Nucleotide variation and balancing selection at the Ckma gene in Atlantic cod: analysis with multiple merger coalescent models

Determinants of rapid adaptation in species with large variance in offspring production

The speed of population adaptation to changing biotic and abiotic environments is determined by the interaction between genetic drift, positive selection and linkage effects. Many marine species (fish, crustaceans), invertebrates and pathogens of humans and crops, exhibit sweepstakes reproduction characterized by the production of a very large amount of offspring (fecundity phase) from which only a small fraction may survive to the next generation (viability phase). Using stochastic simulations, we investigate whether the occurrence of sweepstakes reproduction affects the efficiency of a positively selected unlinked locus, and thus, the speed of adaptation since fecundity and/or viability have distinguishable consequences on mutation rate, probability and fixation time of advantageous alleles. We observe that the mean number of mutations at the next generation is always the function of the population size, but the variance increases with stronger sweepstakes reproduction when mutations occur in the parents. On the one hand, stronger sweepstakes reproduction magnifies the effect of genetic drift thus increasing the probability of fixation of neutral allele and decreasing that of selected alleles. On the other hand, the time to fixation of advantageous (as well as neutral) alleles is shortened by stronger sweepstakes reproduction. Importantly, fecundity and viability selection exhibit different probabilities and times to fixation of advantageous alleles under intermediate and weak sweepstakes reproduction. Finally, alleles under both strong fecundity and viability selection display a synergistic efficiency of selection. We conclude that measuring and modelling accurately fecundity and/or viability selection are crucial to predict the adaptive potential of species with sweepstakes reproduction.

Sweepstakes reproduction facilitates rapid adaptation in highly fecund populations

Adaptation enables natural populations to survive in a changing environment. Understanding the mechanics of adaptation is therefore crucial for learning about the evolution and ecology of natural populations. We focus on the impact of random sweepstakes on selection in highly fecund haploid and diploid populations partitioned into two genetic types, with one type conferring selective advantage. For the diploid populations, we incorporate various dominance mechanisms. We assume that the populations may experience recurrent bottlenecks. In random sweepstakes, the distribution of individual recruitment success is highly skewed, resulting in a huge variance in the number of offspring contributed by the individuals present in any given generation. Using computer simulations, we investigate the joint effects of random sweepstakes, recurrent bottlenecks and dominance mechanisms on selection. In our framework, bottlenecks allow random sweepstakes to have an effect on the time to fixation, and in diploid populations, the effect of random sweepstakes depends on the dominance mechanism. We describe selective sweepstakes that are approximated by recurrent sweeps of strongly beneficial allelic types arising by mutation. We demonstrate that both types of sweepstakes reproduction may facilitate rapid adaptation (as defined based on the average time to fixation of a type conferring selective advantage conditioned on fixation of the type). However, whether random sweepstakes cause rapid adaptation depends also on their interactions with bottlenecks and dominance mechanisms. Finally, we review a case study in which a model of recurrent sweeps is shown to essentially explain population genomic data from Atlantic cod.

Sweepstakes reproductive success via pervasive and recurrent selective sweeps

Highly fecund natural populations characterized by high early mortality abound, yet our knowledge about their recruitment dynamics is somewhat rudimentary. This knowledge gap has implications for our understanding of genetic variation, population connectivity, local adaptation, and the resilience of highly fecund populations. The concept of sweepstakes reproductive success, which posits a considerable variance and skew in individual reproductive output, is key to understanding the distribution of individual reproductive success. However, it still needs to be determined whether highly fecund organisms reproduce through sweepstakes and, if they do, the relative roles of neutral and selective sweepstakes. Here, we use coalescent-based statistical analysis of population genomic data to show that selective sweepstakes likely explain recruitment dynamics in the highly fecund Atlantic cod. We show that the Kingman coalescent (modelling no sweepstakes) and the Xi-Beta coalescent (modelling random sweepstakes), including complex demography and background selection, do not provide an adequate fit for the data. The Durrett-Schweinsberg coalescent, in which selective sweepstakes result from recurrent and pervasive selective sweeps of new mutations, offers greater explanatory power. Our results show that models of sweepstakes reproduction and multiple-merger coalescents are relevant and necessary for understanding genetic diversity in highly fecund natural populations. These findings have fundamental implications for understanding the recruitment variation of fish stocks and general evolutionary genomics of high-fecundity organisms.

Multiple Merger Genealogies in Outbreaks of Mycobacterium tuberculosis

The Kingman coalescent and its developments are often considered among the most important advances in population genetics of the last decades. Demographic inference based on coalescent theory has been used to reconstruct the population dynamics and evolutionary history of several species, including Mycobacterium tuberculosis (MTB), an important human pathogen causing tuberculosis. One key assumption of the Kingman coalescent is that the number of descendants of different individuals does not vary strongly, and violating this assumption could lead to severe biases caused by model misspecification. Individual lineages of MTB are expected to vary strongly in reproductive success because 1) MTB is potentially under constant selection due to the pressure of the host immune system and of antibiotic treatment, 2) MTB undergoes repeated population bottlenecks when it transmits from one host to the next, and 3) some hosts show much higher transmission rates compared with the average (superspreaders).

Here, we used an approximate Bayesian computation approach to test whether multiple-merger coalescents (MMC), a class of models that allow for large variation in reproductive success among lineages, are more appropriate models to study MTB populations. We considered 11 publicly available whole-genome sequence data sets sampled from local MTB populations and outbreaks and found that MMC had a better fit compared with the Kingman coalescent for 10 of the 11 data sets. These results indicate that the null model for analyzing MTB outbreaks should be reassessed and that past findings based on the Kingman coalescent need to be revisited.

Gene flow as a simple cause for an excess of high-frequency-derived alleles

Most human populations exhibit an excess of high-frequency variants, leading to a U-shaped site-frequency spectrum (uSFS). This pattern has been generally interpreted as a signature of ongoing episodes of positive selection, or as evidence for a mis-assignment of ancestral/derived allelic states, but uSFS has also been observed in populations receiving gene flow from a ghost population, in structured populations, or after range expansions. In order to better explain the prevalence of high-frequency variants in humans and other populations, we describe here which patterns of gene flow and population demography can lead to uSFS by using extensive coalescent simulations. We find that uSFS can often be observed in a population if gene flow brings a few ancestral alleles from a well-differentiated population. Gene flow can either consist in single pulses of admixture or continuous immigration, but different demographic conditions are necessary to observe uSFS in these two scenarios. Indeed, an extremely low and recent gene flow is required in the case of single admixture events, while with continuous immigration, uSFS occurs only if gene flow started recently at a high rate or if it lasted for a long time at a low rate. Overall, we find that a neutral uSFS occurs under more restrictive conditions in populations having received single pulses of gene flow than in populations exposed to continuous gene flow. We also show that the uSFS observed in human populations from the 1000 Genomes Project can easily be explained by gene flow from surrounding populations without requiring past episodes of positive selection. These results imply that uSFS should be common in non-isolated populations, such as most wild or domesticated plants and animals.

Evolutionary Genomics of High Fecundity

Natural highly fecund populations abound. These range from viruses to gadids. Many highly fecund populations are economically important. Highly fecund populations provide an important contrast to the low-fecundity organisms that have traditionally been applied in evolutionary studies. A key question regarding high fecundity is whether large numbers of offspring are produced on a regular basis, by few individuals each time, in a sweepstakes mode of reproduction. Such reproduction characteristics are not incorporated into the classical Wright-Fisher model, the standard reference model of population genetics, or similar types of models, in which each individual can produce only small numbers of offspring relative to the population size. The expected genomic footprints of population genetic models of sweepstakes reproduction are very different from those of the Wright-Fisher model. A key, immediate issue involves identifying the footprints of sweepstakes reproduction in genomic data. Whole-genome sequencing data can be used to distinguish the patterns made by sweepstakes reproduction from the patterns made by population growth in a population evolving according to the Wright-Fisher model (or similar models). If the hypothesis of sweepstakes reproduction cannot be rejected, then models of sweepstakes reproduction and associated multiple-merger coalescents will become at least as relevant as the Wright-Fisher model (or similar models) and the Kingman coalescent, the cornerstones of mathematical population genetics, in further discussions of evolutionary genomics of highly fecund populations.

Identifying loci under positive selection in complex population histories

Detailed modeling of a species' history is of prime importance for understanding how natural selection operates over time. Most methods designed to detect positive selection along sequenced genomes, however, use simplified representations of past histories as null models of genetic drift. Here, we present the first method that can detect signatures of strong local adaptation across the genome using arbitrarily complex admixture graphs, which are typically used to describe the history of past divergence and admixture events among any number of populations. The method-called graph-aware retrieval of selective sweeps (GRoSS)-has good power to detect loci in the genome with strong evidence for past selective sweeps and can also identify which branch of the graph was most affected by the sweep. As evidence of its utility, we apply the method to bovine, codfish, and human population genomic data containing panels of multiple populations related in complex ways. We find new candidate genes for important adaptive functions, including immunity and metabolism in understudied human populations, as well as muscle mass, milk production, and tameness in specific bovine breeds. We are also able to pinpoint the emergence of large regions of differentiation owing to inversions in the history of Atlantic codfish.

Codweb: Whole-genome sequencing uncovers extensive reticulations fueling adaptation among Atlantic, Arctic, and Pacific gadids

Introgressive hybridization creates networks of genetic relationships across species. Among marine fish of the Gadidae family, Pacific cod and walleye pollock are separate invasions of an Atlantic cod ancestor into the Pacific. Cods are ecological success stories, and their ecologies allow them to support the largest fisheries of the world. The enigmatic walleye pollock differs morphologically, behaviorally, and ecologically from its relatives, representing a niche shift. Here, we apply whole-genome sequencing to Pacific, Arctic, and Atlantic gadids and reveal extensive introgression among them with the ABBA-BABA test and pseudolikelihood phylogenetic network analysis. We propose that walleye pollock resulted from extensive adaptive introgression or homoploid hybrid speciation. The path of evolution of these taxa is more web than a tree. Their ability to invade and expand into new habitats and become ecologically successful may depend on genes acquired through adaptive introgression or hybrid speciation.

Phylogeographic mitogenomics of Atlantic cod Gadus morhua: Variation in and among trans-Atlantic, trans-Laurentian, Northern cod, and landlocked fjord populations

The historical phylogeography, biogeography, and ecology of Atlantic cod (Gadus morhua) have been impacted by cyclic Pleistocene glaciations, where drops in sea temperatures led to sequestering of water in ice sheets, emergence of continental shelves, and changes to ocean currents. High-resolution, whole-genome mitogenomic phylogeography can help to elucidate this history. We identified eight major haplogroups among 153 fish from 14 populations by Bayesian, parsimony, and distance methods, including one that extends the species coalescent back to ca. 330 kya. Fish from the Barents and Baltic Seas tend to occur in basal haplogroups versus more recent distribution of fish in the Northwest Atlantic. There was significant differentiation in the majority of trans-Atlantic comparisons (ΦST = .029-.180), but little or none in pairwise comparisons within the Northwest Atlantic of individual populations (ΦST = .000-.060) or defined management stocks (ΦST = .000-.023). Monte Carlo randomization tests of population phylogeography showed significantly nonrandom trans-Atlantic phylogeography versus absence of such structure within various partitions of trans-Laurentian, Northern cod (NAFO 2J3KL) and other management stocks, and Flemish Cap populations. A landlocked meromictic fjord on Baffin Island comprised multiple identical or near-identical mitogenomes in two major polyphyletic clades, and was significantly differentiated from all other populations (ΦST = .153-.340). The phylogeography supports a hypothesis of an eastern origin of genetic diversity ca. 200-250 kya, rapid expansion of a western superhaplogroup comprising four haplogroups ca. 150 kya, and recent postglacial founder populations.

Coalescent inferences in conservation genetics: should the exception become the rule?

Genetic estimates of effective population size (Ne) are an established means to develop informed conservation policies. Another key goal to pursue the conservation of endangered species is keeping the connectivity across fragmented environments, to which genetic inferences of gene flow and dispersal greatly contribute. Most current statistical tools for estimating such population demographic parameters are based on Kingman's coalescent (KC). However, KC is inappropriate for taxa displaying skewed reproductive variance, a property widely observed in natural species. Coalescent models that consider skewed reproductive success-called multiple merger coalescents (MMCs)-have been shown to substantially improve estimates of Ne when the distribution of offspring per capita is highly skewed. MMCs predictions of standard population genetic parameters, including the rate of loss of genetic variation and the fixation probability of strongly selected alleles, substantially depart from KC predictions. These extended models also allow studying gene genealogies in a spatial continuum, providing a novel theoretical framework to investigate spatial connectivity. Therefore, development of statistical tools based on MMCs should substantially improve estimates of population demographic parameters with major conservation implications.

Coalescent Processes with Skewed Offspring Distributions and Nonequilibrium Demography

Nonequilibrium demography impacts coalescent genealogies leaving detectable, well-studied signatures of variation. However, similar genomic footprints are also expected under models of large reproductive skew, posing a serious problem when trying to make inference. Furthermore, current approaches consider only one of the two processes at a time, neglecting any genomic signal that could arise from their simultaneous effects, preventing the possibility of jointly inferring parameters relating to both offspring distribution and population history. Here, we develop an extended Moran model with exponential population growth, and demonstrate that the underlying ancestral process converges to a time-inhomogeneous psi-coalescent. However, by applying a nonlinear change of time scale-analogous to the Kingman coalescent-we find that the ancestral process can be rescaled to its time-homogeneous analog, allowing the process to be simulated quickly and efficiently. Furthermore, we derive analytical expressions for the expected site-frequency spectrum under the time-inhomogeneous psi-coalescent, and develop an approximate-likelihood framework for the joint estimation of the coalescent and growth parameters. By means of extensive simulation, we demonstrate that both can be estimated accurately from whole-genome data. In addition, not accounting for demography can lead to serious biases in the inferred coalescent model, with broad implications for genomic studies ranging from ecology to conservation biology. Finally, we use our method to analyze sequence data from Japanese sardine populations, and find evidence of high variation in individual reproductive success, but few signs of a recent demographic expansion.

Evolution of highly fecund haploid populations

We consider a model of viability selection in a highly fecund haploid population with sweepstakes reproduction. We use simulations to estimate the time until the allelic type with highest fitness has reached high frequency in a finite population. We compare the time between two reproduction modes of high and low fecundity. We also consider the probability that the allelic type with highest fitness is lost from the population before reaching high frequency. Our simulation results indicate that highly fecund populations can evolve faster (in some cases much faster) than populations of low fecundity. However, high fecundity and sweepstakes reproduction also confer much higher risk of losing the allelic type with highest fitness from the population by chance. The impact of selection on driving alleles to high frequency varies depending on the trait value conferring highest fitness; in some cases the effect of selection can hardly be detected.

Ancient DNA reveals the Arctic origin of Viking Age cod from Haithabu, Germany

Knowledge of the range and chronology of historic trade and long-distance transport of natural resources is essential for determining the impacts of past human activities on marine environments. However, the specific biological sources of imported fauna are often difficult to identify, in particular if species have a wide spatial distribution and lack clear osteological or isotopic differentiation between populations. Here, we report that ancient fish-bone remains, despite being porous, brittle, and light, provide an excellent source of endogenous DNA (15-46%) of sufficient quality for whole-genome reconstruction. By comparing ancient sequence data to that of modern specimens, we determine the biological origin of 15 Viking Age (800-1066 CE) and subsequent medieval (1066-1280 CE) Atlantic cod (Gadus morhua) specimens from excavation sites in Germany, Norway, and the United Kingdom. Archaeological context indicates that one of these sites was a fishing settlement for the procurement of local catches, whereas the other localities were centers of trade. Fish from the trade sites show a mixed ancestry and are statistically differentiated from local fish populations. Moreover, Viking Age samples from Haithabu, Germany, are traced back to the North East Arctic Atlantic cod population that has supported the Lofoten fisheries of Norway for centuries. Our results resolve a long-standing controversial hypothesis and indicate that the marine resources of the North Atlantic Ocean were used to sustain an international demand for protein as far back as the Viking Age.

Genetic load in marine animals: a review

Marine invertebrates and fish are well known for their remarkable genetic diversity, which is commonly explained by large population size and the characteristic dispersive nature of their early, planktonic life history. Other potential sources of diversity in marine animals, such as a higher mutation rate, have been much less considered, though evidence for a high genetic load in marine bivalves has been accumulating for nearly half a century. In this review, I examine evidence for a higher genetic load in marine animals from studies of molecular marker segregation and linkage over the last 40 years, and survey recent work examining mutational load with molecular evolution approaches. Overall, marine animals appear to have higher genetic load than terrestrial animals (higher dn/ds ratios, inbreeding load, and segregation dis`tortion), though results are mixed for marine fish and data are lacking for many marine animal groups. Bivalves (oysters) have the highest loads observed among marine animals, comparable only to long-lived plants; however, more data is needed from other bivalves and more marine invertebrate taxa generally. For oysters, a higher load may be related to a chronically lower effective population size that, in concert with a higher mutational rate, elevate the number of deleterious mutations observed. I suggest that future studies use high-throughput sequencing approaches to examine (1) polymorphism in genome-scale datasets across a wider range of marine animals at the population level and (2) intergenerational mutational changes between parents and offspring in crosses of aquaculture species to quantify mutation rates.

Evaluating the adaptive potential of the European eel: is the immunogenetic status recovering?

The recent increased integration of evolutionary theory into conservation programs has greatly improved our ability to protect endangered species. A common application of such theory links population dynamics and indices of genetic diversity, usually estimated from neutrally evolving markers. However, some studies have suggested that highly polymorphic adaptive genes, such as the immune genes of the Major Histocompatibility Complex (MHC), might be more sensitive to fluctuations in population dynamics. As such, the combination of neutrally- and adaptively-evolving genes may be informative in populations where reductions in abundance have been documented. The European eel (Anguilla anguilla) underwent a drastic and well-reported decline in abundance in the late 20th century and still displays low recruitment. Here we compared genetic diversity indices estimated from neutral (mitochondrial DNA and microsatellites) and adaptive markers (MHC) between two distinct generations of European eels. Our results revealed a clear discrepancy between signatures obtained for each class of markers. Although mtDNA and microsatellites showed no changes in diversity between the older and the younger generations, MHC diversity revealed a contemporary drop followed by a recent increase. Our results suggest ongoing gain of MHC genetic diversity resulting from the interplay between drift and selection and ultimately increasing the adaptive potential of the species.

Three chromosomal rearrangements promote genomic divergence between migratory and stationary ecotypes of Atlantic cod

Identification of genome-wide patterns of divergence provides insight on how genomes are influenced by selection and can reveal the potential for local adaptation in spatially structured populations. In Atlantic cod – historically a major marine resource – Northeast-Arctic- and Norwegian coastal cod are recognized by fundamental differences in migratory and non-migratory behavior, respectively. However, the genomic architecture underlying such behavioral ecotypes is unclear. Here, we have analyzed more than 8.000 polymorphic SNPs distributed throughout all 23 linkage groups and show that loci putatively under selection are localized within three distinct genomic regions, each of several megabases long, covering approximately 4% of the Atlantic cod genome. These regions likely represent genomic inversions. The frequency of these distinct regions differ markedly between the ecotypes, spawning in the vicinity of each other, which contrasts with the low level of divergence in the rest of the genome. The observed patterns strongly suggest that these chromosomal rearrangements are instrumental in local adaptation and separation of Atlantic cod populations, leaving footprints of large genomic regions under selection. Our findings demonstrate the power of using genomic information in further understanding the population dynamics and defining management units in one of the world’s most economically important marine resources.

Hybrid-Lambda: simulation of multiple merger and Kingman gene genealogies in species networks and species trees

BACKGROUND

There has been increasing interest in coalescent models which admit multiple mergers of ancestral lineages; and to model hybridization and coalescence simultaneously.

RESULTS

Hybrid-Lambda is a software package that simulates gene genealogies under multiple merger and Kingman's coalescent processes within species networks or species trees. Hybrid-Lambda allows different coalescent processes to be specified for different populations, and allows for time to be converted between generations and coalescent units, by specifying a population size for each population. In addition, Hybrid-Lambda can generate simulated datasets, assuming the infinitely many sites mutation model, and compute the F ST statistic. As an illustration, we apply Hybrid-Lambda to infer the time of subdivision of certain marine invertebrates under different coalescent processes.

CONCLUSIONS

Hybrid-Lambda makes it possible to investigate biogeographic concordance among high fecundity species exhibiting skewed offspring distribution.

Trans-species polymorphism at antimicrobial innate immunity cathelicidin genes of Atlantic cod and related species

Natural selection, the most important force in evolution, comes in three forms. Negative purifying selection removes deleterious variation and maintains adaptations. Positive directional selection fixes beneficial variants, producing new adaptations. Balancing selection maintains variation in a population. Important mechanisms of balancing selection include heterozygote advantage, frequency-dependent advantage of rarity, and local and fluctuating episodic selection. A rare pathogen gains an advantage because host defenses are predominantly effective against prevalent types. Similarly, a rare immune variant gives its host an advantage because the prevalent pathogens cannot escape the host's apostatic defense. Due to the stochastic nature of evolution, neutral variation may accumulate on genealogical branches, but trans-species polymorphisms are rare under neutrality and are strong evidence for balancing selection. Balanced polymorphism maintains diversity at the major histocompatibility complex (MHC) in vertebrates. The Atlantic cod is missing genes for both MHC-II and CD4, vital parts of the adaptive immune system. Nevertheless, cod are healthy in their ecological niche, maintaining large populations that support major commercial fisheries. Innate immunity is of interest from an evolutionary perspective, particularly in taxa lacking adaptive immunity. Here, we analyze extensive amino acid and nucleotide polymorphisms of the cathelicidin gene family in Atlantic cod and closely related taxa. There are three major clusters, Cath1, Cath2, and Cath3, that we consider to be paralogous genes. There is extensive nucleotide and amino acid allelic variation between and within clusters. The major feature of the results is that the variation clusters by alleles and not by species in phylogenetic trees and discriminant analysis of principal components. Variation within the three groups shows trans-species polymorphism that is older than speciation and that is suggestive of balancing selection maintaining the variation. Using Bayesian and likelihood methods positive and negative selection is evident at sites in the conserved part of the genes and, to a larger extent, in the active part which also shows episodic diversifying selection, further supporting the argument for balancing selection.