The advent and maturation of algorithms for estimating species trees—phylogenetic trees that allow gene tree heterogeneity and whose tips represent lineages, populations and species, as opposed to genes—represent an exciting confluence of phylogenetics, phylogeography, and population genetics, and ushers in a new generation of concepts and challenges for the molecular systematist. In this essay I argue that to better deal with the large multilocus datasets brought on by phylogenomics, and to better align the fields of phylogeography and phylogenetics, we should embrace the primacy of species trees, not only as a new and useful practical tool for systematics, but also as a long-standing conceptual goal of systematics that, largely due to the lack of appropriate computational tools, has been eclipsed in the past few decades. I suggest that phylogenies as gene trees are a “local optimum” for systematics, and review recent advances that will bring us to the broader optimum inherent in species trees. In addition to adopting new methods of phylogenetic analysis (and ideally reserving the term “phylogeny” for species trees rather than gene trees), the new paradigm suggests shifts in a number of practices, such as sampling data to maximize not only the number of accumulated sites but also the number of independently segregating genes; routinely using coalescent or other models in computer simulations to allow gene tree heterogeneity; and understanding better the role of concatenation in influencing topologies and confidence in phylogenies. By building on the foundation laid by concepts of gene trees and coalescent theory, and by taking cues from recent trends in multilocus phylogeography, molecular systematics stands to be enriched. Many of the challenges and lessons learned for estimating gene trees will carry over to the challenge of estimating species trees, although adopting the species tree paradigm will clarify many issues (such as the nature of polytomies and the star tree paradox), raise conceptually new challenges, or provide new answers to old questions.

Barriers to gene flow can arise at any stage in the reproductive sequence. Most studies of reproductive isolation focus on premating or postzygotic phenotypes, leaving the importance of differences in fertilization rate overlooked. Two closely related species of house mice, Mus domesticus and M. musculus, form a narrow hybrid zone in Europe, suggesting that one or more isolating factors operate in the face of ongoing gene flow. Here, we test for differences in fertilization rate using laboratory matings as well as in vitro sperm competition assays. In noncompetitive matings, we show that fertilization occurs significantly faster in conspecific versus heterospecific matings and that this difference arises after mating and before zygotes form. To further explore the mechanisms underlying this conspecific advantage, we used competitive in vitro assays to isolate gamete interactions. Surprisingly, we discovered that M. musculus sperm consistently outcompeted M. domesticus sperm regardless of which species donated ova. These results suggest that in vivo fertilization rate is mediated by interactions between sperm, the internal female environment, and/or contributions from male seminal fluid. We discuss the implications of faster conspecific fertilization in terms of reproductive isolation among these two naturally hybridizing species.

Optimal male and female mating rates rarely coincide. Males often shift the rate in their favor by either increased signaling and by overcoming female resistance to copulation. The concept of sensory exploitation posits that males produce signals that mimic naturally selected benefits and so deceitfully attract females. However, males also have to overcome female resistance to actual copulation. Males may do so by copulating during situations when the female's ability to resist is decreased because of competing naturally selected demands. Males of the common bedbug, Cimex lectularius, an obligate blood feeder, mate at a rate, and in a manner that is harmful to females. Females have to feed regularly to produce eggs, and during feeding female body volume increases by 300%. Choice trials using unfed and either fed or experimentally enlarged but unfed females showed that the increased postfeeding body volume of females attracted more male mating attempts, strongly reduced female resistance to male mating attempts and resulted in a net increase in female mating rate. Our results, therefore, suggest that males have increased mating success in a situation that females cannot avoid because it is naturally selected. Such “situation exploitation” of low resistance may be a common phenomenon.

Sex has many costs with respect to asexual reproduction, so its ubiquity is a puzzle. There has been a continuing effort to identify general circumstances in which aspects of sex generate an evolutionary advantage over asexual reproduction. Here we focus on the generality that individuals can experience good and bad “luck” at various stages of their life history regardless of genotype, and on the interindividual nature of sex. Sexual outcrossing combines genetic information from individuals with potentially different experiences, so it is conceivable that sex might reduce the contribution of individual luck to noise in inheritance. In a simple way, we derive expressions for noise in inheritance in terms of some sources of within-generation ecological noise. We demonstrate that interindividual reproduction can indeed dampen the effects of ecological noise better than lone-individual modes, but there are conditions under which it does not. Empirical and theoretical work on plants, modeled here, suggest noise dampening conditions. Ecological noise dampening operates alongside other features of sex such as recombination and segregation and, because noise in inheritance weakens the role of selection in genetic change, we speculate that noise dampening may offer a benefit to be deducted from the costs of sex. We also suggest that the amount of selfing relative to outcrossing observed in natural populations may be influenced by the amount of individual-level ecological noise in a given habitat.

A survey of 117 species of arthropods and 17 species of vertebrates showed a strong trend for male genitalia to have relatively low static allometric values. This trend contrasts with the allometry of other structures under sexual selection, which usually show steep allometric slopes. The trend to low allometric genital values is less consistent in mammals than in arthropods. Data not in accord with the previous the “one-size-fits-all” explanation for low allometric slopes in genitalia, which was based on sexual selection by female choice, suggest a more general version that includes both natural selection and sexual selection, and involves both mechanical fit and stimulation. Less-complete data on the female genitalia of arthropods suggest a trend to similar low allometric slopes, and may also be explained by mechanical fit and stimulatory one-size-fits-all arguments.

Although recent studies have demonstrated that female crickets prefer novel males to previous mates, the relative contribution of pre- and postcopulatory behaviors to this advantage remain unknown, as do the reproductive consequences to males. I paired females either with previous or novel mates, and recorded the latency to mating and the time after mating at which the female removed the male's spermatophore, terminating sperm transfer. Females that mated with familiar males removed their spermatophores sooner than females that mated with novel males. Females paired with novel males also mated more quickly than females paired with familiar males, but this difference was not statistically significant. A molecular-based paternity analysis was used to determine whether the postcopulatory preference of females for novel males influences a male's fertilization success. Females were assigned to either mate three times with the same male and then once with a novel male, or four times with four different males. The paternity of the last male was higher when the female previously had mated repeatedly with the same male than when she had mated previously with different males. These results suggest that female spermatophore removal behavior influences male paternity such that novel males receive a fertility benefit.

For many taxa, species are defined by the morphologies of reproductive structures. In many odonates, these structures are the cerci of males (used to hold females during mating) and the thoracic plates of females where the male cerci contact the females' bodies. A previous study showed that the shapes of cerci of Enallagma males (Zygoptera: Coenagrionidae) are best explained by an evolutionary model of punctuated change at the time of speciation, with a homogeneous rate of change across the entire phylogeny of the genus. In the present study, we examine the evolution of shape change in the corresponding female plates. We found that, like male cerci, the shapes of Enallagma female thoracic plates could best be explained by an evolutionary model of punctuated change at the time of speciation, with a homogeneous rate of change across the clade. Moreover, the evolutionary contrasts quantifying the rates of change in male cerci and female thoracic plates were positively related across the history of the clade, demonstrating that these male and female structures evolve in a correlated fashion. This pattern of evolution suggests that these structures are primary signals of species identity during mating.

Transitions from sexual reproduction to parthenogenesis may occur along multiple evolutionary pathways and involve various cytological mechanisms to produce diploid eggs. Here, we investigate routes to parthenogenesis in Timema stick insects, a genus comprising five obligate parthenogens. By combining information from microsatellites and karyotypes with a previously published mitochondrial phylogeny, we show that all five parthenogens likely evolved spontaneously from sexually reproducing species, and that the sexual ancestor of one of the five parthenogens was probably of hybrid origin. The complete maintenance of heterozygosity between generations in the five parthenogens strongly suggests that eggs are produced by apomixis. Virgin females of the sexual species were also able to produce parthenogenetic offspring, but these females produced eggs by automixis. High heterozygosity levels stemming from conserved ancestral alleles in the parthenogens suggest, however, that automixis has not generated the current parthenogenetic Timema lineages but that apomixis appeared abruptly in several sexual species. A direct transition from sexual reproduction to (at least functional) apomixis results in a relatively high level of allelic diversity and high efficiency for parthenogenesis. Because both of these traits should positively affect the demographic success of asexual lineages, spontaneous apomixis may have contributed to the origin and maintenance of asexuality in Timema.

Most organisms experience strong selection to develop mechanisms to resist or tolerate their pathogens or parasites. Limits to adaptation are set by correlated responses to selection, for example reduced abilities to detect other parasites or trade-offs with other fitness components. For a few model systems it is now becoming possible to compare the evolutionary response to a broad range of natural enemies. In Drosophila, the evolutionary responses to ectoparasitic mites, parasitoids, and fungal and bacterial pathogens have previously been studied. Here replicate lines of D. melanogaster were exposed to the microsporidian parasite Tubulinosema kingi over a period of 61 weeks, with overlapping generations. Compared to controls, exposed lines had higher early-life fecundity and increased longevity when infected suggesting successful selection for resistance or tolerance. In the absence of the pathogen, exposed lines had lower fecundity when reared under harsh environmental conditions, and were poorer larval competitors than controls. They also had relatively higher densities of haemocytes, a component of the cellular immune system. Defense against this pathogen resembles more that against macroparasites than microsparasites, and this is interpreted in the light of what is known about the mechanisms of resistance to microsporidians.

Slight departures from bilateral symmetry are usually associated with reduced fitness. Here we show that an insular freshwater population of Gasterosteus aculeatus exhibits spatial and temporal segregation according to the incidence and direction of asymmetry in the number of bony lateral plates, which are important predator-defense structures. We analyzed 11,263 fish collected from 19 full lake transects over three years, and found that signed asymmetries for plate number were slightly left-side biased. Asymmetries occurred in 55% of the stickleback with more asymmetrics found during cold weather, and more left-biased individuals found during windy conditions, possibly due to environmentally driven activity levels that differ among asymmetric forms. Absolute plate asymmetries were randomly distributed in the lake, but there was a strong shift in signed plate asymmetry from a mean of zero in littoral zones to left-side bias in limnetic zones, probably due to microhabitat choices among asymmetric forms. Video data of avian piscivores on the lake show laterality in prey handling, providing a potential mechanism for asymmetric prey morphology. Our results imply a complex relationship between slight asymmetries and niche space that is relevant to the broader literature on the evolutionary implications of developmental instability and intrapopulation variability.

Predator-driven divergent selection may cause differentiation in defensive armor in threespine stickleback: (1) predatory fish and birds favor robust armor, whereas (2) predaceous aquatic insects favor armor reduction. Although (1) is well established, no direct experimental evidence exists for (2). I examined the phenotypic and genetic consequences of insect predation using F₂ families from crosses between freshwater and marine stickleback populations. I measured selection on body size, and size-adjusted spine (dorsal and pelvic) and pelvic girdle length, by splitting juvenile F₂ families between control and insect predation treatments, set in pond enclosures. I also examined the effect of insect predation on Ectodysplasin (Eda), a gene physically linked to quantitative trait loci for lateral plate number, spine length, and body shape. Insect predation resulted in: (1) significant selection for larger juvenile size, and shorter dorsal spine and pelvic girdle length, (2) higher mortality of individuals missing the pelvic girdle, and (3) selection in favor of the low armor Eda allele. Predatory insects favor less stickleback armor, likely contributing to the widespread reduction of armor in freshwater populations. Because size strongly influences mate choice, predator-driven divergent selection on size may play a substantial role in byproduct reproductive isolation and speciation in threespine stickleback.

Whether chromosomal rearrangements promote speciation by providing barriers to gene exchange between populations is one of the long-standing debates in evolutionary biology. This question can be addressed by studying patterns of gene flow and selection in hybrid zones between chromosomally diverse taxa. Here we present results of the first study of the genetic structure of a hybrid zone between chromosomal races of morabine grasshoppers Vandiemenella viatica, P24(XY) and viatica17, on Kangaroo Island, Australia. Chromosomal and 11 nuclear markers revealed a narrow hybrid zone with strong linkage disequilibrium and heterozygote deficits, most likely maintained by a balance between dispersal and selection. Widths and positions of clines for these markers are concordant and coincident, suggesting that selection is unlikely to be concentrated on a few chromosomes. In contrast, a mitochondrial marker showed a significantly wider cline with centre offset toward the P24(XY) side. We argue that the discordance between the mitochondrial and nuclear/chromosomal clines and overall asymmetry of the clines suggest a secondary origin of the contact zone and potential movement of the zone after contact. Genome-wide scans using many genetic markers and chromosomal mapping of these markers are needed to investigate whether chromosomal differences directly reduce gene flow after secondary contact.

Changes in mating signals among populations contribute to species formation. Often these signals involve a suite of display traits of different sensory modalities (“multimodal signals”); however, few studies have tested the consequences of multimodal signal divergence with most focusing on only a single divergent signal or suite of signals of the same sensory modality. Populations of the chestnut-bellied flycatcher Monarcha castaneiventris vary in song and plumage color across the Solomon Islands. Using taxidermic mount presentation and song playback experiments, we tested for the relative roles of divergent song and color in homotypic (“same type”) recognition between one pair of recently diverged sister taxa (the nominate chestnut-bellied M. c. castaneiventris and the white-capped M. c. richardsii forms). We found that both plumage and song type influenced the intensity of aggressive response by territory-owners, with plumage color playing a stronger role. These results indicate that differences in plumage and song are used in homotypic recognition, suggesting the importance of multimodal signal divergence in the evolution of premating reproductive isolation.

Wolbachia are maternally inherited bacteria that infect a large number of insects and are responsible for different reproductive alterations of their hosts. One of the key features of Wolbachia biology is its ability to move within and between host species, which contributes to the impressive diversity and range of infected hosts. Using multiple Wolbachia genes, including five developed for Multi-Locus Sequence Typing (MLST), the diversity and modes of movement of Wolbachia within the wasp genus Nasonia were investigated. Eleven different Wolbachia were found in the four species of Nasonia, including five newly identified infections. Five infections were acquired by horizontal transmission from other insect taxa, three have been acquired by hybridization between two Nasonia species, which resulted in a mitochondrial-Wolbachia sweep from one species to the other, and at least three have codiverged during speciation of their hosts. The results show that a variety of transfer mechanisms of Wolbachia are possible even within a single host genus. Codivergence of Wolbachia and their hosts is uncommon and provides a rare opportunity to investigate long-term Wolbachia evolution within a host lineage. Using synonymous divergence among codiverging infections and host nuclear genes, we estimate Wolbachia mutation rates to be approximately one-third that of the nuclear genome.

Summit metabolic rate (M_sum, maximum cold-induced metabolic rate) is positively correlated with cold tolerance in birds, suggesting that high M_sum is important for residency in cold climates. However, the phylogenetic distribution of high M_sum among birds and the impact of its evolution on current distributions are not well understood. Two potential adaptive hypotheses might explain the phylogenetic distribution of high M_sum among birds. The cold adaptation hypothesis contends that species wintering in cold climates should have higher M_sum than species wintering in warmer climates. The flight adaptation hypothesis suggests that volant birds might be capable of generating high M_sum as a byproduct of their muscular capacity for flight; thus, variation in M_sum should be associated with capacity for sustained flight, one indicator of which is migration. We collected M_sum data from the literature for 44 bird species and conducted both conventional and phylogenetically informed statistical analyses to examine the predictors of M_sum variation. Significant phylogenetic signal was present for log body mass, log mass-adjusted M_sum, and average temperature in the winter range. In multiple regression models, log body mass, winter temperature, and clade were significant predictors of log M_sum. These results are consistent with a role for climate in determining M_sum in birds, but also indicate that phylogenetic signal remains even after accounting for associations indicative of adaptation to winter temperature. Migratory strategy was never a significant predictor of log M_sum in multiple regressions, a result that is not consistent with the flight adaptation hypothesis.

Understanding the role of competition in explaining phenotypic diversity is a challenging problem, given that the most divergent species may no longer compete today. However, convergent evolution of extreme body sizes across communities may offer evidence of past competition. For example, many treefrog assemblages around the world have convergently evolved species with very large and small body sizes. To better understand this global pattern, we studied body-size diversification within the small, endemic radiation of Caribbean treefrogs (Osteopilus). We introduce a suite of analyses designed to help reveal the signature of past competition. Diet analyses show that Osteopilus are generalist predators and that prey size is strongly associated with body size, suggesting that body-size divergence facilitates resource partitioning. Community assembly models indicate that treefrog body-size distributions in Jamaica and Hispaniola are consistent with expectations from competition. Phylogenetic analyses show that similar body-size extremes in Jamaica and Hispaniola have originated through parallel evolution on each island, and the rate of body-size evolution in Osteopilus is accelerated relative to mainland treefrogs. Together, these results suggest that competition may have driven the rapid diversification of body sizes in Caribbean treefrogs to the extremes seen in treefrog communities around the world.

Although studied in many taxa, directional macroevolution remains difficult to detect and quantify. We present an approach for detecting directional evolution in subclades of species when relatively few species are sampled, and apply it to studying the evolution of stockiness in Phrynosomatine lizards. Our approach is more sensitive to detecting the tempo of directional evolution than other available approaches. We use ancestral reconstruction and phylogenetic mapping of morphology to characterize the direction and magnitude of trait evolution. We demonstrate a directional trend toward stockiness in horned lizards, but not their sister groups, finding that stockier species tend to have relatively short and wide bodies, and relatively short heads, tails, and limbs. Ornstein-Uhlenbeck models show that the directional trend in horned lizards is due to a shift in selective regime and stabilizing selection as opposed to directional selection. Bayesian evolutionary correlation analyses indicate that stockier species run more slowly and eat a larger proportion of ants. Furthermore, species with larger horns tend to be slower and more ant-specialized. Directional evolution toward a stocky body shape has evolved in conjunction with changes in a suite of traits, representing a complex example of directional macroevolution.

Eastern North America is the location of the world's most species-rich temperate freshwater fish fauna. Hypotheses regarding the geographic and temporal scale of teleost diversification in this region have not been broadly investigated using absolute divergence time estimates among the constituent lineages. This study used time-calibrated molecular phylogenies estimated from mitochondrial and nuclear genes to investigate the temporal and geographic signatures of diversification within barcheek darters, a clade of allopatrically distributed species endemic to the Eastern Highlands. Results from divergence time estimates using an uncorrelated lognormal model suggest that the barcheek darters are an ancient group with a crown node estimate of 16.3 mya, 95% highest posterior density (HPD): [12.4, 20.5], and the clade is characterized by substantial intraspecific divergence times within several species. In particular, the Caney Fork endemic Etheostoma basilare comprises five strongly supported and deeply divergent clades with a most recent common ancestor estimated at 8.0 mya, 95% HPD: [5.6, 10.7]. These results are concordant with the hypothesis that geologically stable areas of eastern North America have facilitated both the generation and preservation of lineages across a substantial breadth of evolutionary time, and that allopatric speciation in darters has occurred at much smaller spatial scales than previously realized.

Understanding the processes that underlie biodiversity requires insight into the evolutionary history of the taxa involved. Accurate estimation of speciation, extinction, and diversification rates is a prerequisite for gaining this insight. Here, we develop a stochastic birth-death model of speciation and extinction that predicts the probability distribution of both extinct and extant numbers of species in a clade. We present two estimation methods based on this model given data on the number of extinct species (from the fossil record) and extant species (from diversity assessments): a multivariate method of moments approach and a maximum-likelihood approach. We show that, except for some special cases, the two estimation methods produce very similar estimates. This is convenient, because the usually preferred maximum-likelihood approach is much more computationally demanding, so the method of moments can serve as a proxy. Furthermore, we introduce a correction for possible bias that can arise by the mere fact that we will normally only consider extant clades. We find that in some cases the bias correction affects the estimates profoundly. Finally, we show how our model can be extended to incorporate incomplete preservation. Preservation rates can, however, not be reliably estimated on the basis of numbers of extant and extinct species alone.

Prey that are unprofitable to attack are typically conspicuous in appearance. Conventional theory assumes that these warning signals have evolved in response to predator receiver biases. However, such biases might be a symptom rather than a cause of warning signals. We therefore examine an alternative theory: that conspicuousness evolves in unprofitable prey to avoid confusion with profitable prey. One might wonder why unprofitable prey do not find a cryptic means to be distinct from profitable prey, reducing both their risk of confusion with profitable prey and their rate of detection by predators. Here we present the first coevolutionary model to allow for Batesian mimicry and signals with different levels of detectability. We find that unprofitable prey do indeed evolve ways of distinguishing themselves using cryptic signals, particularly when appearance traits can evolve in multiple dimensions. However, conspicuous warning signals readily evolve in unprofitable prey when there are more ways to look different from the background than to match it. Moreover, the more unprofitable the prey species, the higher its evolved conspicuousness. Our results provide strong support for the argument that unprofitable species evolve conspicuous signals to avoid confusion with profitable prey and indicate that peak shift in conspicuousness-linked traits is a major factor in its establishment.

The idea of coevolution originated with Darwin's proposal that long-proboscid pollinators and long-tubed flowers might be engaged in reciprocal selection, but this has not been demonstrated. Here we test key aspects of Darwin's hypothesis of reciprocal selection in an experiment with naturally interacting populations of extremely long-proboscid flies (Moegistorhynchus longirostris: Nemestinidae) and long-tubed irises (Lapeirousia anceps: Iridaceae). We show that the benefit derived by both the fly (volume of nectar consumed) and the plant (number pollen grains received) depends on the relative length of their interacting organs. Each trait is shown to act both as agent and target in directional reciprocal selection, potentially leading to a race. This understanding of how fitness in both species varies in relation to the balance of their armament allows us to make tentative predictions about the nature of selection across multiple communities. We find that in each community a core group of long-tubed plant species might together be involved in diffuse coevolution with the fly. In poorly matched populations, the imbalance in armament is too great to allow reciprocal selection to act, and these species might instead experience one-sided selection that leads to convergence with the core species. Reciprocal selection drives the evolution of the community, then, additional species become attached to the network of interacting mutualists by convergence.

The idea of a general independence between the phenotypic plasticity and the mean value of a trait is, presently, a consensus. Here, we use the reaction norm of abdominal pigmentation (number of dark spots) of Drosophila mediopunctata in response to temperature, to test this idea. We raised eight strains, bearing two different chromosomal inversions and with varying mean phenotypic values, under 11 temperatures in a thermal gradient to test for predictions concerning mean phenotypic values, chromosomal inversions, and reaction norms. Our results revealed a strong effect of different phenotypic groups and no effect of different karyotypes on reaction norms. Moreover, we found a significant negative correlation between mean phenotypic value and the curvature of the reaction norms, revealing a high dependency of the reaction norm shape on mean phenotypic value. These results clearly reject the idea of genetic independence between mean value and phenotypic plasticity, and may indicate a pattern of correlation, which may include results from other traits and species, with an importance that has not been fully appreciated.

Periodical cicadas are known for unusually long and prime-numbered life cycles (13 and 17 years) for insects. To explain the evolution of prime-numbered reproductive intervals (life cycles), the hybridization hypothesis claims that prime numbers greatly reduce the chance of hybridization with other life cycles. We investigate the hybridization hypothesis using a simulation model. This model is a deterministic, discrete population model with three parameters: larval survival per year, clutch size, and emergence success. Reproductive intervals from 10 years to 20 years compete for survival in the simulations. The model makes three key assumptions: a Mendelian genetic system, random mating among broods of different life-cycle lengths, and integer population sizes. Longer life cycles have larger clutch sizes but suffer higher total mortality than shorter life cycles. Our results show that (1) nonprime-numbered reproductive intervals disappear rapidly in comparison to the selection among the various prime-numbered life cycles, (2) the selection of prime-numbered intervals happens only when populations are at the verge of extinction, and (3) the 13- and 17-year prime phenotypes evolve under certain conditions of the model and may coexist. The hybridization hypothesis is discussed in light of other hypotheses for the evolution of periodical cicada life cycles.

A 5000-year fossil series of minute submarine cave bivalves was studied using morphometric and evolutionary analyses. The obtained results indicate that the shapes of larval shells of studied species were labile, whereas the size of the larval shell was stable in each species studied. This result is different than that previously reported in most other studies in which size change is more common than shape change. This unique evolutionary pattern of these bivalves might be attributed to their refugial lifestyle.