the S. pugilis mitochondrial genome for all but the paleontological shells, with consistent ratios of mitochondrial to nuclear mapped reads across sample types. Our methods can be applied to diverse archaeological sites to facilitate reconstructions of the long-term impacts of human behavior on mollusc evolutionary biology.

evolutionary biology↗

bioRxiv2019

Death is on Our Side: Paleontological Data Drastically Modify Phylogenetic Hypotheses

Fossils are the only remaining evidence of the majority of species that have ever existed, providing a direct window into events in evolutionary history that shaped the diversification of life on Earth. Phylogenies underpin our ability to make sense of evolution but are routinely inferred only from data available from living organisms. Although extinct taxa have been shown to add crucial information for inferring macroevolutionary patterns and processes including ancestral states, paleobiogeography and diversification dynamics, the role that fossils play in inferring the tree of life itself is controversial. Since the early years of phylogenetic systematics, different studies have dismissed the impact of fossils due to their incompleteness, championed their ability to overturn phylogenetic hypotheses or concluded that their behavior is indistinguishable from that of extant taxa. Here we show paleontological data has a remarkable effect in phylogenetic inference. Fossils often have higher levels of topological influence than extant taxa, while inducing unique topological rearrangements. Previous studies have proposed a suite of explanations for the topological behavior of fossils, such as their retention of unique morphologies or their ability to break long branches. We develop predictive models that demonstrate that the possession of distinctive character state combinations is the primary predictor of the degree of induced topological change, and that the relative impact of taxa (fossil and extant) can be predicted to some extent before any analysis. Our results bolster the consensus of recent empirical studies by showing the unique role of paleontological data in phylogenetic inference, and provide the first quantitative assessment of its determinants, with broad consequences for the design of taxon sampling in both morphological and total-evidence analyses.

evolutionary biology↗

bioRxiv2023

Low-invasive sampling method for taxonomic for the identification of archaeological and paleontological bones by proteomics of their collagens

Collagen from paleontological bones is an important organic material for isotopic measurement, radiocarbon and paleoproteomic analyzes, to provide information on diet, dating and taxonomy. Current paleoproteomics methods are destructive and require from a few milligrams to several tenths of milligrams of bone for analysis. In many cultures, bones are raw materials for artefact which are conserved in museum which hampers to damage these precious objects during sampling. Here, we describe a low-invasive sampling method that identifies collagen, taxonomy and post-translational modifications from Holocene and Upper Pleistocene bones dated to 130,000 and 150 BC using dermatological skin tape-discs for sampling. The sampled bone micro-powders were digested following our highly optimized eFASP protocol, then analyzed by MALDI FTICR MS and LC-MS/MS for identifying the genus taxa of the bones. We show that this low-invasive sampling does not deteriorate the bones and achieves results similar to those obtained by more destructive sampling. Moreover, this sampling method can be performed at archaeological sites or in museums.

paleontology↗

bioRxiv2024

Resolving the "Ontogeny Problem" in Vertebrate Paleontology

Ontogenetic change is a major source of phenotypic variation among members of a species and is often of greater magnitude than the anatomical differences that distinguish closely related species. Ontogeny has therefore become a problematic confounding variable in vertebrate paleontology, especially in study systems distant from extant crown clades, rendering taxonomic hypothesis testing (a fundamental process in evolutionary biology) rife with difficulty. Paleontologists have adopted quantitative methods to compensate for the perception that juvenile specimens lack diagnostic apomorphies seen in their adult conspecifics. Here, I critically evaluate these methods and the assumptions that guide their interpretation using a {micro}CT dataset comprising growth series of American and Chinese alligator. I find that several widespread assumptions are scientifically unjustifiable, and that two popular methods - geometric morphometrics and cladistic analysis of ontogeny - have unacceptably high rates of type II error and present numerous procedural difficulties. However, I also identify a suite of ontogenetically invariant characters that differentiate the living species of Alligator throughout ontogeny. These characters overwhelmingly correspond to anatomical systems that develop prior to (and play a signaling role in) the development of the cranial skeleton itself, suggesting that their ontogenetic invariance is a consequence of the widely conserved vertebrate developmental program. These observations suggest that the architecture of the cranium is fixed early in embryonic development, and that ontogenetic remodeling does not alter the topological relationships of the cranial bones or the soft tissue structures they house. I propose a general model for future taxonomic hypothesis tests in the fossil record, in which the hypothesis that two specimens different ontogenetic stages of a single species can be falsified by the discovery of character differences that cannot be attributed plausibly to ontogenetic variation.

paleontology↗

bioRxiv2025

Ancient DNA Reveals Hominoid Evolution: Intermediate DNA Sequences and Advances in Molecular Paleontology

AbstractFossils and ancient crude pottery vessels function as physical "DNA containers," preserving oriDNA (original, in situ DNA) and accumulating eDNA (environmental DNA) over time. Ancient DNA (aDNA) serves as molecular fossils, chronicling evolutionaryhistory. Using "nano-affinitybead technology", we extracted and sequenced DNAfrom Lycoptera fossils in the Jehol region and a "round-bellied jar (Jar)" from the Erlitou period in Guangwu Town, yielding 236,545 primate sequences from the fossils and 86,908 from the pottery. We observed that the AFF value of DNA sequences negatively corre lates with species divergence time1, offering a quantitative measure of DNA preservation and host divergence. Some fragments distinct from modern genomic sequences, termed "intermediate DNAsequences" (IDS), have been identified. Many IDS exhibit an upper age limit, preserving characteristics of the last common ancestor (LCA) of the Hominidae and offering molecular insights into "Darwins puzzle". Among IDS, the SRRA subtype (Sequence Reversal and Rearrangement), identified in mRNA-coding exonic sequences, arises from the incorporation of a complementary antisense strand upstream of the sense strand, either adjacent to it or separated bya sequence interval. This introduces a novel post-transcriptional regulatory mechanism at the mRNA level, driven by SRRA, which presets hairpin structures and Indels in the UTR or CDS of exonic sequences, modulating gene variation. We propose: "SRRAs played a critical trial-and-error role in early Hominidae evolution, facilitating adaptive genomic changes, with some SRRA sequences later excised from exons", positioning SRRAas an evolutionary "genetic switch". Additionally, seven species -specific fragments (SSFs) of non-human primates (NHPs) linked to Asian Homo erectus were identified in the fossils, and pottery DNA reveale d sequences from tropical species (e.g., zebrass, oil palms), providing evidence of climate-driven local extinction and supporting paleo-ecological and paleo-environmental reconstruction. This method of analyzing aDNA from non-skeletal materials opens new avenues in paleontology, archaeology, and geology, guiding the tracing of ancient migration patterns and fossil searches. DNAfragments preserved within "DNA containers " exhibit an "old-few, new-many" turnover pattern, with many aDNA fragments displaying non-deamination. This evidence challenges prevailing perspectives, the authenticity criteria for aDNA, and the capabilities and scope of the traditional research method, necessitating a thorough reevaluation of the relevant knowledge framework. Furthermore, this study opens new opportunities for frontier research.

paleontology↗

bioRxiv2022

Trait-based paleontological niche prediction demonstrates deep time parallel ecological occupation in specialized ant predators

Understanding the paleoecology of species is fundamental to reconstructions of paleoecological communities, analyses of changing paleoenvironments, and the evolutionary history of many lineages. One method of establishing paleoecology is through comparing the morphology of extant analogs to extinct species; this method has been applied to many vertebrate groups using predictive linear models, but has been rarely applied using invertebrate taxa or non-linear frameworks. The ant fossil record, which frequently preserves specimens in three-dimensional fidelity, chronicles putative faunal turnover during the Late Cretaceous and into Cenozoic. The earliest fossil species comprise enigmatic stem-groups that underwent extinction concomitant with crown ant diversification. Here, we apply a wide-ranging extant ecomorphological dataset to demonstrate the utility of Random Forest machine learning classification in predicting the ecology of stem-group "hell ants". We reconstruct a predicted ecomorphological assemblage of this phenotypically aberrant group of extinct ants, and compare predicted hell ant ecologies to the ecological occupations of their closest living analogs, lineages of solitary predators with highly specialized mandibular morphology. In contrast to previous hypotheses, we find that hell ants were primarily leaf litter or ground-nesting and foraging taxa, and that the ecological breadth of this unusual lineage mirrored that of living groups. Results suggest ecological coherence between the Mesozoic and modern communities, even as the earliest occupants of predatory niches were phylogenetically and morphologically distinct.

ecology↗

bioRxiv2023

When paleontology meets genomics: complete mitochondrial genomes of two saber-toothed cats' species (Felidae: Machairodontinae)

Within the Machairodontinae subfamily, commonly referred as saber-toothed cats, it is worth noting that only two species, namely Homotherium latidens, recognized as the scimitar-toothed cat, and Smilodon populator, renowned as the saber-toothed tiger, possess partial mitochondrial genomes accessible in the NCBI database. These sequences, however, do not include the mitogenome control region (D-loop) and have several gaps in their genes, including protein-coding genes (PCGs) that are widely used in phylogenetic analysis. In this study, we aimed to obtain a complete assembly of the mitogenomes of these two species from next-generation sequencing data available at NCBIs SRA. The de novo assemblies showed complete mitogenomes with 17,323bp (H. latidens) and 16,769 bp (S. populator), both with 13 PCGs, 22tRNAs, two rRNAs and the D-loop (Control region), with all genes following the standard order and position of most vertebrate mitogenomes. Our phylogeny and molecular dating, despite being generally very similar to previous studies, reveals an earliest divergence between North American and North Sea H. latidens specimens which may be related to an Early Pleistocene migration across Beringia.

genomics↗

bioRxiv2025

PAMPA: a software for peptide markers and taxonomic identification for ZooMS samples in Archaeology and Paleontology

ZooMS (Zooarchaeology by Mass Spectrometry) offers a rapid and cost-effective method for species identification of animal remains through peptide mass fingerprinting. After mass spectrum generation, a mostly used way to perform taxonomic identification is to compare the mass fingerprints to a reference database of diagnostic peptide markers to determine the species of origin. This analytical stage, however, is tedious and error-prone, often necessitating manual examination of spectra. In this paper, we present a comprehensive approach to automate and standardize the usage of peptide markers and the classification of ZooMS spectra. We have developed a software called PAMPA (Protein Analysis by Mass Spectrometry for Ancient Species), for which we demonstrate the effectiveness using a variety of spectral data from bone samples generated by MALDI-TOF and MALDI-FTICR. PAMPA is open-source and comes with a database of peptide markers and collection of curated COL1A1 and COL1A2 sequences. We believe it will be a valuable resource for the scientific community.

bioinformatics↗

bioRxiv2022

Metagenomic analysis of coprolites from three Late Pleistocene megaherbivores from the Southwestern United States.

1.BackgroundDetermining the life-history traits of extinct species is often difficult from skeletal remains alone, limiting the accuracy of studies modeling past ecosystems. However, the analysis of the degraded endogenous bacterial DNA present in paleontological fecal matter (coprolites) may enable the characterization of specific traits such as the hosts digestive physiology and diet. An issue when evaluating the microbial composition of coprolites is the degree to which the microbiome is representative of the hosts original gut community versus the changes that occur in the weeks following deposition due to desiccation. Analyses of paleontological microorganisms are also relevant in the light of recent studies linking the Late Pleistocene and Early Holocene extinctions with modern-day zoonotic pathogen outbreaks. MethodsShotgun sequencing was performed on ancient DNA (aDNA) extracted from coprolites of the Columbian mammoth (Mammuthus Columbi), Shasta ground sloth (Nothrotheriops shastensis) and paleontological bison (Bison sp.) collected from caves on the Colorado Plateau, Southwestern USA. The novel metagenomic classifier MTSv, parameterized for studies of aDNA, was used to assign bacterial taxa to sequencing reads. The resulting bacterial community of coprolites was then compared to those from modern fecal specimens of the African savannah elephant (Loxodonta africana), the brown-throated sloth (Bradypus variegatus) and the modern bison (Bison bison). Both paleontological and modern bison fecal bacterial communities were also compared to those of progressively dried cattle feces to determine whether endogenous DNA from coprolites had a microbiome signal skewed towards aerobic microorganisms typical of desiccated fecal matter. ResultsThe diversity of phyla identified from coprolites was lower than modern specimens. The relative abundance of Actinobacteria was increased in coprolites compared to modern specimens, with fewer Bacteroidetes and Euryarchaeota. Firmicutes had a reduced relative abundance in the mammoth and bison coprolites, compared to the African savanna elephants and modern bison. There was a significant separation of samples in NMDS plots based on their classification as either paleontological or modern, and to a lesser extent, based on the host species. Increasingly dried cattle feces formed a continuum between the modern and paleontological bison samples. ConclusionOur results reveal that any coprolite metagenomes should always be compared to desiccated modern fecal samples from closely related hosts fed a comparable diet to determine the degree to which the coprolite metagenome is a result of desiccation versus true dissimilarities between the modern and paleontological hosts. Also, a large-scale desiccation study including a variety of modern species may shed light on life-history traits of extinct species without close extant relatives, by establishing the proximity of coprolite metagenomes with those from dried modern samples.

paleontology↗

bioRxiv2026

It runs in the family: New extinct species from charismatic clades are more likely to be published in high-impact journals than those from non-charismatic clades

The cultural landscape of paleontology is dominated by dinosaurs and a few other charismatic clades that are more likely to be depicted in media and to be recognized by the public. There is a prevailing belief among researchers that these biases extend to scholarly publishing - that certain clades enjoy a 'taxonomic advantage' that renders them more likely to be published in high-impact journals like Nature and Science. Given the importance of publishing in high-impact journals for career advancement, quantitative testing of this hypothesis can inform on potential biases in this area. I examined articles describing new species that were published between 2000 and mid-2026 in one of thirteen journals (n = 4,248 articles, 8,331 new species), ranging from high-profile, multidisciplinary titles like Nature to lower-profile, specialist titles like the Journal of Paleontology. Comparisons of the taxonomic composition of new species between journals revealed a positive correlation between a journal's prestige (approximated by its impact factor) and the relative proportion of new species that belong to charismatic clades. Avemetatarsalians and mammaliamorphs represent more than 50% of new species in Nature and Science but less than 15% of new species in the control group of paleontological journals. These results provide support for the perception that there is a bias between extinct taxa as it relates to publication in high-impact journals. Given the potential for researchers to accrue cumulative advantage through publishing in prestigious journals, bias in favor of charismatic clades creates the potential for opportunities and knowledge generation to become increasingly skewed and consolidated towards these clades, at the expense of less charismatic clades and the people studying them. This threatens the discipline's ability to continue to construct a holistic understanding of the full history of life that can be disseminated to the public. Further attention should be directed towards examining potential biases in paleontological publications as the primary currency in academia.

scientific communication and education↗

bioRxiv2020

Authentic field experiences for STEM teachers: Collecting Florida fossils

The extensive sedimentary sequence of Florida preserves evidence of prehistoric life spanning some 40 million years into the past. This paper describes the results of a three-pronged professional development (PD) program conducted in November 2019 in which Florida teachers from eight counties gained knowledge and experience about the process and content of paleontology at an active field research site in northern Florida. Working alongside scientists, 15 elementary, middle, and high school teachers collected 5-million-year-old fossil vertebrates and made scientifically important discoveries that advance understanding of Floridas prehistoric life. The PD included three components: (1) a pre-trip webinar; (2) a morning tour of our museum exhibits to scaffold teachers understanding of the kinds of fossils they would find; and (3) the actual day-long field experience collecting fossils. A post-PD evaluation revealed gains in knowledge about, and experience with, fossils and paleontology. We also found that overall satisfaction with the PD underscored the importance of each of the three components supporting one-another--resulting in a more informative and rewarding learning experience for the participants. Fossils and the science of paleontology are a gateway for STEM learning and this subject and its extensions are applicable to existing standards in earth and life sciences at many grade levels.

scientific communication and education↗

bioRxiv2025

Addressing the open world: detecting and segmenting pollen on palynological slides with deep learning

In the "open world", categorical classes are imbalanced, test classes are not known a priori, and test data are captured across different domains. Paleontological data can be described as open-world, as specimens may include new, unknown taxa, and the data collected, such as measurements or images, may not be standardized across different studies. Fossil pollen analysis is one example of an open-world problem in paleontology. Pollen samples capture large numbers of specimens, including not only common types but also rare and even novel taxa. Pollen is diverse morphologically and features can be altered during fossilization. Additionally, there is little standardization in the methods used to capture and catalog pollen images and most collections are mounted on microscope slides. Therefore, generalized workflows for automated pollen analysis require techniques that are robust to these differences and can work with microscope images. We focus on a critical first step, the detection of pollen specimens on a palynological slide and review how existing methods can be employed to build robust and generalizable analysis pipelines. First, we demonstrate how a mixture-of-experts approach - the fusion of a general pollen detector with an expert model trained on minority classes - can be used to address taxonomic biases in detections, particularly the missed detections of rarer pollen types. Second, we demonstrate the efficiency of domain fine-tuning in addressing domain gaps - differences in image magnification and resolution across microscopes, and of taxa across different sample sources. Third, we demonstrate the importance of continual learning workflows, which integrate expert feedback, in training detection models from incomplete data. Finally, we demonstrate how cutting-edge segmentation models can be used to refine and clean detections for downstream deep learning classification models. Non-technical AbstractFossil pollen analysis presents challenges that result from the complexity of the "open world". It is not possible to anticipate all the taxa that will be encountered in geologic samples. Each sample has the potential to produce new species and introduce specimens with unique shapes and sizes. Pollen embodies diverse morphologies, its appearance can be altered depending on the conditions under which it was fossilized, and there is little standardization in the microscopy equipment used to image and catalog pollen images. AI applications in palynology need to address this complexity. We applied four machine learning methods (mixture-of-expert models, domain fine-tuning, continual learning, and foundation models for segmentation) to fossil pollen data to demonstrate their effectiveness in the detection and isolation of pollen specimens on a pollen sample slide.

paleontology↗

bioRxiv2025

Archaeological Bone Assemblages Trace Changes in Turtle and Tortoise Diversity in Continental Southeast Asia

Among tropical regions, continental Southeast Asia is a major hotspot of biodiversity. However, due to rapid urban expansion and severe deforestation, this area is recognized as one of the top global conservation priorities. As in other tropical regions, the prevailing idea is that the decline of local biodiversity in this region is a direct result of the overwhelming environmental changes that have occurred over the last 80 years. However, paleoecological data indicate that tropical forests have been exploited by human populations since at least the Late Pleistocene, and forest clearance for farming began several thousand years ago. To gain a complete overview of the long-term evolution of vertebrate fauna in continental Southeast Asia, it is necessary to investigate the past. This task is currently out of reach, mainly due to the lack of paleontological and historical studies regarding small animals, including emblematic taxa like turtles. Indeed, although some evidence suggests that the biodiversity of turtles in continental Southeast Asia may have changed over the last millennia, the paucity of historical records and archaeological assemblages studies currently precludes further assessment of the potential effect of past environmental changes, including potential human disturbances. The present study consists of a paleontological analysis of turtle bone assemblages collected from four prehistoric sites in Thailand and Cambodia. The aim is to test the hypothesis of changes in turtle biodiversity over the last 10,000 years. Our results indicate that turtle assemblages in most areas have experienced only limited changes across the Holocene, except for Laang Spean in Cambodia. However, a few rare taxa may represent extirpated or extinct species of Testudinidae in continental Southeast Asia at an unknown time during the Holocene. We also observed significant changes in the geographic distribution of some genera, such as Batagur, Cyclemys, and Amyda. The fact that turtle fauna has been rather resilient and unchanged for several millennia shows that past human impact in most investigated areas had limited effects on these taxa. The strong modifications observed in Cambodia could, however, serve as a warning about the potential fate of turtle biodiversity in this region if further loss of natural environments occurs.

paleontology↗

bioRxiv2021

Functional divergence and spectral tuning of microbial rhodopsins from an ancestral proton pump

For billions of years, life has continuously adapted to dynamic physical conditions near the Earths surface. Fossils and other preserved biosignatures in the paleontological record are the most direct evidence for reconstructing the broad historical contours of this adaptive interplay. However, biosignatures dating to Earths earliest history are exceedingly rare. Here, we combine phylogenetic inference of primordial rhodopsin proteins with modeled spectral features of the Precambrian Earth environment to reconstruct the paleobiological history of this essential family of photoactive transmembrane proteins. Our results suggest that ancestral microbial rhodopsins likely acted as light-driven proton pumps and were spectrally tuned toward the absorption of green light, which would have enabled their hosts to occupy depths in a water column or biofilm where UV wavelengths were attenuated. Subsequent diversification of rhodopsin functions and peak absorption frequencies was enabled by the expansion of surface ecological niches induced by the accumulation of atmospheric oxygen. Inferred ancestors retain distinct associations between extant functions and peak absorption frequencies. Our findings suggest that novel information encoded by biomolecules can be used as "paleosensors" for conditions of ancient, inhabited niches of host organisms not represented elsewhere in the paleontological record. The coupling of functional diversification and spectral tuning of this taxonomically diverse protein family underscores the utility of rhodopsins as universal testbeds for inferring remotely detectable biosignatures on inhabited planetary bodies.

evolutionary biology↗

bioRxiv2021

On the reproductive mechanisms of Gram-positive protocells

Prokaryotes are hypothesized to have evolved from more primitive protocells. Unlike present-day cells, protocells are thought to have been devoid of complex molecular biological processes. They are believed to have mediated reproduction entirely by biophysical forces under favorable environmental conditions. Despite this proposition, little is known about the actual mechanism of their reproduction. To understand the reproduction process of protocells in their native habitat, here we used a top-down approach to transform bacterial cells into a primitive lipid vesicle-like state. Given that environmental conditions are thought to have played an essential role in mediating protocell reproduction, we then studied these cells under the presumed environmental conditions of Archaean Eon Earth. Even in the absence of functioning biological processes, cells in our study reproduced in a defined sequence of steps, always leading to the formation of viable daughter cells. Their reproduction mechanism can be explained by the interaction between intracellular metabolism, physicochemical properties of cell constituents, and, most importantly, environmental conditions. Given the simplicity of this reproduction mechanism and its suitability to environmental conditions of early Earth, we propose that protocells reproduced by this process. Moreover, this method of reproduction is also in tune with the earlier theoretical propositions on protocells, the results of the top- down approach of building a minimal cell, and the paleontological record of the Achaean Eon. Our study is the first to bridge the gap between non-living systems like lipid vesicles, living cells, and the paleontology of the Archaean Eon.

biophysics↗

bioRxiv2022

How Important is Budding Speciation for Comparative Studies?

The acknowledgment of evolutionary dependence among species has fundamentally changed how we ask biological questions. Phylogenetic models became the standard approach for studies with three or more lineages, in particular those using extant species. Most phylogenetic comparative methods (PCMs) translate relatedness into covariance, meaning that evolutionary changes before lineages split should be interpreted together whereas after the split lineages are expected to change independently. This clever realization has shaped decades of research. Here we discuss one element of the comparative method often ignored or assumed as unimportant: if nodes of a phylogeny represent the dissolution of the ancestral lineage into two new ones or if the ancestral lineage can survive speciation events (i.e., budding). Budding speciation is often reported in paleontological studies, due to the nature of the evidence for budding in the fossil record, but it is surprisingly absent in comparative methods. Here we show that many PCMs assume that divergence happens as a symmetric split, even if these methods dont explicitly mention this assumption. We discuss the properties of trait evolution models for continuous and discrete traits and their adequacy under a scenario of budding speciation. We discuss the effects of budding speciation under a series of plausible evolutionary scenarios and show when and how these can influence our estimates. We also propose that long-lived lineages that have survived through a series of budding speciation events and given birth to multiple new lineages can produce evolutionary patterns that challenge our intuition about the most parsimonious history of trait changes in a clade. We hope our discussion can help bridge comparative approaches in paleontology and neontology as well as foster awareness about the assumptions we make when we use phylogenetic trees.

evolutionary biology↗

bioRxiv2022

Assessing the utility of death assemblages as reference conditions in a common benthic index (M-AMBI) with simulations

Incorporating paleontological data into the methods and formats already familiar to conservation practitioners may facilitate greater use of paleontological data in conservation practice. Benthic indices (e.g., Multivariate - AZTI Marine Biotic Index; M-AMBI) already incorporate reference conditions and are a good candidate for integration. In simulations of living communities under constant and changing environmental conditions, we evaluate the capacity of death assemblage reference conditions to replicate M-AMBI values when used in place of reference conditions from the final ten generations of the simulation or all five hundred simulated generations. Reference conditions from all death assemblage scenarios successfully replicated correct remediation decisions in the majority of simulation runs with environmental change and stability. Variations in M-AMBI values were due to overestimated richness and diversity in the death assemblages but effects of changes to these parameters varied across scenarios, emphasizing the importance of evaluating multiple metrics. Time averaging was largely beneficial, particularly when environmental change occurred and short-term ecological observations (ten generations) produced incorrect remediation decisions. When the duration of time averaging is known, death assemblages can provide valuable long-term perspectives with the potential to outperform temporally constrained baseline information from monitoring the living community. Supplementary materialAll R code used to produce the simulation, analyze outputs, and create figures is available at: https://doi.org/10.5281/zenodo.6355921. The simulated data is also available at this location. Supplementary figures and analyses referred to in the text are available at the end of this document.

ecology↗