SEARCH · bioRxiv Science

Results for “Evolutionary Biology”

Search indexed bioRxiv preprints in genomics, neuroscience, cell biology and bioinformatics. Read source abstracts and check manuscript versions; preprints are not peer reviewed.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 325 records · Page 18Linked to original sources

bioRxiv2019

Accurate inference of tree topologies from multiple sequence alignments using deep learning

Reconstructing the phylogenetic relationships between species is one of the most formidable tasks in evolutionary biology. Multiple methods exist to reconstruct phylogenetic trees, each with their own strengths and weaknesses. Both simulation and empirical studies have identified several "zones" of parameter space where accuracy of some methods can plummet, even for four-taxon trees. Further, some methods can have undesirable statistical properties such as statistical inconsistency and/or the tendency to be positively misleading (i.e. assert strong support for the incorrect tree topology). Recently, deep learning techniques have made inroads on a number of both new and longstanding problems in biological research. Here we designed a deep convolutional neural network (CNN) to infer quartet topologies from multiple sequence alignments. This CNN can readily be trained to make inferences using both gapped and ungapped data. We show that our approach is highly accurate, often outperforming traditional methods, and is remarkably robust to bias-inducing regions of parameter space such as the Felsenstein zone and the Farris zone. We also demonstrate that the confidence scores produced by our CNN can more accurately assess support for the chosen topology than bootstrap and posterior probability scores from traditional methods. While numerous practical challenges remain, these findings suggest that deep learning approaches such as ours have the potential to produce more accurate phylogenetic inferences.

evolutionary biology↗

bioRxiv2026

Breaking the species barrier: recurrent genomic introgressions from very distant lineages in a ciliate

The process of speciation, through which two reproductively isolated species emerge from an ancestral population, is often gradual, including a period during which gene flow still occurs, and hence speciation remains reversible. However, if isolation persists, the progressive accumulation of genetic incompatibilities ultimately locks the speciation process, reaching the point where hybrid offspring are inviable or sterile. In plants and animals, the establishment of species barriers is quite rapid: beyond a net genetic divergence of 0.02 substitutions per synonymous site, interspecific introgressions become extremely rare. Here we report that in ciliates, species barriers can be broken despite huge genetic divergence. We show that the genome of Paramecium sonneborni contains hundreds of DNA segments that were acquired by recurrent horizontal transfers from multiple very distant lineages (synonymous divergence [~]1 substitution/site). These segments approach the size of full-length chromosomes, which indicates that they were introgressed by inter-specific mating. These data show that in the ancestry of P. sonneborni, hybridization events with highly divergent species occurred repeatedly and led to viable and fertile offspring. We propose that this unexpected promiscuous sexual behavior is made possible by the fact that paramecia separate somatic and germline functions in two types of nuclei: the elimination of non-self DNA fragments during the development of the somatic genome allows individuals of a species to remain phenotypically the same, despite recurrent genetic flow from distant species into their germline. Significance StatementAn important issue in evolutionary biology is to understand the process of speciation, i.e. how two reproductively isolated species emerge from an ancestral population. Various factors can initiate the speciation process, but whatever the initial factor, once two populations become reproductively isolated, they start accumulating genetic incompatibilities. In plants and animals these incompatibilities accumulate rapidly, preventing the formation of viable and fertile hybrids, except between very closely related species. We show here that this rule does not apply to all eukaryotes. We discovered that the unicellular eukaryote Paramecium sonneborni recurrently acquired large DNA segments via hybridization with very distantly related species. This unexpected phenomenon highlights the diversity of factors that affect the delineation of species across eukaryotes.

evolutionary biology↗

bioRxiv2020

Loss of genetic variation in the two-locus multiallelic haploid model

In the evolutionary biology literature, it is generally assumed that in deterministic haploid selection models, in the absence of variation-generating mechanisms such as mutation, no polymorphic equilibrium can be stable. However, results corroborating this claim are scarce and almost always depend upon additional assumptions. Using ideas from game theory, we establish a condition on the fitness parameters of haplotypes formed by two loci such that a monomorphism is a global attractor. Further, we show that no isolated equilibrium exists, at which an unequal number of alleles from two loci is present. Under the assumption of convergence of trajectories to equilirium points, we settle the two-locus three-allele case for a fitness scheme formally equivalent to the classical symmetric viability model.

evolutionary biology↗

bioRxiv2026

Ancient Reconstructed Proteins: A Framework for Resurrecting Protein Structures from Million-Year-Old Metagenomes

DNA sequences derived from ancient samples provide insights into human history, paleoenvironments, and evolutionary biology. Advances in laboratory techniques and computational tools have established ancient DNA research as a distinct field. However, current analyses focus mainly on the DNA level, while the protein space remains under-explored. Recent progress in the de novo assembly of ancient metagenomes and the availability of protein structure prediction tools, such as AlphaFold 2, enable the reconstruction of protein structures from these degraded sequences. Here, we present a computational framework to assemble contigs, evaluate their authenticity as ancient sequences, predict open reading frames, and fold ancient protein structures directly from highly damaged metagenomic data. Applying this pipeline to two-million-year-old datasets from the Kap Kobenhavn Formation, we successfully rescued ancient proteins involved in methane metabolism. By generating structural models with AlphaFold 2 and comparing them to modern predicted reference structures, we demonstrate that these ancient proteins can be reconstructed and aligned with high confidence. We showcase this by analyzing an archaeal V/A-type ATP synthase protein recovered from the 2M-year-old Greenlandic data. Ultimately, our work proves that ancient proteins can be reliably recovered from highly degraded palaeogenomic material, establishing a new computational avenue for evolutionary and biochemical research.

evolutionary biology↗

bioRxiv2022

Analysis of Sexual vs Asexual Reproduction Using Four Measurements

The prevalence of sexual reproduction has long been an outstanding problem of evolutionary biology. In accordance with the mathematical approach employed by past researchers, we propose a mathematical framework to address this problem. We define and derive four measurements, diversity measure DVM, diffusion measure DFM, optimality measure OPM, and survivability measure SVM to compare sexual reproduction with asexual reproduction. We show that DVM increases exponentially in sexual reproduction, while only linearly in asexual reproduction. Hence, sexual reproduction allows species more opportunity to adapt. We also show that DFM is bounded in sexual reproduction and OPM is inversely related to DFM. Thus, sexual reproduction leads to smaller DFM and hence a larger OPM. We further show that SVM is a monotonic increasing function of OPM. Hence, sexual reproduction is better by virtue of producing a more homogeneous population.

evolutionary biology↗

bioRxiv2023

Standing genetic variation and de novo mutations underlie parallel evolution of island bird phenotypes

Parallel evolution occurs when the same trait evolves in closely related lineages in response to similar ecological contexts and provides some of the best examples of determinism in evolutionary biology. However, from a genetic standpoint, this process can be driven by either new mutations that appear independently in each diverging population or by selection on existing genetic variation common to both lineages. Small-bodied birds, for example, tend to increase in size after they colonise a new island, following what is known as the island rule. Such is the case of the silvereye (Zosterops lateralis), a prolific natural coloniser of southwest Pacific islands. Island forms of this bird species increase in body size after they establish, with the pattern and pace of change consistent with directional natural selection and evident even in the most recent colonisations within the last 200 years. The system provides an exceptional opportunity to explore the genomic basis of repeated body size evolution. We sequenced 377 whole genomes from 31 different silvereye populations, which revealed that both mechanisms are at play: in some lineages, new mutations are highly associated with body and bill size, but there are also highly associated polymorphisms present across all populations. Our research sheds light on the genomic basis of repeated body size evolution and emphasises that multiple molecular mechanisms can underlie similar evolutionary trajectories even within a single taxon.

evolutionary biology↗

bioRxiv2020

A transplantation experiment yields no evidencefor phenotypic plasticity in shell band width in Cepaea nemoralis

The common European grove snail, Cepaea nemoralis (Helicidae), has been a model species in genetics and evolutionary biology for over a century thanks largely to its genetic shell colour polymorphism. Although most aspects of its shell colour variation are known to be purely genetic, with little or no phenotypic plasticity involved, the width of the spiral bands has been suspected to display a certain amount of plasticity. To test this, we conducted a transplantation experiment, in which 548 growing banded snails were marked and transplanted, either within the same habitat (open or closed vegetation, displaying 19% and 61% band fusion, respectively) or between habitat types. The numbers recaptured were low: 8%, 5% after removal of individuals that had not grown. Based on these samples, we did not find any substantial influence of transplantation on band width.

evolutionary biology↗

bioRxiv2020

SlicerMorph: An open and extensible platform to retrieve, visualize and analyze 3D morphology

Large scale digitization projects such as #ScanAllFishes and oVert are generating high-resolution microCT scans of vertebrates by the thousands. Data from these projects are shared with the community using aggregate 3D specimen repositories like MorphoSource through various open licenses. MorphoSource currently hosts tens of thousands of 3D scans of eukaryotes. Along with the data from similarly scoped projects such as 10kPhenomes, DigiMorph and many others, soon hundreds of thousands of specimens that represent biodiversity of extinct and extant organisms will be conveniently available to researchers. We anticipate an explosion of quantitative research in organismal biology with the convergence of available data and the methodologies to analyze them. Though the data are available, the road from a series of images to analysis is fraught with challenges for most biologists. It involves tedious tasks of data format conversions, preserving spatial scale of the data accurately, 3D visualization and segmentations, acquiring measurements and annotations. When scientists use commercial software with proprietary formats, a roadblock for data exchange, collaboration, and reproducibility is erected that hurts the efforts of the scientific community to broaden participation in research. Another relevant concern is that ultimate derivative data from individual research projects (e.g., 3D models of segmentation) are shared in formats that do not preserve the correct spatial scale of the data. In this paper, we present our effort to tackle challenges biologists face when conducting 3D specimen-based research. We developed SlicerMorph as an extension of 3D Slicer, a biomedical visualization and analysis ecosystem with extensive visualization and segmentation capabilities built on proven python-scriptable open-source libraries such as Visualization Toolkit and Insight Toolkit. In addition to the core functionalities of Slicer, SlicerMorph provides users with modules to conveniently retrieve open-access 3D models or import users own 3D volumes, to annotate 3D curve and patch-based landmarks, generate canonical templates, conduct geometric morphometric analyses of 3D organismal form using both landmark-driven and landmark-free approaches, and create 3D animations from their results. We highlight how these individual modules can be tied together to establish complete workflow(s) from image sequence to morphospace. Our software development efforts were supplemented with short courses and workshops that cover the fundamentals of 3D imaging and morphometric analyses as it applies to study of organismal form and shape in evolutionary biology, and extensive links to the existing tutorials are provided as supplemental material. Our goal is to establish a community of organismal biologists centered around Slicer and SlicerMorph to facilitate easy exchange of data and results and collaborations using 3D specimens. Our proposition to our colleagues is that using a common open platform supported by a large user and developer community ensures the longevity and sustainability of the tools beyond the initial development effort.

evolutionary biology↗

bioRxiv2026

Olfactory-mediated host tracking and rapid local adaptation in a seed-feeding wasp

Understanding how specialized herbivores track divergence among their hosts is central to evolutionary biology. Congruent genetic structure between hosts and herbivores is often interpreted as evidence of long-term codivergence, but similar patterns may also arise when herbivores rapidly adapt to pre-existing host differentiation. Here, we integrate population genomics, host volatile profiling, and behavioral assays to examine host-associated divergence in the obligate seed-feeding wasp Megastigmus daduheensis and its conifer host Cupressus chengiana across three river valleys on the eastern Qinghai-Tibet Plateau. Despite strong phylogeographic congruence between each of the three wasp and host lineages, calibrated demographic analyses indicate that wasp divergence occurred during the early Holocene, substantially later than the Pliocene-Pleistocene divergence of host lineages. This temporal mismatch is inconsistent with strict long-term codivergence and instead supports rapid host tracking in a topographic complex region. Host lineages differed in volatile organic compound profiles, and behavioral assays showed that wasps were preferentially attracted to volatiles from their local host lineages. These results identify olfactory-mediated host recognition as a plausible mechanism promoting host fidelity and reinforcing host-associated genomic and behavioral differentiation. Our findings show that apparently concordant host-herbivore divergence can emerge over compressed evolutionary timescales through rapid local adaptation, highlighting how ecological differentiation can accumulate within species through host tracking.

evolutionary biology↗

bioRxiv2020

How do ecological and social environments reflect parental roles in birds? A comparative analysis

Parental roles are highly diverse in animal taxa. Since caring is an important determinant of fitness, understanding the origin and maintenance of various parental care strategies is a key question in evolutionary biology. Here we investigate parental care patterns in birds, which exhibit a remarkable diversity of parental sex roles. By means of phylogenetically informed comparative analyses we investigate whether and how care provisioning is predicted by ecology and social environment. Making use of the most comprehensive dataset including 1101 species that represent 126 avian families, we show that sex differences in parental care are neither related to food type nor to nest type, two key ecological factors. However, we found an effect of the social environment, as males tend to care relatively more in in colonial species than in non-colonial species. Taken together, these results highlight the importance of social effects for evolution of diverse parental sex roles.

evolutionary biology↗

bioRxiv2014

Quantifying the effects of anagenetic and cladogenetic evolution

An ongoing debate in evolutionary biology is whether phenotypic change occurs predominantly around the time of speciation or whether it instead accumulates gradually over time. In this work I propose a general framework incorporating both types of change, quantify the effects of speciational change via the correlation between species and attribute the proportion of change to each type. I discuss results of parameter estimation of Hominoid body size in this light. I derive mathematical formulae related to this problem, the probability generating functions of the number of speciation events along a randomly drawn lineage and from the most recent common ancestor of two randomly chosen tip species for a conditioned Yule tree. Additionally I obtain in closed form the variance of the distance from the root to the most recent common ancestor of two randomly chosen tip species.

Evolutionary Biology↗

bioRxiv2022

Evaluating the accuracy of methods for detecting correlated rates of molecular and morphological evolution

Determining the link between genomic and phenotypic evolution is a fundamental goal in evolutionary biology. Insights into this link can be gained by using a phylogenetic approach to test for correlations between rates of molecular and morphological evolution. However, there has been persistent uncertainty about the relationship between these rates, partly because conflicting results have been obtained using various methods that have not been examined in detail. We carried out a simulation study to evaluate the performance of five statistical methods for detecting correlated rates of evolution. Our simulations explored the evolution of molecular sequences and morphological characters under a range of conditions. Of the methods tested, Bayesian relaxed-clock estimation of branch rates was able to detect correlated rates of evolution correctly in the largest number of cases. This was followed by correlations of root-to-tip distances, Bayesian model selection, independent sister-pairs contrasts, and likelihood-based model selection. As expected, the power to detect correlated rates increased with the amount of data, both in terms of tree size and number of morphological characters. Likewise, the performance of all five methods improved when there was greater rate variation among lineages. We then applied these methods to a data set from flowering plants and did not find evidence of a correlation in evolutionary rates between genomic data and morphological characters. The results of our study have practical implications for phylogenetic analyses of combined molecular and morphological data sets, and highlight the conditions under which the links between genomic and phenotypic rates of evolution can be evaluated quantitatively.

evolutionary biology↗

bioRxiv2024

Passive accumulation of alkaloids in putatively non-toxic frogs challenges paradigms of the origins of acquired chemical defenses

Understanding the origins of novel, complex phenotypes is a major goal in evolutionary biology. Poison frogs of the family Dendrobatidae have evolved the novel ability to acquire alkaloids from their diet for chemical defense at least three times. However, taxon sampling for alkaloids has been biased towards colorful species, without similar attention paid to inconspicuous ones that are often assumed to be undefended. As a result, our understanding of how chemical defense evolved in this group is incomplete. Here we provide new data showing that, in contrast to previous studies, species from each undefended poison frog clade have measurable yet low amounts of alkaloids. We confirm that undefended dendrobatids regularly consume mites and ants, which are known sources of alkaloids. Thus, our data suggest that diet is insufficient to explain the defended phenotype. Our data support the existence of a phenotypic intermediate between toxin consumption and sequestration -- passive accumulation -- that differs from sequestration in that it involves no derived forms of transport and storage mechanisms yet results in low levels of toxin accumulation. We discuss the concept of passive accumulation and its potential role in the origin of chemical defenses in poison frogs and other toxin-sequestering organisms. In light of ideas from pharmacokinetics we incorporate new and old data from poison frogs into an evolutionary model that could help explain the origins of acquired chemical defenses in animals and provide insight into the molecular processes that govern the fate of ingested toxins. ResumenComprender los origenes de fenotipos novedosos y complejos es un objetivo central en biologia evolutiva. Las ranas venenosas de la familia Dendrobatidae han desarrollado una novedosa habilidad para adquirir alcaloides de su dieta como defensas quimicas, al menos tres veces. Sin embargo, el muestreo de taxones en busca de alcaloides ha estado sesgado hacia las especies coloridas, sin prestar atencion similar a las poco conspicuas que a menudo se presume, no tienen defensas. Como resultado, nuestra comprension de como evolucionan las defensas quimicas en este grupo es incompleta. Aqui, proporcionamos nuevos datos que muestran que, en contraste con estudios anteriores, las especies de cada clado de ranas venenosas no defendidas tienen cantidades bajas pero cuantificables de alcaloides. Confirmamos que los dendrobatidos no defendidos consumen regularmente acaros y hormigas, que son fuentes conocidas de alcaloides. Por lo tanto, nuestros datos sugieren que la dieta es insuficiente para explicar el fenotipo defendido. Nuestros datos respaldan la existencia de un fenotipo intermedio entre consumo y secuestro de toxinas (acumulacion pasiva), que difiere del secuestro en que no implica formas derivadas de mecanismos de transporte y almacenamiento, pero da lugar a bajos niveles de acumulacion de toxinas. Discutimos el concepto de acumulacion pasiva y su potencial rol en el origen de defensas quimicas en ranas venenosas y otros organismos que secuestran toxinas. Considerando ideas de farmacocinetica, incorporamos datos nuevos y antiguos de ranas venenosas dentro de un modelo evolutivo que podria ayudar a explicar los origenes de defensas quimicas adquiridas en animales, y proporcionar una vision de los procesos moleculares que regulan el destino de las toxinas ingeridas.

evolutionary biology↗

bioRxiv2023

Predicting rapid adaptation in time from adaptation in space: a 30-year field experiment in marine snails

Predicting the outcomes of adaptation is a major goal of evolutionary biology. When temporal changes in the environment mirror spatial gradients, it opens up the potential for predicting the course of adaptive evolution over time based on patterns of spatial genetic and phenotypic variation. We assessed this approach in a 30-year transplant experiment in the marine snail Littorina saxatilis. In 1992, snails were transplanted from a predation-dominated environment to one dominated by wave action. Based on spatial patterns, we predicted transitions in shell size and morphology, allele frequencies at positions throughout the genome, and chromosomal rearrangement frequencies. Observed changes closely agreed with predictions. Hence, transformation can be both dramatic and rapid, and predicted from knowledge of the phenotypic and genetic variation among populations.

evolutionary biology↗

bioRxiv2025

Molecular Clock Dating of Deep-Time Evolution Using Complex Mixture Models

Molecular clocks are a fundamental technique in evolutionary biology for establishing the timing and tempo of organismal divergence. However, currently available molecular clock methods, which often rely on simple homogeneous substitution models, can produce inaccurate time estimates, particularly for deep-time or rapidly evolving lineages where substitution heterogeneity and saturation are common. Hereby, we introduce phyloHessian (https://github.com/evolbeginner/phyloHessianWrapper), a Julia-based software to enable the use of complex mixture substitution models in molecular dating. phyloHessian computes the phylogenetic Hessian matrix and integrates it into PAML-MCMCtrees approximate likelihood framework to conduct dating analyses. Simulations mimicking phylogenies at different timescales demonstrate that complex mixture substitution models significantly enhance the accuracy of divergence time and substitution rate estimates in deep-time phylogenies. This pattern remains consistent across a wide range of uncertainties associated with molecular clock analysis. Additionally, mixture models display greater robustness to model and calibration specifications compared to their homogeneous counterparts. Empirical analysis of ancient symbiont lineages Microsporidia and Rickettsiales with different substitution models shows that mixture models, compared to homogeneous models, yield accelerated substitution rates and in some cases significantly different divergence times, leading to a revised understanding of their host association origins. Our findings underscore the importance of incorporating complex mixture substitution models for constructing reliable evolutionary timelines and elucidating the evolutionary history of deep-time or fast-evolving lineages.

evolutionary biology↗

bioRxiv2026

Evolutionary contingency facilitates scent divergence in an emergent orchid population

Reproductive isolation can evolve rapidly even among populations with extensive genetic similarity, but the mechanisms underlying this divergence remain an open question in evolutionary biology. Here, we investigate the genetic basis of floral scent divergence, a key trait mediating differential pollinator attraction, in a group of nascent Gongora orchid lineages that occur in sympatry. We combined whole-genome resequencing and floral transcriptomics to characterize the transition from the monoterpene-emitting 'M chemotype' to the pollinator-isolated phenylpropanoid-emitting 'A chemotype' nested within it. While overall genetic differentiation was low, a few highly differentiated regions contained candidate genes in biosynthetic pathways. Of particular interest was a putative o-methyltransferase exhibiting evidence of a recent selective sweep in the A chemotype, with much higher expression in scent-emitting floral tissues of A than in M. Transcriptomic comparison with a more distantly related monoterpene-emitting lineage ('X chemotype') further revealed the coordinated and elevated expression of phenylpropanoid biosynthetic genes in M despite its absence of aromatic floral volatiles, including a putative key enzyme potentially involved in directing metabolic flux towards monolignol biosynthesis. Together, our results support a model in which pre-existing activity in a metabolic pathway may facilitate the evolution of a novel floral scent phenotype, potentially making transitions across the adaptive landscape of scent more accessible than others. We propose that such evolutionary contingency may help explain how divergent scent profiles, and consequently, reproductive isolation, can evolve rapidly via few genetic changes.

evolutionary biology↗

bioRxiv2022

A high throughput method for egg size measurement in Drosophila

Life-history traits are used as proxies of fitness in insects including Drosophila. Egg size is an adaptive and ecologically important trait potentially with genetic variation across different populations. However, the low throughput of manual measurement of egg size has hampered the widespread use of this trait in evolutionary biology and population genetics. We established a method for accurate and high throughput measurement of Drosophila egg size using large particle flow cytometry (LPFC). The size estimates using LPFC are accurate and highly correlated with the manual measurements. The measurement of egg size is high throughput (average of 214 eggs measured per minute) and viable eggs of a specific size can be sorted rapidly (average of 70 eggs per minute). Sorting by LPFC does not reduce the survival of eggs making it a suitable approach for sorting eggs for downstream analyses. This protocol can be applied to any organism within the detectable size range (10-1500 m) of the large particle flow cytometers. We discuss the potential applications of this method and provide recommendations for optimizing the protocol for other organisms.

evolutionary biology↗

bioRxiv2022

Topological incongruence between Median-Joining Networks and Bayesian inference phylogenies

1Inferring phylogenies among intraspecific individuals often yields unresolved relationships (i.e., polytomies). Consequently, methods that compute distance-based abstract networks, like Median-Joining Networks (MJNs), are thought to be more appropriate tools for reconstructing such relationships than traditional trees. MJNs visualize all routes of relationships in the form of cycles, if needed, when traditional approaches cannot resolve them. However, the MJN method is a distance-based phenetic approach that does not involve character transformations and makes no reference to ancestor-descendant relationships. Although philosophical and theoretical arguments challenging the implication that MJNs reflect phylogenetic signal in the traditional sense have been presented elsewhere, an empirical comparison with a character-based approach is needed given the increasing popularity of MJN analysis in evolutionary biology. Here, we use the conservative Approximately Unbiased (AU) test to compare 85 cases of branching patterns of cycle-free MJNs and Bayesian Inference (BI) phylogenies using datasets from 55 empirical studies. By rooting the MJN analyses to provide directionality, analyses find substantial disagreement between computed MJNs and posterior distributions on BI phylogenies. The branching patterns in MJNs and BI phylogenies show significantly different relationships in 37.6% of cases. Among the relationships that were not significantly different, 96.2% show different sets of relationships. Our results indicate that the two methods provide different measures of relatedness in a phylogenetic sense. Finally, our analyses also support previous observations of the statistical hypothesis testing by reconfirming the over-conservativeness of the Shimodaira-Hasegawa test versus the AU test.

evolutionary biology↗