A high-density scan of the Z chromosome in Ficedula flycatchers reveals candidate loci for diversifying selection.

Theoretical and empirical data suggest that genes located on sex chromosomes may play an important role both for sexually selected traits and for traits involved in the build-up of hybrid incompatibilities. We investigated patterns of genetic variation in 73 genes located on the Z chromosomes of two species of the flycatcher genus Ficedula, the pied flycatcher and the collared flycatcher. Sequence data were evaluated for signs of selection potentially related to genomic differentiation in these young sister species, which hybridize despite reduced fitness of hybrids. Seven loci were significantly more divergent between the two species than expected under neutrality and they also displayed reduced nucleotide diversity, consistent with having been influenced by directional selection. Two of the detected candidate regions contain genes that are associated with plumage coloration in birds. Plumage characteristics play an important role in species recognition in these flycatchers suggesting that the detected genes may have been involved in the evolution of sexual isolation between the species.

Speciation genetics: current status and evolving approaches.

The view of species as entities subjected to natural selection and amenable to change put forth by Charles Darwin and Alfred Wallace laid the conceptual foundation for understanding speciation. Initially marred by a rudimental understanding of hereditary principles, evolutionists gained appreciation of the mechanistic underpinnings of speciation following the merger of Mendelian genetic principles with Darwinian evolution. Only recently have we entered an era where deciphering the molecular basis of speciation is within reach. Much focus has been devoted to the genetic basis of intrinsic postzygotic isolation in model organisms and several hybrid incompatibility genes have been successfully identified. However, concomitant with the recent technological advancements in genome analysis and a newfound interest in the role of ecology in the differentiation process, speciation genetic research is becoming increasingly open to non-model organisms. This development will expand speciation research beyond the traditional boundaries and unveil the genetic basis of speciation from manifold perspectives and at various stages of the splitting process. This review aims at providing an extensive overview of speciation genetics. Starting from key historical developments and core concepts of speciation genetics, we focus much of our attention on evolving approaches and introduce promising methodological approaches for future research venues.

Evolutionary implications of non-neutral mitochondrial genetic variation.

Sequence variation in mitochondrial DNA (mtDNA) was traditionally considered to be selectively neutral. However, an accumulating body of evidence indicates that this assumption is invalid. Furthermore, recent advances indicate that mtDNA polymorphism can be maintained within populations via selection on the joint mitochondrial-nuclear genotype. Here, we review the latest findings that show mitochondrial and cytoplasmic genetic variation for life-history traits and fitness. We highlight the key importance of the mitochondrial-nuclear interaction as a unit of selection and discuss the consequences of mitochondrially encoded fitness effects on several key evolutionary processes. Our goal is to draw attention to the profound, yet neglected, influence of the mitochondrial genome on the fields of ecology and evolution.

Simple identification of mitochondrial lineages in contact zones based on lineage-selective primers.

A variety of research projects focus on genetic variation among and within maternal lineages as encompassed by mitochondrial DNA (mtDNA). While mtDNA often differs substantially between species, large differences may also be found within species. The evaluation of such divergent lineages, for example in intraspecific contact zones (hybrid zones), commonly involves sequencing numerous individuals. Large-scale sequencing is both expensive and labour-intensive. Based on sequences from 15 individuals, we devised a simple and quick polymerase chain reaction assay for identification of divergent mtDNA lineages in a secondary contact zone of the side-blotched lizard (Uta stansburiana). The application uses lineage-selective primers to amplify a lineage-diagnostic product, and is based on each group of mtDNA haplotypes being a monophyletic assemblage of haplotypes sharing the same maternal ancestry, deeply divergent from the other group. The assay was tested on a larger sample (n = 147) of specimens from the contact zone, confirming its usefulness in quick and reliable identification of mtDNA lineages. This approach can be modified for other species, provided diagnostic lineage variation is available, and may also be performed in simple laboratory settings while conducting fieldwork.

Deep genealogical history without population differentiation: discordance between mtDNA and allozyme divergence in the zebra-tailed lizard (Callisaurus draconoides).

The peninsula of Baja California has a complex geological history that has strongly affected the regional biota. Genealogical histories of many species have revealed congruent patterns, which suggest that the peninsula was temporarily submerged at two locations. We sequenced a total of 1953 base pairs (bp) of the mitochondrial genome for 42 specimens of the zebra-tailed lizard (Callisaurus draconoides). The resulting maternal genealogy supports the former existence of a mid-peninsular seaway and a Plio-Quaternary seaway across the Isthmus of La Paz. In addition, a genealogical break is revealed in the vicinity of Loreto. This genealogical break may have resulted from prolonged submergence of the Loreto Basin during Pliocene. The mid-peninsular seaway may have occurred as early as late Miocene, at a time significantly earlier than previously hypothesized. Comparison with other genealogies and geological evidence suggests that current models on the evolution of Baja California's fauna are temporally shallow. The deep genealogical patterns of C. draconoides also disagree with the very limited population differentiation previously reported for allozyme markers, suggesting that maternal history may not be an appropriate approximation for population differentiation.

Inbreeding depression and male fitness in black grouse.

The male lifetime lekking performance was studied, and related to inbreeding-outbreeding in a wild population of black grouse (Tetrao tetrix) in central Finland between 1989 and 1995. Inbreeding was measured as the mean heterozygosity and mean d(2) of 15 microsatellite loci. We found a significantly positive relationship between mean d(2) and lifetime copulation success (LCS), while the relationship between heterozygosity and LCS was close to significant. We also found that males that never obtained a lek territory had significantly lower mean heterozygosity than males that were observed on a territory at least during one mating season in their life. Furthermore, among males that were successful in obtaining a lek territory, LCS and mean d(2) were highest for those males that held central territories. We suggest that inbred males have a disadvantage (or outbred males have an advantage) in the competition for territories that may explain the relationships with LCS and inbreeding. Furthermore, the fact that mean d(2) was positively correlated with LCS whereas heterozygosity was not when we restricted the analysis to territorial males, suggests that mean d(2) provides more information about levels of inbreeding-outbreeding than heterozygosity alone, and potentially highlights the effects of heterosis. To our knowledge, this is the first time that measures of inbreeding and lifetime fitness have been linked in a non-isolated population. This is important in establishing that the relationships found in previous studies are not artefacts of low gene flow created by limited dispersal but a general feature of wild vertebrate populations.