Rxivist combines preprints from bioRxiv with data from Twitter to help you find the papers being discussed in your field. Currently indexing 67,354 bioRxiv papers from 296,559 authors.
Most downloaded bioRxiv papers, since beginning of last month
in category evolutionary biology
4,398 results found. For more information, click each entry to expand.
12,696 downloads evolutionary biology
Mammals progress through similar physiological stages during life, from early development to puberty, aging, and death. Yet, the extent to which this conserved physiology reflects conserved molecular events is unclear. Here, we map common epigenetic changes experienced by mammalian genomes as they age, focusing on evolutionary comparisons of humans to dogs, an emerging model of aging. Using targeted sequencing, we characterize the methylomes of 104 Labrador retrievers spanning a 16 year age range, achieving >150X coverage within mammalian syntenic blocks. Comparison with human methylomes reveals a nonlinear relationship which translates dog to human years, aligns the timing of major physiological milestones between the two species, and extends to mice. Conserved changes center on specific developmental gene networks which are sufficient to capture the effects of anti-aging interventions in multiple mammals. These results establish methylation not only as a diagnostic age readout but as a cross-species translator of physiological aging milestones.
3,899 downloads evolutionary biology
The defining feature of the eukaryotic cell is the possession of a nucleus that uncouples transcription from translation. This uncoupling of transcription from translation depends on a complex process employing hundreds of eukaryotic specific genes acting in concert and requires the 7-methylguanylate (m7G) cap to prime eukaryotic mRNA for splicing, nuclear export, and cytoplasmic translation. The origin of this complex system is currently a paradox since it is not found or needed in prokaryotic cells which lack nuclei, yet it was apparently present and fully functional in the Last Eukaryotic Common Ancestor (LECA). According to the Viral Eukaryogenesis (VE) hypothesis the abrupt appearance of the nucleus in the eukaryotic lineage occurred because the nucleus descends from the viral factory of a DNA phage that infected the archaeal ancestor of the eukaryotes. Consequently, the system for uncoupling of transcription from translation in eukaryotes is predicted by the VE hypothesis to be viral in origin. In support of this hypothesis it is shown here that m7G capping apparatus that primes the uncoupling of transcription from translation in eukaryotes is present in viruses of the Mimiviridae but absent from bona-fide archaeal relatives of the eukaryotes such as Lokiarchaeota. Furthermore, phylogenetic analysis of the m7G capping pathway indicates that eukaryotic nuclei and Mimiviridae obtained this pathway from a common ancestral source that predated the origin of LECA. These results support the VE hypothesis and suggest the eukaryotic nucleus and the Mimiviridae descend from a common First Eukaryotic Nuclear Ancestor (FENA).
941 downloads evolutionary biology
The European continent was subject to two major migrations of peoples during the Holocene: the northwestward movement of Anatolian farmer populations during the Neolithic and the westward movement of Yamnaya steppe peoples during the Bronze Age. These movements changed the genetic composition of the continent's inhabitants, via admixture and population replacement processes. The Holocene was also characterized by major changes in vegetation composition, which altered the environment occupied by the original hunter-gatherer populations. Here, we use a combination of paleogenomics and geostatistical modelling to produce detailed maps of the movement of these populations over time and space, and to understand how these movements impacted the European vegetation landscape. We find that the dilution of hunter-gatherer ancestries and the Yamnaya steppe migration coincided with a reduction in the amount of broad-leaf forest and an increase in the amount of pasture lands in the continent. We also show that climate played a role in these vegetational changes. Additionally, we find that the spread of Neolithic farmer ancestry had a two-pronged wavefront, in agreement with similar findings based on patterns of the cultural spread of farming from radiocarbon-dated archaeological sites. With thousands of ancient genomes publicly available and in production, we foresee that the integration of ancient DNA with geostatistical techniques and large-scale archaeological datasets will revolutionize the study of ancient populations movements, and their effects on local fauna and flora.
637 downloads evolutionary biology
Accurately inferring the genome-wide landscape of recombination rates in natural populations is a central aim in genomics, as patterns of linkage influence everything from genetic mapping to understanding evolutionary history. Here we describe ReLERNN, a deep learning method for estimating a genome-wide recombination map that is accurate even with small numbers of pooled or individually sequenced genomes. Rather than use summaries of linkage disequilibrium as its input, ReLERNN takes columns from a genotype alignment, which are then modeled as a sequence across the genome using a recurrent neural network. We demonstrate that ReLERNN improves accuracy and reduces bias relative to existing methods and maintains high accuracy in the face of demographic model misspecification, missing genotype calls, and genome inaccessibility. We apply ReLERNN to natural populations of African Drosophila melanogaster and show that genome-wide recombination landscapes, while largely correlated among populations, exhibit important population-specific differences. Lastly, we connect the inferred patterns of recombination with the frequencies of major inversions segregating in natural Drosophila populations.
585 downloads evolutionary biology
IQ-TREE (http://www.iqtree.org) is a user-friendly and widely used software package for phylogenetic inference using maximum likelihood. Since the release of version 1 in 2014, we have continuously expanded IQ-TREE to integrate a plethora of new models of sequence evolution and efficient computational approaches of phylogenetic inference to deal with genomic data. Here, we describe notable features of IQ-TREE version 2 and highlight the key advantages over other software.
478 downloads evolutionary biology
Along with the publication of 137 ancient human genomes retrieved from archaeological remains of the Eurasian steppe, [Damgaard et al., 2018] identified two individuals infected with Yersinia pestis , yielding one genome with 0.24x average coverage (DA147, 6th–9th c. AD) and another with 8.7x (DA101, 2nd–3rd c. AD). A phylogenetic analysis performed on the latter placed it in a position ancestral to a 6th-century Justinianic genome from Aschheim, Germany. These results are used to fuel an argument that the Justinianic Plague (541–544 AD) “was brought to Europe towards the end of the Hunnic period through the Silk Road along the southern fringes of the steppes” in contrast to the leading hypothesis of introduction via the Red Sea that is supported by historical accounts. In our reanalysis, we question the contested historical context of the presented genomes with the Justinianic Plague and show that the lower coverage genome might be rather related to the Black Death (1346–1353 AD). : #ref-11
408 downloads evolutionary biology
Interactions among microbial cells can generate new chemistries and functions, but exploitation requires establishment of communities that reliably recapitulate community-level phenotypes. Using mechanistic mathematical models, we show how simple manipulations to population structure can exogenously impose Darwinian-like properties on communities. Such imposition causes communities to participate directly in the process of evolution by natural selection and drives the evolution of cell-level interactions to the point where, despite underlying stochasticity, derived communities give rise to offspring communities that faithfully re-establish parental phenotype. The mechanism (developmental correction) is akin to a developmental process that arises from density dependent interactions among cells. Knowledge of ecological factors affecting evolution of developmental correction has implications for understanding the evolutionary origin of egalitarian transitions in individuality, symbioses, and for top-down engineering of microbial communities.
391 downloads evolutionary biology
Alexander Immel, Christoph Rinne, John Meadows, Rodrigo Barquera, Andras Szolek, Federica Pierini, Julian Susat, Lisa Boehme, Janina Dose, Joanna Bonczarowska, Clara Drummer, Katharina Fuchs, David Ellinghaus, Jan Christian Kaessens, Martin Furholt, Oliver Kohlbacher, Sabine Schade-Lindig, Iain Mathieson, Andre Franke, Johannes Krause, Johannes Mueller, Tobias L Lenz, Almut Nebel, Ben Krause-Kyora
The Wartberg culture (WBC, 3,500-2,800 BCE) dates to the Late Neolithic period, a time of important demographic and cultural transformations in western Europe. We perform a genome-wide analysis of 42 individuals who were interred in a WBC collective burial in Niedertiefenbach, Germany (3,300-3,200 cal. BCE). Our results highlight that the Niedertiefenbach population indeed emerged at the beginning of the WBC. This farming community was genetically heterogeneous and carried a surprisingly large hunter-gatherer ancestry component (40%). We detect considerable differences in the human leukocyte antigen gene pool between contemporary Europeans and the Niedertiefenbach individuals whose immune response was primarily geared towards defending viral infections.
387 downloads evolutionary biology
In humans, most germline mutations are inherited from the father. This observation is widely interpreted as resulting from the replication errors that accrue during spermatogenesis. If so, the male bias in mutation should be substantially lower in a closely related species with similar rates of spermatogonial stem cell divisions but a shorter mean age of reproduction. To test this hypothesis, we resequenced two 3-4 generation nuclear families (totaling 29 individuals) of olive baboons ( Papio anubis ), who reproduce at ~10 years of age on average. We inferred sex-specific mutation rates by analyzing the data in parallel with three three-generation human pedigrees (26 individuals). The mutation rate per generation in baboons is 0.55×10−8 per base pair, approximately half that of humans. Strikingly, however, the degree of male mutation bias is approximately 3:1, similar to that of humans; in fact, a similar male bias is seen across mammals that reproduce months, years or decades after birth. These results echo findings in humans that the male bias is stable with parental ages and cast further doubt on the assumption that germline mutations track cell divisions. Our mutation rate estimates for baboons raise a further puzzle in suggesting a divergence time between apes and Old World Monkeys of 67 My, too old to be consistent with the fossil record; reconciling them now requires not only a slowdown of the mutation rate per generation in humans but also in baboons.
370 downloads evolutionary biology
The evolution and diversification of animal reproductive modes have been pivotal questions in behavioral ecology. Amphibians present the highest diversity of reproductive modes among vertebrates, involving various behavioral, physiological and morphological traits. One of such features is the amplexus, the clasp or embrace of males on females during reproduction, which is almost universal to anurans. Hypotheses about the origin amplexus are limited and have not been thoroughly tested, nor had they taken into account evolutionary relationships in most comparative studies. However, these considerations are crucial to understand the evolution of reproductive modes. Here, using an evolutionary framework, we reconstruct the ancestral state of amplexus in 686 anuran species; investigate whether the amplexus type is a conserved trait; and test whether sexual size dimorphism (SSD) could have influenced the amplexus type or male performance while clasping females. Overall, we found evidence of at least 35 evolutionary transitions in amplexus type across anurans. We also found that amplexus exhibits a high phylogenetic signal (it is conserved across Anura evolutionary history) and the amplexus type does not evolve in association with SSD. We discuss the implications of our findings on the diversity of amplexus types across anurans.
342 downloads evolutionary biology
With the aim of supporting ecological analyses in butterflies, the third most species-rich superfamily of Lepidoptera, this paper presents the first time-calibrated phylogeny of all 496 extant butterfly species in Europe, including 18 very localized endemics for which no public DNA sequences had been available previously. It is based on a concatenated alignment of the mitochondrial gene COI and up to 11 nuclear gene fragments, using Bayesian inference of phylogeny. To avoid analytical biases that could result from our region-focus sampling, our European tree was grafted upon a global genus-level backbone butterfly phylogeny for analyses. In addition to a consensus tree, we provide the posterior distribution of trees and the fully-concatenated alignment for future analyses.
340 downloads evolutionary biology
Studies of life rely on classifying organisms into species. However, since Darwin, there is no agreement about how to separate species from varieties. Contrary to a frequent belief, quantitative standards for species delineation are lacking and overdue, and debates about species delimitation create obstacles for conservation biology, agriculture, legislation, and education. To tackle this key biological question, we have chosen butterflies as model organisms. We sequenced and analyzed transcriptomes of 188 specimens representing pairs of close but clearly distinct species, populations, and taxa that are debated among experts. We find that species are robustly separated from populations by the combination of two measures computed on Z-linked genes: fixation index that detects hiatus between species, and the extent of gene flow that quantifies reproductive isolation. These criteria suggest that all 9 butterfly pairs that caused experts' disagreement are distinct species, not populations. When applied to Homo, our criteria agree that all modern humans are the same species distinct from Neanderthals, suggesting relevance of this study beyond butterflies. Furthermore, we found that proteins involved in interactions with DNA (including proteins encoded by trans-regulatory elements), circadian clock, pheromone sensing, development, and immune response recurrently correlate with speciation. A significant fraction of these proteins is encoded by the Z-chromosome, which appears to be resistant to introgression. Taken together, we find common speciation mechanisms in butterflies, reveal the central role of Z-chromosome in speciation, and suggest quantitative criteria for species delimitation using genomic data, which is vital for the exploration of biodiversity.
334 downloads evolutionary biology
Urbanization significantly alters natural ecosystems and has accelerated globally. Urban wildlife populations are often highly fragmented by human infrastructure, and isolated populations may adapt in response to local urban pressures. However, relatively few studies have identified genomic signatures of adaptation in urban animals. We used a landscape genomics approach to examine signatures of selection in urban populations of white-footed mice (Peromyscus leucopus) in New York City. We analyzed 154,770 SNPs identified from transcriptome data from 48 P. leucopus individuals from three urban and three rural populations, and used outlier tests to identify evidence of urban adaptation. We accounted for demography by simulating a neutral SNP dataset under an inferred demographic history as a null model for outlier analysis. We also tested whether candidate genes were associated with environmental variables related to urbanization. In total, we detected 381 outlier loci and after stringent filtering, identified and annotated 19 candidate loci. Many of the candidate genes were involved in metabolic processes, and have well-established roles in metabolizing lipids and carbohydrates. Our results indicate that white-footed mice in NYC are adapting at the biomolecular level to local selective pressures in urban habitats. Annotation of outlier loci suggest selection is acting on metabolic pathways in urban populations, likely related to novel diets in cities that differ from diets in less disturbed areas.
325 downloads evolutionary biology
Biological organisms are modular. Theory predicts that natural selection would steadily improve modules towards their performance optima up to the margin of effective neutrality. This classical theory may break down for populations evolving in the clonal interference regime because natural selection may focus on some modules while adaptation of others stalls. Such evolutionary stalling has not been observed and it is unclear whether it limits the power of natural selection to optimize module performance. To empirically characterize evolutionary stalling, we evolved populations of Escherichia coli with genetically perturbed translation machineries (TMs). We show that populations with different suboptimal TMs embark on statistically distinct trajectories of TM optimization. Yet, before TMs approach the margin of effective neutrality, the focus of natural selection shifts to other cellular modules, and TM optimization stalls. Our results suggest that module optimization within an organism may take much longer than suggested by classical theory.
288 downloads evolutionary biology
When one species gradually splits into two, divergent selection on specific traits can cause peaks of differentiation in the genomic regions encoding those traits. Whether speciation is initiated by strong selection on a few genomic regions with large effects or by more diffused selection on many regions with small effects remains controversial. Differentiated phenotypes between differentiating lineages are commonly involved in reproductive isolation, thus their genetic underpinnings are key to the genomics architecture of speciation. When two species hybridize, recombination over multiple generations can help reveal the genetic regions responsible for the differentiated phenotypes against a genomic background that has been homogenized via backcrossing and introgression. We used admixture mapping to investigate genomic differentiation and the genetic basis of differentiated plumage features (relative melanin and carotenoid pigment) between hybridizing sister species in the early stage of speciation: Townsend’s ( Setophaga townsendi ) and Hermit warblers ( S. occidentalis ). We found a few narrow and dispersed divergent regions between allopatric parental populations, consistent with the ‘divergence with gene flow’ model of speciation. One of the divergent peaks involves three genes known to affect pigmentation: ASIP, EIF2S2, and RALY (the ASIP-RALY gene block). After controlling for population substructure, we found that a single nucleotide polymorphism (SNP) inside the intron of RALY displays a strong pleiotropic association with cheek, crown, and breast coloration. In addition, we detect selection on the ASIP-RALY gene block, as the geographic cline of the RALY marker of this gene block has remained narrower than the plumage cline, which remained narrower than expected under neutral diffusion over two decades. Despite extensive gene flow between these species across much of the genome, the selection on ASIP-RALY gene block maintains stable genotypic and plumage difference between species allowing further differentiation to accumulate via linkage to its flanking genetic region or linkage-disequilibrium genome-wide.
285 downloads evolutionary biology
Differences in nutrient availability have led to the evolution of diverse metabolic strategies across species, but within species these strategies are expected to be similar. Here, we discovered that the galactose metabolic pathway in the yeast Saccharomyces cerevisiae exists in two functionally distinct, incompatible states maintained by ancient balancing selection. We identified a genetic interaction for growth in galactose among the metabolic genes GAL2, GAL1/10/7, and PGM1. We engineered strains with all allelic combinations at these loci and showed that the reference allele of PGM1 is incompatible with the alternative alleles of the other genes. We observed a strong signature of ancient balancing selection at all three loci and found that the alternative alleles diverged from the reference alleles before the birth of the Saccharomyces sensu stricto species cluster 10-20 million years ago. Strains with the alternative alleles are found primarily in galactose-rich dairy environments, and they grow faster in galactose, but slower in glucose, revealing a tradeoff on which balancing selection may have acted.
251 downloads evolutionary biology
Biodiversity is distributed unevenly from the poles to the equator, and among branches of the tree of life, yet how those patterns are related is unclear. We investigated global speciation-rate variation across crown Mammalia using a novel time-scaled phylogeny ( N =5,911 species, ~70% with DNA), finding that trait- and latitude-associated speciation has caused uneven species richness among groups. We identify 24 branch-specific shifts in net diversification rates linked to ecological traits. Using time-slices to define clades, we show that speciation rates are a stronger predictor of clade richness than age. Mammals that are low dispersal or diurnal diversify the fastest, indicating roles for geographic and ecological speciation, respectively. Speciation is slower in tropical than extra-tropical lineages, consistent with evidence that longer tropical species durations underpin the latitudinal diversity gradient. These findings juxtapose modes of lineage diversification that are alternatively turnover-based, and thus non-adaptive, or persistence-based as associated with resource adaptations.
247 downloads evolutionary biology
Selection of mutants in a microbial population depends on multiple cellular traits. In serial-dilution evolution experiments, three key traits are the lag time when transitioning from starvation to growth, the exponential growth rate, and the yield (number of cells per unit resource). Here we investigate how these traits evolve in laboratory evolution experiments using a minimal model of population dynamics, where the only interaction between cells is competition for a single limiting resource. We find that the fixation probability of a beneficial mutation depends on a linear combination of its growth rate and lag time relative to its immediate ancestor, even under clonal interference. The relative selective pressure on growth rate and lag time is set by the dilution factor; a larger dilution factor favors the adaptation of growth rate over the adaptation of lag time. The model shows that yield, however, is under no direct selection. We also show how the adaptation speeds of growth and lag depend on experimental parameters and the underlying supply of mutations. Finally, we investigate the evolution of covariation between these traits across populations, which reveals that the population growth rate and lag time can evolve a nonzero correlation even if mutations have uncorrelated effects on the two traits. Altogether these results provide useful guidance to future experiments on microbial evolution.
243 downloads evolutionary biology
The neutral theory has been used as a null model for interpreting nature and produced the Recent Out of Africa model of anatomically modern humans. Recent studies, however, have established that genetic diversities are mostly at maximum saturation levels maintained by selection, therefore challenging the explanatory power of the neutral theory and rendering the present molecular model of human origins untenable. Using improved methods and public data, we have revisited human evolution and found sharing of genetic variations among racial groups to be largely a result of parallel mutations rather than recent common ancestry and admixture as commonly assumed. We derived an age of 1.86-1.92 million years for the first split in modern human populations based on autosomal diversity data. We found evidence of modern Y and mtDNA originating in East Asia and dispersing via hybridization with archaic humans. Analyses of autosomes, Y and mtDNA all suggest that Denisovan and Neanderthal were archaic Africans with Eurasian admixtures and ancestors of South Asia Negritos and Aboriginal Australians. Verifying our model, we found more ancestry of Southern Chinese from Hunan in Africans relative to other East Asian groups examined. These results suggest multiregional evolution of autosomes and replacements of archaic Y and mtDNA by modern ones originating in East Asia, thereby leading to a coherent account of modern human origins.
240 downloads evolutionary biology
An organism's ability to disperse influences many fundamental processes in ecology. However, standardised estimates of dispersal ability are rarely available, and thus the patterns and drivers of broad-scale variation in dispersal ability remain unclear. Here we present a global dataset of avian hand-wing index (HWI), an estimate of wingtip pointedness widely adopted as a proxy for flight efficiency and dispersal in birds. We show that HWI is correlated with geography and ecology across 10,391 (>99 %) bird species, increasing at higher latitudes and in migratory and/or non-territorial species. After controlling for these effects, the strongest predictor of HWI is temperature variability (i.e. seasonality), with secondary effects of diet and habitat type. Our analyses (1) reveal a prominent latitudinal gradient in HWI shaped by ecological and environmental factors, and (2) provide a global index of avian dispersal ability for wider use in community ecology, macroecology, and macroevolution.
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