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Speciation genetics research in diverse organisms shows the X‐chromosome to be exceptional in how it contributes to "rules" of speciation. Until recently, however, the nematode phylum has been nearly silent on this issue, despite the model organism Caenorhabditis elegans having touched most other topics in biology. Studies of speciation with Caenorhabditis accelerated with the recent discovery of species pairs showing partial interfertility. The resulting genetic analyses of reproductive isolation in nematodes demonstrate key roles for the X‐chromosome in hybrid male sterility and inviability, opening up new understanding of the genetic causes of Haldane's rule, Darwin's corollary to Haldane's rule, and enabling tests of the large‐X effect hypothesis. Studies to date implicate improper chromatin regulation of the X‐chromosome by small RNA pathways as integral to hybrid male dysfunction. Sexual transitions in reproductive mode to self‐fertilizing hermaphroditism inject distinctive molecular evolutionary features into the speciation process for some species. Caenorhabditis also provides unique opportunities for analysis in a system with XO sex determination that lacks a Y‐chromosome, sex chromosome‐dependent sperm competition differences and mechanisms of gametic isolation, exceptional accessibility to the development process and rapid experimental evolution. As genetic analysis of reproductive isolation matures with investigation of multiple pairs of Caenorhabditis species and new species discovery, nematodes will provide a powerful complement to more established study organisms for deciphering the genetic basis of and rules to speciation. [ABSTRACT FROM AUTHOR]

The genomic density of sequence polymorphisms critically affects the sensitivity of inferences about ongoing sequence evolution, function and demographic history. Most animal and plant genomes have relatively low densities of polymorphisms, but some species are hyperdiverse with neutral nucleotide heterozygosity exceeding 5%. Eukaryotes with extremely large populations, mimicking bacterial and viral populations, present novel opportunities for studying molecular evolution in sexually reproducing taxa with complex development. In particular, hyperdiverse species can help answer controversial questions about the evolution of genome complexity, the limits of natural selection, modes of adaptation and subtleties of the mutation process. However, such systems have some inherent complications and here we identify topics in need of theoretical developments. Close relatives of the model organisms Caenorhabditis elegans and Drosophila melanogaster provide known examples of hyperdiverse eukaryotes, encouraging functional dissection of resulting molecular evolutionary patterns. We recommend how best to exploit hyperdiverse populations for analysis, for example, in quantifying the impact of noncrossover recombination in genomes and for determining the identity and micro-evolutionary selective pressures on noncoding regulatory elements. [ABSTRACT FROM AUTHOR]

Everyone appreciates the happy fiction that species conform to the simple theoretical convenience of a single panmictic population. In speciation genetics, a further standard simplification is that it is only those genetic differences that are fixed between diverging populations that need concern us in order to understand the accumulation of intrinsic barriers to reproduction. To a first approximation, of course, both of these assumptions are appropriate and theory based on them provides compelling insights into diverse evolutionary phenomena (Orr & Turelli ). But what else can we learn about the begetting of biodiversity, speciation, by considering explicitly some less convenient realities of natural populations? Specifically, how does genetic variation at incompatibility loci within a species influence interspecies hybridization upon secondary contact? And, in nature, how repeatable among distinct bouts of secondary contact are the genomic outcomes of hybridization? Mandeville et al. () tackle exactly this question in their new study in Molecular Ecology on five species of suckers, fish of the genus Catostomus, that overlap sympatrically in different portions of their subdivided ranges that occupy different rivers. They document substantial genomic heterogeneity in realized hybridization in nature, both among species pairs and among the source populations for hybrids of a given species pair. This imperfect repeatability of episodes of hybridization implies greater permeability of species barriers in some parts of their range, with intriguing consequences for how the integrity of species as independently evolving units could be susceptible to collapse. [ABSTRACT FROM AUTHOR]