Incipient sympatric speciation in blind mole rat, Spalax galili, in Israel, caused by sharp ecological divergence of abutting chalk-basalt ecologies, has been proposed previously based on mitochondrial and whole-genome nuclear DNA. Here, we present new evidence, including transcriptome, DNA editing, microRNA, and codon usage, substantiating earlier evidence for adaptive divergence in the abutting chalk and basalt populations. Genetic divergence, based on the previous and new evidence, is ongoing despite restricted gene flow between the two populations. The principal component analysis, neighbor-joining tree, and genetic structure analysis of the transcriptome clearly show the clustered divergent two mole rat populations. Gene-expression level analysis indicates that the population transcriptome divergence is displayed not only by soil divergence but also by sex. Gene ontology enrichment of the differentially expressed genes from the two abutting soil populations highlights reproductive isolation. Alternative splicing variation of the two abutting soil populations displays two distinct splicing patterns. L-shaped FST distribution indicates that the two populations have undergone divergence with gene flow. Transcriptome divergent genes highlight neurogenetics and nutrition characterizing the chalk population, and energetics, metabolism, musculature, and sensory perception characterizing the abutting basalt population. Remarkably, microRNAs also display divergence between the two populations. The GC content is significantly higher in chalk than in basalt, and stress-response genes mostly prefer nonoptimal codons. The multiple lines of evidence of ecological-genomic and genetic divergence highlight that natural selection overrules the gene flow between the two abutting populations, substantiating the sharp ecological chalk-basalt divergence driving sympatric speciation.

• Klíčová slova
• DNA editing, ecological adaptive speciation, microRNA regulation, natural selection, nonoptimal codon usage,
• MeSH
• ekosystém MeSH
• mikro RNA metabolismus   MeSH
• půda MeSH
• silikáty MeSH
• Spalax genetika   metabolismus   MeSH
• sympatrie * MeSH
• tok genů MeSH
• transkriptom * MeSH
• uhličitan vápenatý MeSH
• vznik druhů (genetika) * MeSH
• zvířata MeSH
• Check Tag
• mužské pohlaví MeSH
• ženské pohlaví MeSH
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• srovnávací studie MeSH
• Názvy látek
• basalt MeSH Prohlížeč
• mikro RNA MeSH
• půda MeSH
• silikáty MeSH
• uhličitan vápenatý MeSH

Reinforcement, the increase of assortative mating driven by selection against unfit hybrids, is conditional on pre-existing divergence. Yet, for ecological divergence to precede the evolution of assortment, strict symmetries between fitnesses in niches must hold, and/or there must be low gene flow between the nascent species. It has thus been argued that conditions favouring sympatric speciation are rarely met in nature. Indeed, we show that under disruptive selection, violating symmetries in niche sizes and increasing strength of the trade-off in selection between the niches quickly leads to loss of genetic variation, instead of evolution of specialists. The region of the parameter space where polymorphism is maintained further narrows with increasing number of loci encoding the diverging trait and the rate of recombination between them. Yet, evolvable assortment and pre-existing assortment both substantially broaden the parameter space within which polymorphism is maintained. Notably, pre-existing niche preference speeds up further increase of assortment, thus facilitating reinforcement in the later phases of speciation. We conclude that in order for sympatric ecological divergence to occur, niche preference must coevolve throughout the divergence process. Even if populations come into secondary contact, having diverged in isolation, niche preference substantially broadens the conditions for coexistence in sympatry and completion of the speciation process. This article is part of the theme issue 'Towards the completion of speciation: the evolution of reproductive isolation beyond the first barriers'.

• Klíčová slova
• Levene model, epistasis, maintenance of polymorphism, polygenic trait, sympatric speciation, trade-off,
• MeSH
• ekosystém * MeSH
• modely genetické MeSH
• multifaktoriální dědičnost MeSH
• polymorfismus genetický MeSH
• reprodukční izolace * MeSH
• selekce (genetika) MeSH
• sympatrie * MeSH
• tok genů * MeSH
• vznik druhů (genetika) * MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH

Spiny mice, Acomys cahirinus, colonized Israel 30,000 y ago from dry tropical Africa and inhabited rocky habitats across Israel. Earlier, we had shown by mtDNA that A. cahirinus incipiently sympatrically speciates at Evolution Canyon I (EC I) in Mount Carmel, Israel because of microclimatic interslope divergence. The EC I microsite consists of a dry and hot savannoid "African" slope (AS) and an abutting humid and cool-forested "European" slope (ES). Here, we substantiate incipient SS in A. cahirinus at EC I based on the entire transcriptome, showing that multiple slope-specific adaptive complexes across the transcriptome result in two divergent clusters. Tajima's D distribution of the abutting Acomys interslope populations shows that the ES population is under stronger positive selection, whereas the AS population is under balancing selection, harboring higher genetic polymorphisms. Considerable sites of the two populations were differentiated with a coefficient of FST = 0.25-0.75. Remarkably, 24 and 37 putatively adaptively selected genes were detected in the AS and ES populations, respectively. The AS genes involved DNA repair, growth arrest, neural cell differentiation, and heat-shock proteins adapting to the local AS stresses of high solar radiation, drought, and high temperature. In contrast, the ES genes involved high ATP associated with energetics stress. The sharp ecological interslope divergence led to strong slope-specific selection overruling the interslope gene flow. Earlier tests suggested slope-specific mate choice. Habitat interslope-adaptive selection across the transcriptome and mate choice substantiate sympatric speciation (SS), suggesting its prevalence at EC I and commonality in nature.

• Klíčová slova
• RNA-seq, adaptive ecological speciation, microclimate, natural selection,
• MeSH
• biologická evoluce MeSH
• jednonukleotidový polymorfismus MeSH
• mikroklima MeSH
• mozek metabolismus   MeSH
• Murinae genetika   MeSH
• tok genů MeSH
• transkriptom MeSH
• vznik druhů (genetika) * MeSH
• zvířata MeSH
• Check Tag
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Geografické názvy
• Izrael MeSH

Speciation mechanisms remain controversial. Two speciation models occur in Israeli subterranean mole rats, genus Spalax: a regional speciation cline southward of four peripatric climatic chromosomal species and a local, geologic-edaphic, genic, and sympatric speciation. Here we highlight their genome evolution. The five species were separated into five genetic clusters by single nucleotide polymorphisms, copy number variations (CNVs), repeatome, and methylome in sympatry. The regional interspecific divergence correspond to Pleistocene climatic cycles. Climate warmings caused chromosomal speciation. Triple effective population size, Ne , declines match glacial cold cycles. Adaptive genes evolved under positive selection to underground stresses and to divergent climates, involving interspecies reproductive isolation. Genomic islands evolved mainly due to adaptive evolution involving ancient polymorphisms. Repeatome, including both CNV and LINE1 repetitive elements, separated the five species. Methylation in sympatry identified geologically chalk-basalt species that differentially affect thermoregulation, hypoxia, DNA repair, P53, and other pathways. Genome adaptive evolution highlights climatic and geologic-edaphic stress evolution and the two speciation models, peripatric and sympatric.

• Klíčová slova
• genomic sequencing, methylation, repeatome, speciation models, subterranean rodents,
• MeSH
• biologická adaptace MeSH
• biologická evoluce * MeSH
• epigeneze genetická MeSH
• genetická variace MeSH
• genom MeSH
• jednonukleotidový polymorfismus MeSH
• molekulární evoluce MeSH
• populační genetika MeSH
• reprodukční izolace MeSH
• Spalax genetika   fyziologie   MeSH
• sympatrie * MeSH
• tok genů MeSH
• variabilita počtu kopií segmentů DNA MeSH
• vazebná nerovnováha MeSH
• zvířata MeSH
• Check Tag
• mužské pohlaví MeSH
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Geografické názvy
• Izrael MeSH

A costly search for food in subterranean rodents resulted in various adaptations improving their foraging success under given ecological conditions. In Spalax ehrenbergi superspecies, adaptations to local ecological conditions can promote speciation, which was recently supposed to occur even in sympatry at sites where two soil types of contrasting characteristics abut each other. Quantitative description of ecological conditions in such a site has been, nevertheless, missing. We measured characteristics of food supply and soil within 16 home ranges of blind mole rats Spalax galili in an area subdivided into two parts formed by basaltic soil and pale rendzina. We also mapped nine complete mole rat burrow systems to compare burrowing patterns between the soil types. Basaltic soil had a higher food supply and was harder than rendzina even under higher moisture content and lower bulk density. Population density of mole rats was five-times lower in rendzina, possibly due to the lower food supply and higher cover of Sarcopoterium shrubs which seem to be avoided by mole rats. A combination of food supply and soil parameters probably influences burrowing patterns resulting in shorter and more complex burrow systems in basaltic soil.

• MeSH
• chování zvířat MeSH
• ekosystém * MeSH
• fyziologická adaptace genetika   MeSH
• půda * MeSH
• Spalax genetika   fyziologie   MeSH
• sympatrie fyziologie   MeSH
• vznik druhů (genetika) * MeSH
• zvířata MeSH
• Check Tag
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• půda * MeSH

First multilocus analysis of the largest Neotropical cichlid genus Crenicichla combining mitochondrial (cytb, ND2, 16S) and nuclear (S7 intron 1) genes and comprising 602 sequences of 169 specimens yields a robust phylogenetic hypothesis. The best marker in the combined analysis is the ND2 gene which contributes throughout the whole range of hierarchical levels in the tree and shows weak effects of saturation at the 3rd codon position. The 16S locus exerts almost no influence on the inferred phylogeny. The nuclear S7 intron 1 resolves mainly deeper nodes. Crenicichla is split into two main clades: (1) Teleocichla, the Crenicichla wallacii group, and the Crenicichla lugubris-Crenicichla saxatilis groups ("the TWLuS clade"); (2) the Crenicichla reticulata group and the Crenicichla lacustris group-Crenicichla macrophthalma ("the RMLa clade"). Our study confirms the monophyly of the C. lacustris species group with very high support. The biogeographic reconstruction of the C. lacustris group using dispersal-vicariance analysis underlines the importance of ancient barriers between the middle and upper Paraná River (the Guaíra Falls) and between the middle and upper Uruguay River (the Moconá Falls). Our phylogeny recovers two endemic species flocks within the C. lacustris group, the Crenicichla missioneira species flock and the herein discovered Crenicichla mandelburgeri species flock from the Uruguay and Paraná/Iguazú Rivers, respectively. We discuss putative sympatric diversification of trophic traits (morphology of jaws and lips, dentition) and propose these species flocks as models for studying sympatric speciation in complex riverine systems. The possible role of hybridization as a mechanism of speciation is mentioned with a recorded example (Crenicichla scottii).

• MeSH
• Bayesova věta MeSH
• cichlidy anatomie a histologie   klasifikace   genetika   MeSH
• fylogeneze * MeSH
• fylogeografie MeSH
• genetická variace MeSH
• multilokusová sekvenční typizace * MeSH
• pravděpodobnostní funkce MeSH
• RNA ribozomální 16S genetika   MeSH
• rybí proteiny genetika   MeSH
• sekvenční seřazení MeSH
• sympatrie MeSH
• vznik druhů (genetika) * MeSH
• zvířata MeSH
• Check Tag
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Geografické názvy
• Paraguay MeSH
• Uruguay MeSH
• Názvy látek
• RNA ribozomální 16S MeSH
• rybí proteiny MeSH

The role of chromosome changes in speciation remains a debated topic, although demographic conditions associated with divergence should promote their appearance. We tested a potential relationship between chromosome changes and speciation by studying two Lake Whitefish (Coregonus clupeaformis) lineages that recently colonized postglacial lakes following allopatry. A dwarf limnetic species evolved repeatedly from the normal benthic species, becoming reproductively isolated. Lake Whitefish hybrids experience mitotic and meiotic instability, which may result from structurally divergent chromosomes. Motivated by this observation, we test the hypothesis that chromosome organization differs between Lake Whitefish species pairs using cytogenetics. While chromosome and fundamental numbers are conserved between the species (2n = 80, NF = 98), we observe extensive polymorphism of subtle karyotype traits. We describe intrachromosomal differences associated with heterochromatin and repetitive DNA, and test for parallelism among three sympatric species pairs. Multivariate analyses support the hypothesis that differentiation at the level of subchromosomal markers mostly appeared during allopatry. Yet we find no evidence for parallelism between species pairs among lakes, consistent with colonization effect or postcolonization differentiation. The reported intrachromosomal polymorphisms do not appear to play a central role in driving adaptive divergence between normal and dwarf Lake Whitefish. We discuss how chromosomal differentiation in the Lake Whitefish system may contribute to the destabilization of mitotic and meiotic chromosome segregation in hybrids, as documented previously. The chromosome structures detected here are still difficult to sequence and assemble, demonstrating the value of cytogenetics as a complementary approach to understand the genomic bases of speciation.

• Klíčová slova
• Coregonus, cytogenetics, polymorphism, salmonids, speciation, standing genetic variation,
• MeSH
• chromozomy genetika   MeSH
• fenotyp MeSH
• heterochromatin genetika   MeSH
• jezera MeSH
• populační genetika * MeSH
• Salmonidae genetika   MeSH
• sympatrie * MeSH
• vznik druhů (genetika) * MeSH
• zvířata MeSH
• Check Tag
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH
• Názvy látek
• heterochromatin MeSH

Understanding how speciation relates to ecological divergence has long fascinated biologists. It is assumed that ecological divergence is essential to sympatric speciation, as a mechanism to avoid competition and eventually lead to reproductive isolation, while divergence in allopatry is not necessarily associated with niche differentiation. The impact of the spatial context of divergence on the evolutionary rates of abiotic dimensions of the ecological niche has rarely been explored for an entire clade. Here, we compare the magnitude of climatic niche shifts between sympatric versus allopatric divergence of lineages in butterflies. By combining next-generation sequencing, parametric biogeography and ecological niche analyses applied to a genus-wide phylogeny of Palaearctic Pyrgus butterflies, we compare evolutionary rates along eight climatic dimensions across sister lineages that diverged in large-scale sympatry versus allopatry. In order to examine the possible effects of the spatial scale at which sympatry is defined, we considered three sets of biogeographic assignments, ranging from narrow to broad definition. Our findings suggest higher rates of niche evolution along all climatic dimensions for sister lineages that diverge in sympatry, when using a narrow delineation of biogeographic areas. This result contrasts with significantly lower rates of climatic niche evolution found in cases of allopatric speciation, despite the biogeographic regions defined here being characterized by significantly different climates. Higher rates in allopatry are retrieved when biogeographic areas are too widely defined-in such a case allopatric events may be recorded as sympatric. Our results reveal the macro-evolutionary significance of abiotic niche differentiation involved in speciation processes within biogeographic regions, and illustrate the importance of the spatial scale chosen to define areas when applying parametric biogeographic analyses.

• Klíčová slova
• climatic niche, macro-evolutionary processes, next-generation sequencing, parametric biogeography,
• MeSH
• biologická evoluce * MeSH
• ekosystém * MeSH
• fylogeneze MeSH
• motýli genetika   fyziologie   MeSH
• podnebí * MeSH
• sympatrie MeSH
• vznik druhů (genetika) MeSH
• zvířata MeSH
• Check Tag
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH
• Geografické názvy
• Asie MeSH
• Evropa MeSH
• severní Afrika MeSH

Our knowledge of the processes involved in speciation of microalgae remains highly limited. In the present study, we investigated a potential role of ecological speciation processes in diversification of the filamentous green alga Klebsormidium. We examined 12 strains representing four different genotypes. The strains were collected from sandstone and limestone rocks and were cultivated at five different pH levels ranging from pH 4 to pH 8. We determined the responses of the 12 strains to the experimental pH conditions by (1) measuring the effective quantum yield of photosystem II, and (2) determining the growth rates after cultivation at different pH levels. Strong differences were found between the results obtained by these two methods. Direct counting of cells revealed a strong ecological differentiation of strains of Klebsormidium isolated from different substrate types. Strains isolated from limestone showed the highest growth rates at higher pH levels; whereas, the strains isolated from sandstone exhibited two distinct growth responses with optima at pH 5 and 6, respectively. In contrast, the effective quantum yield of photosystem II was always down-regulated at lower pH values, probably due to dissolved inorganic carbon limitation. In general, we determined distinct ecophysiological differentiation among distantly and closely related lineages, thereby corroborating our hypothesis that the sympatric speciation of terrestrial algae is driven by ecological divergence. We clearly showed that pH is a critical ecological factor that influences the diversity of autotrophic protists in terrestrial habitats.

• Klíčová slova
• Diversity, Klebsormidium, Protist, Speciation, pH,
• Publikační typ
• časopisecké články MeSH

The sympatric occurrence of closely related lineages displaying conserved morphological and ecological traits is often characteristic of free-living microbes. Gene flow, recombination, selection, and mutations govern the genetic variability between these cryptic lineages and drive their differentiation. However, sequencing conservative molecular markers (e.g., 16S rRNA) coupled with insufficient population-level sampling hindered the study of intra-species genetic diversity and speciation in cyanobacteria. We used phylogenomics and a population genomic approach to investigate the extent of local genomic diversity and the mechanisms underlying sympatric speciation of Laspinema thermale. We found two cryptic lineages of Laspinema. The lineages were highly genetically diverse, with recombination occurring more frequently within than between them. That suggests the existence of a barrier to gene flow, which further maintains divergence. Genomic regions of high population differentiation harbored genes associated with possible adaptations to high/low light conditions and stress stimuli, although with a weak diversifying selection. Overall, the diversification of Laspinema species might have been affected by both genomic and ecological processes.

• Klíčová slova
• cryptic species, cyanobacteria, gene flow, phylogenomics, recombination, sympatric speciation,
• Publikační typ
• časopisecké články MeSH