Inferring inter- and intrachromosomal Dobzhansky-Muller incompatibilities from imbalanced segregation of recombinant haplotypes in hybrid populations

Dobzhansky-Muller incompatibilities (DMIs) are a major component of reproductive isolation between species. DMIs imply negative epistasis, exposed when two diverged populations hybridize. Mapping the locations of DMIs has largely relied on classical genetic mapping, but these approaches are stymied by low power and the challenge of identifying DMI loci on the same chromosome, because strong initial linkage of parental haplotypes weakens statistical tests. Here, we propose new statistics to infer negative epistasis from haplotype frequencies in hybrid populations. When two divergent populations hybridize, the variance of two-locus heterozygosity decreases faster with time at DMI loci than at random pairs of loci. If two populations hybridize at near-even admixture proportions, the deviation of the observed variance from its expectation is negative, which enables us to detect signals of intermediate to strong negative epistasis both within and between chromosomes. When the initial proportion of the two parental populations is uneven, only strong DMIs can be detected with our method, unless migration reintroduces haplotypes from the minor parental population. We use the two new statistics to infer candidate DMIs from three hybrid populations of swordtail fish. We identify numerous new DMI candidates some of which are inferred to interact with several loci within and between chromosomes. Moreover, we discuss our results in the context of an expected enrichment in intrachromosomal over interchromosomal DMIs.

Predictability and parallelism in the contemporary evolution of hybrid genomes

Hybridization between species is widespread across the tree of life. As a result, many species, including our own, harbor regions of their genome derived from hybridization. Despite the recognition that this process is widespread, we understand little about how the genome stabilizes following hybridization, and whether the mechanisms driving this stabilization tend to be shared across species. Here, we dissect the drivers of variation in local ancestry across the genome in replicated hybridization events between two species pairs of swordtail fish: Xiphophorus birchmanni × X. cortezi and X. birchmanni × X. malinche. We find surprisingly high levels of repeatability in local ancestry across the two types of hybrid populations. This repeatability is attributable in part to the fact that the recombination landscape and locations of functionally important elements play a major role in driving variation in local ancestry in both types of hybrid populations. Beyond these broad scale patterns, we identify dozens of regions of the genome where minor parent ancestry is unusually low or high across species pairs. Analysis of these regions points to shared sites under selection across species pairs, and in some cases, shared mechanisms of selection. We show that one such region is a previously unknown hybrid incompatibility that is shared across X. birchmanni × X. cortezi and X. birchmanni × X. malinche hybrid populations.

Antagonistic selection on body size and sword length in a wild population of the swordtail fish, Xiphophorus multilineatus: potential for intralocus tactical conflict

Alternative reproductive tactics (ARTs) have provided valuable insights into how sexual selection and life history tradeoffs can lead to variation within a sex. However, the possibility that tactics may constrain evolution through intralocus tactical conflict (IATC) is rarely considered. In addition, when IATC has been considered, the focus has often been on the genetic correlations between the ARTs, while evidence that the ARTs have different optima for associated traits and that at least one of the tactics is not at its optima is often missing. Here we investigate selection on three traits associated with the ARTs in the swordtail fish Xiphophorus multilineatus; body size, body shape and the sexually selected trait for which these fishes were named, sword length (elongation of the caudal fin). All three traits are tactically dimorphic, with courter males being larger, deeper bodied and having longer swords, and the sneaker males being smaller, more fusiform and having shorter swords. Using measures of reproductive success in a wild population we calculated selection differentials, linear and quadratic gradients, demonstrate that the tactics have different optima and at least one of the tactics is not at its optima for body size and sword length. Our results provide the first evidence of selection in the wild on the sword, an iconic trait for sexual selection. In addition, given the high probability that these traits are genetically correlated to some extent between the two tactics, our study suggests that IATC is constraining both body size and the sword from reaching their phenotypic optima. We discuss the importance of considering the role of IATC in the evolution of tactical dimorphism, how this conflict can be present despite tactical dimorphism, and how it is important to consider this conflict when explaining not only variation within a species but differences across species as well.

The determination of oxidative damage caused by fluoxetine hydrocloride in swordtail fish (Xiphophorus hellerii)

In this study, it was aimed to determine the oxidative stress in the tissues of the swordtail fish (Xiphophorus hellerii Heckel, 1848) after exposed to the active ingredient of Prozac® and one of the SSRI (Selective Serotonine Reuptake Inhibitor) group antidepressants, Fluoxetine Hydrochloride, which is considered to be safe cardiovascular. It is widely used in the treatment of depression, which is one of the increasing health problems in the World. Fluoxetine-HCl has been found 0.012 μg/L in surface waters and in the dose range of 0.54-0.929 μg/L in wastewater (Sehonova et al., 2018). In line with this information, 0.1 μg / L and 1 μg / L Fluoxetine-HCl was administered to swordtails. At the end of 96 hours, heart and liver tissues of the fish were dissected under antiseptic conditions and homogenized. Later, malondialdehyde (MDA), total glutathione (GSH), catalase (CAT) enzyme activity, superoxide dismutase (SOD) enzyme activity and total protein amount were determined by spectrophotometric methods. As a result, while CAT enzyme activity and MDA level decreased in heart tissue, SOD enzyme activity and GSH level increased. In liver tissue, while CAT enzyme activity and GSH amount increased, SOD enzyme activity and MDA level decreased. As a result of the comparisons with the control group, it was determined that Fluoxetine-HCl is effective in regulating the stress response by affecting the stress pathways in swordtails.

Rheotaxis Response Based on Sexual Dimorphism in the Green Swordtail Fish, Xiphophorus hellerii

Morphological distinctions between males and females of a species are referred to by sexual dimorphism. It may result from various selection pressures affecting either sex or both and may occur in any dioecious species, including Green Swordtail fish, which are sexually reproductive. This study examined the different rheotaxis responses of Xiphophorus hellerii based on different sexes and morphological features. We analyzed ten adult males, ten gravid females, and ten non-gravid females of Xiphophorus helleri collected down the river and transferred into the column. We counted the number of the individual that performed positive rheotaxis (+), negative rheotaxis (-), and indifference response (0). The result showed different rheotaxis responses shown by male, non-gravid female, and gravid female X. hellerii. The highest percentage of positive rheotaxis response (movement against the current) was shown by non-gravid female X. hellerii, reaching up to 89%. Morphological differences between male, non-gravid female, and gravid female X. hellerii appear to affect the orientation and ability of X. hellerii in giving response against current and certainly has an impact on their survival in nature.

Two new hybrid zones expand the swordtail hybridization model system

Natural hybridization events provide unique windows into the barriers that keep species apart as well as the consequences of their breakdown. Here we characterize hybrid populations formed between the northern swordtail fish Xiphophorus cortezi and X. birchmanni from collection sites on two rivers. We develop sensitive and accurate local ancestry calling for this system based on low coverage whole genome sequencing. Strikingly, we find that hybrid populations on both rivers consist of two genetically distinct subpopulations: a cluster of nearly pure X. birchmanni individuals and one of phenotypically intermediate hybrids that derive ~85-90% of their genome from X. cortezi. Simulations and empirical data suggest that at both sites initial hybridization occurred ~150 generations ago, with little evidence for contemporary gene flow between subpopulations, likely due to strong assortative mating. The patterns of population structure uncovered here mirror those seen in hybridization between X. birchmanni and its sister species, X. malinche. Future comparisons will provide a window into the repeatability of the outcomes of hybridization not only across independent hybridization events between the same species but also across distinct species pairs.

Estimating the time since admixture from phased and unphased molecular data

After admixture, recombination breaks down genomic blocks of contiguous ancestry. The break down of these blocks forms a new ‘molecular’ clock, that ticks at a much faster rate than the mutation clock, enabling accurate dating of admixture events in the recent past. However, existing theory on the break down of these blocks, or the accumulation of delineations between blocks, so called ‘junctions’, has been limited to using regularly spaced markers on phased data. Here, we present an extension to the theory of junctions using the Ancestral Recombination Graph that describes the expected number of junctions for any distribution of markers along the genome. Furthermore, we provide a new framework to infer the time since admixture using unphased data. We demonstrate both the phased and unphased methods on simulated data and show that our new extensions perform much better than previous methods, especially for more ancient admixture times. Lastly, we demonstrate the applicability of our method on an empirical dataset of labcrosses of yeast (Saccharomyces cerevisae) and on two case studies of hybridization in swordtail fish and Populus trees.