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bioRxiv2015

Site-specific amino-acid preferences are mostly conserved in two closely related protein homologs

Evolution drives changes in a proteins sequence over time. The extent to which these changes in sequence lead to shifts in the underlying preference for each amino acid at each site is an important question with implications for comparative sequence-analysis methods such as molecular phylogenetics. To quantify the extent that site-specific amino-acid preferences shift during evolution, we performed deep mutational scanning on two homologs of human influenza nucleoprotein with 94% amino-acid identity. We found that only a modest fraction of sites exhibited shifts in amino-acid preferences that exceeded the noise in our experiments. Furthermore, even among sites that did exhibit detectable shifts, the magnitude tended to be small relative to differences between non-homologous proteins. Given the limited change in amino-acid preferences between these close homologs, we tested whether our measurements could inform site-specific substitution models that describe the evolution of nucleoproteins from more diverse influenza viruses. We found that site-specific evolutionary models informed by our experiments greatly outperformed non-site-specific alternatives in fitting phylogenies of nucleoproteins from human, swine, equine, and avian influenza. Combining the experimental data from both homologs improved phylogenetic fit, partly because measurements in multiple genetic contexts better captured the evolutionary average of the amino-acid preferences for sites with shifting preferences. Our results show that site-specific amino-acid preferences are sufficiently conserved that measuring mutational effects in one protein provides information that can improve quantitative evolutionary modeling of nearby homologs.

Evolutionary Biology↗

bioRxiv2015

Selection for Intermediate Genotypes Enables a Key Innovation in Phage Lambda

The evolution of qualitatively new functions is fundamental for shaping the diversity of life. Such innovations are rare because they require multiple coordinated changes. We sought to understand the evolutionary processes involved in a particular key innovation, whereby phage {lambda} evolved the ability to exploit a novel receptor, OmpF, on the surface of Escherichia coli cells. Previous work has shown that this transition repeatedly evolves in the laboratory, despite requiring four mutations in specific regions of a single gene. Here we examine how this innovation evolved by studying six intermediate genotypes that arose during independent transitions to use OmpF. In particular, we tested whether these genotypes were favored by selection, and how a coevolved change in the hosts influenced the fitness of the phage genotypes. To do so, we measured the fitness of the intermediate types relative to the ancestral {lambda} when competing for either ancestral or coevolved host cells. All six intermediates had improved fitness on at least one host, and four had higher fitness on the coevolved host than on the ancestral host. These results show that the evolution of the phages new ability to use OmpF was repeatable because the intermediate genotypes were adaptive and, in many cases, because coevolution of the host favored their emergence.

Evolutionary Biology↗

bioRxiv2015

Detecting recent selective sweeps while controlling for mutation rate and background selection

A composite likelihood ratio test implemented in the program SweepFinder is a commonly used method for scanning a genome for recent selective sweeps. SweepFinder uses information on the spatial pattern of the site frequency spectrum (SFS) around the selected locus. To avoid confounding effects of background selection and variation in the mutation process along the genome, the method is typically applied only to sites that are variable within species. However, the power to detect and localize selective sweeps can be greatly improved if invariable sites are also included in the analysis. In the spirit of a Hudson-Kreitman-Aguade test, we suggest to add fixed differences relative to an outgroup to account for variation in mutation rate, thereby facilitating more robust and powerful analyses. We also develop a method for including background selection modeled as a local reduction in the effective population size. Using simulations we show that these advances lead to a gain in power while maintaining robustness to mutation rate variation. Furthermore, the new method also provides more precise localization of the causative mutation than methods using the spatial pattern of segregating sites alone.

Evolutionary Biology↗

bioRxiv2015

Climatic niches in phylogenetic comparative studies: a review of challenges and approaches

Studying the evolution of climatic niches through time in a phylogenetic comparative framework combines species distribution modeling with phylogenies. Phylogenetic comparative studies aid the understanding of the evolution of species environmental preferences by revealing the underlying evolutionary processes and causes, detecting the differences among groups of species or relative to evolutionary pattern of other phenotypic traits, but also act as a yardstick to gauge the adaptational potential under climate change. Because several alternatives exist on how to compute and represent the climatic niche, we here review and discuss the current state of the art and propose a best practice to use in comparative studies. Moreover we outline the common evolutionary models and available model-fitting methods and describe the procedure for ancestral niche reconstruction with the intention to give a broad overview and highlight the most advanced approaches for optimal niche-related comparative studies.

Evolutionary Biology↗

bioRxiv2015

Driven to Extinction: On the Probability of Evolutionary Rescue from Sex-Ratio Meiotic Drive

Many evolutionary processes result in sufficiently low mean fitness that they pose a risk of species extinction. Sex-ratio meiotic drive was recognized by W.D. Hamilton (1967) to pose such a risk, because as the driving sex chromosome becomes common, the opposite sex becomes rare. We expand on Hamiltons classic model by allowing for the escape from extinction due to evolution of suppressors of X and Y drivers. We explore differences in the two systems in their probability of escape from extinction. Several novel conclusions are evident, including a) that extinction time scales approximately with the log of population size so that even large populations may go extinct quickly, b) extinction risk is driven by the relationship between female fecundity and drive strength, c) anisogamy and the fact that X and Y drive result in sex ratios skewed in opposite directions, mean systems with Y drive are much more likely to go extinct than those with X drive, and d) suppressors are most likely to become established when the strength of drive is intermediate, since weak drive leads to weak selection for suppression and strong drive leads to rapid extinction.

Evolutionary Biology↗

bioRxiv2015

A Chronological Atlas of Natural Selection in the Human Genome during the Past Half-million Years

The spatiotemporal distribution of recent human adaptation is a long standing question. We developed a new coalescent-based method that collectively assigned human genome regions to modes of neutrality or to positive, negative, or balancing selection. Most importantly, the selection times were estimated for all positive selection signals, which ranged over the last half million years, penetrating the emergence of anatomically modern human (AMH). These selection time estimates were further supported by analyses of the genome sequences from three ancient AMHs and the Neanderthals. A series of brain function-related genes were found to carry signals of ancient selective sweeps, which may have defined the evolution of cognitive abilities either before Neanderthal divergence or during the emergence of AMH. Particularly, signals of brain evolution in AMH are strongly related to Alzheimers disease pathways. In conclusion, this study reports a chronological atlas of natural selection in Human.

Evolutionary Biology↗

bioRxiv2015

Theoretical consequences of the Mutagenic Chain Reaction for manipulating natural populations

ABTRACTThe use of recombinant genetic technologies for population manipulation has mostly remained an abstract idea due to the lack of a suitable means to drive novel gene constructs to high frequency in populations. Recently Gantz and Bier showed that the use of CRISPR/Cas9 technology could provide an artificial drive mechanism, the so-called Mutagenic Chain Reaction (MCR), which could lead to rapid fixation of even a deleterious introduced allele. We establish the equivalence of this system to models of meiotic drive and review the results of simple models showing that, when there is a fitness cost to the MCR allele, an internal equilibrium exists that is usually unstable. Introductions must be at a frequency above this critical point for the successful invasion of the MCR allele. These modeling results have important implications for application of MCR in natural populations.

Evolutionary Biology↗

bioRxiv2015

Bayesian Inference of Divergence Times and Feeding Evolution in Grey Mullets (Mugilidae)

Grey mullets (Mugilidae, Ovalentariae) are coastal fishes found in near-shore environments of tropical, subtropical, and temperate regions within marine, brackish, and freshwater habitats throughout the world. This group is noteworthy both for the highly conserved morphology of its members--which complicates species identification and delimitation--and also for the uncommon herbivorous or detritivorous diet of most mullets. In this study, we first attempt to identify the number of mullet species, and then--for the resulting species--estimate a densely sampled time-calibrated phylogeny using three mitochondrial gene regions and three fossil calibrations. Our results identify two major subgroups of mullets that diverged in the Paleocene/Early Eocene, followed by an Eocene/Oligocene radiation across both tropical and subtropical habitats. We use this phylogeny to explore the evolution of feeding preference in mullets, which indicates multiple independent origins of both herbivorous and detritivorous diets within this group. We also explore correlations between feeding preference and other variables, including body size, habitat (marine, brackish, or freshwater), and geographic distribution (tropical, subtropical, or temperate). Our analyses reveal: (1) a positive correlation between trophic index and habitat (with herbivorous and/or detritivorous species predominantly occurring in marine habitats); (2) a negative correlation between trophic index and geographic distribution (with herbivorous species occurring predominantly in subtropical and temperate regions), and; (3) a negative correlation between body size and geographic distribution (with larger species occurring predominantly in subtropical and temperate regions).

Evolutionary Biology↗

bioRxiv2015

Mitochondria, mutations and sex: a new hypothesis for the evolution of sex based on mitochondrial mutational erosion

The evolution of sex in eukaryotes represents a paradox, given the \"two-fold\" fitness cost it incurs. We hypothesize that the mutational dynamics of the mitochondrial genome would have favoured the evolution of sexual reproduction. Mitochondrial DNA (mtDNA) exhibits a high mutation rate across most eukaryote taxa, and several lines of evidence suggest this high rate is an ancestral character. This seems inexplicable given mtDNA-encoded genes underlie the expression of lifes most salient functions, including energy conversion. We propose that negative metabolic effects linked to mitochondrial mutation accumulation would have invoked selection for sexual recombination between divergent host nuclear genomes in early eukaryote lineages. This would provide a mechanism by which recombinant host genotypes could be rapidly shuffled and screened for the presence of compensatory modifiers that offset mtDNA-induced harm. Under this hypothesis, recombination provides the genetic variation necessary for compensatory nuclear coadaptation to keep pace with mitochondrial mutation accumulation.

Evolutionary Biology↗

bioRxiv2015

Coalescent times and patterns of genetic diversity in species with facultative sex: effects of gene conversion, population structure and heterogeneity

Many diploid organisms undergo facultative sexual reproduction. However, little is currently known concerning the distribution of neutral genetic variation amongst facultative sexuals except in very simple cases. Under-standing this distribution is important when making inferences about rates of sexual reproduction, effective population size and demographic history. Here, we extend coalescent theory in diploids with facultative sex to consider gene conversion, selfing, population subdivision, and temporal and spatial heterogeneity in rates of sex. In addition to analytical results for two-sample coalescent times, we outline a coalescent algorithm that accommodates the complexities arising from partial sex; this algorithm can be used to generate multi-sample coalescent distributions. A key result is that when sex is rare, gene conversion becomes a significant force in reducing diversity within individuals, which can remove genomic signatures of infrequent sex (the Meselson Effect) or entirely reverse the predictions. Our models offer improved methods for assessing the null model (I.e. neutrality) of patterns of molecular variation in facultative sexuals.

Evolutionary Biology↗

bioRxiv2015

Coregulation of tandem duplicate genes slows evolution of subfunctionalization in mammals.

Gene duplication is a fundamental process in genome evolution. However, most young duplicates are degraded into pseudogenes by loss-of-function mutations, and the factors that allow some duplicate pairs to survive long-term remain controversial. One class of models to explain duplicate retention invokes sub- or neofunctionalization, especially through evolution of gene expression, while other models focus on sharing of gene dosage. While studies of whole genome duplications tend to support dosage sharing, the primary mechanisms in mammals-where duplications are small-scale and thus disrupt dosage balance- are unclear. Using RNA-seq data from 46 human and 26 mouse tissues we find that sub-functionalization of expression evolves slowly, and is rare among duplicates that arose within the placental mammals. A major impediment to subfunctionalization is that tandem duplicates tend to be co-regulated by shared genomic elements, in contrast to the standard assumption of modularity of gene expression. Instead, consistent with the dosage-sharing hypothesis, most young duplicates are down-regulated to match expression of outgroup singleton genes. Our data suggest that dosage sharing of expression is a key factor in the initial survival of mammalian duplicates, followed by slower functional adaptation enabling long-term preservation.

Evolutionary Biology↗

bioRxiv2015

Molecular Fossils from Microorganisms Preserved in Glacial Ice

The study of microbial evolution is hindered by the fact that microbial populations leave few fossils. We hypothesized that bacterial cells preserved in ancient ice could be used as a molecular fossil record if their DNA could be extracted and sequenced. Channels formed along triple junctions of ice crystals contain liquid \"veins\" in which microbial cells may be preserved intact. Since vertical motion through the ice matrix is impossible, microbes found in ice cores are representative of microbes present at the time the ice was formed. We detected chlorophyll fluorescence in intact ice cores taken from Greenland and Antarctica. Flow cytometric analysis localized at least some of this fluorescence to particles < 1 m in diameter. Metagenomic analysis of meltwater indeed revealed sequences similar to modern strains of the picocyanobacterial genera Synechococcus and Prochlorococcus, and some of these sequences were distinct from any sequences known from modern oceans or glacial environments. Our study is a first proof-of-concept of the use of ice cores as records of microbial evolution, and we suggest that future genetic studies with higher vertical resolution in the cores might shed light on the pace and character of evolution of these ecologically important cells.

Evolutionary Biology↗

bioRxiv2015

Worldwide population structure, long term demography, and local adaptation of Helicobacter pylori

Helicobacter pylori is an important human pathogen associated with serious gastric diseases. Owing to its medical importance and close relationship with its human host, understanding genomic patterns of global and local adaptation in H. pylori may be of particular significance for both clinical and evolutionary studies. Here we present the first such whole-genome analysis of 60 globally distributed strains, from which we inferred worldwide population structure and demographic history and shed light on interesting global and local events of positive selection, with particular emphasis on the evolution of San-associated lineages. Our results indicate a more ancient origin for the association of humans and H. pylori than previously thought. We identify several important perspectives for future clinical research on candidate selected regions that include both previously characterized genes (e.g. transcription elongation factor NusA and tumor Necrosis Factor Alpha-Inducing Protein Tip) and hitherto unknown functional genes.

Evolutionary Biology↗

bioRxiv2015

Shifts in diversification rates linked to biogeographic movement into new areas, an example of disparate continental distributions and a recent radiation in the Andes

AcknowledgementsWe would like to thank S. Mathews for kindly sharing genomic DNA for some taxa used in this study. J. Sullivan, L. Harmon, E. Roalson, J. Beaulieu, B. Moore, N. Nurk, M. Pennell, T. Peterson, and two anonymous reviewers for helpful suggestions or comments on the manuscript. J. Beaulieu, L. Harmon, C. Blair and the University of Idaho Institute for Bioinformatics and Evolutionary Studies (NIH/NCRR P20RR16448 and P20RR016454) for computational aid. Funding for this work was provided by NSF DEB-1210895 to DCT for SUC, NSF DEB-1253463 to DCT, and Graduate Student Research Grants to SUC from the Botanical Society of America (BSA), the Society of Systematic Biologists (SSB), the American Society of Plant Taxonomists (ASPT), and the University of Idaho Stillinger Herbarium Expedition Funds.\n\nPremise of the studyClade specific bursts in diversification are often associated with the evolution of key innovations. However, in groups with no obvious morphological innovations, observed upticks in diversification rates have also been attributed to the colonization of a new geographic environment. In this study, we explore the systematics, diversification dynamics, and historical biogeography of the plant clade Rhinantheae in the Orobanchaceae, with a special focus on the Andean clade of the genus Bartsia L..\n\nMethodsWe sampled taxa from across Rhinantheae, including a representative sample of Andean Bartsia species. Using standard phylogenetic methods, we reconstructed evolutionary relationships, inferred divergence times among the clades of Rhinantheae, elucidated their biogeographic history, and investigated diversification dynamics.\n\nKey resultsWe confirmed that the South American Bartsia species form a highly supported monophyletic group. The median crown age of Rhinantheae was determined to be ca. 30 Ma, and Europe played an important role in the biogeographic history of the lineages. South America was first reconstructed in the biogeographic analyses around 9 Ma, and with a median age of 2.59 Ma, this clade shows a significant uptick in diversification.\n\nConclusionsIncreased net diversification of the South American clade corresponds with biogeographic movement into the New World. This happened at a time when the Andes were reaching the necessary elevation to host an alpine environment. Although a specific route could not be identified with certainty, we provide plausible hypotheses to how the group colonized the New World.

Evolutionary Biology↗

bioRxiv2015

A Coalescent Model of a Sweep from a Uniquely Derived Standing Variant

The use of genetic polymorphism data to understand the dynamics of adaptation and identify the loci that are involved has become a major pursuit of modern evolutionary genetics. In addition to the classical \"hard sweep\" hitchhiking model, recent research has drawn attention to the fact that the dynamics of adaptation can play out in a variety of different ways, and that the specific signatures left behind in population genetic data may depend somewhat strongly on these dynamics. One particular model for which a large number of empirical examples are already known is that in which a single derived mutation arises and drifts to some low frequency before an environmental change causes the allele to become beneficial and sweeps to fixation. Here, we pursue an analytical investigation of this model, bolstered and extended via simulation study. We use coalescent theory to develop an analytical approximation for the effect of a sweep from standing variation on the genealogy at the locus of the selected allele and sites tightly linked to it. We show that the distribution of haplotypes that the selected allele is present on at the time of the environmental change can be approximated by considering recombinant haplotypes as alleles in the infinite alleles model. We show that this approximation can be leveraged to make accurate predictions regarding patterns of genetic polymorphism following such a sweep. We then use simulations to highlight which sources of haplotypic information are likely to be most useful in distinguishing this model from neutrality, as well as from other sweep models, such as the classic hard sweep, and multiple mutation soft sweeps. We find that in general, adaptation from a uniquely derived standing variant will be difficult to detect on the basis of genetic polymorphism data alone, and when it can be detected, it will be difficult to distinguish from other varieties of selective sweeps.

Evolutionary Biology↗

bioRxiv2015

Endless forms most beau-toe-ful: evolution of the human hallux

BackgroundThe adduction of the first pedal ray in humans, such that the hallux is incapable of functional opposability, is a major feature of the evolution of the hominin foot (e.g. Darwin 1872, Haeckel 1879, Latimer and Lovejoy 1990). While hallucal adduction facilitates obligate bipedalism, it inhibits but does not eliminate arboreal grasping ability. The angle of the hallux (as determined by the longitudinal axis of the first metatarsal) relative to the rest of the foot (as determined by the longitudinal axis of the second metatarsal) is a product of both hard-and soft-tissues. Given the failure of soft tissue to fossilize, direct evidence for hallucal angle evolution is scanty, and consensus has not emerged as to when and how the modern human condition of hallucal non-opposability evolved.\n\nMethodology/Principal FindingsAnalysis of a large sample (n = 331) of radiographs taken from the dorsal aspect of living human feet elucidates the relationship between osteological measures and the magnitude of hallucal adduction, which is resultant of both hard-and soft-tissue anatomy (Lovejoy et al. 2009). I describe the correlation of hallucal convergence with first metatarsal posterior articular facet morphology, which allows inference of hallucal convergence in the absence of the medial cuneiform. I report parameters of modern human hallucal convergence variation and offer insight into the hominin fossil record. I infer that the hallucal convergence of the recently reported specimen from Burtele (BRT-VP-2/73) falls within the range of living human variation, inconsistent with the interpretation that this hominin retained the ability to oppose its great toe for the purpose of arboreal locomotion (Haile-Selassie et al. 2012). Of the fossil hominin first metatarsals surveyed, all fall within the range of living human variation, consistent with previous research on medial cuneiform (McHenry and Jones 2006) and first metatarsal (Berillon 1999) morphology.\n\nConclusions/SignificanceThis study finds that the modern human condition of hallucal non-opposability was present in the genus Australopithecus. However, while the Burtele specimen (BRT-VP-2/73) falls within the range of living human variation, it displays a markedly divergent hallux compared to most living humans. This study suggests that, as in humans today, there was variation in hallucal divergence in Plio-Pleistocene hominins. Rather than using the terms opposability and the ambiguously synonymous grasping, I suggest here the term clamping (as in the motion performed by a clamp) be used to describe the less powerful and less dexterous ability of modern humans to place and hold a thin, narrow object between the great toe and second toe ray in a limited, albeit functional, manner.

Evolutionary Biology↗

bioRxiv2015

Genomic epidemiology of the current wave of artemisinin resistant malaria

Artemisinin resistant Plasmodium falciparum is advancing across Southeast Asia in a soft selective sweep involving at least 20 independent kelch13 mutations. In a large global survey, we find that kelch13 mutations which cause resistance in Southeast Asia are present at low frequency in Africa. We show that African kelch13 mutations have originated locally, and that kelch13 shows a normal variation pattern relative to other genes in Africa, whereas in Southeast Asia there is a great excess of non-synonymous mutations, many of which cause radical amino-acid changes. Thus, kelch13 is not currently undergoing strong selection in Africa, despite a deep reservoir of standing variation that could potentially allow resistance to emerge rapidly. The practical implications are that public health surveillance for artemisinin resistance should not rely on kelch13 data alone, and interventions to prevent resistance must account for local evolutionary conditions, shown by genomic epidemiology to differ greatly between geographical regions.

Evolutionary Biology↗

bioRxiv2015

RAD sequencing enables unprecedented phylogenetic resolution and objective species delimitation in recalcitrant divergent taxa

Species delimitation is problematic in many taxa due to the difficulty of evaluating predictions from species delimitation hypotheses, which chiefly relay on subjective interpretations of morphological observations and/or DNA sequence data. This problem is exacerbated in recalcitrant taxa for which genetic resources are scarce and inadequate to resolve questions regarding evolutionary relationships and uniqueness. In this case study we demonstrate the empirical utility of restriction site associated DNA sequencing (RAD-seq) by unambiguously resolving phylogenetic relationships among recalcitrant octocoral taxa with divergences greater than 80 million years. We objectively infer robust species boundaries in the genus Paragorgia, which contains some of the most important ecosystem engineers in the deep-sea, by testing alternative taxonomy-guided or unguided species delimitation hypotheses using the Bayes factors delimitation method (BFD*) with genome-wide single nucleotide polymorphism data. We present conclusive evidence rejecting the current morphological species delimitation model for the genus Paragorgia and indicating the presence of cryptic species boundaries associated with environmental variables. We argue that the suitability limits of RAD-seq for phylogenetic inferences in divergent taxa cannot be assessed in terms of absolute time, but depend on taxon-specific factors such as mutation rate, generation time and effective population size. We show that classic morphological taxonomy can greatly benefit from integrative approaches that provide objective tests to species delimitation hypothesis. Our results pave the way for addressing further questions in biogeography, species ranges, community ecology, population dynamics, conservation, and evolution in octocorals and other marine taxa.

Evolutionary Biology↗