[Show abstract][Hide abstract] ABSTRACT: 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.
[Show abstract][Hide abstract] ABSTRACT: 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.
Philosophical Transactions of The Royal Society B Biological Sciences 06/2010; 365(1547):1717-33. · 6.23 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: Herein we assess the phylogenetic relationships and taxonomy of geckos of the genus Phyllodactylus inhabiting the peninsula of Baja California, Mexico using five mitochondrial and two nuclear genes. Phylogenetic analysis using maximum parsimony (MP) and Bayesian inference (BI) recovered three distinct peninsular clades with high statistical support. Sequence divergence estimates between peninsular taxa approached 13%. Two of the species, P. unctus and P. xanti are Cape Region endemics, whereas P. nocticolus is widespread throughout much of the peninsula and extreme southern California. Monophyly of the peninsular taxa was strongly supported. In the MP analysis, P. unctus rooted at the base of the peninsular clade, resolving P. xanti and P. nocticolus as sister taxa. Conversely, BI placed P. nocticolus and P. unctus as sister taxa. These data provide further evidence for a trans-peninsular seaway near the Isthmus of La Paz, severing the Cape Region from the rest of the peninsula. The analysis also supports the validity of P. nocticolus as a distinct species and suggests a single invasion to the peninsula from mainland Mexico, presumably during tectonic activity during the Miocene.
[Show abstract][Hide abstract] ABSTRACT: 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.
[Show abstract][Hide abstract] ABSTRACT: 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.
[Show abstract][Hide abstract] ABSTRACT: The use of molecular markers has greatly increased our understanding of unionoid systematics. However, it is critical that their use in phylogenetic studies be conducted with the correct methodologies in order to ensure that the correct interpretations of evolutionary history are made. The phylogenetic relationships of a selection of Anodonta were investigated by Hoeh (1990), who found variation in 23 allozyme loci. These allozymes were coded using the presence/absence of alleles, yielding 67 characters used in a phylogenetic analysis. The resulting phylogeny was used as evidence to recommend the elevation of Pyganodon and Utterbackia to full generic status. Since the publication of Hoeh (1990) the coding of characters using the presence/absence of alleles has been shown to be invalid and has been superseded by mutation coding, with the locus as the character. The phylogenetic analysis of 20 characters, coded using mutation coding, yielded two equally parsimonious trees and an interpretation markedly different from that of Hoeh (1990). Both trees supported the monophyly of Pyganodon and Utterbackia. However, the genus Anodonta was paraphyletic with respect to both Pyganodon and Utterbackia. The one Eurasian species (Anodonta cygnea) was resolved as the sister of the remaining ingroup taxa, including Pyganodon, Utterbackia, and the North American Anodonta. These findings lead to a taxonomic problem, requiring further phylogenetic analysis of the Anodontinae. In order to test the phylogenetic hypotheses presented herein, we strongly recommend the construction of a phylogeny for all anodontine taxa using a combination of mitochondrial and nuclear DNA sequences.
Proceedings of the Academy of Natural Sciences of Philadelphia 05/2007; · 0.83 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: Geological forces and long-term climate changes can have profound effects on species. Such effects may be manifested in the pattern and magnitude of genealogical diversity, as revealed by mitochondrial DNA (mtDNA) lineages. The relative importance of the different forces on a regional biota must be evaluated along with a good understanding of geological and climatological history. The peninsula of Baja California of north-western Mexico is one area where both geology and climate have affected the historical biogeography of the regional biota. Molecular studies based on the genealogical relationships among mtDNA lineages have contributed greatly towards elucidating the historical biogeography of Baja California. Perhaps most noticeably, numerous concordant breaks in mtDNA genealogies half-way along the peninsula suggest a vicariant history in which the mid-peninsula was temporarily submerged. This vicariant explanation has recently been criticized, as no conclusive geological evidence exists for a continuous submergence of the mid-peninsula. As an alternative, a scenario based on climatological factors has been suggested. Here we discuss the validity of the hypothesized mid-peninsular vicariance event and the climate-based alternative in explaining the concordant genealogical breaks. We argue that, despite the significant changes in climate brought about by the glacial cycles throughout the Quaternary, a vicariant history involving a mid-peninsular seaway remains the most parsimonious explanation of the observed patterns in mtDNA genealogies.
[Show abstract][Hide abstract] ABSTRACT: 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.
Molecular Phylogenetics and Evolution 10/2005; 36(3):682-94. · 4.07 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: As a case study for single-nucleotide polymorphism (SNP) identification in species for which little or no sequence information is available, we investigated several approaches to identifying SNPs in two passerine bird species: pied and collared flycatchers (Ficedula hypoleuca and F. albicollis). All approaches were successful in identifying sequence polymorphism and over 50 candidate SNPs per species were identified from approximately 9.1 kb of sequence. In addition, 17 sites were identified in which the frequency of alternative bases differed by > 50% between species (termed interspecific SNPs). Interestingly, polymorphism of microsatellite/intron loci in the source species appeared to be a positive predictor of nucleotide diversity in homologous flycatcher sequences. The overall nucleotide diversity of flycatchers was 2.3-2.7 x 10(-3), which is approximately 3-6 times higher than observed in recent studies of human SNPs. Higher nucleotide diversity in the avian genome could be due to the relatively older age of flycatcher populations, compared with humans, and/or a higher long-term effective population size.
[Show abstract][Hide abstract] ABSTRACT: Evolutionary history of Muscicapidae flycatchers is inferred from nuclear and mitochondrial DNA (mtDNA) sequence comparisons and population genetic analysis of nuclear and mtDNA markers. Phylogenetic reconstruction based on sequences from the two genomes yielded similar trees with respect to the order at which the species split off. However, the genetic distances fitted a nonlinear, polynomial model reflecting diminishing divergence rate of the mtDNA sequences compared to the nuclear DNA sequences. This could be explained by Haldane's rule because genetic isolation might evolve more rapidly on the mitochondrial rather than the nuclear genome in birds. This is because hybrid sterility of the heterogametic sex (females) would predate that of the homogametic sex (males), leading to sex biased introgression of nuclear genes. Analyses of present hybrid zones of pied (Ficedula hypoleuca) and collared flycatchers (F. albicollis) may indicate a slight sexual bias in rate of introgression, but the introgression rates were too low to allow proper statistical analyses. It is suggested, however, that the observed deviation from linearity can be explained by a more rapid mutational saturation of the mtDNA sequences than of the nuclear DNA sequences, as supported by analyses of third codon position transversions at two protein coding mtDNA genes. A phylogeographic scenario for the black and white flycatcher species is suggested based on interpretation of the genetic data obtained. Four species appear to have diverged from a common ancestor relatively simultaneously during the Pleistocene. After the last glaciation period, pied and collared flycatchers expanded their breeding ranges and eventually came into secondary contact in Central and Eastern Europe and on the Baltic Isles.