Lukas Choleva

• The Czech Academy of Sciences

Interspecific gene flow may profoundly impact genome integrity and adaptive evolution in hybridizing species, leading to novelties such as transgressive traits, supergenes, or, sometimes, the emergence of asexually reproducing lineages. Conventionally, introgression is thought to proceed between reproductively interacting species, mediated by recom...

The distribution of the neutral component of genetic diversity is the interplay of historical and ongoing processes resulting in the species-specific genetic structure of populations, which can, however, be disrupted by interspecific hybridisation and introgression. In this study, we focused on two species of water frogs, Pelophylax epeiroticus and...

European water frogs from the Pelophylax esculentus complex include two sexual species, P. ridibundus and P. lessonae, and their hybrids, which usually clonally transmit one of the parental species' genomes. This unique reproductive strategy allows hybrids to reproduce with one or both parental species, creating diverse population systems. Unlike m...

Gametogenesis produces gametes as a piece of genetic information transmitted to the offspring. While during sexual reproduction, progeny inherits a mix of genetic material from both parents, asexually reproducing organisms transfer a copy of maternal or paternal DNA to the progeny clonally. Parthenogenetic, gynogenetic and hybridogenetic animals ha...

Developmental anomalies and malformations in amphibians serve as a marker of extreme or unstable environmental conditions and can affect the reproduction and viability of amphibians. In the Czech Republic, anomalies were reported for amphibians from the Elbe and the Danube rivers basins, but not from the Oder River. Here, we report anomalies in thr...

Karyotype divergence may strongly affect the degree of hybridization between species. Western Palearctic slow worms (Anguis) are legless lizards forming different types of secondary contact zones. To identify the level of chromosomal variation in slow worms, we examined karyotype in multiple populations of all species except one and Pseudopus apodu...

Hybrid taxa from the genus Pelophylax can propagate themselves in a modified way of sexual reproduction called hybridogenesis ensuring the formation of clonal gametes containing the genome of only one parental (host) species. Pelophylax grafi from South-Western Europe is a hybrid composed of P. ridibundus and P. perezi genomes and it lives with a h...

Asexual reproduction can be triggered by interspecific hybridization, but its emergence is supposedly rare, relying on exceptional combinations of suitable genomes. To examine how genomic and karyotype divergence between parental lineages affect the incidence of asexual gametogenesis, we experimentally hybridized fishes (Cobitidae) across a broad p...

Meiosis is a conservative process in all sexual organisms which ensures fertility and is central for producing genetic diversity by recombination and random segregation of parental chromosomes. Yet unexplored mechanisms may disrupt it and cause loss of sex followed by the emergence of clonal modes of reproduction. Interspecific hybridization is the...

Asexual reproduction can be triggered by interspecific hybridization, but its emergence is supposedly rare, relying on exceptional combinations of suitable genomes. To examine how genomic and karyotype divergence between parental lineages affect the incidence of asexual gametogenesis, we experimentally hybridized fishes (Cobitidae) across a broad p...

Asexual reproduction can be triggered by interspecific hybridization, but its emergence is supposedly rare, relying on exceptional combinations of suitable genomes. To examine how genomic and karyotype divergence between parental lineages affect the incidence of asexual gametogenesis, we experimentally hybridized fishes (Cobitidae) across a broad p...

Asexual reproduction can be triggered by interspecific hybridization, but its emergence is supposedly rare, relying on exceptional combinations of suitable genomes. To examine how genomic and karyotype divergence between parental lineages affect the incidence of asexual gametogenesis, we experimentally hybridized fishes (Cobitidae) across a broad p...

The genus Pelophylax (water frogs) includes relatively common, widely distributed, and even invasive species, but also endemic taxa with small ranges and limited knowledge concerning their ecology and evolution. Among poorly studied species belong endemics of the southwestern Balkans, namely Pelophylax shqipericus, P. epeiroticus and P. kurtmueller...

Asexual reproduction can be triggered by interspecific hybridization, but its emergence is supposedly rare, relying on exceptional combinations of suitable genomes. To examine how genomic and karyotype divergence between parental lineages affect the incidence of asexual gametogenesis, we experimentally hybridized fishes (Cobitidae) across a broad p...

Interspecific hybridization can disrupt canonical gametogenic pathways, leading to the emergence of clonal and hemiclonal organisms. Such gametogenic alterations usually include genome endoreplication and/or premeiotic elimination of one of the parental genomes. The hybrid frog Pelophylax esculentus exploits genome endoreplication and genome elimin...

Background: Hybrid taxa exist in nature, but their fitness can vary greatly. Hybrids are usually thought to have lower viability and survival rate than parental species due to the occurrence of two different genomes and divergent evolution in each species. On the other hand, the hybrid vigour of the F1 generation may give hybrids an advantage in m...

Habitat selectivity has become an increasingly acknowledged mechanism shaping the structure of freshwater communities; however, most studies have focused on the effect of predators and competitors, neglecting habitat complexity and specialization. In this study, we examined the habitat selection of semiaquatic (amphibians: Bufonidae; odonates: Libe...

Previous studies on the phylogenetic relationships between lamprey species relied either on a low number of morphological characters related to the feeding apparatus, or on a low number of molecular mitochondrial DNA markers. Here, we apply a multilocus approach to assess the phylogenetic relationships of northern hemisphere lampreys, with a specia...

Metazoans usually reproduce sexually, blending the unique identity of parental genomes for the next generation through functional crossing-over and recombination in meiosis. However, some metazoan lineages have evolved reproductive systems where offspring are either full (clonal) or partial (hemiclonal) genetic replicas. In the latter group, the pr...

The southwestern Balkans is inhabited by three endemic water frog species, Pelophylax shqipericus, P. epeiroticus and P. kurtmuelleri. Although these species are genetically and bioacoustically distinct from each other, their morphological differentiation is less pronounced as is generally observed in the genus Pelophylax. In this study, we analyze...

Hybridogenesis is a reproductive tool for sexual parasitism. Hybridogenetic hybrids use gametes from their sexual host for their own reproduction, but sexual species gain no benefit from such matings as their genome is later eliminated. Here, we examine the presence of sexual parasitism in water frogs through crossing experiments and genome-wide da...

The maternal origin of isolated populations of the common wall lizard (Podracis muralis) in the Czech Republic, representing the northeastern range border of the species, was addressed. We compared mitochondrial DNA sequences of the cytochrome b gene of samples from these populations with those from within the continuous range in Slovakia, the nort...

South-east Europe, along with the adjacent region of south-west Asia, is an important biodiversity hotspot with high local endemism largely contributed by contemporary continental lineages that retreated to southern refugia during colder Quaternary periods. We investigated the genetic diversity of the European bitterling fish (Rhodeus amarus) speci...

The karyotype of Greek cobitid fish Cobitisstrumicae Karaman, 1955, from Lake Volvi, Greece, a representative of one of its two major intraspecific phylogenetic lineages, was analysed by means of sequential Giemsa-staining, C-banding, silver-staining, CMA 3 fluorescence banding and also by in situ hybridization (FISH) with rDNA probe. The diploid c...

Background: Sexual parasites offer unique insights into the reproduction of unisexual and sexual populations. Because unisexuality is almost exclusively linked to the female sex, most studies addressed host-parasite dynamics in populations where sperm-dependent females dominate. Pelophylax water frogs from Central Europe include hybrids of both se...

Pelophylax esculentus is a vertebrate animal with hemiclonal heredity, attracting the interest of many reproductive and evolutionary biologists. It is a hybrid between P. ridibundus and P. lessonae. These three taxa form the so-called Pelophylax esculentus complex with a population structure usually comprising a hybrid taxa and one parental species...

Conservation translocations (including reintroductions) are potentially powerful tools for wildlife conservation, and their use has increased worldwide. However, most studies have focused on vertebrates, with the long-term impact and ecological progress of translocations being neglected. Moreover, such projects rarely target insects. The present st...

The crucian carp Carassius carassius (Linnaeus, 1758), is native to many European freshwaters. Despite its wide distribution, the crucian carp is declining in both the number and sizes of populations across much of its range. Here we studied 30 individuals of a putative pure population from Helsinki, Finland. Despite clear external morphological fe...

Hybrid sterility is a common first step in the evolution of postzygotic reproductive isolation. According to Haldane's Rule it affects predominantly the heterogametic sex. While the genetic basis of hybrid male sterility in organisms with heterogametic males has been studied for decades, the genetic basis of hybrid female sterility in organisms wit...

Although sexual reproduction is ubiquitous throughout nature, the molecular machinery behind it has been repeatedly disrupted during evolution, leading to the emergence of asexual lineages in all eukaryotic phyla. Despite intensive research, little is known about what causes the switch from sexual reproduction to asexuality. Interspecific hybridiza...

Background: The ability to eliminate a parental genome from a eukaryotic germ cell is a phenomenon observed mostly in hybrid organisms displaying an alternative propagation to sexual reproduction. For most taxa, the underlying cellular pathways and timing of the elimination process is only poorly understood. In the water frog hybrid Pelophylax esc...

Speciation usually proceeds in a continuum from intensively hybridizing populations until the formation of irreversibly isolated species. Restriction of interspecific gene flow may often be achieved by gradual accumulation of postzygotic incompatibilities with hybrid infertility typically evolving more rapidly than inviability. A reconstructed hist...

Interspecific hybridization, polyploidization and transitions from sexuality to asexuality considerably affect organismal genomes. Especially the last mentioned process has been assumed to play a significant role in the initiation of chromosomal rearrangements, causing increased rates of karyotype evolution. We used cytogenetic analysis and molecul...

Hybrid individuals used for karyotyping presented in S1 Fig. (DOCX)

List of hybrid individuals used for GISH experiments presented in S3 Fig. (DOCX)

Representative karyotypes of hybrid biotypes after DAPI/Giemsa staining. (A-C) EN hybrids. (D-F) EEN hybrids. (G-I) ENN hybrids. (J-L) ET hybrids. (M-O) EET hybrids. (P-R) ETT hybrids. Chromosomes were arranged in a decreasing size order and classified in four morphological groups: metacentric (m), submetacentric (sm), subtelocentric (st) and acroc...

Maximum likelihood phylogenetic tree of Cobitis and Sabanejewia species. ML phylogenetic tree constructed from cytochrome b gene sequences from Tang et al. [46] and from Doadrio and Perdices [47]. Calibration point follows Doadrio and Perdices [47]. Widths of branches are proportional to ML estimate of substitution rate. Cobitis species are highlig...

Hybrid individuals used for GISH experiments presented in Fig 1. (DOCX)

Representative metaphases of hybrid biotypes after GISH experiments. (A, B) EN hybrids. (C, D) EEN hybrids. (E, F) ENN hybrids. (G, H) ET hybrids. (I, J) EET hybrids. (K, L) ETT hybrids. Probes labelled with biotin-16-dUTP were detected with streptavidin-FITC (green signals on chromosomes); probes labelled with digoxigenin-11-dUTP were detected wit...

Speciation process often occurs in the face of hybridisation between forming species. Hybrid genomic constitution of many clonal organisms including fish, amphibians and reptiles also indicates tight linkage between hybridization, clonality and malfunction of sex in hybrids. To address the causal links between these phenomena, we investigated the e...

Polyploidization is a rare yet sometimes successful way for animals to rapidly create geno- and phenotypes that may colonize new habitats and quickly adapt to environmental changes. In this study, we use water frogs of the Pelophylax esculentus complex, comprising two species (Pelophylax lessonae, genotype LL; Pelophylax ridibundus, RR) and various...

Polyploidization is a rare yet sometimes successful way for animals to rapidly create geno- and phenotypes that may colonize new habitats and quickly adapt to environmental changes. In this study, we use water frogs of the Pelophylax esculentus complex, comprising two species (Pelophylax lessonae, genotype LL; Pelophylax ridibundus, RR) and various...

The scarcity of parthenogenetic vertebrates is often attributed to their ‘inferior’ mode of clonal reproduction, which restricts them to self-reproduce their own genotype lineage and leaves little evolutionary potential with regard to speciation and evolution of sexual reproduction. Here, we show that for some taxa such uniformity does not hold. By...

Distinguishing between hybrid introgression and incomplete lineage sorting causing incongruence among gene trees in that they exhibit topological differences requires application of statistical approaches that are based on biologically relevant models. Such study is especially challenging in hybrid systems, where usual vectors mediating interspecif...

The past decade has witnessed a tremendous increase in interest in polyploidy, which may partly be related to the development of new powerful genetic and genomic tools. These have provided numerous insights into mainly genetic and genomic consequences of polyploidy, dramatically improving our understanding of the dynamics of the polyploidization pr...

Population genetics patterns of marine fish in general and of Southern Ocean fish in particular range from virtual panmixia over ocean-wide scale to deeply fragmented populations. However the causes underlying these different patterns are not properly understood. In this paper, we tested the hypotheses that population connectivity is positively rel...

Given the hybrid genomic constitutions and increased ploidy of many asexual animals, the identification of processes governing the origin and maintenance of clonal diversity provides useful information about the evolutionary consequences of interspecific hybridization, asexuality and polyploidy. In order to understand the processes driving observed...

Schema of performed IBM simulation - two sexual species occur in region 1 and 2, which are interconnected by a migration rate m. Interspecific hybridisation leads to the formation of clonal hybrids, which originate either in the region 1 or 2. At every 200th generation, we calculate the distribution of Hartigan’s D for dist.mut and dist.bp indices....

Summary of the locality ID, microsatellite data, ploidy level, genomic composition and MLG of individuals in the study. (PDF)

Allelic diversity within populations of microsatellite loci for diploid specimens. (PDF)

Locality information, IDs an in Figure 1c . (PDF)

Microsatellite allelic diversity for diploid biotypes. (PDF)

Detailed description of methods applied to delimit the clonal lineages and to estimate the distribution of clonal ages. (DOC)

For each clone (MLL), we indicate genomes of the ancestral species, abundance, ploidy, included MLG, ancestral clone (if recognized), number of polyploid derivatives (if any), cyt b haplotype, and values of age indices (calculated only for individuals sampled in years 2005–2007). (* denotes haplotypes from hybrids that were also found in Odra R. po...

Because most clonal vertebrates have hybrid genomic constitutions, tight linkages are assumed among hybridization, clonality, and polyploidy. However, predictions about how these processes mechanistically relate during the switch from sexual to clonal reproduction have not been validated. Therefore, we performed a crossing experiment to test the hy...

1. As a first approximation, whole-body metabolic rate can be considered as the sum of metabolic rates of constituent cells. Yet, among several current explanations of metabolic rate scaling, only two explicitly invoke cell architecture of organisms: (1) the Metabolic Theory of Ecology, which predicts size invariance of metabolically active cells,...

Exact location and number of glacial refugia still remain unclear for many European cold-blooded terrestrial vertebrates. We performed a fine-scaled multilocus phylogeographic analysis of two Bombina species combining mitochondrial variation of 950 toads from 385 sites and nuclear genes (Rag-1, Ncx-1) from a subset of samples to reconstruct their c...

Habitat fragmentation may influence the genetic make-up and adaptability of endangered populations. To facilitate genetic monitoring of the endangered European ground squirrel (EGS), we analyzed 382 individuals from 16 populations in Central Europe, covering almost half of its natural range. We tested how fragmentation affects the genetic architect...

The Western Palearctic water frogs Pelophylax ridibundus and P. lessonae were identified as parental (sexual) species and P. esculentus as their interspecific, hybridogenetically reproducing hybrid with hemiclonal heredity. We used genomic in situ hybridization (GISH) to identify parental chromosomes of P.lessonae and P.ridibundus in diploid P. esc...

Interspecific hybridization may result in asexual hybrid lineages that reproduce via parthenogenesis. Contrary to true parthenogens, sperm-dependent asexuals (gynogens and hybridogens) are restricted to the range of bisexual species, generally the parental taxa, by their need for a sperm donor. It has been documented that asexual lineages may rarel...

The Black and Caspian Seas have experienced alternating periods of isolation and interconnection over many Milankovitch climate oscillations and most recently became separated when the meltwater overflow from the Caspian Sea ceased at the end of the last glaciation. Climate-induced habitat changes have indisputably had profound impacts on distribut...

Using mitochondrial DNA (mtDNA) variations, the phylogenetic position of Croatian populations of spined loaches within the European genus Cobitis was assessed. Spined loaches from the Matica, Neretva, Cetina, Zrmanja, Jadova, Sava, Drava and Kupa Rivers are included in two previously described groups: a) Cobitis sensu stricto group, and b) Adriatic...

Between 2003 and 2006, almost 80 localities in all main hydrological systems in Albania were sampled and data on the distribution of loach fishes gathered. The spined loach Cobitis ohridana Karaman, 1928 was found to be a common species in Albania, occurring in most of its river systems, from the Ohrid-Drin-Shkodra system in the east and north to t...

Although the unique features of asexual reproduction and hybridization among European spined loaches (genus Cobitis) have recently attracted the attention of conservation biologists, faunists and evolutionary biologists, the research has suffered from uncertain identification of specimens and their genomes because of the extreme morphological simil...