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PubMed2006

Hybridization between mtDNA-defined phylogeographic lineages of black ratsnakes (Pantherophis sp.).

Phylogeographic analyses using mitochondrial DNA (mtDNA) have revealed many examples of apparently deep historical subdivisions ('phylogroups') within many vertebrates. It remains unclear whether these phylogroups represent independently evolving, adaptively differentiated lineages or groups that show little functional differentiation and, hence, will merge on contact. Here, we use mtDNA sequence data to evaluate the phylogeographic relationships between two of the northernmost populations of black ratsnakes (Pantherophis obsoletus complex) in Ontario, Canada and previously analysed populations in the United States. We then use population-level analyses to evaluate the level of adaptive divergence between previously established mtDNA phylogroups. Phylogenetic analyses show that southern Ontario snakes have mtDNA haplotypes that fall within the Central mtDNA phylogroup, as designated by Burbrink et al. (2000). In contrast, snakes in eastern Ontario carry either Central or Eastern-specific haplotypes. Within the hybrid region, we found highly variable frequencies of mtDNA haplotypes among isolated sub-populations, no association between variation in cytonuclear (mtDNA) and nuclear (microsatellite DNA) markers, no difference in survival or reproductive success among snakes with different mtDNA haplotypes, and no effect of mate similarity in mtDNA on female clutch size. These results argue that the Eastern and Central phylogroups have merged in this region, likely due to a lack of adaptive differentiation between individuals in each lineage. Hence, in these snakes, phylogeographic structure in mtDNA is more a reflection of historical isolation rather than adaptive divergence. The observed reticulation between lineages and lack of evidence for hybrid disgenesis also bears on the classification of these lineages as distinct species.

Adaptation, Physiological↗
PubMed2006

Deleterious epistatic interactions between electron transport system protein-coding loci in the copepod Tigriopus californicus.

The nature of epistatic interactions between genes encoding interacting proteins in hybrid organisms can have important implications for the evolution of postzygotic reproductive isolation and speciation. At this point very little is known about the fitness differences caused by specific closely interacting but evolutionarily divergent proteins in hybrids between populations or species. The intertidal copepod Tigriopus californicus provides an excellent model in which to study such interactions because the species range includes numerous genetically divergent populations that are still capable of being crossed in the laboratory. Here, the effect on fitness due to the interactions of three complex III proteins of the electron transport system in F2 hybrid copepods resulting from crosses of a pair of divergent populations is examined. Significant deviations from Mendelian inheritance are observed for each of the three genes in F2 hybrid adults but not in nauplii (larvae). The two-way interactions between these genes also have a significant impact upon the viability of these hybrid copepods. Dominance appears to play an important role in mediating the interactions between these loci as deviations are caused by heterozygote/homozygote deleterious interactions. These results suggest that the fitness consequences of the interactions of these three complex III-associated genes could influence reproductive isolation in this system.

Animals↗
PubMed2026

AdmixLD: fast genome-scale inference of ancestry disequilibrium in hybrid zones.

SUMMARY: Hybrid zones represent powerful natural systems for studying reproductive isolation and speciation. One key genomic signature of genetic incompatibilities and epistatic interactions is linkage disequilibrium (LD)-non-random associations between loci from different lineage backgrounds, generated by selection against maladaptive allele combinations. However, admixture alone induces strong genome-wide LD in hybrid populations, obscuring selection-driven signals. Here, we present AdmixLD, a fast, scalable C++ tool for genome-wide LD scanning in hybrid zones that estimates LD using partial correlation to control for individual hybrid index. By removing admixture-driven covariance, AdmixLD enhances detection of locus-specific associations and enables genome-scale identification of candidate barrier loci and interacting genomic regions. AVAILABILITY: The software and its code source are available at https://github.com/yzfranci/AdmixLD, and scripts for the data analysis are available at https://github.com/yzfranci/AdmixLDAnalysis.

Linkage Disequilibrium↗
PubMed2005

Tempo of hybrid inviability in centrarchid fishes (Teleostei: Centrarchidae).

Hybrid viability decreases with divergence time, a pattern consistent with a so-called speciation clock. However, the actual rate at which this clock ticks is poorly known. Most speciation-clock studies have used genetic divergence as a proxy for time, adopting a molecular clock and often far-distant calibration points to convert genetic distances into age. Because molecular clock assumptions are violated for most genetic datasets and distant calibrations are of questionable utility, the actual rate at which reproductive isolation evolves may be substantially different than current estimates suggest. We provide a robust measure of the tempo at which hybrid viability declines with divergence time in a clade of freshwater fishes (Centrarchidae). This incompatibility clock is distinct from a speciation clock because speciation events in centrarchids appear to be driven largely by prezygotic isolation. Our analyses used divergence times estimated with penalized likelihood applied to a phylogeny derived from seven gene regions and calibrated with six centrarchid fossils. We found that hybrid embryo viability declined at mean rate of 3.13% per million years, slower than in most other taxa investigated to date. Despite measurement error in both molecular estimated ages and hatching success of hybrid crosses, divergence time explained between 73% and 90% of the variation in hybrid viability among nodes. This high correlation is consistent with the gradual accumulation of many genetic incompatibilities of small effect. Hybrid viability declined with the square of time, consistent with an increasing rate of accumulation of incompatibilities between divergent genomes (the snowball effect). However, the quadratic slope is due to a lag phase resulting from heterosis among young species pairs, a phenomenon rarely considered in predictions of hybrid fitness. Finally, we found that reciprocal crosses often show asymmetrical hybrid viabilities. We discuss several alternative explanations for this result including possible deleterious cytonuclear interactions. Speciation-clock studies have been a small cottage industry recently, but there are still novel insights to be gained from analyses of more taxonomic groups. However, between-group comparisons require more careful molecular-clock calibration than has been the norm.

Animals↗
PubMed1989

Advances in the genetics of reproductive isolation in Drosophila.

Speciation genetics is defined as the study of genetic events and processes that differentiate the probabilities that genetic material from individual members of a population will co-occur in individuals of some future generation. It follows that phenotypic attributes that contribute to this differentiation of probabilities (e.g., mating preferences, sterility, or infertility of individuals from certain types of matings) constitute the phenotype of speciation, and genetic loci that may affect these phenotypic attributes can be considered as speciation genes. The literature on genetic differences between hybridizable species of Drosophila that are responsible for morphological differences, mating preferences, hybrid inviability, and hybrid sterility are reviewed with special reference to the species pair D. mojavensis - D. arizonensis. The case for the involvement of karyotypic changes in speciation in rodents is briefly discussed. It is concluded that no major advance has been made in the speciation genetics of Drosophila since Dobzhansky initiated the field 40 years ago. Yet, the identification of several gene loci that cause hybrid inviability or sterility may open the way to the understanding of reproductive isolation at the molecular level. It is not clear whether this approach will lead to general molecular mechanisms underlying the speciation process.

Animals↗
PubMed1993

Tuberculous spondylitis as a complication of intravesical bacillus Calmette-Guerin therapy.

We report a case of tuberculous spondylitis following intravesical bacillus Calmette-Guerin (BCG) instillation. A 90-year-old male physician living in South Africa received an uncomplicated 6-week course of intravesical BCG (Japanese 172 strain) for high grade superficial bladder carcinoma. He experienced a sudden onset of debilitating lower back pain 16 months following this treatment. A lytic lesion involving the anterior T11 and T12 vertebral bodies was diagnosed and subsequently biopsied. An acid-fast organism was isolated after 3 weeks of incubation and was confirmed through deoxyribonucleic acid probe hybridization as a mycobacterium. High performance liquid chromatography analysis speciated the organism as Mycobacterium bovis BCG, proving that it was acquired through the intravesical therapy.

Aged↗
PubMed2006

The relative influence of natural selection and geography on gene flow in guppies.

Two general processes may influence gene flow among populations. One involves divergent selection, wherein the maladaptation of immigrants and hybrids impedes gene flow between ecological environments (i.e. ecological speciation). The other involves geographic features that limit dispersal. We determined the relative influence of these two processes in natural populations of Trinidadian guppies (Poecilia reticulata). If selection is important, gene flow should be reduced between different selective environments. If geography is important, gene flow should be impeded by geographic distance and physical barriers. We examined how genetic divergence, long-term gene flow, and contemporary dispersal within a watershed were influenced by waterfalls, geographic distance, predation, and habitat features. We found that waterfalls and geographic distance increased genetic divergence and reduced dispersal and long-term gene flow. Differences in predation or habitat features did not influence genetic divergence or gene flow. In contrast, differences in predation did appear to reduce contemporary dispersal. We suggest that the standard predictions of ecological speciation may be heavily nuanced by the mating behaviour and life history strategies of guppies.

Animals↗
PubMed1992

Chromosomal rearrangements and speciation of sportive lemurs (Lepilemur species).

Theoretical configurations of meiotic chromosomes of potential hybrids between the different Lepilemur species were examined, and the classification of this genus was reviewed in the light of this information. Among the chromosomal rearrangements that occurred during the chromosomal evolution of the sportive lemurs, only those which would generate a pronounced reproductive barrier were considered in relation to the geographic distribution of this genus. The analysis showed that the pattern of geographic distribution is compatible with the inferred chronological occurrence of these chromosomal rearrangements in the phylogenetic tree of the genus Lepilemur.

Animals↗
PubMed2006

Global variation in the diversification rate of passerine birds.

Net diversification rates were estimated for samples of primarily tribe-to-family-level clades of passerine birds, taking into account extinction as well as speciation. Two samples were used. The first consisted of 37 clades of primarily temperate North American and primarily tropical South American passerines; the second comprised a global set of 90 clades, each distributed within one or more zoogeographic regions. Circumscription and ages of clades were taken from Sibley and Ahlquist's phylogeny based on DNA hybridization, with updates from more recent sequence analysis. Under a homogeneous speciation (rate = lamda) and extinction (rate = mu) process, the expected number of species (N) after t units of time can be described by the expression, N(t)= [exp(lamda(1 - kappa) t - kappa]/(1 - kappa), where kappa = mu/lamda. A nonlinear least-squares regression for the temperate and tropical American clades with more than one species estimated kappa = 0.938 +/- 0.076 (mean +/- SE), suggesting a high rate of turnover of lineages within clades. Because of the broad confidence limits in kappa, I used values ranging from 0.80 to 0.98 to calculate speciation rates in subsequent analyses, assuming that kappa is uniform among clades and does not vary with latitude. Speciation rate among South American clades exceeded that among North American clades for all kappa, whether monophyletic lineages were included or not. The estimated speciation rate was negatively related to clade age, suggesting that proliferation within clades slows with time. In the global data set, rate of speciation decreased with clade age and increased with the area of the region or regions within which a clade is distributed, and for any given value of kappa the speciation rate was significantly higher in tropical than in temperate regions. Relaxing the assumption of latitude independence in kappa, larger clade size in the tropics could be achieved by various combinations of relative speciation and extinction rates that obscure the underlying causes of global biodiversity patterns. Nonetheless, the results of this analysis clearly indicate that a higher rate of diversification in the tropics contributes to the pervasive latitudinal gradient in diversity observed in passerine birds.

Animals↗
PubMed2002

Alps, genes, and chromosomes: their role in the formation of species in the Sorex araneus group (Mammalia, Insectivora), as inferred from two hybrid zones.

During the Pleistocene glaciations, the Alps were an efficient barrier to gene flow between isolated populations, often leading to allopatric speciation. Afterwards, the Alps strongly influenced the post-glacial recolonization of Europe and represent a major suture zone between differentiated populations. Two hybrid zones in the Swiss and French Alps between genetically and chromosomally well-differentiated species-the Valais shrew, Sorex antinorii, and the common shrew, S. araneus-were studied karyotypically and by analyzing the distribution of seven microsatellite loci. In the center of the Haslital hybrid zone the two species coexist over a distance of 900 m. Hybrid karyotypes, among them the most complex known in Sorex, are rare. F-statistics based on microsatellite data revealed a strong heterozygote deficit only in the center of the zone, due to the sympatric distribution of the two species with little hybridization between them. Structuring within the species (both F(IS) and F(ST)) was low. An hierarchical analysis showed a high level of interspecific differentiation. Results were compared with those previously reported in another hybrid zone located at Les Houches in the French Alps. Genetic structuring within and between species was comparable in both hybrid zones, although chromosomal incompatibilities are more important in Haslital, where a linkage block of the race-specific chromosomes should additionally impede gene flow. Evidence for a more restricted gene flow in Haslital comes from the genetically intermediate hybrid karyotypes, whereas in Les Houches, hybrid karyotypes are genetically identical to individuals of the pure karyotypic races. Genic and chromosomal introgression was observed in Les Houches, but not in Haslital. The possible influence of a river, separating the two species at Les Houches, on gene flow is discussed.

Altitude↗
PubMed2002

A test of ecologically dependent postmating isolation between sympatric sticklebacks.

Ecological speciation occurs when reproductive isolation evolves ultimately as a result of divergent natural selection between populations inhabiting different environments or exploiting alternative resources. I tested a prediction of the ecological model concerning the fitness of hybrids between two young, sympatric species of threespine sticklebacks (Benthics and Limnetics). The two species are ecologically and morphologically divergent: the Benthic is adapted to feeding on invertebrates in the littoral zone of the lake whereas the Limnetic is adapted to feeding on zooplankton in the open water. The growth rate of two types of hybrids, the Benthic backcross and the Limnetic backcross, as well as both parent species, was evaluated in enclosures in both parental habitats in the lake. The use of backcrosses is ideal because a comparison of their growth rates in the two habitats estimates an ecologically dependent component of their fitness while controlling for any intrinsic genetic incompatibilities that may exist between the Benthic and Limnetic genomes. The backcross results revealed a striking pattern of ecological dependence: in the littoral zone, Benthic backcrosses grew at approximately twice the rate of Limnetic backcrosses, while in the open water, Limnetic backcrosses grew at approximately twice the rate of Benthic backcrosses. Such a reversal of relative fitness of the two cross-types in the two environments provides strong evidence that divergent natural selection has played a central role in the evolution of postmating isolation between Benthics and Limnetics. Although the rank order of growth rates of all cross-types in the littoral zone was Benthic > Benthic backcross > Limnetic backcross > Limnetic, neither backcross differed significantly from the parent from which it was mainly derived. Implications of this result are discussed in terms of ecological speciation and possible introgressive hybridization between the species. Results in the open water were less clear and were not fully consistent with the ecological model of speciation, mainly as a result of the low growth rate of Limnetics. However, analysis of the diet of the fish in the open water suggests that these enclosures may not have been fully successful at replicating the food regimes characteristic of this habitat.

Animals↗
PubMed2026

Digest: Speciation involves both barriers and bridges in the tropical Andes.

Mountains are important centers of biodiversity and studies of speciation. In particular, the north-south linear orientation of the Andes allows examination of how geographic isolation, elevation, and latitude influence divergence in closely related species such as Myioborus warblers (Parulidae), the focal taxa of this study. Traditional models of Andean speciation have emphasized allopatric divergence due to geographic barriers, but thanks to the limited sampling of hybrid zones and lack of genome-wide datasets in tropical taxa, we may have underestimated of the role of gene flow in shaping patterns of divergence in the region. Using ddRAD-seq genomic data, Céspedes Arias et al. (2026) demonstrated that geographic isolation and hybridization both contribute to the generation and maintenance of Andean warbler lineages. Their results revealed how complex patterns of genetic divergence, introgression, and isolation-by-distance contribute to the historical buildup of biodiversity in the Andes, challenging strictly isolationist models of mountain evolution.

Animals↗
PubMed2000

Do the constraints of human speciation cause expression of the same set of genes in brain, testis, and placenta?

Evolution appears to be especially rapid during speciation, and the genes involved in speciation should be evident in species such as humans that have recently speciated or are presently in the process of speciation. Haldane's rule is that when one sex is sterile or inviable in interspecific F(1) hybrids, it is usually the heterogametic sex. For mammals, this implicates genes on the X chromosome as those particularly responsible for speciation. A preponderance of sex- and reproduction-related genes on the X chromosome has been shown repeatedly, but also mental retardation genes are more frequent on the X chromosome. We argue that brain, testis, and placenta are those organs most responsible for human speciation. Furthermore, the high degree of complexity of the vertebrate genome demands coordinate evolution of new characters. This coordination is best attained when the same set of genes is redeployed for these new characters in the brain, testis, and placenta.

Biological Evolution↗
PubMed2000

Genetic analysis of speciation by means of introgression into Drosophila melanogaster.

In the last decade, the genetic basis of reproductive isolation has been shown to be surprisingly polygenic, and yet even the most efficient system currently in use could lend itself to molecular analysis only in highly selected cases. By extending the recent discovery of fertility rescue between Drosophila melanogaster and Drosophila simulans, we show that this hybridization can permit systematic and precise delineation of the genetic and molecular basis of speciation. In a region of 5% of the D. simulans genome introgressed into D. melanogaster, we discover at least six genes of hybrid male sterility and none for female sterility by deficiency mapping. A single case of hybrid inviability has been tracked down to a 3-Kb element that was inserted into the Cyclin E locus during species hybridization. The extent of interspecific genetic divergence underlying hybrid male sterility, especially in contrast with the low degree of inviability and female sterility, is far greater than expected from previous studies.

Animals↗
PubMed2005

Adaptation to environmental stress: a rare or frequent driver of speciation?

Recent results of evolutionary genomics and other research programmes indicate an important role for environment-dependent selection in speciation, but the conceptual frameworks of speciation genetics and environmental stress physiology have not been fully integrated. Only a small number of model systems have been established for cross-disciplinary studies of this type in animals and plants. In these taxa (e.g. Drosophila and Arabidopsis/Arabis), studies of the mechanistic basis of various stress responses are increasingly combined with attempts to understand their evolutionary consequences. Our understanding of the role of environmental stress in speciation would benefit from studies of a larger variety of taxa. We pinpoint areas for future study and predict that in many taxa 'broad' hybrid zones maintained by ecological selection will be valuable venues for addressing the link between environmental stress, adaptation, and speciation.

Adaptation, Biological↗
PubMed2006

The coexistence of hybrid and parental Daphnia: the role of parasites.

Parasite driven time-lagged negative frequency-dependent selection of hosts has been studied in natural populations by following changes in host genotype frequencies over time. However, such dynamics have not been considered at higher taxonomic levels, for example, between parental species and their hybrids. In a field study on a Daphnia hybrid system, we observed that one Daphnia taxon first was relatively under-infected, but became over-infected after a strong increase in frequency. This finding is consistent with the idea of parasite evolution towards the most frequent host taxon. In two experiments, we investigated whether the assumptions made by a model of negative frequency-dependent selection apply to our host taxa system. First, we showed that the parasite can change the outcome of taxa competition and secondly, we confirmed that the over-infection of one host taxon observed in the field has a genetic basis. Our results indicate that the incorporation of host-parasite interactions at the species level may allow us to gain a more complete picture of forces driving dynamic taxa coexistence in Daphnia hybrid systems. More generally, we suggest that if hybrids coexist in sympatry with parental taxa, the infection patterns as observed under natural conditions may be rather temporal and unstable.

Animals↗
PubMed1992

A dual level model for speciation by multiple pericentric inversions.

A considerable body of evidence suggests that the deleterious meiotic effects of pericentric inversions in F1 hybrids can be overcome by changes in chiasma location and various means of non-homologous pairing. Such overriding mechanisms may render pericentric inversions benign and increase the likelihood of their fixation in population isolates. It has been argued that overriding mechanisms of this type negate the involvement of pericentric inversions as reproductive isolating mechanisms in speciation. It is suggested, however, that the involvement of pericentric inversions in speciation should be considered on two levels. First, that by reducing meiotic effects in F1 hybrids, overriding mechanisms facilitate the fixation of pericentric inversions. Secondly, when contact hybridization occurs between the chromosomally derived and parental populations second-level effects may be encountered. That is, the recombinational effects of pericentric inversion differences on coadapted gene complexes (sensu Brncic, 1954, Shaw & Coates, 1983) enforce profound inviability barriers in F2 and backcross matings. In this way, multiple pericentric inversions may act as significant post-mating isolating mechanisms, whereas individual inversions with less significant second-level effects may not.

Animals↗
PubMed2000

Reproductive mode and speciation: the viviparity-driven conflict hypothesis.

In birds and frogs, species pairs retain the capacity to produce viable hybrids for tens of millions of years, an order of magnitude longer than mammals. What accounts for these differences in relative rates of pre- and postzygotic isolation? We propose that reproductive mode is a critically important but previously overlooked factor in the speciation process. Viviparity creates a post-fertilization arena for genomic conflicts absent in egg-laying species. With viviparity, conflict can arise between: mothers and embryos; sibling embryos in the womb, and maternal and paternal genomes within individual embryos. Such intra- and intergenomic conflicts result in perpetual antagonistic coevolution, thereby accelerating interpopulation postzygotic isolation. In addition, by generating intrapopulation genetic incompatibility, viviparity-driven conflict favors polyandry and limits the potential for precopulatory divergence. Mammalian diversification is characterized by rapid evolution of incompatible feto-maternal interactions, asymmetrical postzygotic isolation, disproportionate effects of genomically-imprinted genes, and "F(2) hybrid enhancement. " The viviparity-driven conflict hypothesis provides a parsimonious explanation for these patterns in mammalian evolution.

Animals↗