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bioRxiv2017

Cone-like rhodopsin expressed in the all cone retina of the colubrid pine snake as a potential adaptation to diurnality

Colubridae is the largest and most diverse family of snakes, with visual systems that reflect this diversity, encompassing a variety of retinal photoreceptor organizations. The transmutation theory proposed by Walls postulates that photoreceptors could evolutionarily transition between cell types in squamates, but few studies have tested this theory. Recently, evidence for transmutation and rod-like machinery in an all cone retina has been identified in a diurnal garter snake (Thamnophis), and it appears that the rhodopsin gene at least may be widespread among colubrid snakes. However, functional evidence supporting transmutation beyond the existence of the rhodopsin gene remains rare. We examined the all cone retina of another diurnal colubrid, Pituophis melanoleucus, distantly related to Thamnophis. We found that P. melanoleucus expresses two cone opsins (SWS1, LWS) and rhodopsin (RH1) within the eye. Immunohistochemistry localized rhodopsin to the outer segment of photoreceptors in the all-cone retina of the snake and all opsin genes produced functional visual pigments when expressed in vitro. Consistent with other studies, we found that P. melanoleucus rhodopsin is extremely blue-shifted. Surprisingly, P. melanoleucus rhodopsin reacted with hydroxylamine, a typical cone opsin characteristic. These results support the idea that the rhodopsin-containing photoreceptors of P. melanoleucus are the products of evolutionary transmutation from rod ancestors, and suggests that this phenomenon may be widespread in colubrid snakes. We hypothesize that transmutation may be an adaptation for diurnal, brighter-light vision, which could result in increased spectral sensitivity and chromatic discrimination with the potential for colour vision.\n\nSummary StatementThe all cone retina of the colubrid snake, Pituophis melanoleucus contains a blue-shifted rhodopsin with cone opsin-like properties, which may have been adaptive in diurnal snakes.

evolutionary biology↗

bioRxiv2017

Immune receptors with exogenous domain fusions form evolutionary hotspots in grass genomes

BackgroundThe plant immune system is innate, encoded in the germline. Using it efficiently, plants are capable of recognizing a diverse range of rapidly evolving pathogens. A recently described phenomenon shows that plant immune receptors are able to recognize pathogen effectors through the acquisition of exogenous protein domains from other plant genes.\n\nResultsWe showed that plant immune receptors with integrated domains are distributed unevenly across their phylogeny in grasses. Using phylogenetic analysis, we uncovered a major integration clade, whose members underwent repeated independent integration events producing diverse fusions. This clade is ancestral in grasses with members often found on syntenic chromosomes. Analyses of these fusion events revealed that homologous receptors can be fused to diverse domains. Furthermore, we discovered a 43 amino acids long motif that was associated with this dominant integration clade and was located immediately upstream of the fusion site. Sequence analysis revealed that DNA transposition and/or ectopic recombination are the most likely mechanisms of NLR-ID formation.\n\nConclusionsThe identification of this subclass of plant immune receptors that is naturally adapted to new domain integration will inform biotechnological approaches for generating synthetic receptors with novel pathogen baits.

evolutionary biology↗

bioRxiv2017

Evolution of Reduced Co-Activator Dependence Led to Target Expansion of a Starvation Response Pathway

In S. cerevisiae, the phosphate starvation (PHO) responsive transcription factors Pho4 and Pho2 are jointly required for induction of phosphate response genes and survival in phosphate starvation conditions. In the related human commensal and pathogen C. glabrata, Pho4 is required but Pho2 is dispensable for survival in phosphate-limited conditions and is only partially required for inducing the phosphate response genes. This reduced dependence on Pho2 evolved in C. glabrata and closely related species. Pho4 orthologs that are less dependent on Pho2 induce more genes when introduced into the S. cerevisiae background, and Pho4 in C. glabrata both binds to more sites and induces more genes with expanded functional roles compared to Pho4 in S. cerevisiae. Our work reveals an evolutionary mechanism for rapidly expanding the targets of a transcription factor by changing its dependence on a co-activator, potentially refining the physiological response it regulates.

evolutionary biology↗

bioRxiv2017

Modern human origins: multiregional evolution of autosomes and East Asia origin of Y and mtDNA

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.

evolutionary biology↗

bioRxiv2017

Modern-Day SIV viral diversity generated by extensive recombination and cross-species transmission

Cross-species transmission (CST) has led to many devastating epidemics, but is still a poorly understood phenomenon. HIV-1 and HIV-2 (human immunodeficiency virus 1 and 2), which have collectively caused over 35 million deaths, are the result of multiple CSTs from chimpanzees, gorillas, and sooty mangabeys. While the immediate history of HIV is known, there are over 45 lentiviruses that infect specific species of primates, and patterns of host switching are not well characterized. We thus took a phylogenetic approach to better understand the natural history of SIV recombination and CST. We modeled host species as a discrete character trait on the viral phylogeny and inferred historical host switches and the pairwise transmission rates between each pair of 24 primate hosts. We identify 14 novel, well-supported, ancient cross-species transmission events. We also find that lentiviral lineages vary widely in their ability to infect new host species: SIVcol (from colobus monkeys) is evolutionarily isolated, while SIVagms (from African green monkeys) frequently move between host subspecies. We also examine the origins of SIVcpz (the predecessor of HIV-1) in greater detail than previous studies, and find that there are still large portions of the genome with unknown origins. Observed patterns of CST are likely driven by a combination of ecological circumstance and innate immune factors.

evolutionary biology↗

bioRxiv2017

asymptoticMK: A web-based tool for the asymptotic McDonald-Kreitman test

The McDonald-Kreitman (MK) test is a widely used method for quantifying the role of positive selection in molecular evolution. One key shortcoming of this test lies in its sensitivity to the presence of slightly deleterious mutations, which can severely bias its estimates. An asymptotic version of the MK test was recently introduced that addresses this problem by evaluating polymorphism levels for different mutation frequencies separately, and then extrapolating a function fitted to that data. Here we present asymptoticMK, a web-based implementation of this asymptotic McDonald-Kreitman test. Our web service provides a simple R-based interface into which the user can upload the required data (polymorphism and divergence data for the genomic test region and a neutrally evolving reference region). The web service then analyzes the data and provides plots of the test results. This service is free to use, open-source, and available at http://benhaller.com/messerlab/asymptoticMK.html.

evolutionary biology↗

bioRxiv2017

Unraveling the population history of Indian Siddis

The Siddis are a unique Indian tribe of African, South Asian and European ancestry. While their ancestral origins have been traced to the Bantu populations from sub-Saharan Africa, their population history has remained an enigmatic question. Here, we have traced the biogeographical origin of the Siddis employing an admixture based algorithm, Geographical Population Structure (GPS). We evaluated 14 Siddi genomes in reference to 5 African populations from the 1000 Genomes project and 7 Bantu populations from the Human Genome Diversity project. GPS assigned the Siddi genomes to west Zambia and the present-day border between Zimbabwe and northeastern Botswana, overlapping with one of the principal areas of secondary Bantu settlement in Africa, ~1700 years before present (YBP). This is concordant with the secondary Bantu dispersal route from the east African Bantu center that brought the African ancestors of the Siddis to settlement sites in southeast Africa, from where they were disseminated to India, by the Portuguese. Our results also suggest that while the Siddi genomes are significantly different from that of the Bantus, they displayed the highest genomic proximity to the Luhyas and North-East Bantus from Kenya, and that ancestral Siddis are likely to have split from the Luhyas, ~2700 YBP, in congruence with known Bantu expansion and population migration routes. Together with historical, linguistic and anthropological evidences our findings shine light on the genetic relatedness between populations, fine-scale population structure and recapitulate the population history of the Siddis, in the ethnohistorical context of India.

evolutionary biology↗

bioRxiv2017

A hierarchical Bayesian approach to estimate endosymbiont infection rates

Endosymbionts may play an important role in the evolution of the Insecta. Bacteria such as Wolbachia, Cardinium, and Rickettsia are known to manipulate host reproduction to facilitate their own. Indeed, there are many documented cases where Wolbachia (Alphaproteobacteria: Rickettsiaceae) induces one of four manipulative phenotypes (cytoplasmic incompatibility, male killing, feminization, and parthenogenesis). The scale of infection among species has been a major subject of investigation, but quantification has been difficult because various approaches have yielded different estimates. One under-appreciated aspect of this problem arises when multiple--yet independent--samples are taken within a taxon. When independent samples within a taxon are treated as levels of a hierarchy, the problem is greatly simplified because data are partially pooled according to taxon. Here, we present a hierarchical Bayesian approach to estimate infection frequency where multiple independent samples were collected across several taxonomic levels. We apply this model to estimate the rates of infection for Wolbachia in the Lepidoptera, and then extend the model to account for phylogenetic non-independence. In addition, we highlight the current knowledge regarding Wolbachia and its effects within Lepidoptera. Our model estimates that the rate of endosymbiont infection for the Lepidoptera is approximately 12%. Given our limited knowledge regarding the phenotypes induced by these endosymbionts and the low infection rate, we urge caution when extrapolating the results of positive assays.

evolutionary biology↗

bioRxiv2017

Density-dependent selection in evolutionary genetics: a lottery model of Grime’s triangle

Selection is commonly described by assigning constant relative fitness values to genotypes. Yet population density is often regulated by crowding. Relative fitness may then depend on density, and selection can change density when it acts on a density-regulating trait. When strong density-dependent selection acts on a density-regulating trait, selection is no longer describable by density-independent relative fitnesses, even in demographically stable populations. These conditions are met in most previous models of density-dependent selection (e.g. \"K-selection\" in the logistic and Lotka-Volterra models), suggesting that density-independent relative fitnesses must be replaced with more ecologically explicit absolute fit-nesses unless selection is weak. Here we show that density-independent relative fitnesses can also accurately describe strong density-dependent selection under some conditions. We develop a novel model of density-regulated population growth with three ecologically intuitive traits: fecundity, mortality, and competitive ability. Our model, unlike the logistic or Lotka-Volterra, incorporates a density-dependent juvenile \"reproductive excess\", which largely decouples density-dependent selection from the regulation of density. We find that density-independent relative fitnesses accurately describe strong selection acting on any one trait, even fecundity, which is both density-regulating and subject to density-dependent selection. Pleiotropic interactions between these traits recovers the familiar K-selection behavior. In such cases, or when the population is maintained far from demographic equilibrium, our model offers a possible alternative to relative fitness.

evolutionary biology↗

bioRxiv2017

The role of gene expression in the recent evolution of resistance in a model host parasite system

Damage by parasites is a perpetual challenge for hosts, often leading to the evolution of elaborate mechanisms of avoidance, immunity, or tolerance. Host resistance can evolve via changes in immune protein coding and/or expression. Heritable population differences in gene expression following infection can reveal mechanisms of immune evolution. We compared gene expression in infected and uninfected threespine stickleback (Gasterosteus aculeatus) from two natural populations that differ in their resistance to a native cestode parasite, Schistocephalus solidus. Genes in both the innate and adaptive immune system were differentially expressed as a function of host population, infection status, and their interaction. These genes were enriched for loci controlling immune functions that we independently verified differ between host populations, or in response to infection. For instance, populations differ strongly in reactive oxygen (ROS) production, and we observed corresponding differences in expression of ROS-affecting loci. Differentially expressed genes also were involved in fibroblast activation, B-cell activation, and leukocyte trafficking. Coexpression network analysis identified two distinct immune processes contributing to stickleback resistance; several modules of genes are correlated with parasite survival while a different set of modules are correlated with suppression of cestode growth. Comparison of networks between populations showed resistant fish have a dynamic expression profile while susceptible fish are static. In summary, recent evolutionary divergence between two vertebrate populations has generated population-specific gene expression responses to parasite infection, which reveal a few immune modules likely to separately affect cestode establishment, and growth.

evolutionary biology↗

bioRxiv2017

The genomic basis of adaptation to the deep water ‘twilight zone’ in Lake Malawi cichlid fishes

Deep water environments are characterized by low levels of available light at increasingly narrow spectra, great hydrostatic pressure and reduced dissolved oxygen - conditions predicted to exert highly specific selection pressures. In Lake Malawi over 800 cichlid species have evolved, and this adaptive radiation extends into the \"twilight zone\" below 100 metres. We use population-level RAD-seq data to investigate whether four endemic deep water species (Diplotaxodon spp.) have experienced divergent selection within this environment. We identify candidate genes including regulators of photoreceptor function, photopigments, lens morphology and haemoglobin, many not previously implicated in cichlid adaptive radiations. Co-localization of functionally linked genes suggests co-adapted \"supergene\" complexes. Comparisons of Diplotaxodon to the broader Lake Malawi radiation using genome resequencing data revealed functional substitutions in candidate genes. Our data provide unique insights into genomic adaptation to life at depth, and suggest genome-level specialisation for deep water habitat as an important process in cichlid radiation.

evolutionary biology↗

bioRxiv2017

Resolution of conflict between parental genomes in a hybrid species

The development of reproductive barriers against parent species is crucial during hybrid speciation, and post-zygotic isolation can be important in this process. Genetic incompatibilities that normally isolate the parent species can become sorted in hybrids to form reproductive barriers towards either parent. However, the extent to which this sorting process is systematically biased and therefore predictable in which loci are involved and which alleles are favored is largely unknown. Theoretically, reduced fitness in hybrids due to the mixing of differentiated genomes can be resolved through rapid evolution towards allelic combinations ancestral to lineage-splitting of the parent species, as these alleles have successfully coexisted in the past. However, for each locus, this effect may be influenced by its chromosomal location, function, and interactions with other loci. We use the Italian sparrow, a homoploid hybrid species that has developed post-zygotic barriers against its parent species, to investigate this prediction. We show significant bias towards fixation of the ancestral allele among 57 nuclear intragenic SNPs, particularly those with a mitochondrial function whose ancestral allele came from the same parent species as the mitochondria. Consistent with increased pleiotropy leading to stronger fitness effects, genes with more protein-protein interactions were more biased in favor of the ancestral allele. Furthermore, the number of protein-protein interactions was especially low among candidate incompatibilities still segregating within Italian sparrows, suggesting that low pleiotropy allows steep intraspecific clines in allele frequencies to form. Finally, we report evidence for pervasive epistatic interactions within one Italian sparrow population, particularly involving loci isolating the two parent species but not hybrid and parent. However there was a lack of classic incompatibilities and no admixture linkage disequilibrium. This suggests that parental genome admixture can continue to constrain evolution and prevent genome stabilization long after incompatibilities have been purged.

evolutionary biology↗

bioRxiv2017

Inferring the Joint Demographic History of Multiple Populations: Beyond the Diffusion Approximation

Understanding variation in allele frequencies across populations is a central goal of population genetics. Classical models for the distribution of allele frequencies, using forward simulation, coalescent theory, or the diffusion approximation, have been applied extensively for demographic inference, medical study design, and evolutionary studies. Here we propose a tractable model of ordinary differential equations for the evolution of allele frequencies that is closely related to the diffusion approximation but avoids many of its limitations and approximations. We show that the approach is typically faster, more numerically stable, and more easily generalizable than the state-of-the-art software implementation of the diffusion approximation. We present a number of applications to human sequence data, including demographic inference with a five-population joint frequency spectrum and a discussion of the transferability of demographic histories across populations.

evolutionary biology↗

bioRxiv2017

Contemporary evolution of a Lepidopteran species, Heliothis virescens, in response to modern agricultural practices

Adaptation to human-induced environmental change has the potential to profoundly influence the genomic architecture of affected species. This is particularly true in agricultural ecosystems, where anthropogenic selection pressure is strong. Heliothis virescens feeds on cotton in its larval stages and US populations have been declining since the widespread planting of transgenic cotton, which endogenously express proteins derived Bacillus thuringiensis (Bt). No physiological adaptation to Bt toxin has been found in the field, so adaptation to this altered environment could involve: 1) shifts in host plant selection mechanisms to avoid cotton, 2) changes in detoxification mechanisms required for cotton-feeding versus feeding on other host plants, or 3) loss of resistance to previously used management practices including insecticides. Here we begin to address the question of whether such changes occurred in H. virescens populations between the years 1997 and 2012. As part of our study, we produced an H. virescens genome assembly and used this in concert with a ddRAD-seq enabled genome scan to identify loci with significant allele frequency changes over the 15 year period after Bt crops became widespread in the agricultural landscape. Confirmation that a known genetic change at a previously described H. virescens target of selection was detectable in our genome scan increased our confidence in this methodology. We quantified the strength of selection required to elicit the observed allele frequency changes at loci under selection. Potential contributions of genes near the loci under selection to adaptive phenotypes in the H. virescens cotton system are discussed.

evolutionary biology↗

bioRxiv2017

The mitochondrial genomes of the acoelomorph wormsParatomella rubra and Isodiametra pulchra

Acoels are small, ubiquitous, but understudied, marine worms with a very simple body plan. Their internal phylogeny is still in parts unresolved, and the position of their proposed phylum Xenacoelomorpha (Xenoturbella+Acoela) is still debated.\n\nHere we describe mitochondrial genome sequences from two acoel species: Paratomella rubra and Isodiametra pulchra. The 14,954 nucleotide-long P. rubra sequence is typical for metazoans in size and gene content. The larger I. pulchra mitochondrial genome contains both ribosomal genes, 21 tRNAs, but only 11 protein-coding genes. We find evidence suggesting a duplicated sequence in the I. pulchra mitochondrial genome.\n\nMitochondrial sequences for both P. rubra and I. pulchra have a unique genome organisation in comparison to other published metazoan mitochondrial genomes. We found a large degree of protein-coding gene and tRNA overlap in P. rubra, with little non-coding sequence making the genome compact. Conversely, the I. pulchra mitochondrial genome has many long non-coding sequences between genes, likely driving the genome size expansion. Phylogenetic trees inferred from concatenated alignments of mitochondrial genes grouped the fast-evolving Acoela and Tunicata, almost certainly due to the systematic error of long branch attraction: a reconstruction artefact that is probably compounded by the fast substitution rate of mitochondrial genes in this taxon.

evolutionary biology↗

bioRxiv2017

Experimental evidence that thermal selection has shaped the latitudinal distribution of mitochondrial haplotypes in Australian fruit flies

Cellular metabolism is regulated by enzyme complexes within the mitochondrion, the function of which are sensitive to the prevailing temperature. Such thermal sensitivity, coupled with the observation that population frequencies of mitochondrial haplotypes tend to associate with latitude, altitude or climatic regions across species distributions, led to the hypothesis that thermal selection has played a role in shaping standing variation in the mitochondrial DNA (mtDNA) sequence. This hypothesis, however, remains controversial, and requires evidence that the distribution of haplotypes observed in nature corresponds with the capacity of these haplotypes to confer differences in thermal tolerance. Specifically, haplotypes predominating in tropical climates are predicted to encode increased tolerance to heat stress, but decreased tolerance to cold stress. We present direct evidence for these predictions, using mtDNA haplotypes sampled from the Australian distribution of Drosophila melanogaster. We show that the ability of flies to tolerate extreme thermal challenges is affected by sequence variation across mtDNA haplotypes, and that the thermal performance associated with each haplotype corresponds with its latitudinal prevalence. The haplotype that predominates at low (subtropical) latitudes confers greater resilience to heat stress, but lower resilience to cold stress, than haplotypes predominating at higher (temperate) latitudes. We explore molecular mechanisms that might underlie these responses, presenting evidence that the effects are in part regulated by SNPs that do not change the protein sequence. Our findings suggest that standing variation in the mitochondrial genome can be shaped by thermal selection, and could therefore contribute to evolutionary adaptation under climatic stress.

evolutionary biology↗

bioRxiv2017

High GC Content Causes De Novo Created Proteins to be Intrinsically Disordered

De novo creation of protein coding genes involves the formation of short ORFs from noncoding regions; some of these ORFs might then become fixed in the populationThese orphan proteins need to, at the bare minimum, not cause serious harm to the organism, meaning that they should for instance not aggregate. Therefore, although the creation of short ORFs could be truly random, the fixation should be subjected to some selective pressure. The selective forces acting on orphan proteins have been elusive, and contradictory results have been reported. In Drosophila young proteins are more disordered than ancient ones, while the opposite trend is present in yeast. To the best of our knowledge no valid explanation for this difference has been proposed.\n\nTo solve this riddle we studied structural properties and age of proteins in 187 eukaryotic organisms. We find that, with the exception of length, there are only small differences in the properties between proteins of different ages. However, when we take the GC content into account we noted that it could explain the opposite trends observed for orphans in yeast (low GC) and Drosophila (high GC). GC content is correlated with codons coding for disorder promoting amino acids. This leads us to propose that intrinsic disorder is not a strong determining factor for fixation of orphan proteins. Instead these proteins largely resemble random proteins given a particular GC level. During evolution the properties of a protein change faster than the GC level causing the relationship between disorder and GC to gradually weaken.\n\nAuthor SummaryWe show that the GC content of a genome is of great importance for the properties of an orphan protein. GC content affects the frequency of the codons and this affects the probability for each amino acid to be included in a de novo created protein. The codons encoding for Ala, Pro and Gly contain 80% GC, while codons for Lys, Phe, Asn, Tyr and Ile contain 20% or less. The three high GC amino acids are all disorder promoting, while Phe, Tyr and Ile are order promoting. Therefore, random protein sequences at a high GC will be more disordered than the ones created at a low GC. The structural properties of the youngest proteins match to a large degree the properties of random proteins when the GC content is taken into account. In contrast, structural properties of ancient proteins only show a weak correlation with GC content. This suggests that even after fixation in the population, proteins largely resemble random proteins given a certain GC content. Thereafter, during evolution the correlation between structural properties and GC weakens.

evolutionary biology↗

bioRxiv2017

Joint estimation of relatedness coefficients and allele frequencies from ancient samples

We develop and test a method to address whether DNA samples sequenced from a group of fossil hominin bone or teeth fragments originate from the same individual or from closely related individuals. Our method assumes low amounts of retrievable DNA, significant levels of sequencing error and contamination from one or more present-day humans. We develop and implement a maximum likelihood method that estimates levels of contamination, sequencing error rates and pairwise relatedness co-efficients in a set of individuals. We assume there is no reference panel for the ancient population to provide allele and haplotype frequencies. Our approach makes use of single nucleotide polymorphisms and does not make assumptions about the underlying demographic model. By artificially mating individual genomes from the 1000 Genomes Project, we determine the numbers of individuals at a given genomic coverage that are required to detect different levels of genetic relatedness with confidence.

evolutionary biology↗