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Results for “Evolutionary Biology”

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bioRxiv2016

Genome-level parameters describe the pan-nuclear fractal nature of eukaryotic interphase chromosomal arrangement

Long-range inter-chromosomal interactions in the interphase nucleus subsume critical genome-level regulatory functions such as transcription and gene expression. To decipher the physical basis of diverse pan-nuclear patterns of chromosomal arrangement that facilitates these processes, we investigate the scaling effects within disparate genomes and compared their total number of genes with chromosome size. First, we derived the pan-nuclear average fractal dimension of inter-chromosomal arrangement in interphase nuclei of different species and corroborated our predictions with independently reported results. Then, we described the different patterns across disparate unicellular and multicellular eukaryotes. We report that, unicellular lower eukaryotes have inter-chromosomal fractal dimension = 1 at the pan-nuclear scales, which is analogous to the multi-polymer crumpled globule model. Multi-fractal dimensions, corresponding to different inter-chromosomal arrangements emerged from multicellular eukaryotes, such that closely related species have relatively similar patterns. Using this theoretical approach, we could distinguish fractal patterns from human acrocentric versus metacentric chromosomes, implying that the multi-fractal nature of inter-chromosomal geometry facilitates viable large-scale chromosomal aberrations, such as Robertsonian translocations. We report that the nature of such an average multi-fractal dimension for nocturnal mammals is very different in diurnal mammals, which suggests a greatly enhanced plasticity in arrangement across different cell types, for example retinal versus dermal fibroblasts. Altogether, our results substantiate that genome-level constraints have also co-evolved with the average pan-nuclear fractal dimension of inter-chromosomal folding during eukaryotic evolution.

evolutionary biology↗

bioRxiv2016

Tempo and timing of ecological trait divergence associated with transitions to coexistence in birds

Summary paragraphOrganismal traits may evolve either gradually or in rapid pulses followed by periods of stasis, but the relative importance of these evolutionary models in generating biodiversity has proven difficult to resolve1,2. In addition, while it is often assumed that pulses of trait evolution are associated with speciation events, few studies have explicitly examined how the tempo of trait divergence varies with respect to different geographical phases of speciation. Thus, we still know little about the trajectories of trait divergence over timescales relevant to speciation, or the extent to which these trajectories are shaped by variation in geographical isolation and overlap (sympatry) among incipient species. Here, we combine divergence time estimates, trait measurements, and geographic range data for avian sister species pairs worldwide to examine the tempo and timing of trait divergence during allopatric speciation. We show that divergence in two important ecological traits--?body mass and beak morphology--is best explained by a model including pulses of divergence and periods of relative stasis. We also infer that trait divergence pulses often precede sympatry, and that pulses leading to greater trait disparity are associated with earlier transitions to sympatry. These findings suggest that early pulses of trait divergence promote subsequent transitions to sympatry, rather than such pulses occurring after sympatry has been established, for example via character displacement3. Incorporating pulsed divergence models into allopatric speciation theory helps to resolve some apparently contradictory observations, including widespread instances of both rapid sympatry and prolonged geographical exclusion4-6.

evolutionary biology↗

bioRxiv2016

An assessment of phylogenetic tools for analyzing the interplay between interspecific interactions and phenotypic evolution

Much ecological and evolutionary theory predicts that interspecific interactions often drive phenotypic diversification and that species phenotypes in turn influence species interactions. Several phylogenetic comparative methods have been developed to assess the importance of such processes in nature; however, the statistical properties of these methods have gone largely untested. Focusing mainly on scenarios of competition between closely-related species, we assess the performance of available comparative approaches for analyzing the interplay between interspecific interactions and species phenotypes. We find that currently used statistical methods largely fail to detect the impact of interspecific interactions on trait evolution, that sister taxa analyses often erroneously detect character displacement where it does not exist, and that recently developed process-based models have more satisfactory statistical properties. In weighing the strengths and weaknesses of different approaches, we hope to provide a clear guide for empiricists testing hypotheses about the reciprocal effect of interspecific interactions and species phenotypes and to inspire further development of process-based models.

evolutionary biology↗

bioRxiv2016

Fractal model of emergence of a proto-plant

The extension of the sectional model of the spruce crowns dynamics into diapason (0, 1) of the fractal parameter has demonstrated the existence of green biomass on branches of three orders in form of photosynthesizing (green) points. We investigated the growth of point sets on an interval as a model of the origin of proto-plants, which are formed due to endosymbiosis of cyanobacteria and protists. The fractal properties of the sets of evenly placed points and group sets were studied using the box-counting method. For the group sets, the character of dependence on the growing total number of points changes radically differently depending on whether the number of the points per group or the number of groups was fixed. As the host does not have the initial infrastructure needed for an increase in cyanobacteria per group, the first path is implemented and decreases from 1 to 0.25 when groups consist of two points per group. If and when the host develops necessary anatomical features (infrastructure), the second pathway is realized and grows to 1. The combined trajectory of initially demonstrates a slow growth of the size of the photosynthetic system and then an exponential growth after the development of the hosts infrastructure. Similar fractal peculiarity also characterizes trees and is an innate property of plants. Assumptions on the morphological recapitulation of proto-plant in higher plants ontogenesis (embryogenesis and seed germination) and also a possibility to fix the number of cyanobacteria per group are discussed.

evolutionary biology↗

bioRxiv2016

Bacterial but not protist gut microbiota align with ecological specialization in a set of lower termite species

The role of microbes in adaptation of higher organisms to the environment is becoming increasingly evident, but remains poorly understood. Protist and bacterial microbes facilitate that lower termites thrive on wood and are directly involved in substrate break down. During the course of evolution lower termites adapted to different diets and lifestyles. In order to test whether there are changes of the termite gut microbiota that co-occur and hence could be related to diet and lifestyle adaptation, we assessed the bacterial and protist communities in a multispecies framework profiling three wood-dwelling and two foraging lower termite species using 16S and 18S rRNA gene amplicon sequencing. Termites were kept under controlled conditions on the same diet to minimize environmental effects on their gut microbiota. We found that protist communities group according to host phylogeny while bacterial communities group according to lifestyle. The change from the ancestral wood-dwelling to a foraging lifestyle coincides with exposure to more diverse and higher concentrations of pathogens as well as a more diverse diet. Accordingly, we identified bacteria that are associated with foraging termites of the genus Reticulitermes and could function as probiotics or be metabolically important on a more diverse diet. Furthermore, protist and bacterial diversity are correlated, suggesting not only that many termite gut bacteria are associated with protists, but also suggesting a role of protist diversity in the evolution of bacterial diversity in the termite gut or vice versa.

evolutionary biology↗

bioRxiv2016

A defensive body plan was pre-adaptive for termitophily in the rove beetle tribe Termitohospitini (Staphylinidae: Aleocharinae)

Termitophily--the symbiosis of organisms with termite societies--has evolved a disproportionate number of times within the rove beetle subfamily Aleocharinae (Staphylinidae). Among aleocharine termitophiles, defensive (limuloid) and mimetic (physogastric & physothoracic) body forms have evolved convergently, but due to lack of a comprehensive aleocharine phylogeny, the context in which termitophily and associated adaptations evolve is unknown. We present the first example of a robust, morphology-based phylogenetic placement of an exclusively termitophilous tribe, the Termitohospitini. Termitohospitini is recovered to be nested within Myllaenini sensu nov, and sister to Myllaena (new synonymy). Furthermore, we also recovered the small tribe Masuriini nested within Myllaenini sensu nov (new status).\n\nReconstructing ecological transitions within this clade, we present evidence that the stem lineage of Myllaenini sensu nov invaded intertidal marine habitats, the common ancestor for Myllaena + Termitohospitini then transitioned to freshwater riparian habitats, with Termitohospitini alone subsequently shifting to termitophily. We conclude that: (1) Termitohospitini was ancestrally a limuloid-bodied riparian inhabitant; (2) a limuloid form may have been pre-adaptive for defense against host attack during the evolution of termitophily; (3) the strongly tapered abdomen of an ancestral limuloid body was a constraint on the evolution of physogastry, leading to the emergence of the unusual physothoracic body form observed in termitohospitines that likely integrates these obligate termitophiles to life inside termite colonies.\n\n\"one of the most astonishing spectacles in all natural history.\" -- Richard Dawkins

evolutionary biology↗

bioRxiv2016

Recombination Suppression is Unlikely to Contribute to Speciation in Sympatric Heliconius Butterflies

Mechanisms that suppress recombination are known to help maintain species barriers by preventing the breakup of co-adapted gene combinations. The sympatric butterfly species H. melpomene and H. cydno are separated by many strong barriers, but the species still hybridise infrequently in the wild, with around 40% of the genome influenced by introgression. We tested the hypothesis that genetic barriers between the species are reinforced by inversions or other mechanisms to reduce between-species recombination rate. We constructed fine-scale recombination maps for Panamanian populations of both species and hybrids to directly measure recombination rate between these species, and generated long sequence reads to detect inversions. We find no evidence for a systematic reduction in recombination rates in F1 hybrids, and also no evidence for inversions longer than 50 kb that might be involved in generating or maintaining species barriers. This suggests that mechanisms leading to global or local reduction in recombination do not play a significant role in the maintenance of species barriers between H. melpomene and H. cydno.\n\nAuthor SummaryIt is now possible to study the process of species formation by sequencing the genomes of multiple closely related species. Heliconius melpomene and Heliconius cydno are two butterfly species that have diverged over the past 2 million years and have different colour patterns, mate preferences and host plants. However, they still hybridise infrequently in the wild and exchange large parts of their genomes. Typically, when genomes are exchanged, chromosomes are recombined and gene combinations are broken up, preventing species from forming. Theory predicts that gene variants that define species might be linked together because of structural differences in their genomes, such as inverted pieces of chromosomes that will not be broken up when the species hybridise. However, in this paper, we use deep sequencing of large crosses of butterflies to show that there are no long chromosome regions that are not broken up during hybridisation, and no long chromosome inversions anywhere between the two genomes. This suggests that hybridisation is rare enough and mate preference is strong enough that inversions are not necessary to maintain the species barrier.

evolutionary biology↗

bioRxiv2016

Level-Based Analysis of Genetic Algorithms and Other Search Processes

Understanding how the time-complexity of evolutionary algorithms (EAs) depend on their parameter settings and characteristics of fitness landscapes is a fundamental problem in evolutionary computation. Most rigorous results were derived using a handful of key analytic techniques, including drift analysis. However, since few of these techniques apply effortlessly to population-based EAs, most time-complexity results concern simplified EAs, such as the (1 + 1) EA.\n\nThis paper describes the level-based theorem, a new technique tailored to population-based processes. It applies to any non-elitist process where o spring are sampled independently from a distribution depending only on the current population. Given conditions on this distribution, our technique provides upper bounds on the expected time until the process reaches a target state.\n\nWe demonstrate the technique on several pseudo-Boolean functions, the sorting problem, and approximation of optimal solutions in combina-torial optimisation. The conditions of the theorem are often straightfor-ward to verify, even for Genetic Algorithms and Estimation of Distribution Algorithms which were considered highly non-trivial to analyse. Finally, we prove that the theorem is nearly optimal for the processes considered. Given the information the theorem requires about the process, a much tighter bound cannot be proved.

evolutionary biology↗

bioRxiv2016

Ancestry in adapting, spatially-extended populations

Selective sweeps reduce neutral genetic diversity. In sexual populations, this \"hitchhiking\" effect is thought to be limited to the local genomic region of the sweeping allele. While this is true in panmictic populations, we find that in spatially-extended populations the combined effects of many unlinked sweeps can affect patterns of ancestry (and therefore neutral genetic diversity) across the whole genome. Even low rates of sweeps can be enough to skew the spatial locations of ancestors such that neutral mutations that occur in an individual living outside a small region in the center of the range have virtually no chance of fixing in the population. The fact that nearly all ancestry rapidly traces back to a small spatial region also means that relatedness between individuals falls off very slowly as a function of the spatial distance between them.

evolutionary biology↗

bioRxiv2016

Minimal-assumption inference from population-genomic data

Samples of multiple complete genome sequences contain vast amounts of information about the evolutionary history of populations, much of it in the associations among polymorphisms at different loci. Current methods that take advantage of this linkage information rely on models of recombination and coalescence, limiting the sample sizes and populations that they can analyze. We introduce a method, Minimal-Assumption Genomic Inference of Coalescence (MAGIC), that reconstructs key features of the evolutionary history, including the distribution of coalescence times, by integrating information across genomic length scales without using an explicit model of recombination, demography or selection. Using simulated data, we show that MAGICs performance is comparable to PSMC on single diploid samples generated with standard coalescent and recombination models. More importantly, MAGIC can also analyze arbitrarily large samples and is robust to changes in the coalescent and recombination processes. Using MAGIC, we show that the inferred coalescence time histories of samples of multiple human genomes exhibit inconsistencies with a description in terms of an effective population size based on single-genome data.

evolutionary biology↗

bioRxiv2016

Ploidy tug-of-war: evolutionary and genetic environments influence the rate of ploidy drive in a human fungal pathogen

Variation in baseline ploidy is seen throughout the tree of life, yet the factors that determine why one ploidy level is selected over another remain poorly understood. Experimental evolution studies using asexual fungal microbes with manipulated ploidy levels intriguingly reveals a propensity to return to the historical baseline ploidy, a phenomenon that we term ploidy drive. We evolved haploid, diploid, and polyploid strains of the human fungal pathogen Candida albicans under three different nutrient limitation environments to test whether these conditions, hypothesized to select for low ploidy levels, could counteract ploidy drive. Strains generally maintained or acquired smaller genome sizes in minimal medium and under phosphorus depletion compared to in a complete medium, while mostly maintained or acquired increased genome sizes under nitrogen depletion. Surprisingly, improvements in fitness often ran counter to changes in total nuclear genome size; in a number of scenarios lines that maintained their original genome size often increased in fitness more than lines that converged towards diploidy. Combined, this work demonstrates a role for both the environment and genotype in determination of the rate of ploidy drive, and highlights questions that remain about the force(s) that cause genome size variation.

evolutionary biology↗

bioRxiv2016

Vertically transmitted rhabdoviruses are found across three insect families and have dynamic interactions with their hosts

A small number of free-living viruses have been found to be obligately vertically transmitted, but it remains uncertain how widespread vertically transmitted viruses are and how quickly they can spread through host populations. Recent metagenomic studies have found several insects to be infected with sigma viruses (Rhabdoviridae). Here, we report that sigma viruses that infect Mediterranean fruit flies (Ceratitis capitata), Drosophila immigrans, and speckled wood butterflies (Pararge aegeria) are all vertically transmitted. We find patterns of vertical transmission that are consistent with those seen in Drosophila sigma viruses, with high rates of maternal transmission, and lower rates of paternal transmission. This mode of transmission allows them to spread rapidly in populations, and using viral sequence data we found the viruses in D. immigrans and C. capitata had both recently swept through host populations. The viruses were common in nature, with mean prevalences of 12% in C. capitata, 38% in D. immigrans and 74% in P. aegeria. We conclude that vertically transmitted rhabdoviruses may be widespread in insects, and that these viruses can have dynamic interactions with their hosts.

evolutionary biology↗

bioRxiv2016

The natural selection of metabolism and mass selects allometric transitions from prokaryotes to mammals

Inter-specific body mass allometries can evolve from the natural selection of mass, with {+/-}1/4 and {+/-}3/4 exponents following from the geometry of intra-specific interactions when density dependent foraging occurs in two spatial dimensions (2D, Witting, 1995). The corresponding values for three dimensional interactions (3D) are {+/-}1/6 and {+/-}5/6.\n\nBut the allometric exponents in mobile organisms are more diverse than the prediction. The exponent for mass specific metabolism tends to cluster around -1/4 and -1/6 in terrestrial and pelagic vertebrates, but it is strongly positive in prokaryotes with an apparent value around 5/6 (DeLong et al., 2010). And a value around zero has been reported in protozoa, and on the macro evolutionary scale from prokaryotes over larger unicells to multicellular vertebrates (Makarieva et al., 2005, 2008).\n\nI show that mass specific metabolism can be selected as the pace of the resource handling that generates net energy for self-replication and the selection of mass, and that this selection of metabolism and mass is sufficient to explain metabolic exponents that decline from 5/6 over zero to -1/6 in 3D, and from 3/4 over zero to -1/4 in 2D. The decline follows from a decline in the importance of mass specific metabolism for the selection of mass, and it suggests i) that the body mass variation in prokaryotes is selected from primary variation in mass specific metabolism, ii) that the variation in multicellular animals are selected from primary variation in the handling and/or densities of the underlying resources, iii) that protozoa are selected as an intermediate lifeform between prokaryotes and multicellular animals, and iv) that macro evolution proceeds along an upper bound on mass specific metabolism.

evolutionary biology↗

bioRxiv2016

Habitat preference predicts genetic diversity and population divergence in Amazonian birds

The ecological traits of organisms may predict important evolutionary parameters such as genetic diversity, population genetic structure, and demographic history. Making these ecological-evolutionary links is difficult because robust, comparable genetic estimates are required from many species with differing ecologies. In Amazonian birds, differences in habitat preference are an important component of ecological diversity. A subset of Amazonian birds is restricted to forest edge and open forest along floodplains, whereas another subset occurs only in the interior of tall, upland forest. Here, we examine the link between habitat and evolutionary metrics using 20 pairs of closely related and co-distributed bird species in which one member of the pair occurs primarily in forest edge and floodplains, and the other occurs in upland forest interior. We use standardized geographic sampling and genomic data from the same set of 2,416 independent markers to estimate genetic diversity, population structure, and demographic history in each species. We find that species of upland forest have higher genetic diversity, greater divergence across the landscape, more genetically distinct populations, and deeper gene histories than floodplain species. Our results reveal that species ecology in the form of habitat preference is an important predictor of genetic diversity and divergence and suggest that floodplain and upland avifaunas in the Amazon may be on separate evolutionary trajectories and require different conservation strategies.

evolutionary biology↗

bioRxiv2016

Inferring the role of habitat dynamics in driving diversification: evidence for a species pump in Lake Tanganyika cichlids

Geographic isolation that drives speciation is often assumed to slowly increase over time, for instance through the formation of rivers, the formation of mountains or the movement of tectonic plates. Cyclic changes in connectivity between areas may occur with the advancement and retraction of glaciers, with water level fluctuations in seas between islands or in lakes that have an uneven bathymetry. These habitat dynamics may act as a driver of allopatric speciation and propel local diversity. Here we present a parsimonious model of the interaction between cyclical (but not necessarily periodic) changes in the environment and speciation, and provide an ABC-SMC method to infer the rates of allopatric and sympatric speciation from a phylogenetic tree. We apply our approach to the posterior sample of an updated phylogeny of the Lamprologini, a tribe of cichlid fish from Lake Tanganyika where such cyclic changes in water level have occurred. We find that water level changes play a crucial role in driving diversity in Lake Tanganyika. We note that if we apply our analysis to the Most Credible Consensus (MCC) tree, we do not find evidence for water level changes influencing diversity in the Lamprologini, suggesting that the MCC tree is a misleading representation of the true species tree. Furthermore, we note that the signature of habitat dynamics is found in the posterior sample despite the fact that this sample was constructed using a species tree prior that ignores habitat dynamics. However, in other cases this species tree prior might erase this signature. Hence we argue that in order to improve inference of the effect of habitat dynamics on biodiversity, phylogenetic reconstruction methods should include tree priors that explicitly take into account such dynamics.

evolutionary biology↗

bioRxiv2016

Phylogenetic relationships and genome size evolution within the genus Amaranthus indicate the ancestors of an ancient crop

The genus Amaranthus consists of 50 to 70 species and harbors several cultivated and weedy species of great economic importance. A small number of suitable traits, phenotypic plasticity, gene flow and hybridization made it difficult to establish the taxonomy and phylogeny of the whole genus despite various studies using molecular markers. We inferred the phylogeny of the Amaranthus genus using genotyping by sequencing (GBS) of 94 genebank accessions representing 35 Amaranthus species and measured their genome sizes. SNPs were called by de novo and reference-based methods, for which we used the distant sugarbeet Beta vulgaris and the closely related Amaranthus hypochondriacus as references. SNP counts and proportions of missing data differed between methods, but the resulting phylogenetic trees were highly similar. A distance-based neighbor joing tree of individual accessions and a species tree calculated with the multispecies coalescent supported a previous taxonomic classification into three subgenera although the subgenus A. Acnida consists of two highly differentiated clades. The analysis of the Hybridus complex within the A. Amaranthus subgenus revealed insights on the history of cultivated grain amaranths. The complex includes the three cultivated grain amaranths and their wild relatives and was well separated from other species in the subgenus. Wild and cultivated amaranth accessions did not differentiate according to the species assignment but clustered by their geographic origin from South and Central America. Different geographically separated populations of Amaranthus hybridus appear to be the common ancestors of the three cultivated grain species and A. quitensis might be additionally be involved in the evolution of South American grain amaranth (A. caudatus). We also measured genome sizes of the species and observed little variation with the exception of two lineages that showed evidence for a recent polyploidization. With the exception of two lineages, genome sizes are quite similar and indicate that polyploidization did not play a major role in the history of the genus.

evolutionary biology↗

bioRxiv2016

Phylogenetic analysis suggests joint control of transmission mode in a grass-endophyte symbiosis

How symbionts are transmitted between hosts is key to determining whether symbioses evolve to be harmful or beneficial. Vertical transmission favors mutualistic symbionts, and horizontal transmission more virulent ones. Transmission mode evolution itself depends on whether the host or symbiont can respond to selection on transmission mode. When hosts control the transmission mode, vertical transmission should evolve under more restrictive circumstances than when symbionts are in control. We take a phylogenetic approach to determine whether the host, symbiont, or both control transmission mode using the pooid grass-epichloid endophyte symbiosis as a model system. This study is the first to investigate control of transmission mode evolution in a phylogenetic context. We find a signal of host phylogeny but only in conjunction with symbiont identity. This pattern suggests joint control of transmission mode by the host and symbiont. It also suggests that non-genetic or non-conserved symbiont traits may determine whether host traits lead to vertical or horizontal transmission.

evolutionary biology↗

bioRxiv2016

Identifying genetic variants that affect viability in large cohorts

A number of open questions in human evolutionary genetics would become tractable if we were able to directly measure evolutionary fitness. As a step towards this goal, we developed a method to examine whether individual genetic variants, or sets of genetic variants, currently influence viability. The approach consists in testing whether the frequency of an allele varies across ages, accounting for variation in ancestry. We applied it to the Genetic Epidemiology Research on Aging (GERA) cohort and to the parents of participants in the UK Biobank. Across the genome, we find only a few common variants with large effects on age-specific mortality: tagging the APOE {varepsilon}4 allele and near CHRNA3. These results suggest that when large, even late onset effects are kept at low frequency by purifying selection. Testing viability effects of sets of genetic variants that jointly influence one of 42 traits, we detect a number of strong signals. In participants of the UK Biobank study of British ancestry, we find that variants that delay puberty timing are enriched in longer-lived parents (P~6x10-6 for fathers and P~2x10-3 for mothers), consistent with epidemiological studies. Similarly, in mothers, variants associated with later age at first birth are associated with a longer lifespan (P~1x10-3). Signals are also observed for variants influencing cholesterol levels, risk of coronary artery disease, body mass index, as well as risk of asthma. These signals exhibit consistent effects in the GERA cohort and among participants of the UK Biobank of non-British ancestry. Moreover, we see marked differences between males and females, most notably at the CHRNA3 locus, and variants associated with risk of coronary artery disease and cholesterol levels. Beyond our findings, the analysis serves as a proof of principle for how upcoming biomedical datasets can be used to learn about selection effects in contemporary humans.

evolutionary biology↗