PERSPECTIVE: MODELS OF SPECIATION: WHAT HAVE WE LEARNED IN 40 YEARS?

Multilocus Characterization of a Woodrat (Genus Neotoma) Hybrid Zone

In order to investigate hybridization between 2 species of woodrats, Neotoma floridana and Neotoma micropus, 103 specimens were collected, in March of 1988, from a known area of sympatry, and compared with reference collections from areas of allopatry. Ten genetic markers, consisting of 7 microsatellite loci, 1 mitochondrial gene (cytochrome-b [Cytb]), and 2 nuclear introns (intron 2 of the vertebrate alcohol dehydrogenase gene [Adh1-I2] and intron 7 of the beta-fibrinogen gene [Fgb-I7]) were used to develop a composite genotype for each individual and for detection of hybridization. Six individuals were identified as pure parental N. micropus, 96 as hybrids, and 1 as pure parental N. floridana Hybrids were formed primarily through matings between complex genotypes, resulting in a high prevalence of individuals classified as backcrosses. The ratio of hybrid classes, population substructure, and presence of significant linkage disequilibrium within the zone of contact could not reject either the hybrid superiority or hybrid equilibrium model as responsible for maintenance of this hybrid zone. The collection date of this dataset (1988) provided not only a point in time assessment of the hybrid zone but also provided opportunities for future comparisons of temporal datasets with the purpose of examining hybrid zone characteristics over multiple generations.

Two-time-scale population evolution on a singular landscape

Under the effect of strong genetic drift, it is highly probable to observe gene fixation or gene loss in a population, shown by singular peaks on a potential landscape. The genetic drift-induced noise gives rise to two-time-scale diffusion dynamics on the bipeaked landscape. We find that the logarithmically divergent (singular) peaks do not necessarily imply infinite escape times or biological fixations by iterating the Wright-Fisher model and approximating the average escape time. Our analytical results under weak mutation and weak selection extend Kramers's escape time formula to models with B (Beta) function-like equilibrium distributions and overcome constraints in previous methods. The constructed landscape provides a coherent description for the bistable system, supports the quantitative analysis of bipeaked dynamics, and generates mathematical insights for understanding the boundary behaviors of the diffusion model.

Evolution of a genetic incompatibility in the genus Xiphophorus

Genetic incompatibilities are commonly observed between hybridizing species. Although this type of isolating mechanism has received considerable attention, we have few examples describing how genetic incompatibilities evolve. We investigated the evolution of two loci involved in a classic example of a Bateson-Dobzhansky-Muller (BDM) incompatibility in Xiphophorus, a genus of freshwater fishes from northern Central America. Hybrids develop a lethal melanoma due to the interaction of two loci, an oncogene and its repressor. We cloned and sequenced the putative repressor locus in 25 Xiphophorus species and an outgroup species, and determined the status of the oncogene in those species from the literature. Using phylogenetic analyses, we find evidence that a repeat region in the proximal promoter of the repressor is coevolving with the oncogene. The data support a hypothesis that departs from the standard BDM model: it appears the alleles that cause the incompatibilities have coevolved simultaneously within lineages, rather than in allopatric or temporal isolation.

Genetic diversification, vicariance, and selection in a polytypic frog

Spatial patterns of heritable phenotypic diversity reflect the relative roles of gene flow and selection in determining geographic variation within a species. We quantified color differentiation and genetic divergence among 20 populations of the red-eyed tree frog (Agalychnis callidryas) in lower Central America. Phylogenetic analyses revealed 5 well-supported mitochondrial DNA clades, and we infer from our phylogeny that geographic barriers have played a large role in structuring populations. Two phenotypic characters varied independently among isolated population groups: Flank coloration distinguished Caribbean from Pacific individuals, whereas leg coloration exhibited a more complex geographic pattern. We detected 3 generalized spatial patterns of genetic and phenotypic diversity: 1) phenotypic differentiation in the presence of historical connectivity, 2) phenotypic uniformity across genetically differentiated regions, and 3) codistribution of genetic and phenotypic characters. These patterns indicate that phenotypic diversification is highly regionalized and can result from spatial variation in localized adaptations, geographic isolation, genetic drift, and/or evolutionary stasis. Although the mode of selection underlying color variation was not the focal objective of this study, we discuss the possible roles of natural and sexual selection in mediating population differentiation. Our study underscores the fact that selection gradients vary across relatively small spatial scales, even in species that occupy relatively homogeneous environments.

RAPID ALLOPATRIC SPECIATION IN LOGPERCH DARTERS (PERCIDAE: PERCINA)

Theory predicts that clades diversifying via sympatric speciation will exhibit high diversification rates. However, the expected rate of diversification in clades characterized by allopatric speciation is less clear. Previous studies have documented significantly higher speciation rates in freshwater fish clades diversifying via sympatric versus allopatric modes, leading to suggestions that the geographic pattern of speciation can be inferred solely from knowledge of the diversification rate. We tested this prediction using an example from darters, a clade of approximately 200 species of freshwater fishes endemic to eastern North America. A resolved phylogeny was generated using mitochondrial DNA gene sequences for logperches, a monophyletic group of darters composed of 10 recognized species. Divergence times among logperch species were estimated using a fossil calibrated molecular clock in centrarchid fishes, and diversification rates in logperches were estimated using several methods. Speciation events in logperches are recent, extending from 4.20 +/- 1.06 million years ago (mya) to 0.42 +/- 0.22 mya, with most speciation events occurring in the Pleistocene. Diversification rates are high in logperches, at some nodes exceeding rates reported for well-studied adaptive radiations such as Hawaiian silverswords. The geographic pattern of speciation in logperches was investigated by examining the relationship between degree of sympatry and the absolute age of the contrast, with the result that diversification in logperches appears allopatric. The very high diversification rate observed in the logperch phylogeny is more similar to freshwater fish clades thought to represent examples of sympatric speciation than to clades representing allopatric speciation. These results demonstrate that the geographic mode of speciation for a clade cannot be inferred from the diversification rate. The empirical observation of high diversification rates in logperches demonstrates that allopatric speciation can occur rapidly.

Accumulating Dobzhansky-Muller incompatibilities: reconciling theory and data

Theoretical models of the accumulation of Dobzhansky-Muller incompatibilities (DMIs) are studied, and in particular, the framework introduced by Orr (1995) and a verbal model introduced by Kondrashov et al. (2002). These models embody very different assumptions about the relationship between the substitution process underlying evolutionary divergence and the formation of incompatibilities. These differences have implications for our ability to make inferences about the divergence from patterns in the relevant data. With this in mind, the models are investigated for their ability to account for three patterns evident in this data: (1) the asymmetrical nature of incompatibilities under reciprocal introgression; (2) the finding that multiple concurrent introgressions may be necessary for an incompatibility to form; and (3) the finding that the probability of obtaining an incompatibility by introgressing a single amino acid remains roughly constant over a wide range of genetic distances. None of the models available in the literature can account for all of the empirical patterns. However, modified versions of the models can do so. Ways of discriminating between the different models are then discussed.

WHEN VICARS MEET: A NARROW CONTACT ZONE BETWEEN MORPHOLOGICALLY CRYPTIC PHYLOGEOGRAPHIC LINEAGES OF THE RAINFOREST SKINK, CARLIA RUBRIGULARIS

Phylogeographic analyses of the fauna of the Australian wet tropics rainforest have provided strong evidence for long-term isolation of populations among allopatric refugia, yet typically there is no corresponding divergence in morphology. This system provides an opportunity to examine the consequences of geographic isolation, independent of morphological divergence, and thus to assess the broader significance of historical subdivisions revealed through mitochondrial DNA phylogeography. We have located and characterized a zone of secondary contact between two long isolated (mtDNA divergence > 15%) lineages of the skink Carlia rubrigularis using one mitochondrial and eight nuclear (two intron, six microsatellite) markers. This revealed a remarkably narrow (width < 3 km) hybrid zone with substantial linkage disequilibrium and strong deficits of heterozygotes at two of three nuclear loci with diagnostic alleles. Cline centers were coincident across loci. Using a novel form of likelihood analysis, we were unable to distinguish between sigmoidal and stepped cline shapes except at one nuclear locus for which the latter was inferred. Given estimated dispersal rates of 90-133 m x gen(-1/2) and assuming equilibrium, the observed cline widths suggest effective selection against heterozygotes of at least 22-49% and possibly as high as 70%. These observations reveal substantial postmating isolation, although the absence of consistent deviations from Hardy-Weinberg equilibrium at diagnostic loci suggests that there is little accompanying premating isolation. The tight geographic correspondence between transitions in mtDNA and those for nuclear genes and corresponding evidence for selection against hybrids indicates that these morphologically cryptic phylogroups could be considered as incipient species. Nonetheless, we caution against the use of mtDNA phylogeography as a sole criterion for defining species boundaries.