The ability to efficiently and accurately determine genotypes is a keystone technology in modern genetics, crucial to studies ranging from clinical diagnostics, to genotype-phenotype association, to reconstruction of ancestry and the detection of selection. To date, high capacity, low cost genotyping has been largely achieved via “SNP chip” microarray-based platforms which require substantial prior knowledge of both genome sequence and variability, and once designed are suitable only for those targeted variable nucleotide sites. This method introduces substantial ascertainment bias and inherently precludes detection of rare or population-specific variants, a major source of information for both population history and genotype-phenotype association. Recent developments in reduced-representation genome sequencing experiments on massively parallel sequencers (commonly referred to as RAD-tag or RADseq) have brought direct sequencing to the problem of population genotyping, but increased cost and procedural and analytical complexity have limited their widespread adoption. Here, we describe a complete laboratory protocol, including a custom combinatorial indexing method, and accompanying software tools to facilitate genotyping across large numbers (hundreds or more) of individuals for a range of markers (hundreds to hundreds of thousands). Our method requires no prior genomic knowledge and achieves per-site and per-individual costs below that of current SNP chip technology, while requiring similar hands-on time investment, comparable amounts of input DNA, and downstream analysis times on the order of hours. Finally, we provide empirical results from the application of this method to both genotyping in a laboratory cross and in wild populations. Because of its flexibility, this modified RADseq approach promises to be applicable to a diversity of biological questions in a wide range of organisms.
It is well established that changes to the chemical environment can impair development, physiology and reproductive biology; by contrast, impacts on communication have not been widely reported. This is surprising given that chemical communication is the most widely used sensory modality in nature, and that variation in the chemical composition of the environment is the rule, not the exception. Here, we show that chemically mediated species recognition in a swordtail fish, Xiphophorus birchmanni, can be hindered by anthropogenic disturbance to the signalling environment. Females have a strong preference for conspecific male chemical cues, yet they hybridize in nature with the congener X. malinche. Wild-caught females showed a strong preference for conspecifics when tested in clean water, but failed to show a preference when tested in stream water subject to sewage effluent and agricultural runoff. We hypothesized that this was due to the interaction between chemical communication systems and humic acid (HA), a ubiquitous, natural product elevated to high levels by anthropogenic processes. When exposed to elevated concentrations of HA, female X. birchmanni again lost their preference for conspecific male chemical cues, while visual mating preferences and motivation to mate were retained. Sub-lethal concentrations of seemingly benign substances can thus have a drastic effect on natural populations through their specific impact on communication systems.
Among the extraordinary adaptations driven by sperm competition is the cooperative behaviour of spermatozoa1. By forming cooperative groups, sperm can increase their swimming velocity and thereby gain an advantage in intermale sperm competition1,2. Accordingly, selection should favour cooperation of the most closely related sperm to maximize fitness3. Here we show that sperm of deer mice (genus Peromyscus) form motile aggregations, then we use this system test predictions of sperm cooperation. We first show that sperm aggregate more often with conspecific than heterospecific sperm, suggesting that individual sperm can discriminate based on genetic relatedness. Next, we provide evidence that the cooperative behaviour of closely-related sperm is driven by sperm competition. In a monogamous species lacking sperm competition, P. polionotus, sperm indiscriminately group with unrelated conspecific sperm. In contrast, in the highly promiscuous deer mouse, P. maniculatus, sperm are significantly more likely to aggregate with those obtained from the same male than sperm from an unrelated conspecific donor. Even when we test sperm from sibling males, we continue to see preferential aggregations of related sperm in P. maniculatus. These results suggest that sperm from promiscuous deer mice discriminate among relatives and thereby cooperate with the most closely-related sperm, an adaptation likely driven by sperm competition.
Natural hybrid zones provide opportunities to study a range of evolutionary phenomena from speciation to the genetic basis of fitness-related traits. We show that widespread hybridization has occurred between two neo-tropical stream fishes with partial reproductive isolation. Phylogenetic analyses of mitochondrial sequence data showed that the swordtail fish Xiphophorus birchmanni is monophyletic and that X. malinche is part of an independent monophyletic clade with other species. Using informative single nucleotide polymorphisms in one mitochondrial and three nuclear intron loci, we genotyped 776 specimens collected from twenty-three sites along seven separate stream reaches. Hybrid zones occurred in replicated fashion in all stream reaches along a gradient from high to low elevation. Genotyping revealed substantial variation in parental and hybrid frequencies among localities. Tests of F(IS) and linkage disequilibrium (LD) revealed generally low F(IS) and LD except in five populations where both parental species and hybrids were found suggesting incomplete reproductive isolation. In these locations, heterozygote deficiency and LD were high, which suggests either selection against early generation hybrids or assortative mating. These data lay the foundation to study the adaptive basis of the replicated hybrid zone structure and for future integration of behaviour and genetics to determine the processes that lead to the population genetic patterns observed in these hybrid zones.
Sperm cooperation has evolved in a variety of taxa and is often considered a response to sperm competition, yet the benefit of this form of collective movement remains unclear. Here, we use fine-scale imaging and a minimal mathematical model to study sperm aggregation in the rodent genus Peromyscus. We demonstrate that as the number of sperm cells in an aggregate increase, the group moves with more persistent linearity but without increasing speed. This benefit, however, is offset in larger aggregates as the geometry of the group forces sperm to swim against one another. The result is a non-monotonic relationship between aggregate size and average velocity with both a theoretically predicted and empirically observed optimum of six to seven sperm per aggregate. To understand the role of sexual selection in driving these sperm group dynamics, we compared two sister-species with divergent mating systems. We find that sperm of Peromyscus maniculatus (highly promiscuous), which have evolved under intense competition, form optimal-sized aggregates more often than sperm of Peromyscus polionotus (strictly monogamous), which lack competition. Our combined mathematical and experimental study of coordinated sperm movement reveals the importance of geometry, motion and group size on sperm velocity and suggests how these physical variables interact with evolutionary selective pressures to regulate cooperation in competitive environments.
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