Laurie S. Stevison

Recombination is an important source of genetic variation and plays a central role in adaptation and genome stability. Although environmental conditions such as temperature can alter recombination rates, much less is known about how multiple environmental stressors act together. Here, we tested the effects of low temperature and hypoxia, both independently and in combination, on recombination in Drosophila melanogaster across five genetic backgrounds. Using a quadruple X-linked marker stock, we measured recombination in 50,209 male backcross progeny from 194 backcrosses exposed to four conditions: control, hypoxia, low temperature, and combined hypoxia and low temperature. Low temperature significantly altered recombination across all three chromosome intervals examined and affected total map length with an average increase of 5 cM. Genetic background strongly influenced the magnitude of altered recombination rate. Hypoxia alone did not significantly change total map length, but its effects differed among genetic backgrounds with significant variation in both the magnitude and direction with an average decrease of 0.96 cM. The response to combined hypoxia and low temperature was not simply the sum of the responses to each stressor alone, with an average increase of 6.78 cM, that also varied across genetic backgrounds in magnitude and direction as well as over time. DGRP_57 and DGRP_508 showed some of the largest increases in recombination under combined stress, whereas DGRP_491 showed a decrease. DGRP_391 was robust across all treatments. Despite these changes in crossover frequency, crossover interference remained largely stable across treatments, with only the y-cv-v interval pair showing a significant treatment-by-genotype interaction. Together, these results show that recombination responses to environmental stress depend strongly on genetic background and on the combination of stressors experienced. Our findings highlight the importance of considering both genetic variation and interacting environmental conditions when predicting how populations may respond to increasingly complex environmental change.

Classic recombination experiments designed to test genetic and environmental treatments do not directly measure chromosomal exchange, instead rates and distribution of crossing-over in F1 meiocytes are inferred from genetic markers in F2 adults. In Drosophila melanogaster females this procedure introduces substantial “missing data problems” because 75% of meiotic chromatids segregate to polar body nuclei and another 11% are transmitted to inviable F2 zygotes which cannot be scored for recombination. To address these sources of uncertainty and bias, we extend the Cx(Co)m data-generating process by assuming: (i) programmed double-strand breaks occur as a Poisson point process, (ii) crossover maturation is a stationary renewal process, (iii) chromosome segregation is random one-half thinning of this process, (iv) fertilization by X- versus Y-bearing sperm is mendelian, and (v) egg-to-adult survival is binomially distributed with a ate parameter determined by F2 marker alleles. To quantify experimental mortality, we performed egg counts for 6-point X chromosome testcrosses and marker-free X chromosome controls on identical genetic backgrounds under standard laboratory conditions. The 19,927 fly dataset revealed 44% F2 experimental mortality, and likelihood ratio tests support a model where 36 of those 44% are due to sex-specific, marker-associated viability defects. Variability in X chromosome genetic map lengths with experimental mortality can be simulated, and we provide case-control 80% power curves to guide experimental design. We propose that differential mortality should be the de facto null hypothesis when comparing F2 recombinant fractions, and we provide probabilistic models of the data-generating process to improve characterization of F1 meiotic crossover patterning.

Plasticity in meiotic recombination is a well-documented phenomenon with an unknown mechanism. Recent studies have shown variation in the magnitude and direction of plasticity with a putative connection to organismal stress. Though there have been many factors shown to contribute to recombination rate plasticity, dietary manipulations are understudied. Here we manipulated caloric density, which is known to contribute to well-known life-history trade-offs, to determine if it altered meiotic recombination rates. To investigate the role of genetic background, we selected two stocks from the Drosophila Genetic Reference Panel (DGRP) with varying susceptibility to starvation stress. We found that overall recombination rates increased as calories decreased consistent with previous dietary plasticity studies in Drosophila. Specifically, while neither 0.5x nor 2x were significantly different from the standard 1x diet, we found significant post hoc differences between the low-calorie (0.5x) versus the high-calorie (2x) dietary treatments in the strain DGRP_42 but not in DGRP_217, confirming the predicted increased sensitivity of DGRP_42 to starvation stress based on prior studies. In addition to measuring changes in crossover frequency and distribution, we also investigated various organismal reproductive and physiological traits. We found significant changes in female body mass, the number of oocytes in female ovaries, and male testis length due to both diet and genetic background. We also noted significant differences in DNA damage during oogenesis via TUNEL assay. Examination of ovarian gene expression confirmed that the strain that had plasticity in recombination (DGRP_42) also had 20x more differentially expressed genes between dietary treatments. Despite diet typically eliciting a tradeoff whereby dietary restriction increases lifespan, here we saw evidence that DGRP_42 did not experience benefits from low-calorie treatment, with evidence of stress response and increased DNA damage, which suggests plasticity in recombination is due to stress. Overall, our study provides additional support for the negative relationship between metabolism and recombination rate, differences between genetic backgrounds, and a connection between organismal traits and plasticity in meiotic recombination.

Classic recombination experiments designed to test genetic and environmental treatments do not directly measure crossing-over, instead rates and distribution of meiotic events in F ₁ meiocytes is inferred from genetic markers in F ₂ adults. In Drosophila melanogaster females this procedure introduces a substantial "missing data problem" because 75% of meiotic chromatids segregate to polar body nuclei and another 11% are transmitted to inviable F ₂ zygotes which cannot be scored for recombination. To address these sources of uncertainty and bias we extend the Cx ( Co ) ^m model of the data-generating process by assuming: 1) programmed double strand breaks occur as a Poisson point process, 2) crossover maturation is a stationary renewal process, 3) chromosome segregation is random one-half thinning of this process, 4) fertilization by X- versus Y-bearing sperm is mendelian, and 5) egg-to-adult survival is binomially distributed with a rate parameter determined by F ₂ marker alleles. To quantify experimental mortality, we performed egg counts in a 6-point X chromosome testcross and marker-free controls on identical genetic backgrounds under standard laboratory conditions. The 19,927 fly dataset reveals 44% F ₂ experimental mortality, and likelihood ratio tests support a model where 36 of the 44% is due to sex-specific, marker-associated viability defects. Variability in X chromosome genetic lengths with experimental mortality can be simulated and we provide case-control 80% power curves to guide experimental design. We propose that differential mortality should be the de facto null hypothesis when comparing F ₂ recombinant fractions and provide probabilistic models of the data-generating process to improve characterization of patterns in F ₁ meiotic events.

Population genetic analyses use information from the site frequency spectrum to infer evolutionary processes. Two summary statistics, Watterson's estimator () of genetic diversity, and Tajima's , used for detecting non‐neutral evolution, are among the most frequently computed statistics utilising this information. However, missing information in genomic data, particularly as encoded in the Variant Call Format (VCF), can bias these estimates, leading to incorrect evolutionary inferences. We assessed the impact of missing data on the estimation of these statistics using various population genetic software packages (VCFtools, PopGenome, pegas and scikit‐allel). By simulating neutral genomic data with varying levels of missing genotypes and sites, we found consistent underestimation of across programs. We found a consequent bias in estimates of Tajima's , though the direction varied by software. We developed and implemented correction methods as functions in an update of the popular pixy software, significantly reducing these biases. Our findings highlight the need for accurate data handling in population genomics to avoid misinterpretations of evolutionary phenomena.

Speciation can involve phases of divergent adaptation in allopatry and ecological/reproductive character displacement in sympatry or parapatry. Reproductive character displacement can result as a means of preventing hybridization, a process known as reinforcement speciation. In this study, we use whole‐genome sequencing (WGS) of two closely related primate species that have experienced introgression in their history, the rhesus (Macaca mulatta) and cynomolgus (M. fascicularis) macaques, to identify genes exhibiting reproductive character displacement and other patterns consistent with reinforcement speciation. Using windowed scans of various population genetic statistics to identify signatures of reinforcement, we find 184 candidate genes associated with a variety of functions, including an overrepresentation of multiple neurological functions and several genes involved in sexual development and gametogenesis. These results are consistent with a variety of genes acting in a reinforcement process between these species. We also find signatures of introgression of the Y‐chromosome that confirm previous studies suggesting male‐driven introgression ofM. mulattaintoM. fascicularispopulations. This study uses WGS to find evidence of the process of reinforcement in primates that have medical and conservation relevance.

Intrinsic postzygotic isolation typically appears as reduced viability or fertility of interspecific hybrids caused by genetic incompatibilities between diverged parental genomes. Dobzhansky–Muller interactions among individual genes, and chromosomal rearrangements causing problems with chromosome synapsis and recombination in meiosis, have both long been considered as major mechanisms behind intrinsic postzygotic isolation. Recent research has, however, suggested that the genetic basis of intrinsic postzygotic isolation can be more complex and involves, for example, overall divergence of the DNA sequence or epigenetic changes. Here, we review the mechanisms of intrinsic postzygotic isolation from genic, chromosomal, genomic, and epigenetic perspectives across diverse taxa. We provide empirical evidence for these mechanisms, discuss their importance in the speciation process, and highlight questions that remain unanswered.

When compared to the approximately 22 other macaque species, Macaca arctoides has many unique phenotypes. These traits fall into various phenotypic categories, including genitalia, coloration, mating, and olfactory traits. Here we used a previously identified whole genome set of 690 outlier genes to look for possible genetic explanations of these unique traits. Of these, 279 genes were annotated miRNAs, which are non-coding. Patterns within the remaining outliers in coding genes were investigated using GO (n = 370) and String (n = 383) analysis, which showed many interconnected immune-related genes. Further, we compared the outliers to candidate pathways associated with M. arcotides’ unique phenotypes, revealing 10/690 outlier genes that overlapped these four pathways: hedgehog signaling, WNT signaling, olfactory, and melanogenesis. Of these, genes in all pathways except olfactory had higher F_ST values than the rest of the genes in the genome based on permutation tests. Overall, our results point to many genes each having a small impact on phenotype, working in tandem to cause large systemic changes. Additionally, these results may indicate pleiotropy. This seems to be especially true with the development and coloration of M. arctoides. Our results highlight that development, melanogenesis, immune function, and miRNAs may be heavily involved in M. arctoides’ evolutionary history.

Speciation can be caused by divergent adaptation in allopatry as a result of ecological or reproductive character displacement in sympatry or parapatry. The latter can result as a means of preventing hybridization, a process known as reinforcement speciation. Though this has been described in a variety of taxonomic systems though the prevalence throughout nature is still unknown. In this study, we use whole-genome sequencing (WGS) of two primate species that have experienced introgression in their history, the rhesus (Macaca mulatta) and cynomolgus (M. fascicularis) macaques, to identify genes exhibiting a pattern of reproductive character displacement consistent with reinforcement speciation. Using windowed scans of various population genetic statistics to identify reproductive character displacement, we find candidate genes associated with a variety of functions, including an overrepresentation of multiple neurological functions and some genes involved in sexual development and gametogenesis. This suggests a variety of genes acting at multiple stages of a reinforcement process between these species. We also find signatures of introgression of the Y-chromosome that confirm previous studies suggesting male-driven introgression of M. mulatta into M. fascicularis populations. This study is among the first to utilize whole-genome sequencing to analyze the phenomenon of reinforcement and among the first to find evidence of this phenomenon in primates, particularly ones that have medical relevance.