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bioRxiv2022

The build-up of the present-day tropical diversity of tetrapods

The extraordinary number of species in the tropics when compared to the extra-tropics is probably the most prominent and consistent pattern in biogeography, suggesting that overarching processes regulate this diversity gradient. A major challenge to characterizing which processes are at play relies on quantifying how the frequency and determinants of tropical and extra-tropical speciation, extinction and dispersal events shaped evolutionary radiations. We address this question by developing and applying spatio-temporal phylogenetic and paleontological models of diversification for tetrapod species incorporating paleoenvironmental variation. Our phylogenetic model results show that area, energy or species richness did not uniformly affect speciation rates across tetrapods and dispute expectations of a latitudinal gradient in speciation rates. Instead, both neontological and fossil evidence coincide in underscoring the role of extra-tropical extinctions and the outflow of tropical species in shaping biodiversity. These diversification dynamics accurately predict present-day levels of species richness across latitudes and uncover temporal idiosyncrasies but spatial generality across the major tetrapod radiations.

evolutionary biology↗

bioRxiv2023

Genetic timeline of human brain and cognitive traits

Human evolution is characterised by extensive changes of body and brain, with perhaps one of the core developments being the fast increase in cranial capacity and brain volume. Paleontological records are the most direct method to study such changes, but they can unfortunately provide a limited view of how soft traits such as brain function and cognitive abilities have evolved in humans. A potential complementary approach is to identify when particular genetic variants associated with human phenotypes (such as height, body mass index, intelligence, and also disease) have emerged in the 6-7 million years since we diverged from chimpanzees. In this study, we combine data from genome-wide association studies on human brain and cognitive traits with estimates of human genome dating. We systematically analyse the temporal emergence of genetic variants associated with modern-day human brain and cognitive phenotypes over the last five million years. Our analysis provides evidence that genetic variants related to neocortex structure (e.g., area, thickness; median evolutionary age = 400,170 years old), cognition (e.g., fluid intelligence; median age = 459,465), education (median age = 637,646), and psychiatric disorders (median age = 412,639) have emerged more recently in human evolution than expected by chance. In contrast, variants related to other physical traits, such as height (median age = 811,305) and body mass index (median age = 794,265), emerged relatively later. We further show that genes containing recent evolutionary modifications (from around 54,000 to 4,000 years ago) are linked to intelligence (P = 2 x 10-6) and neocortical surface area (P = 6.7 x 10-4), and that these genes tend to be highly expressed in cortical areas involved in language and speech (pars triangularis, P = 6.2 x 10-4). Elucidating the temporal dynamics of genetic variants associated with brain and cognition is another source of evidence to advance our understanding of human evolution.

genetics↗

bioRxiv2023

Seasonal fluctuations in the bone microstructure of Sciurus vulgaris fuscoater humeri: a case study using phenomics on μCT-scans

Sciurus vulgaris Linnaeus, 1758, the red squirrel, is a small, mostly arboreally living rodent, spread across the Palearctic. It is mostly vegetarian, feeding on plants, fungi and seeds, and is less active in the winter months, but does not hibernate. In this lateral study, the humeri of the subspecies Sciurus vulgaris fuscoater, the Central European red squirrel, were analysed to uncover potential intraspecific variation between individuals found in different seasons. The {micro}CT-scans were obtained with a resolution of 26 microns. Five bone parameters were calculated and statistically evaluated with regards to seasonal variations: total volume, bone volume, endocortical surface, cortical thickness, and average trabecular thickness. Bone volume, trabecular thickness and endocortical thickness correlate with bone size, whereas cortical thickness does not. Seasonal differences were observed between the warmer summer and autumn months versus the colder winter and spring months for all parameters. We, speculatively, relate the observed seasonal variation to nutrient intake, notably calcium. These results offer a deeper understanding of intraindividual variation in red squirrels, that may be useful in further ecological, taxonomic, and paleontological research.

zoology↗

bioRxiv2023

Ecological and spatial overlap indicate interspecific competition during North American Canid radiation

Understanding biodiversity patterns and the processes that generate them are key goals in ecology and macroevolutionary studies. Diversity-dependent models of diversification have been used to indirectly infer the relevance of interspecific competition on driving speciation and extinction dynamics. In this study, we develop a new approach that more explicitly incorporated spatial and eco-morphological overlap among species to test how interspecific competition my affect diversification dynamics at deep time. We built different metrics that capture not only species temporal coexistence, but also their coexistence in space and morphospace to test the hypothesis that an increase in the intensity of competition would result in both a decrease in speciation rate and an increase in extinction rate. We tested our predictions using the North American fossil record of the family Canidae, a group that has been extensively studied and well characterized both from the eco-morphological and paleontological points of view. We found that interspecific competition only affected diversification dynamics during the early stages of Canidae radiation, resulting only in the suppression of speciation rate at the time the clade was expanding in diversity. We found no association between the intensity of the competition and extinction dynamics as expected by a competitive model, nor an association between changes in speciation and extinction rates and changes in global temperature, suggesting that extinction dynamics might be more related to external factors, such as clade-competition. We discuss the relevance of different factors on driving diversification dynamics changes over time and how evaluating the role of interspecific competition using different metrics that better capture the intensity of competition (as opposed to diversity dependent models), might be a way forward to investigate the role of biotic interactions at deep time.

evolutionary biology↗

bioRxiv2024

Anatomy of the mandibular corpus of extant cercopithecids : taxonomy and variation

This study aims to discriminate cercopithecid taxa of higher taxonomic levels (subfamily, tribe, subtribe, and genus) on the basis of corpus shape in transverse cross-section at the M1-M2 junction and to assess its variation using 2D geometric morphometrics. Specifically, we evaluated the effect of allometry and sexual dimorphism on differences in corpus shape at interspecific and intraspecific levels, respectively. We also investigated whether corpus variation among cercopithecids was following Brownian motion using Pagels {lambda}. Taxonomic discrimination and sexual dimorphism were established using Analysis of Variance on Principal Component scores. Allometry was studied using phylogenetic least-squares regressions and partial least-squares regressions. We demonstrated that, using corpus shape, extant cercopithecids can be significantly discriminated at the subfamilial, tribal, and subtribal levels. In addition, the main axis of variation of the Principal Component Analysis follows a distribution expected under Brownian motion, validating the presence of a phylogenetic signal in corpus shape. Colobines exhibit a robust corpus (superoinferiorly short and transversely broad) with large lateral prominences while cercopithecines have a gracile corpus (superoinferiorly long and transversely thin in its distal portion) with marked corpus fossae in African papionins. Exception to the typical subfamilial or tribal shape pattern exist, with the best examples being Trachypithecus, Presbytis and Pygathrix within colobines, Allenopithecus within Cercopithecini, and Macaca, Theropithecus and Cercocebus within Papionini. Sexual dimorphism is a confounding factor in shape discrimination, as there are significant differences between sexes, notably in Papio anubis, Nasalis larvatus and Procolobus verus . Intriguingly, sexual dimorphism in corpus shape does not seem to follow the dimorphism deduced in canine and molar crown dimensions. This discrepancy is illustrated by the low degree of dimorphism in corpus shape in Piliocolobus badius, despite dimorphic canine and molar dimensions. Overall, our findings concerning corpus shape variation in cercopithecids will greatly benefit to paleontological studies that seek to identify taxa in the fossil record, and to neontological studies aiming to explore the ecomorphological value of the cercopithecid mandible.

zoology↗

bioRxiv2024

Emergence and evolution of heterocyte glycolipid biosynthesis enabled specialized nitrogen fixation in cyanobacteria

Paleontological and phylogenomic observations have shed light on the evolution of cyanobacteria. Nevertheless, the emergence of heterocytes, specialized cells for nitrogen fixation, remains unclear. Heterocytes are surrounded by heterocyte glycolipids (HGs), which contribute to protection of the nitrogenase enzyme from oxygen. Here, by comprehensive HG identification and screening of HG biosynthesis genes throughout cyanobacteria, we identify HG analogs produced by specific and distantly related non-heterocytous cyanobacteria. These structurally less complex molecules probably acted as precursors of HGs, suggesting that HGs arose after a genomic reorganization and expansion of ancestral biosynthetic machinery, enabling the rise of cyanobacterial heterocytes in an increasingly oxygenated atmosphere. Subsequently, HG chemical structure evolved convergently in response to environmental pressures. Our results open a new chapter in the potential use of diagenetic products of HGs and HG analogs as fossils for reconstructing the evolution of multicellularity and division of labor in cyanobacteria.

microbiology↗

bioRxiv2024

SAFARI: Pangenome Alignment of Ancient DNA Using Purine/Pyrimidine Encodings

Aligning DNA sequences retrieved from fossils or other paleontological artifacts, referred to as ancient DNA, is particularly challenging due to the short sequence length and chemical damage which creates a specific pattern of substitution (C[->]T and G[->]A) in addition to the heightened divergence between the sample and the reference genome thus exacerbating reference bias. This bias can be mitigated by aligning to pangenome graphs to incorporate documented organismic variation, but this approach still suffers from substitution patterns due to chemical damage. We introduce a novel methodology introducing the RYmer index, a variant of the commonly-used minimizer index which represents purines (A,G) and pyrimidines (C,T) as R and Y respectively. This creates an indexing scheme robust to the aforementioned chemical damage. We implemented SAFARI, an ancient DNA damage-aware version of the pangenome aligner vg giraffe which uses RYmers to rescue alignments containing deaminated seeds. We show that our approach produces more correct alignments from ancient DNA sequences than current approaches while maintaining a tolerable rate of spurious alignments. In addition, we demonstrate that our algorithm improves the estimate of the rate of ancient DNA damage, especially for highly damaged samples. Crucially, we show that this improved alignment can directly translate into better insights gained from the data by showcasing its integration with a number of extant pangenome tools.

bioinformatics↗

bioRxiv2024

Arthropod Diversity at Two Sites with Different Disturbance Levels at the Texas A&M International University

This research aimed to measure arthropod species richness in two different sites with different disturbance levels in the Texas A&M International University campus to determine the overall biological diversity of the two sites and compare these measurements. As part of the research and methods, the Paleontological Statistics (PAST) software was used to calculate statistical indices in ecology that can help determine the difference between East and South sites. Some indices employed were the Shannons Diversity Index or the Simpsons Index of Diversity, the Bray-Curtis matrix, and the iNaturalist app. Results showed that the abundance of arthropods differed significantly from one site to the other, with the South site having a greater quantity, which was the site with less degradation created by humans. The site with the degraded ecosystem (East site) did not show a clear disadvantage regarding the diversity of arthropods. Thus, this article is relevant considering abundance and diversity to discover which is more important in each location. Finally, the study provides more insight into the arthropod community in the South Texas region, which can help with land and ecosystem management.

plant biology↗

bioRxiv2024

Development and use of integrated wetland condition index for lacustrine fringe wetlands of Lake Tana, Ethiopia

The primary objective of this research was to develop an integrated wetland condition index (IWCI) for lacustrine fringe wetlands (LFWs) in Lake Tana, Ethiopia, which has been highly impacted by recessionary agriculture, water hyacinth infestation, and both short- and long-term water level fluctuations (WLFs), as well as a heavy sediment load. The index of lacustrine wetland condition was developed based on four wetland characteristics that define wetlands: hydrology, water quality, sediment quality, and wetland biota. The value obtained from field and laboratory measurements of each wetland hydrology, water chemistry, and sediment characteristics indicator was normalized by allocating scores based on literature information and the results of this research project from three different disturbance-level lacustrine wetlands in Lake Tana. Macrophyte, diatom, and zooplankton indicator species tests (IndVal% and p (raw)) were calculated using PAST (PAleontological STatistics). Scores were allocated on a scale from 1 to 10, in such a way that the highest scores reflected the best conditions and the lowest scores the most disturbed and unhealthy conditions. Within four sub-indexes, there is more than one measure, with each measure given equal weighting, whereas the four wetland components (hydrology, water chemistry, sediment, and biota) are weighted as per their contribution to the overall wetland condition. Weights were assigned using the Decision Support System Software of DEFINITE. Finally, the total IWCI was classified into five wetland condition categories, namely: very poor or very far from the reference (0-3), poor (3-5), moderate (5-7), good (7-9), and excellent wetland condition or reference condition (9-10). According to the IWCI of the low water level period, eight wetland sampling sites were found within a moderately impacted condition (44.44%); similarly, eight wetland sampling sites were found within a good or mildly impacted condition; and only two wetland sampling sites (11.11%) were found in an excellent or reference condition. Thus, this IWCI developed and tested in this study could be a powerful tool to inform decision-makers on lacustrine wetland conservation and restoration priorities throughout the Lake Tana Ecosystem.

ecology↗

bioRxiv2024

From Ice Cores to Dinosaurs: Physical Collections Managers' Research Data Curation Perceptions and Behaviors

Physical collections provide the tangible objects that when analyzed become data informing all sciences. Physical collection managers aim to make physical objects discoverable, accessible, and reusable. The volume and variety of physical collections acquired, described, and stored across decades, and in some cases centuries, results from large public and private investments. The purpose of this study is to understand the curation perceptions and behaviors of physical collection managers across domains to inform cross-disciplinary research data management. Ten focus groups were conducted with thirty-two participants across several physical collection communities. Participants responded to open-ended questions about the data lifecycle of their physical objects. Results indicated that physical collections attempt to use universal metadata and data storage standards to increase discoverability, but interdisciplinary physical collections and derived data reuse require more investments to increase reusability of these invaluable items. This study concludes with a domain-agnostic discussion of the results to inform investment in cyberinfrastructure tools and services. Author summaryPhysical collections across the life and geosciences provide the tangible objects used to analyze and gain knowledge. There are collection managers in many museums and other information agencies working hard to curate these items in a way to keep them secure for long-term use. This study conducted focus groups with collection managers across several physical collection communities, including anthropology, archaeology, paleontology, ichthyology, herbaria, entomology, herpetology, and geology. Participants discussed their collection management approaches using the stages of the data lifecycle to frame how they make their items discoverable and reusable. Results indicated metadata and data storage standards help increase discoverability, but more work could be done to ensure better interdisciplinary reuse through increased investment and user-informed design of the cyberinfrastructure that preserves and makes available these invaluable items.

bioinformatics↗

bioRxiv2025

Geometric morphometrics enables accurate predictions of paleoecology and reveals unique adaptations to an expanded niche space in extinct waterfowl

Establishing the relationships between organismal phenotypes and their environment is a key component to understanding evolutionary history. Comparative evaluations of extant and extinct species can reveal how lineages have adapted to changing environmental conditions over time. However, the understanding of paleoecologies is predicated on a robust understanding of how modern species have been shaped by adaptation. Waterfowl may present an ideal group to study adaptive evolution as much of their morphology is apparently shaped by their dietary ecology. Here we use a large geometric morphometric dataset of waterfowl combined with random forest, a supervised machine learning algorithm, and linear discriminate analysis, to predict the dietary ecologies of nine extinct waterfowl species. We find that both model types reliably predict ecology for extinct species with well-established diets. Interestingly, we also found that the Hawaiian moa-nalo and the New Zealand Cnemiornis calcitrans likely occupied ecological niches no longer present in modern waterfowl as they were not morphologically or ecologically convergent with modern geese as previously asserted. Our study demonstrates that waterfowl are an excellent model group for the study of adaptive evolution, and underscores the utility of predictive modelling for paleontological studies.

evolutionary biology↗

bioRxiv2025

Patterns of aDNA Damage Through Time end Environments, lessons from herbarium specimens

Herbarium collections are a vast but underutilized resource for ancient DNA research, containing over 400 million specimens with detailed metadata and spanning centuries of global biodiversity. Understanding patterns of DNA preservation in natural collections is crucial for optimizing ancient DNA studies and informing future curation practices. We analysed genomic data for 573 herbarium specimens from six plant species from the genera Hordeum and Oryza collected from the Americas and Eurasia over 220 years. Using standardized laboratory protocols and shotgun sequencing, we quantified DNA degradation and elucidated factors that accelerate it. We find significant age-dependent DNA fragmentation rates, indicating temporal degradation processes not detected in prehistoric samples. In our analysis, DNA decay rates in herbarium specimens were almost eight times faster than in moa bones, reflecting fundamental differences in tissue composition and preservation environments. Environmental conditions at the time of specimen collection emerged as the major determinants of post-mortem damage rates, with the interaction term between temperature and genus being the dominant driver of cytosine deamination. We find no effect of sample storage on DNA damage and degradation. These findings provide insights into how climatic origin, preservation environment, taxonomic identity and age influence DNA preservation while highlighting opportunities for improving institutional preservation practices. Due to standardised preservation conditions, museum collections can provide better insights into DNA damage and degradation over time than archaeological and paleontological samples.

molecular biology↗

bioRxiv2017

Complex multicellularity in fungi: evolutionary convergence, single origin, or both?

Complex multicellularity comprises the most advanced level of organization evolved on Earth. It has evolved only a few times in metazoans, green plants, brown and red algae and fungi. Compared to other lineages, the evolution of multicellularity in fungi follows different principles; both simple and complex multicellularity evolved via unique mechanisms not seen in other lineages. In this article we review ecological, paleontological, developmental and genomic aspects of complex multicellularity in fungi and discuss the general principles of the evolution of complex multicellularity in light of its fungal manifestations. Fungi represent the only lineage in which complex multicellularity shows signatures of convergent evolution: it appears 8-12 distinct fungal lineages, which show a patchy phylogenetic distribution, yet share some of the genetic mechanisms underlying complex multicellular development. To mechanistically explain the patchy distribution of complex multicellularity across the fungal tree of life we identify four key observations that need to be considered: the large number of apparently independent complex multicellular clades; the lack of documented phenotypic homology between these; the universal conservation of gene circuits regulating the onset of complex multicellular development; and the existence of clades in which the evolution of complex multicellularity is coupled with limited gene family diversification. We discuss how these patterns and known genetic aspects of fungal development can be reconciled with the genetic theory of convergent evolution to explain its pervasive occurrence in across the fungal tree of life.

evolutionary biology↗

bioRxiv2018

Bayesian and likelihood placement of fossils on phylogenies from quantitative morphometrics

AO_SCPLOWBSTRACTC_SCPLOWJointly developing a comprehensive tree of life from living and fossil taxa has long been a fundamental goal in evolutionary biology. One major challenge has stemmed from difficulties in merging evidence from extant and extinct organisms. While these efforts have resulted in varying stages of synthesis, they have been hindered by their dependence on qualitative descriptions of morphology. Though rarely applied to phylogenetic inference, traditional and geometric morphometric data can improve these issues by generating more rigorous ways to quantify variation in morphological structures. They may also facilitate the rapid and objective aggregation of large morphological datasets. I describe a new Bayesian method that leverages quantitative trait data to reconstruct the positions of fossil taxa on fixed reference trees composed of extant taxa. Unlike most formulations of phylogenetic Brownian motion models, this method expresses branch lengths in units of morphological disparity, suggesting a new framework through which to construct Bayesian node calibration priors for molecular dating and explore comparative patterns in morphological disparity. I am hopeful that the approach described here will help to facilitate a deeper integration of neo- and paleontological data to move morphological phylogenetics further into the genomic era.

evolutionary biology↗

bioRxiv2018

Bracketing phenotypic limits of mammalian hybridization

An increasing number of mammalian species have been shown to have a history of hybridization and introgression based on genetic analyses. Only relatively few fossils, however, preserve genetic material and morphology must be used to identify the species and determine whether morphologically intermediate fossils could represent hybrids. Because dental and cranial fossils are typically the key body parts studied in mammalian paleontology, here we bracket the potential for phenotypically extreme hybridizations by examining uniquely preserved cranio-dental material of a captive hybrid between gray and ringed seals. We analyzed how distinct these species are genetically and morphologically, how easy it is to identify the hybrids using morphology, and whether comparable hybridizations happen in the wild. We show that the genetic distance between these species is more than twice the modern human-Neanderthal distance, but still within that of morphologically similar species-pairs known to hybridize. In contrast, morphological and developmental analyses show gray and ringed seals to be highly disparate, and that the hybrid is a predictable intermediate. Genetic analyses of the parent populations reveal introgression in the wild, suggesting that gray-ringed seal hybridization is not limited to captivity. Taken together, gray and ringed seals appear to be in an adaptive radiation phase of evolution, showing large morphological differences relative to their comparatively modest genetic distance. Because morphological similarity does not always correlate with genetic distance in nature, we postulate that there is considerable potential for mammalian hybridization between phenotypically disparate taxa.

evolutionary biology↗

bioRxiv2018

Counterbalancing the time-dependence effect on the human mitochondrial DNA molecular clock

We propose a new method for estimating the coalescent age of phylogenetically related sequences that takes into account the observed time dependency of molecular rate estimates. Applying this method to human mitochondrial DNA data we have obtained significantly older ages for the main events of human evolution than in previous estimates. These ages are in close agreement with the most recent archaeological and paleontological records.

evolutionary biology↗

bioRxiv2018

Time calibrated morpho-molecular classification of Nassellaria (Radiolaria)

Nassellaria are marine radiolarian protists belonging to the Rhizaria lineage. Their skeleton, made of opaline silica, exhibit an excellent fossil record, extremely valuable in micro-paleontological studies for paleo-environmental reconstruction. Yet, to date very little is known about the extant diversity and ecology of Nassellaria in contemporary oceans, and most of it is inferred from their fossil record. Here we present an integrative classification of Nassellaria based on taxonomical marker genes (18S and 28S ribosomal DNA) and morphological characteristics obtained by optical and scanning electron microscopy imaging. Our phylogenetic analyses distinguished 11 main morpho-molecular clades relying essentially on the overall morphology of the skeleton and not on internal structures as previously considered. Using fossil calibrated molecular clock we estimated the origin of Nassellaria among radiolarians primitive forms in the Devonian (ca. 420 Ma), that gave rise to living nassellarian groups in the Triassic (ca. 250 Ma), during the biggest diversification event over their evolutionary history. This morpho-molecular framework provides both a new morphological classification easier to identify under light microscopy and the basis for future molecular ecology surveys. Altogether, it brings a new standpoint to improve our scarce understanding of the ecology and worldwide distribution of extant nassellarians.

molecular biology↗

bioRxiv2018

Insights from Bacillus anthracis strains isolated from permafrost in the tundra zone of Russia

This article describes Bacillus anthracis strains isolated during an outbreak of anthrax on the Yamal Peninsula in the summer of 2016 and independently in Yakutia in 2015. A common feature of these strains is their conservation in permafrost, from which they were extracted either due to the thawing of permafrost (Yamal strains) or as the result of paleontological excavations (Yakut strains). All strains isolated on the Yamal share an identical genotype belonging to lineage B.Br.001/002, pointing to a common source of infection in a territory over 250 km in length. In contrast, during the excavations in Yakutia, three genetically different strains were recovered from a single pit. One strain belongs to B.Br.001/002, as the Yamal strains. Despite the remoteness of Yamal from Yakutia, whole genome sequence analysis showed that the B.Br.001/002 strains are very closely related. The two other strains contribute to two different branches of A.Br.008/011, one of the remarkable polytomies described so far in B. anthracis population. The geographic distribution of the strains belonging to this polytomy is suggesting that this polytomy emerged in the thirteenth century, in combination with the constitution of a unified Mongol empire extending from China to Eastern Europe. We propose an evolutionary model for B. anthracis recent evolution in which the B lineage spread throughout Eurasia and was subsequently replaced by the A lineage except in some geographically isolated areas.

microbiology↗