Biology subjects

Kontopoulos, D. - G.

Publications and source records attributed to Kontopoulos, D. - G..

11 recordsLinked to original sources

bioRxiv2026

Side-necked turtle genomes reveal chromosomal dynamics, skeletal innovation and cancer resistance

Turtles exhibit a highly derived body plan, exceptional longevity, cancer resistance, and striking diversity in karyotypes and sex determination systems. However, the genomic basis of these innovations remains unresolved, largely because reference genomes were lacking for one of two extant turtle clades, the side-necked turtles (Pleurodira). As part of the Vertebrate Genomes Project, we generated seven reference-quality Pleurodira genomes and reconstructed the most comprehensive genome-wide turtle phylogeny. Combining demographic inference with historical climate and biome reconstructions indicates that ancient climate fluctuations shaped long-term population dynamics, while recent declines mainly reflect population structure. Ancestral genome reconstructions reveal that rare bursts of chromosome fusions and fissions, likely facilitated by repetitive elements, drove turtle karyotype diversity. By identifying sex chromosomes and tracing their evolutionary history, we resolve a long-standing debate and demonstrate a single origin of genetic sex determination in Chelidae on a microchromosome over 80 million years ago. Contrary to previous hypotheses, we find no evidence of coevolution between genetic sex determination and chromosome number in turtles. Comparative genomic analyses further identify gene losses and signatures of adaptive evolution associated with key turtle traits. Gene losses causing disproportionate dwarfism phenotypes may have contributed to skeletal adaptations underlying the compact turtle body plan. In addition, gene losses and adaptive changes in stress response and tumor suppressor pathways likely enhance oxidative stress tolerance and cancer resistance. Together, these findings illuminate turtle genome evolution, revealing chromosomal dynamics, sex chromosome evolution, molecular insights into skeletal innovation and cancer resistance, and implicate gene losses as a recurrent contributor to evolutionary novelty.

genomics↗

bioRxiv2025

Comparative genomics indicate multiple genetic routes to the evolution of torpor in placental mammals

Torpor is a key survival strategy that many avian and mammalian lineages evolved in response to challenging environmental conditions. Whether the independent evolution of torpor in different lineages involved changes in the same genes remains poorly understood. Here, we performed comparative screens across 190 placental mammal genomes to comprehensively examine associations between loss, positive selection and evolutionary rate shifts in individual protein-coding genes and evolutionary shifts in torpor use. We find that gene-torpor associations are highly clade-specific, with no gene being able to explain the majority of torpor shifts across the phylogeny of placental mammals. Instead, a relatively higher but limited extent of evolutionary convergence can be detected at the pathway level. Our results suggest that torpor emerged through several genetic routes in placental mammals, which likely explains the vast diversity of torpor use patterns that can be observed among torpor-capable species today. SignificanceA fundamental question in evolutionary genomics is whether independent gains and losses of a convergent trait may be achieved through similar or distinct genetic paths. Here, we address this question by focusing on the evolution of torpor across placental mammals, a key trait that likely emerged independently in several lineages. By conducting multiple comparative genomics screens across 190 placental mammal species, we find that individual protein-coding genes have a low explanatory power for evolutionary shifts in torpor. In contrast, there is slightly stronger evidence for pathway-level convergence. Our findings suggest that the wide diversity of patterns of torpor use across placental mammals may, in part, be due to the existence of multiple genetic paths to torpor.

evolutionary biology↗

bioRxiv2025

Comprehensive phylogenetic reconstructions support ancestral omnivory in the ecologically diverse bat family Phyllostomidae

Adaptive radiations often occur with an early burst of ecological diversification, which requires not only various available niches but also a generalist ancestor with wide ecological niche breadths. However, ancestral generalism remains hard to test in empirical cases. The New World leaf-nosed bats (family Phyllostomidae) represent an unparalleled mammalian adaptive radiation with diverse dietary niches including arthropods, blood, terrestrial vertebrates, nectar, and fruits. However, when and how often phyllostomid bats transitioned from insectivory to fruit or nectar feeding remains unclear. Here we tested the hypotheses of ancestral insectivory versus ancestral omnivory in Phyllostomidae (141 species) using improved trait reconstructions based on multi-response phylogenetic threshold models, while explicitly accounting for phylogenetic uncertainty. Our results indicate that complementary fruit feeding has fully evolved at the early burst of the phyllostomid radiation and started to evolve in the most recent common ancestor of the family, supporting the ancestral omnivory hypothesis. In addition, fruit feeding probably evolved before nectar eating in Phyllostomidae, in contrast to the claims of previous studies. Extending this analysis to all bat families (621 species) reveals independent evolution of ancestral fruit feeding in four families, namely the Pteropodidae (Old World fruit bats) and three families from the Noctilionoidea superfamily. Despite the ancestral omnivory of these fruit-eating families, only Phyllostomidae and Pteropodidae show high species diversity and evolved predominant and strict fruit feeding. Therefore, our results reveal that ancestral generalism (i.e., omnivory) may be a precondition of but does not necessarily lead to adaptive radiations which also require subsequent niche partitioning and speciation.

evolutionary biology↗

bioRxiv2024

Changes in flexibility but not in compactness underlie the thermal adaptation of prokaryotic adenylate kinases

Understanding the structural changes that enable enzymes to remain active in extreme thermal conditions is of broad scientific interest for both fundamental and applied biological research. Three key mechanisms that underlie the thermal adaptation of enzymes are modifications in structural flexibility, compactness, and the contacts formed among amino acids. However, most previous studies on these topics have been limited to small sample sizes or a narrow taxonomic focus, and the importance of these factors to thermal adaptation remains poorly understood. In this study, we combined molecular dynamics simulations and phylogenetic comparative analyses to thoroughly analyse the structural factors underlying thermal adaptation in adenylate kinase--a key enzyme involved in cellular energy balance and homeostasis--across 70 prokaryotic species. We detect systematic increases in the flexibility of the enzyme with temperature, both across and within species. In contrast, structural compactness appears to be almost completely independent of temperature. Finally, we uncover a remarkable diversity in the number and types of amino acid contacts observed in different adenylate kinases that cannot be explained solely by temperature. Our results suggest that there are multiple paths toward the adaptation of prokaryotic adenylate kinases to extreme thermal environments and that these paths are generally accessible through changes in flexibility. Lay summaryThe structure of a given enzyme can vary considerably among species, reflecting local environmental conditions to an extent. To this day, we do not have a clear picture of the impacts of the thermal environment on enzyme structure. To fill this gap, we performed a structural comparison of the enzyme adenylate kinase (ADK) from 70 species of bacteria and archaea. We find that rises in temperature tend to increase the flexibility of the enzyme. However, at any given temperature, ADKs from cold environments tend to be more flexible than those from hot environments. In contrast, the compactness of the enzyme did not vary consistently with temperature. Finally, we found that the pattern of amino acid contacts can vary dramatically across ADKs of different species, in a manner that cannot be predicted by temperature alone. Overall, our study shows that there are multiple ways to evolve an enzyme structure that can tolerate extreme temperatures, with a key constraint being maintaining sufficient flexibility at temperatures typically experienced by each species.

evolutionary biology↗

bioRxiv2023

Numerous independent gains of torpor and hibernation across endotherms, linked with adaptation to diverse environments

Many endotherms from diverse taxonomic groups can respond to environmental changes through dormancy, i.e., by greatly reducing their energy expenditure for up to 24 hours (daily torpor) or longer (hibernation). We currently have a poor understanding of how dormancy evolved across endotherms and its associations with physiological traits and ecological factors. To fill this gap, we thoroughly examine the evolutionary patterns of dormancy and its links with 21 key ecophysiological variables across 1,338 extant endotherms. We find that daily torpor and hibernation are parts of a dormancy continuum, and that there are several, albeit weak, associations between dormancy and species physiological or environmental characteristics. Furthermore, we show that early endotherm ancestors likely did not hibernate and that this trait evolved multiple times in independent lineages. Overall, our results provide an explanation for the remarkable variation in dormancy patterns, even among species occupying highly similar niches.

ecology↗

bioRxiv2023

No model to rule them all: a systematic comparison of 83 thermal performance curve models across traits and taxonomic groups

In ectotherms, the performance of physiological, ecological and life-history traits universally increases with temperature to a maximum before decreasing again. Identifying the most appropriate thermal performance model for a specific trait type has broad applications, from metabolic modelling at the cellular level to forecasting the effects of climate change on population, ecosystem and disease transmission dynamics. To date, numerous mathematical models have been designed, but a thorough comparison among them is lacking. In particular, we do not know if certain models consistently outperform others and how factors such as sampling resolution and trait or organismal identity influence model performance. To fill this knowledge gap, we compile 2,739 thermal performance datasets from diverse traits and taxa, to which we fit a comprehensive set of 83 existing mathematical models. We detect remarkable variation in model performance that is not primarily driven by sampling resolution, trait type, or taxonomic information. Our results reveal a surprising lack of well-defined scenarios in which certain models are more appropriate than others. To aid researchers in selecting the appropriate set of models for any given dataset or research objective, we derive a classification of the 83 models based on the average similarity of their fits.

ecology↗

bioRxiv2023

Variation in temperature of peak trait performance will constrain adaptation of arthropod populations to climatic warming.

The capacity of arthropod populations to adapt to long-term climatic warming is uncertain. Here, we combine theory and extensive data on diverse arthropod taxa to show that their rate of thermal adaptation to climatic warming will be constrained in two fundamental ways. First, the rate of thermal adaptation is predicted to be limited by the rate of shift in the temperature of peak performance of four life-history traits in a specific order: juvenile development, adult fecundity, juvenile mortality, and adult mortality. Second, thermal adaptation will be constrained due to differences in the temperature of peak performance among these four traits, which are expected to persist because of trade-offs. By compiling a new global dataset of 61 diverse arthropod species, we find strong evidence that contemporary populations have indeed evolved under these constraints. Our results provide a basis for using relatively feasible trait measurements to predict the adaptive capacity of diverse arthropod populations to climatic warming.

ecology↗

bioRxiv2021

Latent functional diversity may accelerate microbial community responses to environmental fluctuations

How complex microbial communities respond to climatic fluctuations remains an open question. Due to their relatively short generation times and high functional diversity, microbial populations harbor great potential to respond as a community through a combination of strain-level phenotypic plasticity, adaptation, and species sorting. However, the relative importance of these mechanisms remains unclear. We conducted a laboratory experiment to investigate the degree to which bacterial communities can respond to changes in environmental temperature through a combination of phenotypic plasticity and species sorting alone. We grew replicate soil communities from a single location at six temperatures between 4{degrees}C and 50{degrees}C. We found that phylogenetically- and functionally-distinct communities emerge at each of these temperatures, with K-strategist taxa favoured under cooler conditions, and r-strategist taxa under warmer conditions. We show that this dynamic emergence of distinct communities across a wide range of temperatures (in essence, community-level adaptation), is driven by the resuscitation of latent functional diversity: the parent community harbors multiple strains pre-adapted to different temperatures that are able to "switch on" at their preferred temperature without immigration or adaptation. Our findings suggest that microbial community function in nature is likely to respond rapidly to climatic temperature fluctuations through shifts in species composition by resuscitation of latent functional diversity.

ecology↗

bioRxiv2020

Higher temperatures worsen the effects of mutations on protein stability

Understanding whether and how temperature increases alter the effects of mutations on protein stability is crucial for understanding the limits to thermal adaptation by organisms. Currently, it is generally assumed that the stability effects of mutations are independent of temperature. Yet, mutations should become increasingly destabilizing as temperature rises due to the increase in the energy of atoms. Here, by performing an extensive computational analysis on the essential enzyme adenylate kinase in prokaryotes, we show, for the first time, that mutations become more destabilizing with temperature both across and within species. Consistent with these findings, we find that substitution rates of prokaryotes decrease nonlinearly with temperature. Our results suggest that life on Earth likely originated in a moderately thermophilic and thermally fluctuating environment, and indicate that global warming should decrease the per-generation rate of molecular evolution of prokaryotes.

evolutionary biology↗

bioRxiv2019

Adaptive evolution explains the present-day distribution of the thermal sensitivity of population growth rate

Developing a thorough understanding of how ectotherm physiology adapts to different thermal environments is of crucial importance, especially in the face of global climate change. A key aspect of an organisms thermal performance curve--the relationship between fitness-related trait performance and temperature--is its thermal sensitivity, i.e., the rate at which trait values increase with temperature within its typically-experienced thermal range. For a given trait, the distribution of thermal sensitivities across species, often quantified as "activation energy" values, is typically right-skewed. Currently, the mechanisms that generate this distribution are unclear, with considerable debate about the role of thermodynamic constraints vs adaptive evolution. Here, using a phylogenetic comparative approach, we study the evolution of the thermal sensitivity of population growth rate across phytoplankton (Cyanobacteria and eukaryotic microalgae) and prokaryotes (bacteria and archaea), two microbial groups that play a major role in the global carbon cycle. We find that thermal sensitivity across these groups is moderately phylogenetically heritable, and that its distribution is shaped by repeated evolutionary convergence throughout its parameter space. More precisely, we detect bursts of adaptive evolution in thermal sensitivity, increasing the amount of overlap among its distributions in different clades. We obtain qualitatively similar results from evolutionary analyses of the thermal sensitivities of two physiological rates underlying growth rate: net photosynthesis and respiration of plants. Furthermore, we find that these episodes of evolutionary convergence are consistent with two opposing forces: decrease in thermal sensitivity due to environmental fluctuations and increase due to adaptation to stable environments. Overall, our results indicate that adaptation can lead to large and relatively rapid shifts in thermal sensitivity, especially in microbes where rapid evolution can occur at short time scales. Thus, more attention needs to be paid to elucidating the implications of rapid evolution in organismal thermal sensitivity for ecosystem functioning. Author summaryChanges in environmental temperature influence the performance of biological traits (e.g., respiration rate) in ectotherms, with the relationship between trait performance and temperature (the "thermal performance curve") being single-peaked. Understanding how thermal performance curves adapt to different environments is important for predicting how organisms will be impacted by climate change. One key aspect of the shape of these curves is the thermal sensitivity near temperatures typically experienced by the species. Whether and how thermal sensitivity responds to different environments is a topic of active debate. To shed light on this, here we perform an evolutionary analysis of the thermal sensitivity of three key traits of prokaryotes, phytoplankton, and plants. We show that thermal sensitivity does not evolve in a gradual manner, but can differ considerably even between closely related species. This suggests that thermal sensitivity undergoes rapid adaptive evolution, which is further supported by our finding that thermal sensitivity varies weakly with latitude. We conclude that variation in thermal sensitivity arises partly from adaptation to environmental factors and that this may need to be accounted for in ecophysiological models.

evolutionary biology↗

bioRxiv2018

Phytoplankton thermal responses adapt in the absence of hard thermodynamic constraints

To better predict how populations and communities respond to climatic temperature variation, it is necessary to understand how the shape of the response of fitness-related traits to temperature evolves (the thermal performance curve). Currently, there is disagreement about the extent to which the evolution of thermal performance curves is constrained. One school of thought has argued for the prevalence of thermodynamic constraints through enzyme kinetics, whereas another argues that adaptation can--at least partly--overcome such constraints. To shed further light on this debate, we perform a phylogenetic meta-analysis of the thermal performance curves of growth rate of phytoplankton--a globally important functional group--, controlling for environmental effects (habitat type and thermal regime). We find that thermodynamic constraints have a minor influence on the shape of the curve. In particular, we detect a very weak increase of maximum performance with the temperature at which the curve peaks, suggesting a weak "hotter-is-better" constraint. Also, instead of a constant thermal sensitivity of growth across species, as might be expected from strong constraints, we find that all aspects of the thermal performance curve evolve along the phylogeny. Our results suggest that phytoplankton thermal performance curves adapt to thermal environments largely in the absence of hard thermodynamic constraints.

evolutionary biology↗