SEARCH · Search bioRxiv

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 Read source abstracts and check manuscript versions; preprints are not peer reviewed.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 37 records · Page 2Linked to original sources

bioRxiv2024

Unifying approaches from statistical genetics and phylogenetics for mapping phenotypes in structured populations

In both statistical genetics and phylogenetics, a major goal is to identify correlations between genetic loci or other aspects of the phenotype or environment and a focal trait. In these two fields, there are sophisticated but disparate statistical traditions aimed at these tasks. The disconnect between their respective approaches is becoming untenable as questions in medicine, conservation biology, and evolutionary biology increasingly rely on integrating data from within and among species, and once-clear conceptual divisions are becoming increasingly blurred. To help bridge this divide, we derive a general model describing the covariance between the genetic contributions to the quantitative phenotypes of different individuals. Taking this approach shows that standard models in both statistical genetics (e.g., Genome-Wide Association Studies; GWAS) and phylogenetic comparative biology (e.g., phylogenetic regression) can be interpreted as special cases of this more general quantitative-genetic model. The fact that these models share the same core architecture means that we can build a unified understanding of the strengths and limitations of different methods for controlling for genetic structure when testing for associations. We develop intuition for why and when spurious correlations may occur using analytical theory and conduct population-genetic and phylogenetic simulations of quantitative traits. The structural similarity of problems in statistical genetics and phylogenetics enables us to take methodological advances from one field and apply them in the other. We demonstrate this by showing how a standard GWAS technique--including both the genetic relatedness matrix (GRM) as well as its leading eigenvectors, corresponding to the principal components of the genotype matrix, in a regression model--can mitigate spurious correlations in phylogenetic analyses. As a case study of this, we re-examine an analysis testing for co-evolution of expression levels between genes across a fungal phylogeny, and show that including covariance matrix eigenvectors as covariates decreases the false positive rate while simultaneously increasing the true positive rate. More generally, this work provides a foundation for more integrative approaches for understanding the genetic architecture of phenotypes and how evolutionary processes shape it.

genomics↗

bioRxiv2017

Spatial resource heterogeneity increases diversity and evolutionary potential

Spatial heterogeneity is believed to be an evolutionary driver of biodiversity. Variability in the distribution of resource patches can allow an environment to support a wider variety of phenotypes for selection to act upon at the ecosystem level, which may lead to more species. However, the generality of this principle has not been thoroughly tested, as the relevant adaptive dynamics occur on evolutionary timescales. We overcame this challenge by performing experiments on populations of digital organisms in the Avida Digital Evolution Platform, in which we investigated the impact of spatial resource heterogeneity on phenotypic diversity. Since an important benefit of diversity may be increased evolutionary potential, we also tracked the probability of a complex trait evolving in the context of various levels of spatial heterogeneity. We found that spatial entropy and phenotypic diversity have a strong positive correlation and this relationship is consistent across various spatial configurations. Diversity also increases evolutionary potential, but has a much smaller impact than other components of environmental composition. The most important of these components was the mean number of resources present in locations across the environment, likely owing to the importance of building blocks for the evolution of complex features. These results suggest that a general relationship exists between spatial heterogeneity and diversity, beyond the specific ecosystems and timescales in which it has previously been studied. By examining this relationship in the context of phenotypic evolution, we advance a mechanistic understanding of the resulting dynamics. Moreover, our results suggest that the likelihood of evolving various traits can be impacted by the spatial configuration of patches in which these traits are advantageous. These findings have implications for both evolutionary biology and evolutionary computation, as generating and maintaining diversity is critical to all forms of evolution.

ecology↗

bioRxiv2017

De novo organelle biogenesis in the cyanobacterium TDX16 released from the green alga Haematococcus pluvialis

It is believed that eukaryotes arise from prokaryotes, which means that organelles can form in the latter. Such events, however, had not been observed previously. Here, we report the biogenesis of organelles in the endosymbiotic cyanobacterium TDX16 that escaped from its senescent/necrotic host cell of green alga Haematococcus pluvialis. In brief, organelle biogenesis in TDX16 initiated with cytoplasm compartmentalization, followed by de-compartmentalization, DNA allocation, and re-compartmentalization, as such two composite organelles-the primitive chloroplast and primitive nucleus sequestering minor and major fractions of cellular DNA respectively were formed. Thereafter, the eukaryotic cytoplasmic matrix was built up from the matrix extruded from the primitive nucleus; mitochondria were assembled in and segregated from the primitive chloroplast, whereby the primitive nucleus and primitive chloroplast matured into nucleus and chloroplast respectively; while most mitochondria turned into double-membraned vacuoles after matrix degradation. Results of pigment analyses, 16S rRNA and genome sequencing revealed that TDX16 is a phycocyanin-containing cyanobacterium resembling Chroococcidiopsis thermalis, which had acquired 9,017,401bp DNAs with 10301 genes form its host. Therefore, organelle biogenesis in TDX16 was achieved by hybridizing the acquired eukaryotic DNAs with its own ones and expressing the hybrid genome.\n\nOrganelle biogenesis in TDX16 results in its transition into a new eukaryotic alga TDX16-DE, which provides a reference to re-understand the development, structure, function and association of organelles in eukaryotes and the reasons behind them, and has implications on other sections of biology, particularly cancer biology and evolutionary biology: (1) the formation and maturation of the small organelle-less nascent cancer cells share striking similarities with TDX16 development and transition, so, it is most likely that cancer cells arise from bacteria; (2) organelle biogenesis in TDX16 uncovers a way of new organelle and new single-celled eukaryote formation, and in light of which, the ancestral organelles were likely formed in rather than transformed form the endosymbiotic prokaryotes that had acquired their hosts DNAs.

cell biology↗

bioRxiv2020

The genetic structure and adaptation of Andean highlanders and Amazonian dwellers is influenced by the interplay between geography and culture

Western South America was one of the worldwide cradles of civilization. The well known Inca Empire was the tip of the iceberg of a cultural and biological evolutionary process that started 14-11 thousand years ago. Genetic data from 18 Peruvian populations reveal that: (1) The between-population homogenization of the central-southern Andes and its differentiation with respect to Amazonian populations of similar latitudes do not extend northward. Instead, longitudinal gene flow between the northern coast of Peru, Andes and Amazonia accompanied cultural and socioeconomic interactions revealed by archeological studies. This pattern recapitulates the environmental and cultural differentiation between the fertile north, where altitudes are lower; and the arid south, where the Andes are higher, acting as a genetic barrier between the sharply different environments of the Andes and Amazonia (2). The genetic homogenization between the populations of the arid Andes is not only due to migration during the Inca Empire or the subsequent colonial period. It started at least during the earlier expansion of the pre-Inca Wari Empire (600-1000 YBP) (3) This demographic history allowed for cases of positive natural selection in the high and arid Andes vs. the low Amazon tropical forest: in the Andes, HAND2-AS1 (heart and neural crest derivatives expressed 2 antisense RNA1, related with cardiovascular function) and DUOX2 (dual oxidase 2, related to thyroid function and innate immunity) genes; in the Amazon, the gene encoding for the CD45 protein, essential for antigen recognition by T/B lymphocytes in viral-host interaction, consistent with the host-virus arms race hypothesis.

evolutionary biology↗

bioRxiv2021

Phenotypic plasticity triggers rapid morphological convergence

Phenotypic convergence, the independent evolution of similar traits, is ubiquitous in nature, happening at all levels of biological organizations and in most kinds of living beings. Uncovering its mechanisms remains a fundamental goal in biology. Evolutionary theory considers that convergence emerges through independent genetic changes selected over long periods of time. We show in this study that convergence can also arise through phenotypic plasticity. We illustrate this idea by investigating how plasticity drives Moricandia arvensis, a mustard species displaying within-individual polyphenism in flowers, across the morphological space of the entire Brassicaceae family. By compiling the multidimensional floral phenotype, the phylogenetic relationships, and the pollination niche of over 3000 Brassicaceae species, we demonstrated that Moricandia arvensis exhibits a plastic-mediated within-individual floral disparity greater than that found not only between species but also between higher taxonomical levels such as genera and tribes. As a consequence of this divergence, M. arvensis moves outside the morphospace region occupied by its ancestors and close relatives, crosses into a new region where it encounters a different pollination niche and converges phenotypically with distant Brassicaceae lineages. Our study suggests that, by inducing phenotypes that explore simultaneously different regions of the morphological space, plasticity triggers rapid phenotypic convergence.

evolutionary biology↗

bioRxiv2023

Vascular microforamina and endocranial surface: normal variation and distribution in adult humans

The term craniovascular traits refers to the imprints left by arteries and veins on the skull bones. These features can be used in anthropology and archaeology to investigate the morphology of the vascular network in extinct species and past populations. Generally, the term refers to macrovascular features of the endocranial cavity, like those associated with the middle meningeal artery, venous sinuses, emissary foramina, and diploic channels. However, small vascular passages (here called microforamina or microchannels) have been occasionally described on the endocranial surface. In this study, we describe and quantify the amount and distribution of these microforamina in adult humans (N = 45) and, preliminarily, in early to late juvenile subjects (N = 7). Adults display more microchannels than juvenile skulls. Females show more channels than males, and it should be evaluated whether this trait can represent a new described sexual features, influenced by sex biology. The distribution of the microforamina is particularly concentrated on the top of the vault, in particular along the sides of the sagittal, metopic, and coronal sutures, matching the course of major venous sinuses. Nonetheless, the density is lower in the region behind the bregma. A preferential pattern of distribution seems to join diagonally the coronal and dorsal parietal regions. Beyond oxygenation, these features are likely involved in endocranial thermal regulation and immune responses, and their distribution and prevalence can hence be of interest in human biology, evolutionary anthropology, and medicine.

evolutionary biology↗

bioRxiv2024

Rate of de novo mutations in the three-spined stickleback

Being a fundamentally important genetic parameter and evolutionary force, estimates of germline mutation rates have many uses in evolutionary biology. However, accurate estimates of de novo mutation (DNM) rates are still relatively scarce even for extensively studied evolutionary biology models. We estimated DNM rates for the three-spined stickleback (Gasterosteus aculeatus), the supermodel of ecology and evolutionary biology. Using a large number of family trios sequenced to depth of 45x coverage, we identified 115 unique mutations genome wide and estimated the DNM rate at {micro} = 5.05 x 10-9/bp/gen without any detectable sex bias. The localised DNM rate was found to be positively correlated with recombination rate supporting the notion that recombination is a mutagenic process. Comparison of {micro} and genomic characteristics to those of the related nine-spined stickleback (Pungitius pungitius) revealed a high degree of similarity suggesting that despite 17.5 million years of independent evolution, the mutational processes in the two species appear to have been conserved.

evolutionary biology↗

bioRxiv2025

Genetic Novelty and Short-Term Evolutionary Dynamics in Drosophila yakuba mayottensis

1Understanding how genetic novelty arises and contributes to population divergence is central to evolutionary biology. On short evolutionary timescales, the relative roles of new mutations and standing variation remain underexplored among structural variation. Here, we compare the contributions of chromosomal rearrangements, tandem duplications, and single-nucleotide polymorphisms (SNPs) to early genomic differentiation in a recently colonized island population, Drosophila yakuba mayottensis, from the island of Mayotte. By comparing the relative impacts of these mutation classes, along with the involvement of transposable elements (TEs), we assess whether certain mutations are more likely to contribute to rapid divergence. We show that TEs are disproportionately involved in the formation of novel structural variants shortly after colonization, particularly through direct insertions. Our results suggest that TE-associated rearrangements may bypass the clocklike pace of SNP accumulation and divergence, where the contributions of coding SNPs, tandem duplications, and TE-facilitated ectopic recombination are constrained to standing variation on short timescales. Although TEs can drive the rapid emergence of novel variants, their full contribution to adaptation likely depends on evolutionary context and time since colonization. Together, our findings reveal time-dependent mutational dynamics and highlight the importance of structural variation, particularly TE-associated rearrangements, in shaping early genomic divergence following habitat shifts.

evolutionary biology↗

bioRxiv2018

Global invasion history of the world’s most abundant pest butterfly: a citizen science population genomics study

A major goal of invasion and climate change biology research is to understand the ecological and evolutionary responses of organisms to anthropogenic disturbance, especially over large spatial and temporal scales. One significant, and sometimes unattainable, challenge of these studies is garnering sufficient numbers of relevant specimens, especially for species spread across multiple continents. We developed a citizen science project, \"Pieris Project\", to successfully amass thousands of specimens of the invasive agricultural pest Pieris rapae, the small cabbage white butterfly, from 32 countries worldwide. We then generated and analyzed genomic (ddRAD) and mitochondrial DNA sequence data for these samples to reconstruct and compare different global invasion history scenarios. Our results bolster historical accounts of the global spread and timing of P. rapae introductions. The spread of P. rapae over the last [~]160 years followed a linear series of at least four founding events, with each introduced population serving as the source for the next. We provide the first molecular evidence supporting the hypothesis that the ongoing divergence of the European and Asian subspecies of P. rapae ([~]1,200 yrBP) coincides with the domestication of brassicaceous crops. Finally, the international success of the Pieris Project allowed us to nearly double the geographic scope of our sampling (i.e., add >1,000 specimens from 13 countries), demonstrating the power of the public to aid scientists in collections-based research addressing important questions in ecology and evolutionary biology.\n\nNon-technical summaryWe provide genetic evidence that the success of the small cabbage white butterfly--its rise to one of the most widespread and abundant butterflies on the planet-- was largely facilitated by human activities, through the domestication of its food plants and the accidental movement of the butterfly by means of trade and human movement (migration). Through an international citizen science project--Pieris Project--people from around the world helped to unravel the global invasion history of this agricultural pest butterfly by collecting samples for DNA analysis. The success of this citizen science project demonstrates the power of the public to aid in collections-based research that address important questions related to ecology and evolutionary biology.

evolutionary biology↗

bioRxiv2021

Evolutionary systems biology reveals patterns of rice adaptation to drought-prone agro-ecosystems

Rice was domesticated around 10,000 years ago and has developed into a staple for half of humanity. The crop evolved and is currently grown in stably wet and intermittently dry agro-ecosystems, but patterns of adaptation to differences in water availability remain poorly understood. While previous field studies have evaluated plant developmental adaptations to water deficit, adaptive variation in functional and hydraulic components, particularly in relation to gene expression, has received less attention. Here, we take an evolutionary systems biology approach to characterize adaptive drought resistance traits across roots and shoots. We find that rice harbors heritable variation in molecular, physiological, and morphological traits that is linked to higher fitness under drought. We identify modules of co-expressed genes that are associated with adaptive drought avoidance and tolerance mechanisms. These expression modules showed evidence of polygenic adaptation in rice subgroups harboring accessions that evolved in drought-prone agro-ecosystems. Fitness-linked expression patterns had predictive value and allowed us to identify the drought-adaptive nature of optimizing photosynthesis and interactions with arbuscular mycorrhizal fungi. Taken together, our study provides an unprecedented, integrative view of rice adaptation to water-limited field conditions.

plant biology↗

bioRxiv2024

An evolutionary cell biology perspective into the diverging mechanisms of clathrin-mediated endocytosis in dikarya fungi

Clathrin-mediated endocytosis is an ancient eukaryotic trafficking pathway, which transports plasma membrane and associated cargo into the cell and is involved in numerous cell- and tissue-level processes. Cargo selection and clathrin-coated vesicle formation is mediated by over 60 proteins that assemble in a regular and sequential manner at the plasma membrane. Decades of endocytosis studies have followed the tenet that uncovering the conserved core molecular mechanisms is sufficient to understand a cellular process. However, this approach also revealed a number of cell type or species-related variations that challenge a universal conserved, core mechanism. In this paper, we refocus on the endocytic diversity to understand how evolution shapes endocytic mechanisms. We define a comparative evolutionary cell biology approach that uses dikarya fungi as a model clade and live-cell fluorescence microscopy to study endocytosis dynamics in three species: Saccharomyces cerevisiae, Schizosaccharomyces pombe and Ustilago maydis. Our results quantitatively define several phenotypic differences between the species. We uncover several differences that impact the endocytic early phase, the protein assembly order, actin regulation, membrane invagination and scission. These findings demonstrate a mosaic evolution of endocytic traits, suggest ancestral states and direction of changes. We also investigate the phenotypic plasticity and robustness against environmental conditions. Lastly, we demonstrate that relatively minor evolutionary changes can majorly impact endocytic phenotypes. These studies force an appreciation of endocytic variation as not auxiliary, but vital to mechanistic understanding of this conserved cellular pathway.

cell biology↗

bioRxiv2021

PRDM9 losses in vertebrates are coupled to the loss of at least three other meiotic genes

In most mammals and likely throughout vertebrates, the gene PRDM9 specifies the locations of meiotic double strand breaks; in mice and humans at least, it also aids in their repair. For both roles, many of the molecular partners remain unknown. Here, we take a phylogenetic approach to identify genes that may be interacting with PRDM9, by leveraging the fact that PRDM9 arose before the origin of vertebrates, but was lost many times, either partially or entirely--and with it, its role in recombination. As a first step, we characterize PRDM9 domain composition across 446 vertebrate species, inferring at least thirteen independent losses. We then use the interdigitation of PRDM9 orthologs across vertebrates to test whether it co-evolved with any of 241 candidate genes co-expressed with PRDM9 in mice or associated with recombination phenotypes in mammals. Accounting for the phylogenetic relationship among species, we find two genes whose presence and absence is unexpectedly coincident with that of PRDM9: ZCWPW1, which was recently shown to facilitate double strand break repair, and its paralog ZCWPW2, as well as more tentative evidence for TEX15 and FBXO47. ZCWPW2 is expected to be recruited to sites of PRDM9 binding; its tight coevolution with PRDM9 across vertebrates suggests that it is a key interactor, with a role either in recruiting the recombination machinery or in double strand break repair. Author SummaryOur understanding of meiotic recombination in mammals has seen great progress over the past 15 years, spurred in part by the convergence of lines of evidence from molecular biology, statistical genetics and evolutionary biology. We now know that in most mammals and likely in many vertebrates, the gene PRDM9 specifies the location of meiotic double strand breaks and that in mice and humans at least, it also aids in their repair. For both roles, however, many of the molecular partners remain unknown. To search for these, we take a phylogenetic approach, leveraging the fact that the complete PRDM9 has been lost at least thirteen times in vertebrates and thus that its presence is interdigitated across species. By this approach, we identify two genes whose presence or absence across vertebrates is coupled to the presence or absence of PRDM9, ZCWPW1 and ZCWPW2, as well as two genes for which the evidence is weaker, TEX15 and FBXO47. ZCWPW1 was recently shown to be recruited to sites of PRDM9 binding and to aid in the repair of double strand breaks. ZCWPW2 is likely recruited to sites of PRDM9 binding as well; its tight coevolution with PRDM9 across vertebrates suggests that it plays an important role either in double strand break formation, potentially as the missing link that recruits the recombination machinery to sites of PRDM9 binding, or in double strand break repair.

evolutionary biology↗

bioRxiv2020

Selection on ancient variations drives the adaptive radiation of Metrosideros across the Hawaiian archipelago

Some of the most spectacular adaptive radiations begin with founder populations on remote islands. How genetically limited founder populations give rise to the striking phenotypic and ecological diversity characteristic of adaptive radiations is a paradox of evolutionary biology. We conducted an evolutionary genomic analysis of genus Metrosideros, a landscape-dominant, incipient adaptive radiation of woody plants that spans a striking range of phenotypes and environments across the Hawaiian Islands. Using nanopore-sequencing, we created a chromosome-level genome assembly for M. polymorpha var. incana and analyzed wholegenome sequences of 131 individuals from 11 taxa sampled across the islands. We found evidence of population structure that grouped taxa by island. Demographic modeling showed concordance between the divergence times of island-specific lineages and the geological formation of individual islands. Gene flow was also detected within and between island taxa, suggesting a complex reticulated evolutionary history. We investigated genomic regions with increased differentiation as these regions may harbor variants involved in local adaptation or reproductive isolation, thus forming the genomic basis of adaptive radiation. We discovered differentiation outliers have arisen from balancing selection on ancient divergent haplotypes that formed before the initial colonization of the archipelago. These regions experienced recurrent divergent selection as lineages colonized and diversified on new islands, and hybridization likely facilitated the transfer of these ancient variants between taxa. Balancing selection on multiple ancient haplotypes-or time-tested variants-may help to explain how lineages with limited gene pools can rapidly diversify to fill myriad ecological niches on remote islands. Significance statementSome of the most spectacular adaptive radiations of plants and animals occur on remote oceanic islands, yet such radiations are preceded by founding events that severely limit genetic variation. How genetically depauperate founder populations give rise to the spectacular phenotypic and ecological diversity characteristic of island adaptive radiations is not known. We generated novel genomic resources for Hawaiian Metrosideros--a hyper-variable incipient adaptive radiation of woody taxa--for insights into the paradox of remote island radiations. We found that Metrosideros colonized each island shortly after formation and diversified within islands through recurrent selection on ancient variations that predate the radiation. Recurring use of ancient variants may explain how genetically depauperate lineages can diversify to fill countless niches on remote islands.

evolutionary biology↗

bioRxiv2021

Long distance migration is a major factor driving local adaptation at continental scale in Coho Salmon

Inferring the genomic basis of local adaptation is a long-standing goal of evolutionary biology. Beyond its fundamental evolutionary implications, such knowledge can guide conservation decisions for populations of conservation and management concern. Here, we investigated the genomic basis of local adaptation in the Coho salmon (Oncorhynchus kisutch) across its entire North American range. We hypothesized that extensive spatial variation in environmental conditions and the species homing behavior may promote the establishment of local adaptation. We genotyped 7,829 individuals representing 217 sampling locations at more than 100,000 high-quality RADseq loci to investigate how recombination might affect the detection of loci putatively under selection and took advantage of the precise description of the demographic history of the species from our previous work to draw accurate population genomic inferences about local adaptation. Results indicated that genetic differentiation scans and genetic-environment association analyses were both significantly affected by variation in recombination rate as low recombination regions displayed an increased number of outliers. By taking these confounding factors into consideration, we revealed that migration distance was the primary selective factor driving local adaptation and partial parallel divergence among distant populations. Moreover, we identified several candidates SNP associated with long distance migration and altitude including a gene known to be involved in adaptation to altitude in other species. The evolutionary implications of our findings are discussed along with conservation applications.

evolutionary biology↗

bioRxiv2023

Sorting of persistent morphological polymorphisms links paleobiological pattern to population process

Biological variation fuels evolutionary change. Across longer timescales, however, polymorphisms at both the genomic and phenotypic levels often persists longer than would be expected under standard population genetic models such as positive selection or genetic drift. Explaining the maintenance of this variation within populations across long timespans via balancing selection has been a major triumph of theoretical population genetics and ecology. Although persistent polymorphisms can often be traced in fossil lineages over long periods through the rock record, paleobiology has had little to say about either the long-term maintenance of phenotypic variation or its macroevolutionary consequences. I explore the dynamics that occur when persistent polymorphisms maintained over long lineage durations are filtered into descendant lineages during periods of demographic upheaval that occur at speciation. I evaluate these patterns in two lineages: Ectocion, a genus of Eocene mammals, and botryocrinids, a Mississippian cladid crinoid family. Following origination, descendants are less variable than their ancestors. The patterns by which ancestral variation is sorted cannot be distinguished from drift. Maintained and accumulated polymorphisms in highly variable ancestral lineages such as Barycrinus rhombiferus (Owen and Shumard 1852) may fuel radiations as character states are sorted into multiple descendant lineages. Interrogating the conditions under which trans-specific polymorphism is either maintained or lost during periods of demographic and ecological upheaval can explain how population-level processes contribute to the emergent macroevolutionary dynamics that shape the history of life as preserved in the fossil record. Non-technical abstractUnderstanding how morphological variation changes within populations over relatively short timescales in response to environmental changes and ecology (i.e., thousands of years) is a major focus of paleontology and evolutionary biology. A distinct focus is in understanding the broad-scale patterns by which lineages have diversified into distinct environments over geologic time (i.e., millions of years). One major challenge has been reconciling how and whether processes acting over shorter timescales shape the patterns observed over long timescales. One way of examining morphological variation at the population level is by examining the distribution of polymorphic character states--discrete anatomical features that vary within a population. Fossil species often maintain such polymorphisms for long periods of time, with such variation even sometimes inherited by new species from their ancestors. In this article, I suggest that examining how these polymorphisms are distributed among incipient descendant lineages might help link the ecological and evolutionary processes that act at the population level (e.g., natural selection, genetic drift, competition, predation) to the paleobiological patterns that are often reconstructed across many species and over long timescales. I explore these dynamics in two lineages: Ectocion, a genus of Eocene mammals, and botryocrinids, a Mississippian cladid crinoid family. I found that new lineages typically have fewer polymorphisms than their ancestors, suggesting that ancestral variation is "sorted" into incipient lineages during speciation. This variation appears to be sorted randomly, which means that it is not possible to detect the influence of natural selection in guiding the inheritance of ancestral morphologies. I suggest that the patterns by which ancestral variation is sorted into new species may explain patterns of lineage diversification over long timescales, highlighting how population processes can extend their influence over longer timescales to shape large-scale evolutionary dynamics.

paleontology↗

bioRxiv2020

Polynomial Phylogenetic Analysis of Tree Shapes

AO_SCPLOWBSTRACTC_SCPLOWPhylogenetic trees are a central tool in evolutionary biology. They demonstrate evolutionary patterns among species, genes, and with modern sequencing technologies, patterns of ancestry among sets of individuals. Phylogenetic trees usually consist of tree shapes, branch lengths and partial labels. Comparing tree shapes is a challenging aspect of comparing phylogenetic trees as there are few tools to describe tree shapes in a quantitative, accurate, comprehensive and easy-to-interpret way. Current methods to compare tree shapes are often based on scalar indices reflecting tree imbalance, and on frequencies of small subtrees. In this paper, we present tree comparisons and applications based on a polynomial that fully characterizes trees. Polynomials are important tools to describe discrete structures and have been used to study various objects including graphs and knots. There are also polynomials that describe rooted trees. We use tree-defining polynomials to compare tree shapes randomly generated by simulations and tree shapes reconstructed from data. Moreover, we show that the comparisons can be used to estimate parameters and to select the best-fit model that generates specific tree shapes.

systems biology↗

bioRxiv2017

Phenotype loss is associated with widespread divergence of the gene regulatory landscape in evolution

Detecting the genomic changes underlying phenotypic changes between species is a main goal of evolutionary biology and genomics. Evolutionary theory predicts that changes in cis-regulatory elements are important for morphological changes. Here, we combine genome sequencing and functional genomics with genome-wide comparative analyses to investigate the fate of regulatory elements in lineages that lost morphological traits. We first show that limb loss in snakes is associated with widespread divergence of limb regulatory elements. We next show that eye degeneration in subterranean mammals is associated with widespread divergence of eye regulatory elements. In both cases, sequence divergence results in an extensive loss of relevant transcription factor binding sites. Importantly, diverged regulatory elements are associated with key genes required for normal limb patterning or normal eye development and function, suggesting that regulatory divergence contributed to the loss of these phenotypes. Together, our results provide the first evidence that genome-wide decay of the phenotype-specific cis-regulatory landscape is a hallmark of lost morphological traits.

genomics↗

bioRxiv2022

Phylogenomics reveals the relationships of butterflies and moths (Lepidoptera): providing the potential landscape using universal single copy orthologues

BackgroundA robust and stable phylogenetic framework is a fundamental goal of evolutionary biology. As the third largest insect order following by Diptera and Coleoptera in the world, lepidoptera (butterflies and moths) play a central role in almost every terrestrial ecosystem as the indicators of environmental change and serve as important models for biologists exploring questions related to ecology and evolutionary biology. However, for such charismatic insect group, the higher-level phylogenetic relationships among its superfamilies are still poorly unresolved. Resultswe increased taxon sampling among Lepidoptera (40 superfamilies and 76 families contained 286 taxa) and filtered the unqualified samples, then acquired a series of large amino-acid datasets from 69,680 to 400,330 for phylogenomic reconstructions. Using these datasets, we explored the effect of different taxon sampling on tree topology by considering a series of systematic errors using ML and BI methods. Moreover, we also tested the effectiveness in topology robustness among the three ML-based models. The results showed that taxon sampling is an important determinant in tree robustness of accurate lepidopteran phylogenetic estimation. Long-branch attraction (LBA) caused by site-wise heterogeneity is a significant source of bias given rise to topologies divergence of ditrysia in phylogenomic reconstruction. Phylogenetic inference showed a most comprehensive framework by far to reveal the relationships among lepidopteran superfamilies, but limited by taxon sampling, it could only represent the current understanding of the lepidopteran tree of life. The relationships within the species-rich and relatively rapid radiation Ditrysia and especially Apoditrysia remain poorly unresolved, which need to increase taxon sampling and adopt lineage-specific genes for further phylogenomic reconstruction. ConclusionsThe present study further expands the taxon sampling of lepidopteran phylogeny and provides a potential phylogenomic foundation for further understanding its current higher-level relationships.

evolutionary biology↗