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Over the past two decades researchers have documented the extent of natural hybridization between closely related species using genomic tools. Many species across the tree of life show evidence of past hybridization with their evolutionary relatives. In some cases, this hybridization is complex – involving gene flow between more than two species. While hybridization is common over evolutionary timescales, some researchers have proposed that it may be even more common in contemporary populations where anthropogenic disturbance has modified myriad aspects of the environments in which organisms live and reproduce. Here, we develop a flexible tool for local ancestry inference in hybrids derived from three source populations and describe a complex, recent hybridization event between distantly related swordtail fish lineages (Xiphophorus) and its potential links to anthropogenic disturbance.Impact SummaryAs sequencing tools have advanced, we have found that barriers between animal species are more porous than once thought. Researchers have found evidence for hybridization between species throughout many branches of the tree of life. In some cases, these hybridization events can involve more than two species. Here, we develop a flexible and user-friendly tool that can be used to identify three-way hybrids and report the discovery of hybrids with ancestry from three swordtail (Xiphophorus) species from an anthropogenically impacted site on the Río Calnali in Hidalgo, Mexico. Researchers have studied hybrids between twoXiphophorusspecies along this river for decades, but this is the first documented case of hybridization involving three species. We explore hypotheses for what drove this hybridization event, including anthropogenic pollutants and reduced water quality.

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 Xiphophorus birchmanni from collection sites on two rivers. We use simulations and new genetic reference panels to develop sensitive and accurate local ancestry calling in this novel system. Strikingly, we find that hybrid populations on both rivers consist of two genetically distinct subpopulations: a cluster of pure X. birchmanni individuals and one of phenotypically intermediate hybrids that derive ∼85-90% of their genome from X. cortezi. Simulations suggest that initial hybridization occurred ∼150 generations ago at both sites, with little evidence for contemporary gene flow between subpopulations. This population structure is consistent with strong assortative mating between individuals of similar ancestry. The patterns of population structure uncovered here mirror those seen in hybridization between X. birchmanni and its sister species, Xiphophorus malinche, indicating an important role for assortative mating in the evolution of hybrid populations. Future comparisons will provide a window into the shared mechanisms driving the outcomes of hybridization not only among independent hybridization events between the same species but also across distinct species pairs.

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 unexpectedly 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., Author summary We now know that hybridization, or the production of offspring between individuals of different species, happens frequently across many plant, animal, and fungi groups. As a result, the genomes of many contemporary species contain material derived from these hybridization events. At the same time, hybridization can have negative consequences on an organism’s ability to survive and reproduce. One major question is whether there are shared principles that determine which parts of the genome can move between species and which cannot. Here, we compare the genomes of several independently formed hybrid populations between the fish species pairs of Xiphophorus birchmanni and X. cortezi as well as X. birchmanni and X. malinche to begin to address this question. We find that across hybrid populations, regions of the genome with especially low recombination rates or especially high gene density are more likely to be derived from the parent species that contributed the majority of the genome to hybrids. Moreover, we identify regions of the genome that negatively interact in both types of hybrid population. Together our results demonstrate that genomic outcomes of hybridization between distinct species pairs are in part predictable.

Urban coastal ecosystems are unique intersections of human development and biodiversity, and monitoring populations in these areas is critical to understanding ecosystem health and function. Three highly urbanized estuary systems, San Diego Bay, San Gabriel River, and Seal Beach National Wildlife Refuge (all in California), are the northernmost foraging habitats for green turtles (Chelonia mydas) in the Eastern Pacific. Here, we report blood biochemistry and morphological parameters for these Southern California green sea turtle foraging aggregations to investigate the current health status of these animals and provide baseline values for future work. Morphometric and blood biochemistry parameters for green turtles captured in this study (n = 39) were clinically reasonable and were generally consistent with previously reported parameters for green turtles.