Ultraconserved elements are novel phylogenomic markers that resolve placental mammal phylogeny when combined with species-tree analysis.

Phylogenomics offers the potential to fully resolve the Tree of Life, but increasing genomic coverage also reveals conflicting evolutionary histories among genes, demanding new analytical strategies for elucidating a single history of life. Here, we outline a phylogenomic approach using a novel class of phylogenetic markers derived from ultraconserved elements and flanking DNA. Using species-tree analysis that accounts for discord among hundreds of independent loci, we show that this class of marker is useful for recovering deep-level phylogeny in placental mammals. In broad outline, our phylogeny agrees with recent phylogenomic studies of mammals, including several formerly controversial relationships. Our results also inform two outstanding questions in placental mammal phylogeny involving rapid speciation, where species-tree methods are particularly needed. Contrary to most phylogenomic studies, our study supports a first-diverging placental mammal lineage that includes elephants and tenrecs (Afrotheria). The level of conflict among gene histories is consistent with this basal divergence occurring in or near a phylogenetic "anomaly zone" where a failure to account for coalescent stochasticity will mislead phylogenetic inference. Addressing a long-standing phylogenetic mystery, we find some support from a high genomic coverage data set for a traditional placement of bats (Chiroptera) sister to a clade containing Perissodactyla, Cetartiodactyla, and Carnivora, and not nested within the latter clade, as has been suggested recently, although other results were conflicting. One of the most remarkable findings of our study is that ultraconserved elements and their flanking DNA are a rich source of phylogenetic information with strong potential for application across Amniotes.

No evidence of sexual selection in a repetition of Bateman's classic study of Drosophila melanogaster.

We are unique in reporting a repetition of Bateman [Bateman AJ (1948) Heredity (Edinb) 2:349-368] using his methods of parentage assignment, which linked sex differences in variance of reproductive success and variance in number of mates in small populations of Drosophila melanogaster. Using offspring phenotypes, we inferred who mated with whom and assigned offspring to parents. Like Bateman, we cultured adults expressing dramatic phenotypes, so that each adult was heterozygous-dominant at its unique marker locus but had only wild-type alleles at all other subjects' marker loci. Assuming no viability effects of parental markers on offspring, the frequencies of parental phenotypes in offspring follow mendelian expectations: one-quarter will be double-mutants who inherit the dominant gene from each parent, the offspring from which Bateman counted the number of mates per breeder; half of the offspring must be single mutants inheriting the dominant gene of one parent and the wild-type allele of the other parent; and one-quarter would inherit neither of their parent's marker mutations. Here we show that inviability of double-mutant offspring biased inferences of mate number and number of offspring on which rest inferences of sex differences in fitness variances. Bateman's method overestimated subjects with zero mates, underestimated subjects with one or more mates, and produced systematically biased estimates of offspring number by sex. Bateman's methodology mismeasured fitness variances that are the key variables of sexual selection.

Polyandry increases offspring viability and mother productivity but does not decrease mother survival in Drosophila pseudoobscura.

Polyandrous mating is common, but the benefits for females of polyandry remain controversial. To test whether mating with multiple males affects female fitness, we compared lifetime components of fitness of three experimental sets of Drosophila pseudoobscura females: monogamous females allowed to copulate one time (MOC); monogamous females held with a male over her entire life and experiencing many copulations (MMC); and polyandrous females with a different male over each day of their lives and also experiencing many copulations (PMC). Consistent with previous studies in this species, females in treatments in which multiple copulations occurred, MMC and PMC, had offspring with significantly higher egg-to-adult survival (i.e., offspring viability) and higher numbers of adult offspring (i.e., productivity) than MOC females, showing that multiple inseminations enhance offspring and mother fitness. In addition, although MMC females laid significantly more eggs than polyandrous (PMC) females, percent egg-to-adult survival and number of adult offspring were higher for PMC than MMC females, showing that polyandrous mating enhances the fitness of females more than multiply mating with only one male. Inconsistent with the cost of reproduction, lifespan was not significantly longer for MOC females than for MMC or PMC females. To our knowledge, this is the first study to examine simultaneously in outbred WT Drosophila pseudoobscura the lifetime costs and benefits to females of polyandry, monogamy with a single copulation, and monogamy with repeat copulations.

Bayesian animals sense ecological constraints to predict fitness and organize individually flexible reproductive decisions.

A quantitative theory of reproductive decisions (Gowaty & Hubbell 2009) says that individuals use updated priors from constantly changing demographic circumstances to predict their futures to adjust actions flexibly and adaptively. Our ecological/evolutionary models of ultimate causes seem consistent with Clark's ideas and thus suggest an opportunity for a unified proximate and ultimate theory of Bayesian animal brains, senses, and actions.

Reproductive decisions under ecological constraints: it's about time.

The switch point theorem (SPT) is the quantitative statement of the hypothesis that stochastic effects on survival, mate encounter, and latency affect individuals' time available for mating, the mean and variance in fitness, and thus, originally favored the evolution of individuals able to make adaptively flexible reproductive decisions. The SPT says that demographic stochasticity acting through variation in (i) individual survival probability, s; (ii) individual encounter probability, e; (iii) latency, l; (iv) the number of potential mates in the population, n; and (v) the distribution of fitness conferred, the w distribution, together affect average lifetime fitness, and induce adaptive switches in individual reproductive decisions. The switch point is the rank of potential mates at which focal individuals switch from accepting to rejecting potential mates, a decision rule that the SPT proves maximizes the average lifetime fitness of a focal individual under given values of ecological constraints on time. The SPT makes many predictions, including that the shape of the distribution of fitness conferred affects individual switch points. All else equal, higher probabilities of individual survival and encounter decrease the fraction of acceptable potential mates, such that focal individuals achieve higher average lifetime fitness by rejecting more potential mates. The primary prediction of the SPT is that each decision a focal individual makes is determined jointly by e, s, l, n, and the w distribution.

Bateman's Data: Inconsistent with "Bateman's Principles".

A.J. Bateman (1948) hypothesized that a metric of sexual selection is in sex differences of intrasexual variance in number of mates (V NM). AJB predicted that (a) males have greater variance in reproductive success (V RS) than females; (b) males have greater V NM than females; and (c) a positive relationship between V NM and V RS is stronger among males. AJB used phenotypically observable mutations in offspring to identify parents and to count subjects' NM and RS. AJB's conclusions matched his predictions, later called "Bateman's Principles." Empirical challenges to his conclusions guided analyses herein. (a) AJB's analysis pseudo-replicated sample sizes, violating a sexual selection assumption: That is, individuals must be in the same population to choose and compete. (b) AJB's methods overestimated subjects with no mates while underestimating subjects with one or more. (c) A replication (Gowaty et al., 2012) showed that offspring inheriting nametags from both parents often died before expressing adult phenotypes, proving some of AJB's methods produced biased data. Science historian Thierry Hoquet located AJB's archived, handwritten laboratory notes, photocopied, and transcribed them. We tested each of the 65 unique populations for expected combinations in offspring of parental mutations: 41.5% failed Punnett's tests: Offspring carrying nametags simultaneously from both parents were missing showing estimates of parents' NM and V NM were undercounted. 58.5% of populations met Punnett's expectations providing an unparalleled opportunity to re-evaluate AJB's predictions. 34 unbiased populations had no sex differences in V RS; 37 had no sex differences in V NM. No sex differences in slopes of RS and NM occurred in any unbiased population. Regressions showed weak, positive, significant associations between V NM and V RS for females and males, contrary to AJB's prediction that the relationship would be positive in males but not in females. AJB's laboratory data are inconsistent with "Bateman's Principles."

Reproductive compensation.

The reproductive compensation hypothesis says that individuals constrained by ecological or social forces to reproduce with partners they do not prefer compensate for likely offspring viability deficits. The reproductive compensation hypothesis assumes that (i) pathogens and parasites evolve more rapidly than their hosts, (ii) mate preferences predict variation in health and viability of offspring, (iii) social and ecological factors keep some individuals from mating with their preferred partners (some are constrained to mate with partners they do not prefer), (iv) all individuals may be induced to compensate, so that (v) variation in compensation is due to environmental and developmental factors affecting between-individual abilities to express compensatory mechanisms. Selection favouring compensation may act through variation in prezygotic physiological mechanisms, zygotic mechanisms, or parental care to eggs or young that enhance offspring health, increasing the likelihood that some offspring survive to reproductive age, often at a survival cost to the parents. Compensation may be through increased number of eggs laid or offspring born, a compensatory effort working during a single reproductive bout that sometimes will match the number of offspring surviving to reproductive age produced by unconstrained parents during the same bout. The reproductive compensation hypothesis therefore predicts trade-offs in components of fitness for breeders, such that parents constrained to mating with a nonpreferred partner, but who compensate sometimes match their current productivity (number of offspring at reproductive age) to unconstrained parents (those breeding with their preferred partners), and, when all else is equal, die faster than unconstrained parents. The reproductive compensation hypothesis emphasizes that reproductive competition is not just between constrained and unconstrained individuals, but also among constrained individuals who do and do not compensate. The reproductive compensation hypothesis may thus explain previously unexplained between-population and within-population, between-individual variation in reproductive success, survival, physiology and behaviour.

A reappraisal of Bateman's classic study of intrasexual selection.

Bateman's (1948) study showing greater variances in number of mates and reproductive success in male than female Drosophila melanogaster is a foundational paper in sexual selection. Here we show for the first time that his methods had flaws, including the elimination of genetic variance, sampling biases, miscalculations of fitness variances, statistical pseudo-replication, and selective presentation of data. We conclude that Bateman's results are unreliable, his conclusions are questionable, and his observed variances are similar to those expected under random mating. Despite our analysis, we do not intend this article as a criticism of Bateman; he accomplished his work without modern computational tools, and his approach was groundbreaking emphasizing the significance of fitness variance for sexual selection. However, this reanalysis has implications for what counts as evidence for sexual selection and we believe that our concerns should be of interest to contemporary students of sexual selection. We call for repetitions of Bateman's study using modern statistical and molecular methods.

Polyandry enhances offspring viability with survival costs to mothers only when mating exclusively with virgin males in Drosophila melanogaster.

A prominent hypothesis for polyandry says that male-male competitive drivers induce males to coerce already-mated females to copulate, suggesting that females are more likely to be harassed in the presence of multiple males. This early sociobiological idea of male competitive drive seemed to explain why sperm-storing females mate multiply. Here, we describe an experiment eliminating all opportunities for male-male behavioral competition, while varying females' opportunities to mate or not with the same male many times, or with many other males only one time each. We limited each female subject's exposure to no more than one male per day over her entire lifespan starting at the age at which copulations usually commence. We tested a priori predictions about relative lifespan and daily components of RS of female Drosophila melanogaster in experimental social situations producing lifelong virgins, once-mated females, lifelong monogamous, and lifelong polyandrous females, using a matched-treatments design. Results included that (1) a single copulation enhanced female survival compared to survival of lifelong virgins, (2) multiple copulations enhanced the number of offspring for both monogamous and polyandrous females, (3) compared to females in lifelong monogamy, polyandrous females paired daily with a novel, age-matched experienced male produced offspring of enhanced viability, and (4) female survival was unchallenged when monogamous and polyandrous females could re-mate with age- and experienced-matched males. (5) Polyandrous females daily paired with novel virgin males had significantly reduced lifespans compared to polyandrous females with novel, age-matched, and experienced males. (6) Polyandrous mating enhanced offspring viability and thereby weakened support for the random mating hypothesis for female multiple mating. Analyzes of nonequivalence of variances revealed opportunities for within-sex selection among females. Results support the idea that females able to avoid constraints on their behavior from simultaneous exposure to multiple males can affect both RS and survival of females and offspring.

A conceptual review of mate choice: stochastic demography, within-sex phenotypic plasticity, and individual flexibility.

Mate choice hypotheses usually focus on trait variation of chosen individuals. Recently, mate choice studies have increasingly attended to the environmental circumstances affecting variation in choosers' behavior and choosers' traits. We reviewed the literature on phenotypic plasticity in mate choice with the goal of exploring whether phenotypic plasticity can be interpreted as individual flexibility in the context of the switch point theorem, SPT (Gowaty and Hubbell 2009). We found >3000 studies; 198 were empirical studies of within-sex phenotypic plasticity, and sixteen showed no evidence of mate choice plasticity. Most studies reported changes from choosy to indiscriminate behavior of subjects. Investigators attributed changes to one or more causes including operational sex ratio, adult sex ratio, potential reproductive rate, predation risk, disease risk, chooser's mating experience, chooser's age, chooser's condition, or chooser's resources. The studies together indicate that "choosiness" of potential mates is environmentally and socially labile, that is, induced - not fixed - in "the choosy sex" with results consistent with choosers' intrinsic characteristics or their ecological circumstances mattering more to mate choice than the traits of potential mates. We show that plasticity-associated variables factor into the simpler SPT variables. We propose that it is time to complete the move from questions about within-sex plasticity in the choosy sex to between- and within-individual flexibility in reproductive decision-making of both sexes simultaneously. Currently, unanswered empirical questions are about the force of alternative constraints and opportunities as inducers of individual flexibility in reproductive decision-making, and the ecological, social, and developmental sources of similarities and differences between individuals. To make progress, we need studies (1) of simultaneous and symmetric attention to individual mate preferences and subsequent behavior in both sexes, (2) controlled for within-individual variation in choice behavior as demography changes, and which (3) report effects on fitness from movement of individual's switch points.

Mutual interest between the sexes and reproductive success in Drosophila pseudoobscura.

The pre-mating behavior of female Drosophila pseudoobscura has been considered passive and "coy" relative to more active, "ardent," and indiscriminate male behavior. To test whether this long-held view-the "received wisdom" about mating behavior in Drosophila-is really true we carried out observations on how often D. pseudoobscura females approached males prior to courtship and copulation. By including only virgin females and males in the experiments, we eliminated the possibility that males are "coy" due to sperm limitation and females flexibly "coy" due to male manipulations that may affect the duration of remating inhibition. We observed the movements of females and males in vials during the first five minutes of exposure to one another. Video records revealed females went toward males as frequently as males toward females; we inferred that females were as interested in males as males in females. The total number of offspring emerging as adults correlated significantly with mutual, precourtship interest of both males and females in their vial-mates and latency to copulation. Thus, we hypothesize that females in nature approach males, perhaps actively soliciting male courtship simply by remaining close to them.

Indiscriminate females and choosy males: within- and between-species variation in Drosophila.

The classic view of choosy, passive females and indiscriminate, competitive males gained theoretical foundations with parental investment theory. When females invest more in offspring than males, parental investment theory says that selection operates so that females discriminate among males for mates (i.e., females are choosy and passive) and males are indiscriminate (i.e., males are profligate and competitive). Here we report tests of predictions using Drosophila pseudoobscura and D. melanogaster, with typical asymmetry in gamete sizes (females > males), and in D. hydei with far less asymmetry in gamete size. Experimental observations revealed that the labels "choosy, passive females" and "profligate, indiscriminate males" did not capture the variation within and between species in premating behavior. In each of the species some females were as active in approaching males (or more so) than males in approaching females, and some males were as discriminating (or more so) than females. In pairs focal males and females responded differently to opposite-sex than to same-sex conspecifics. Drosophila hydei were less sex-role stereotyped than the other two species consistent with parental investment theory. However, D. pseudoobscura females approached males more often than did D. melanogaster females, and male D. hydei approached females as often as males of the other two species, both results inconsistent with parental investment theory. Male D. pseudoobscura and D. hydei were more likely to approach males in same-sex pairs than male D. melanogaster, inconsistent with parental investment theory.

Mendel's law reveals fatal flaws in Bateman's 1948 study of mating and fitness.

Bateman's experimental study of Drosophila melanogaster produced conclusions that are now part of the bedrock premises of modern sexual selection. Today it is the most cited experimental study in sexual selection, and famous as the first experimental demonstration of sex differences in the relationship between number of mates and relative reproductive success. We repeated the experimental methodology of the original to evaluate its reliability. The results indicate that Bateman's methodology of visible mutations to assign parentage and reproductive success to subject adults is significantly biased. When combined in offspring, the mutations decrease offspring survival, so that counts of mate number and reproductive success are mismeasured. Bateman's method overestimates the number of subjects with no mates and underestimates the number with one or more mates for both sexes. Here we discuss why Bateman's paper is important and present additional analyses of data from our monogamy trials. Monogamy trials can inform inferences about the force of sexual selection in populations because in monogamy trials male-male competition and female choice are absent. Monogamy trials also would have provided Bateman with an a priori test of the fit of his data to Mendel's laws, an unstated, but vital assumption of his methodology for assigning parentage from which he inferred the number of mates per individual subject and their reproductive success. Even under enforced monogamous mating, offspring frequencies of double mutant, single mutant and no mutant offspring were significantly different from Mendelian expectations proving that Bateman's method was inappropriate for answering the questions he posed. Double mutant offspring (those with a mutation from each parent) suffered significant inviability as did single mutant offspring whenever they inherited their mother's marker but the wild-type allele at their father's marker locus. These inviability effects produced two important inaccuracies in Bateman's results and conclusions. (1) Some matings that actually occurred were invisible and (2) reproductive success of some mothers was under-estimated. Both observations show that Bateman's conclusions about sex differences in number of mates and reproductive success were unwarranted, based on biased observations. We speculate about why Bateman's classic study remained without replication for so long, and we discuss why repetition almost 60 years after the original is still timely, necessary and critical to the scientific enterprise. We highlight overlooked alternative hypotheses to urge that modern tests of Bateman's conclusions go beyond confirmatory studies to test alternative hypotheses to explain the relationship between mate number and reproductive success.

The evolution of multiple mating: Costs and benefits of polyandry to females and of polygyny to males.

Polyandry is a paradox: why do females mate multiple times when a single ejaculate often provides enough sperm for lifetime egg production? Gowaty et al. addressed explanations for polyandry in Drosophila pseudoobscura from the perspective of hypotheses based on sex differences in costs of reproduction (CoR). Contrary to CoR, Gowaty et al. showed that (1) a single ejaculate was inadequate for lifetime egg production; (2) polyandry provided fitness benefits to females beyond provision of adequate sperm and (3) fitness benefits of polyandry were not offset by costs. Here, I discuss predictions of the ad hoc hypotheses of CoR and three alternative hypotheses to CoR to facilitate a discussion and further development of a strong inference approach to experiments on the adaptive significance of polyandry for females. Each of the hypotheses makes testable predictions; simultaneous tests of the predictions will provide a strong inference approach to understanding the adaptive significance of multiple mating. I describe a sex-symmetric experiment meant to evaluate variation in fitness among lifelong virgins (V); monogamous females and males with one copulation (MOC); monogamous females and males with multiple copulations (MMC); PAND, polyandrous females; and PGYN, polygynous males. Last, I recommend the study of many different species, while taking care in choice of study species and attention to the assumptions of specific hypotheses. I particularly urge the study of many more Drosophila species both in laboratory and the wild to understand the "nature of flies in nature," where opportunities and constraints mold evolutionary responses.

Preference status does not indicate intrinsic quality differences in Drosophila pseudoobscura.

The good genes hypothesis states that choosers prefer individuals of high intrinsic quality to individuals of lower intrinsic quality. Variation in longevity is thought to reflect, in part, intrinsic quality differences of individuals in addition to the costs of mating and reproduction. Here we report longevity variation of Drosophila pseudoobscura, a species in which previous experiments have demonstrated that individual mate preferences (pre-touching mate assessments) of females and males are associated with enhanced numbers of eclosed (adult) offspring and higher egg-to-adult survival (offspring viability). Using mate assessment arenas and protocols similar to those in a previous experiment that demonstrated fitness benefits to breeders and their offspring of mating with individuals they preferred, we tested the following predictions: (i) preferred discriminatees live longer than non-preferred discriminatees; (ii) males live longer than females; and (iii) virgins live longer than mated individuals. The experiment yielded 938 individuals for longevity analysis. Sex and mating status affected longevity: males lived longer than females, virgin females lived longer than mated females, but there were no differences in longevity for mated and virgin males. Non-preferred discriminatees of both sexes survived as long as preferred discriminatees, a result inconsistent with the prediction of the good genes hypothesis for mate preferences. To our knowledge, this is the first demonstration of the cost of reproduction for females in D. pseudoobscura and of longevity variation of preferred and non-preferred discriminatees.

Microsatellite markers isolated from Drosophila hydei.

We isolated and characterized 10 polymorphic microsatellite loci in Drosophila hydei. The number of alleles per locus ranged from 3 to 8 (N = 23 individuals). Polymorphic information content ranged from 0.316 to 0.750 and observed heterozygosity from 0.261 to 0.913. These markers will be valuable in studies of sexual selection and parental investment in D. hydei.

Experimental constraints on mate preferences in Drosophila pseudoobscura decrease offspring viability and fitness of mated pairs.

Using Drosophila pseudoobscura, we tested the hypothesis that social constraints on the free expression of mate preferences, by both females and males, decrease offspring viability and reproductive success of mating pairs. Mate preference arenas eliminated intrasexual combat and intersexual coercion. The time female and male choosers spent in arena tests near either of two opposite-sex individuals measured the preferences of choosers. We placed choosers in breeding trials with their preferred or nonpreferred discriminatee when they met the minimum criteria for showing the same preference in two consecutive tests. There was no statistically significant difference in the frequency of female and male choosers meeting minimal preference criteria. There was a significant difference between female and male choosers for offspring viability, with female choice having the greater effect, but there was not a significant difference in the overall reproductive success of male and female choosers. There were significant differences in fitness between matings to preferred and nonpreferred partners. Female and male choosers paired with their nonpreferred discriminatees had offspring of significantly lower viability, as predicted by the constraints hypothesis. Reproductive success, our measure of overall fitness, was greater when males or females mated with the partner they preferred rather than the one they did not prefer.

The hypothesis of reproductive compensation and its assumptions about mate preferences and offspring viability.

The Compensation Hypothesis says that parents and prospective parents attempt to make up for lowered offspring viability by increasing reproductive effort to produce healthy, competitive offspring and by increasing investment in less viable, but still-living progeny (parental effects). The hypothesis assumes that offspring viability is lower when individuals are constrained (often through sexual conflict) to breed with individuals they do not prefer. We review results of experimental tests of the offspring-viability assumption in Tanzanian cockroaches, fruit flies, pipefish, wild mallards, and feral house mice. Experimental constraints on mating preferences lowered offspring viability in each of the studies. Females breeding under constraints laid more eggs or gave birth to more young than females breeding without or with fewer constraints on their mating preferences, and males mating under constraints on their mate preferences ejaculated more sperm than males mating without constraints. The number of eggs laid or offspring born was higher when female choosers were experimentally constrained to reproduce with males they did not prefer. Constrained females may increase fecundity to enhance the probability that they produce adult offspring with rarer phenotypes with survival benefits against offspring generation pathogens. Similarly, ejaculation of more sperm when males are paired with females they do not prefer may be a mechanism that provides more variable sperm haplotypes for prospective mothers or that may provide nutritional benefits to mothers and zygotes.