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bioRxiv2024

Phylogenomics of the North American Desert Radiation Linanthus (Polemoniaceae) Reveals Mixed Trait Lability and No Single Geographic Mode of Speciation

PremiseUnderstanding how arid-adapted plants have diversified in harsh environments is a central question in evolutionary biology. Linanthus (Polemoniaceae) occurs in biodiverse dry areas of Western North America and exhibits extensive floral trait variation, multiple color polymorphisms, differences in blooming time, and variation in life history strategies. Here, we reconstruct the evolutionary history of this group. MethodsWe generated restriction-site associated (ddRAD) sequences for 180 individuals and target capture (TC) sequences for 63 individuals, with complete species sampling. Using maximum likelihood and pseudo-coalescent approaches, we inferred phylogenies of Linanthus and used these phylogenies to model the evolution of phenotypic traits and investigate the geographic speciation history of this genus. Key resultsShallow relationships are consistent and well supported with both ddRAD and TC data. Most species are monophyletic despite rampant local sympatry and range overlap, suggesting strong isolating barriers. The non-monophyly of some species is possibly due to rapid speciation or issues with current species delimitation. Perenniality likely evolved from annuality, a rare shift in angiosperms. Night blooming evolved three times independently. Flower color polymorphism is an evolutionarily labile trait and is likely ancestral. No single geographic mode of speciation characterizes the radiation but most species overlap in range, suggesting they evolved in parapatry. ConclusionsOur results illustrate the complexity of phylogenetic inference for recent radiations, even with multiple sources of genomic data and extensive sampling. This analysis provides a foundation to understand aridity adaptations, such as evolution of flower color polymorphisms, night blooming, and perenniality, as well as speciation mechanisms.

evolutionary biology↗

bioRxiv2025

Identifying rare spontaneous mutations through wildtype E. coli population sequencing

Understanding the rate and types of mutations occurring in different populations is fundamental to our ability to predict and potentially manipulate evolution. Common techniques for microbial mutation rate estimation fall into 2 camps; rapid, locus specific, generally liquid-culture based fluctuation assays; and slow, genome-wide, generally solid-culture based mutation accumulation experiments. This constrains the hypotheses which can be tested, notably the mutagenic effects of liquid environments cannot be rapidly quantified at a genome-wide scale. One example of such effect is the negative association previously observed between population density and mutation rates at many marker loci using the fluctuation assay. Because homogeneous population density is specifically relevant in liquid culture, this association has not been tested at a truly genome-wide scale. We fill this methodological gap by developing a novel pipeline that relies on population sequencing to capture how mutation rates are affected by population density in liquid cultures. We simulate expected mutation counts in a growing population along with random sampling during sequencing to estimate the necessary sequencing coverage as [≥]1,000-fold. We then carry out PCR-free sequencing of 95 wildtype E. coli populations at this coverage, calling rare variants with both reference-based and reference-free methods. These variant-calling methods are prone to different sources of error which can be minimised by considering only mutations called by both pipelines. This approach identifies 119 mutations across all cultures, with (non)coding/(non)synonymous and mutational spectrum profiles consistent with being samples of spontaneous mutation unbiased by selection. The distribution of these mutations also supports the motivating hypothesis, finding that mutation counts across the genome are strongly negatively associated with population density. This demonstrates the utility of population sequencing for the rapid testing of many previously inaccessible evolutionary biology hypotheses.

evolutionary biology↗

bioRxiv2021

Protracted speciation under the state-dependent speciation and extinction approach

How long does speciation take? What are the speciation processes that generated a species group? The answers to these important questions in evolutionary biology lie in the genetic difference not only among species, but also among lineages within each species. With the advance of genome sequencing in non-model organisms and the statistical tools to improve accuracy in inferring evolutionary histories among recently diverged lineages, we now have the lineage-level trees to answer these questions. However, we do not yet have an analytical tool for inferring speciation processes from these trees. What is needed is a model of speciation processes that generates both the trees and species identities of extant lineages. The model should allow calculation of the probability that certain lineages belong to certain species and have an evolutionary history consistent with the tree. Here we propose such a model and test the model performance on both simulated data and real data. We show that maximum likelihood estimates of the model are highly accurate and give estimates from real data that generate patterns consistent with observations. We discuss how to extend the model to account for different rates and types of speciation processes across lineages in a species group. By linking evolutionary processes on lineage level to species level, the model provides a new phylogenetic approach to study not just when speciation happened, but how speciation happened.

evolutionary biology↗

bioRxiv2020

Maximizing cooperation in the prisoner's dilemma evolutionary game via optimal control

The prisoners dilemma (PD) game offers a simple paradigm of competition between two players who can either cooperate or defect. Since defection is a strict Nash equilibrium, it is an asymptotically stable state of the replicator dynamical system that uses the PD payoff matrix to define the fitness landscape of two interacting evolving populations. The dilemma arises from the fact that the average payoff of this asymptotically stable state is sub-optimal. Coaxing the players to cooperate would result in a higher payoff for both. Here we develop an optimal control theory for the prisoners dilemma evolutionary game in order to maximize cooperation (minimize the defector population) over a given cycle-time T, subject to constraints. Our two time-dependent controllers are applied to the off-diagonal elements of the payoff matrix in a bang-bang sequence that dynamically changes the game being played by dynamically adjusting the payoffs, with optimal timing that depends on the initial population distributions. Over multiple cycles nT (n > 1), the method is adaptive as it uses the defector population at the end of the nth cycle to calculate the optimal schedule over the n + 1st cycle. The control method, based on Pontryagins maximum principle, can be viewed as determining the optimal way to dynamically alter incentives and penalties in order to maximize the probability of cooperation in settings that track dynamic changes in the frequency of strategists, with potential applications in evolutionary biology, economics, theoretical ecology, and other fields where the replicator system is used. PACS numbers02.50.Le; 02.30.Yy; 05.45.-a; 87.23.Kg; 87.23.Cc

evolutionary biology↗

bioRxiv2025

Single capsid mutations modulating phage adsorption, persistence, and plaque morphology shape evolutionary trajectories in {Phi}X174

The evolutionary success of lytic bacteriophages depends on key life-history traits, including adsorption, lysis time, burst size, and persistence in the environment. However, how these traits evolve to allow adaptation to different environments remains poorly understood. Here, we explored this question in {Phi}X174, combining experimental evolution and mathematical modelling. By investigating how serial transfer conditions shape evolutionary outcomes in liquid culture, we found that the time between transfers imposes divergent selection on adsorption and context-dependent directional selection on persistence. Longer transfer intervals, which allow multiple infection cycles until host depletion, favoured fast-adsorbing, highly persistent mutants that could rapidly initiate infections and remained viable in the absence of the host. In contrast, shorter transfer intervals selected for slower adsorption without substantially altering persistence. Mathematical modelling of phage population dynamics predicted that adsorption evolution during short transfers reflects a trade-off between two opposing selective forces within each transfer: an early phase in which susceptible hosts are abundant and adsorption is productive, favouring fast adsorption, and a later phase in which most hosts are already infected and adsorption primarily removes phage particles via attachment to already infected cells, favouring slower adsorption. A single-point mutation in the major capsid protein was sufficient to drive these changes in adsorption. In the case of fast-adsorbing mutants, this mutation was positively pleiotropic and also enhanced environmental persistence. Our findings show how simple changes in propagation conditions can steer phage phenotypes, providing insights relevant to evolutionary biology and phage therapy.

evolutionary biology↗

bioRxiv2024

Navigating "tip fog": Embracing uncertainty in tip measurements

Nature is full of messy variation, which serves as the raw material for evolution. However, in comparative biology this variation is smoothed into averages. Overlooking this variation not only weakens our analyses but also risks selecting inaccurate models, generating false precision in parameter estimates, and creating artificial patterns. Furthermore, the complexity of uncertainty extends beyond traditional "measurement error," encompassing various sources of intraspecific variance. To address this, we propose the term "tip fog" to describe the variance between the true species mean and what is recorded, without implying a specific mechanism. We show why accounting for tip fog remains critical by showing its impact on continuous comparative models and discrete comparative and diversification models. We rederive methods to estimate this variance and use simulations to assess its feasibility and importance in a comparative context. Our findings reveal that ignoring tip fog substantially affects the accuracy of rate estimates, with higher tip fog levels showing greater biases from the true rates, as well as affecting which models are chosen. The findings underscore the importance of model selection and the potential consequences of neglecting tip fog, providing insights for improving the accuracy of comparative methods in evolutionary biology.

evolutionary biology↗

bioRxiv2018

Convergence in form and function overcomes non-parallel evolutionary histories in Arctic charr

Understanding the extent to which evolution is predictable under multifarious selection is a longstanding question in evolutionary biology. However, the interplay of stochastic and contingent factors influencing the extent of parallelism in nature is not well understood. To test the predictability of evolution, we studied a natural experiment on different organismal levels across lakes and evolutionary lineages of a freshwater salmonid fish, Arctic charr (Salvelinus alpinus). We identified significant phenotypic parallelism between Arctic charr ecotype pairs within a continuum of parallel evolution and highly parallel adaptive morphological traits. Variability in phenotypic predictability was explained by complex demographic histories, differing genomic backgrounds and genomic responses to selection, variable genetic associations with ecotype, and environmental variation. Remarkably, gene expression was highly similar across ecotype replicates, and explained the observed parallelism continuum. Our findings suggest that parallel evolution by non-parallel evolutionary routes is possible when the regulatory molecular phenotype compensates for divergent histories.

evolutionary biology↗

bioRxiv2018

Evolution of correlated complexity in the radically different courtship signals of birds-of-paradise

Ornaments used in courtship often vary wildly among species, reflecting the evolutionary interplay between mate preference functions and the constraints imposed by natural selection. Consequently, understanding the evolutionary dynamics responsible for ornament diversification has been a longstanding challenge in evolutionary biology. However, comparing radically different ornaments across species, as well as different classes of ornaments within species, is a profound challenge to understanding diversification of sexual signals. Using novel methods and a unique natural history dataset, we explore evolutionary patterns of ornament evolution in a group - the birds-of-paradise - exhibiting dramatic phenotypic diversification widely assumed to be driven by sexual selection. Rather than the tradeoff between ornament types originally envisioned by Darwin and Wallace, we found positive correlations among cross-modal (visual/acoustic) signals indicating functional integration of ornamental traits into a composite unit - the courtship phenotype. Furthermore, given the broad theoretical and empirical support for the idea that systemic robustness - functional overlap and interdependency - promotes evolutionary innovation, we posit that birds-of-paradise have radiated extensively through ornamental phenotype space as a consequence of the robustness in the courtship phenotype that we document at a phylogenetic scale. We suggest that the degree of robustness in courtship phenotypes among taxa can provide new insights into the relative influence of sexual and natural selection on phenotypic radiations.\n\nAuthor SummaryAnimals frequently vary widely in ornamentation, even among closely related species. Understanding the patterns that underlie this variation is a significant challenge, requiring comparisons among drastically different traits - like comparing apples to oranges. Here, we use novel analytical approaches to quantify variation in ornamental diversity and richness across the wildly divergent birds-of-paradise, a textbook example of how sexual selection can profoundly shape organismal phenotypes. We find that color and acoustic complexity, along with behavior and acoustic complexity, are positively correlated across evolutionary time-scales. Positive covariation among ornament classes suggests that selection is acting on correlated suites of traits - a composite courtship phenotype - and that this integration may be partially responsible for the extreme variation we see in birds-of-paradise.

evolutionary biology↗

bioRxiv2023

Whole-genome sequencing confirms multiple species of Galapagos giant tortoises

Galapagos giant tortoises are endemic to the Galapagos Archipelago, where they are found in isolated populations. While these populations are widely considered distinguishable in morphology, behavior, and genetics, the recent divergence of these taxa has made their status as species controversial. Here, we apply multispecies coalescent methods for species delimitation to whole genome resequencing data from 38 tortoises across all 13 extant taxa to assess support for delimiting these taxa as species. In contrast to previous studies based solely on divergence time, we find strong evidence to reject the hypothesis that all Galapagos giant tortoises belong to a single species. Instead, a conservative interpretation of model-based and divergence-based results indicates that these taxa form a species complex consisting of a minimum of 9 species, with some analyses supporting as many as 13 species. There is mixed support for the species status of taxa living on the same island, with some methods delimiting them as separate species and others suggesting multiple populations of a single species per island. These results make clear that Galapagos giant tortoise taxa represent different stages in the process of speciation, with some taxa further along in that evolutionary process than others. A better understanding of the more complex parts of that process is urgently needed, given the threatened status of Galapagos giant tortoises. Lay SummarySpecies delimitation is a challenging problem in evolutionary biology, but one that is central to the field. Distinguishing species can affect conservation management practices, from conservation status assessments to strategies for breeding programs. More fundamentally, understanding species boundaries affects our ability to assess biodiversity and to study evolutionary processes. The Galapagos Archipelago presents several radiations of closely related taxa that inspired Charles Darwin to develop his theory of evolution by natural selection and later led to foundational case studies in speciation. The Galapagos giant tortoises were one such inspiration. Nearly two centuries later, there is still an ongoing debate about the taxonomic status of these tortoises, with opinions on their status ranging from barely differentiated populations to separate species. Here, we present the first genomic species delimitation of Galapagos giant tortoises and provide convincing evidence that this group is a complex consisting of between 9 and 13 species. These results provide valuable guidance to conservation stakeholders in the Galapagos, while also adding an important case study to the delimitation of island species.

evolutionary biology↗

bioRxiv2026

Natural limits on male mating sustain costly female choice, exaggerated displays, and genetic variation

The persistence of costly female preferences, exaggerated male sexual displays, and the genetic variation underlying those displays remains a central puzzle in evolutionary biology. Classical Fisherian models explain preference-driven display exaggeration but not how costly preference and display can persist without runaway or collapse. These models assume that preferred males remain available regardless of previous mating success, precluding feedback through declining availability. Here I use a gene-centered analysis to show that allelic realized relatedness governs the indirect benefits of choice and that unlimited availability allows relatedness to remain high until genetic variation is lost. Individual-based simulations relaxing this idealization exposed negative feedback: as preference spread and concentrated mating success, preferred males reached capacity and became unavailable. Choosy females became less able to steer indirect fitness benefits toward additional copies of the preference allele, reducing allelic realized relatedness and constraining further evolution of preference and display. This transformed Fisherian runaway into stable exaggeration, allowing costly preference and display to persist for tens of thousands of generations across broad ranges of preference strength, mating capacity, and recombination rate. With autosomal display and a 1% viability cost of preference, stable exaggeration reached 16.5 additive-genetic standard deviations above matched no-preference baselines. Negative feedback generated disruptive selection on display, amplifying additive genetic variation beyond mutation-selection balance by as much as 32-fold, providing a resolution to the lek paradox--the persistence of display variation despite strong sexual selection--without invoking biased mutation or condition dependence. Z linkage of display loci, relevant to birds and other taxa with ZW sex determination, expanded the conditions supporting persistent preference and display, increased exaggeration, and further amplified genetic variation. Once inherent biological limits on male mating success are recognized, Fisherian sexual selection is revealed as a self-regulating form of gene-level cooperation.

evolutionary biology↗

bioRxiv2022

Polytypy and systematics: diversification of Papilio swallowtail butterflies in the biogeographically complex Indo-Australian Region

A long-standing problem in evolutionary biology and systematics is defining patterns of diversification and speciation, which is compounded by allopatric distributions of polytypic taxa in biogeographically fragmented landscapes. In this paper we revisit this enduring systematic challenge using Mormon swallowtail butterflies (Papilio subgenus Menelaides)--an evolutionary and genetic model system. Menelaides is speciose and intensively sampled, with nearly 260 years of systematic study complicated by polytypy resulting from discontinuous morphological variation. This variation is structured by the mainland-island matrix of the geologically complex Indo-Australian Region, where drawing species boundaries has been difficult. We sampled variation across the biogeographic range of Menelaides, covering 97% of currently recognized species and nearly half of all subspecies. We generated a well-supported mito-nuclear phylogeny, on which we delineated species based on two species delimitation methods (GMYC and mPTP) and strongly supported reciprocal monophyly. These analyses showed that the true species diversity in this group may be up to 25% greater than traditional taxonomy suggests, and prompts extensive taxonomic restructuring. Biogeographic analyses showed that Menelaides have diversified largely in allopatry in Indo-Australian subregions by repeated dispersals across key biogeographic barriers. These results provide critical insights into the diversification process in this morphologically diverse and taxonomically complicated model group. These results will also be informative in future studies on systematics, biogeography, speciation and morphological diversification in the Indo-Australian Region--arguably the most complex geological land/seascape in the world.

evolutionary biology↗

bioRxiv2024

Dominant contribution of Asgard archaea to eukaryogenesis

The origin of eukaryotes is one of the key problems in evolutionary biology 1,2. The demonstration that the Last Eukaryotic Common Ancestor (LECA) already contained the mitochondrion, an endosymbiotic organelle derived from an alphaproteobacterium, and the discovery of Asgard archaea, the closest archaeal relatives of eukaryotes 3-7, inform and constrain evolutionary scenarios of eukaryogenesis 8. We undertook a comprehensive analysis of the origins of core eukaryotic genes tracing to the LECA within a rigorous statistical framework centered around evolutionary hypotheses testing using constrained phylogenetic trees. The results reveal dominant contributions of Asgard archaea to the origin of most of the conserved eukaryotic functional systems and pathways. A limited contribution from Alphaproteobacteria was identified, primarily relating to the energy transformation systems and Fe-S cluster biogenesis, whereas ancestry from other bacterial phyla was scattered across the eukaryotic functional landscape, without clear consistent trends. These findings suggest a model of eukaryogenesis in which key features of eukaryotic cell organization evolved in the Asgard lineage leading to the LECA, followed by the capture of the Alphaproteobacterial endosymbiont, and augmented by numerous but sporadic horizontal acquisition of genes from other bacteria both before and after endosymbiosis.

evolutionary biology↗

bioRxiv2023

Large-scale phylogenomics uncovers a complex evolutionary history and extensive ancestral gene flow in an African primate radiation

Understanding the drivers of speciation is fundamental in evolutionary biology, and recent studies highlight hybridization as a potential facilitator of adaptive radiations. Using whole-genome sequencing data from 22 species of guenons (tribe Cercopithecini), one of the worlds largest primate radiations, we show that rampant gene flow characterizes their evolutionary history, and identify ancient hybridization across deeply divergent lineages differing in ecology, morphology and karyotypes. Lineages experiencing gene flow tend to be more species-rich than non-admixed lineages. Mitochondrial transfers between distant lineages were likely facilitated by co-introgression of co-adapted nuclear variants. Although the genomic landscapes of introgression were largely lineage specific, we found that genes with immune functions were overrepresented in introgressing regions, in line with adaptive introgression, whereas genes involved in pigmentation and morphology may contribute to reproductive isolation. This study provides important insights into the prevalence, role and outcomes of ancestral hybridization in a large mammalian radiation.

evolutionary biology↗

bioRxiv2016

Host-selected mutations converging on a global regulator drive an adaptive leap by bacteria to symbiosis

Even though eukaryote health relies on beneficial symbionts, host defenses targeting pathogens create substantial obstacles for the establishment of these essential partnerships. To reveal mechanisms of symbiotic adaptation, we experimentally evolved ecologically distinct bioluminescent Vibrio fischeri through Euprymna scolopes squid light organs. Serial passaging of V. fischeri populations through squid hosts produced eight distinct mutations in the binK sensor kinase gene that conferred an exceptional selective advantage demonstrated through both empirical and theoretical analysis. Squid-adaptive binK alleles promoted colonization and immune evasion behavior which was mediated by symbiotic polysaccharide (Syp). binK variation also produced metabolic convergence with native symbionts, and altered quorum sensing and luminescence. Preexisting coordination of symbiosis traits facilitated an efficient solution where altered function of a regulator was the key to unlock multiple colonization barriers. These results identify a genetic basis for microbial adaptability and underscore the importance of hosts as selective agents that shape emergent symbiont populations.\n\nImpact statementSquid selection on non-native Vibrio fischeri drove rapid adaptation through convergent mutations of large effect, unmasking preexisting coordinate regulation of symbiosis.\n\nMajor subject areas, keywords, and research organism(s)\n\nMajor subject area: Genomics and evolutionary biology

Evolutionary Biology↗

bioRxiv2024

Estimation of spatial demographic maps from polymorphism data using a neural network

A fundamental goal in population genetics is to understand how variation is arrayed over natural landscapes. From first principles we know that common features such as heterogeneous population densities and barriers to dispersal should shape genetic variation over space, however there are few tools currently available that can deal with these ubiquitous complexities. Geographically referenced single nucleotide polymorphism (SNP) data are increasingly accessible, presenting an opportunity to study genetic variation across geographic space in myriad species. We present a new inference method that uses geo-referenced SNPs and a deep neural network to estimate spatially heterogeneous maps of population density and dispersal rate. Our neural network trains on simulated input and output pairings, where the input consists of genotypes and sampling locations generated from a continuous space population genetic simulator, and the output is a map of the true demographic parameters. We benchmark our tool against existing methods and discuss qualitative differences between the different approaches; in particular, our program is unique because it infers the magnitude of both dispersal and density as well as their variation over the landscape, and it does so using SNP data. Similar methods are constrained to estimating relative migration rates, or require identity by descent blocks as input. We applied our tool to empirical data from North American grey wolves, for which it estimated mostly reasonable demographic parameters, but was affected by incomplete spatial sampling. Genetic based methods like ours complement other, direct methods for estimating past and present demography, and we believe will serve as valuable tools for applications in conservation, ecology, and evolutionary biology. An open source software package implementing our method is available from https://github.com/kr-colab/mapNN.

evolutionary biology↗

bioRxiv2025

Foraging behavior and ecology drive the evolution of humeral shape in hummingbirds

Understanding how locomotion-related skeletal elements evolve under biomechanical and ecological constraints is central to animal evolutionary biology. In hummingbirds (Trochilidae), the humerus plays a key role in force transmission during hovering and flapping flight, yet the drivers of its shape evolution have not been examined. We combined geometric morphometrics with phylogenetic comparative analyses to examine humeral shape variation, evolutionary rates, and phenotypic integration in male hummingbirds from 78 species. Our analyses identified humerus allometry as the dominant predictor of shape, revealing a pattern in which larger humeri show broader proximal epiphyses, increased shaft robustness, and reduced curvature. In addition to this scaling pattern, we find that male humerus shape differs subtly among hummingbird species that differ in the use of aggression during nectar foraging. Evolutionary rates of humeral shape were heterogeneous and decoupled from ecological predictors. We also find phenotypic integration between the proximal and distal regions of the humerus, indicating coordinated evolution. Together, these results show that humeral evolution in hummingbirds is governed primarily by biomechanical scaling and internal integration, with foraging ecology introducing secondary, size-dependent modifications. This work highlights the importance of considering scaling and internal integration when interpreting morphological evolution in locomotor systems across vertebrates.

evolutionary biology↗

bioRxiv2017

Extensive phenotypic plasticity in a seasonal butterfly limits potential for evolutionary responses to environmental change

Understanding how populations adapt to changing environments is a major goal in evolutionary biology and ecology, and particularly urgent for predicting resilience to climate change. Phenotypic plasticity, the ability to express multiple phenotypes from the same genome, is a widespread adaptation to short-term environmental fluctuations, but whether it facilitates adaptation to environmental change on evolutionary timescales, such as those under climate change, remains contentious. Here, we investigate plasticity and adaptive potential in an African savannah butterfly displaying extensive plasticity as adaptation to predictable dry-wet seasonality. We assess the transcriptional architecture of seasonal plasticity and find pervasive gene expression differences between the seasonal phenotypes, reflecting a genome-wide plasticity programme. Strikingly, intra-population genetic variation for this response is highly depleted, possibly reflecting strong purifying selection in its savannah habitat where an environmental cue (temperature) reliably predicts seasonal transitions and the cost of a mismatched phenotype is high. Under climate change the accuracy of such cues may deteriorate, rendering dominant reactions norm maladaptive. Therefore, depleted variation for plasticity as reported here may crucially limit evolutionary potential when conditions change, and seasonally plastic species may in fact be especially vulnerable to climate change.

evolutionary biology↗

bioRxiv2025

Climate associated natural selection in the human mitochondrial genome

Mitochondria are essential for cellular energy production and biosynthesis, thermogenesis, and cell signalling, and thus help coordinate physiological responses to changing environments. Humans (Homo sapiens) have adapted to cope with a wide range of climatic conditions, however the role of the mitochondrial genome (mtDNA) in mediating this process remains poorly understood. Here we curated a dataset of 23,790 publicly available full human mitochondrial genomes, an approximate 40-fold increase on earlier studies, paired with modern climate and reconstructed paleoclimate variables. Using a Generalised Linear Model approach, we identify 18 independent candidate variants significantly associated with climatic conditions, suggesting local adaptation in human mitochondrial genomes. Candidate variants are distributed across multiple loci in regulatory, tRNA, rRNA and protein-coding regions - including prominently in ND2 and ND4 complex I subunits. Specific variants are predicted to impact mtDNA transcription, ribosome or protein structure, and multiple have been associated with disease pathologies. We further show that candidate variant genotype distributions are each best modelled by different paleo-bioclimatic variables, consistent with environmental stressors linked to our measured variables exerting subtly distinct selective effects. These stressors may reflect dietary changes or different thermogenic demands at lower temperatures. Our results provide genetic evidence to support the accumulating body of work from functional studies that mitochondria can modulate adaptation to diverse environments. This work underscores the importance of mtDNA in evolutionary biology and its relevance for understanding both disease and physiological variation in global populations.

evolutionary biology↗