The relative importance of introgression for diversification has long been a highly disputed topic in speciation research and remains an open question despite the great attention it has received over the past decade. Gene flow leaves traces in the genome similar to those created by incomplete lineage sorting (ILS), and identification and quantification of gene flow in the presence of ILS is challenging and requires knowledge about the true phylogenetic relationship among the species. We use whole nuclear, plastid and organellar genomes from 12 species in the rapidly radiated, ecologically diverse, actively hybridizing genus of peatmoss (Sphagnum) to reconstruct the species phylogeny and quantify introgression using a suite of phylogenomic methods. We found extensive phylogenetic discordance among nuclear and organellar phylogenies, as well as across the nuclear genome and the nodes in the species tree, best explained by extensive ILS following the rapid radiation of the genus rather than by post-speciation introgression. Our analyses support the idea of ancient introgression among the ancestral lineages followed by ILS, whereas recent gene flow among the species is highly restricted despite widespread interspecific hybridization known in the group. Our results contribute to phylogenomic understanding of how speciation proceeds in rapidly radiated, actively hybridizing species groups, and demonstrate that employing a combination of diverse phylogenomic methods can facilitate untangling complex phylogenetic patterns created by ILS and introgression.

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Studying any system requires development of ways to describe the variety of its conditions. Such development includes three steps. The first one is to identify groups of similar systems (associative typology). The second one is to identify groups of objects which are similar in characteristics important for their description (analytic typology). The third one is to arrange systems into groups based on their predicted common future (dynamic typology).We propose a method to build such a dynamic topology for a system. The first step is to build a simulation model of studied systems. The model must be undetermined and simulate stochastic processes. The model generates distribution of the studied systems output parameters with the same initial parameters. We prove the correctness of the model by aligning the parameters sets generated by the model with the set of the original systems conditions evaluated empirically. In case of a close match between the two, we can presume that the model is adequately describing the dynamics of the studied systems. On the next stage, we should determine the probability distribution of the systems transformation outcome. Such outcomes should be defined based on the simulation of the transformation of the systems during the time sufficient to determine its fate. If the systems demonstrate asymptotic behavior, its phase space can be divided into pools corresponding to its different future state prediction. A dynamic typology is determined by which of these pools each system falls into.We implemented the pipeline described above to study water frog hemiclonal population systems. Water frogs (Pelophylax esculentus complex) is an animal group displaying interspecific hybridization and non-mendelian inheritance.

Conserving species and their genetic variation are a global priority to safeguard evolutionary potential in a rapidly changing world. Species are fundamental units in research and nature management, but taxonomic work is increasingly undermined. Increasing knowledge on the species genetic diversity would aid in prioritizing conservation efforts. Sphagnum is a diverse, well-known bryophyte genus, which makes the genus suited to study speciation and cryptic variation. The species share specific characteristics and can be difficult to separate in the field. By combining molecular data with thorough morphological examination, new species have recently been discovered.Still, there are taxonomic uncertainties, even for species assessed on the IUCN Red List of threatened species. Here, we use molecular data to examine three rare species within the subgenus Acutifolia described based on morphological characters. All species have narrow distributions and limited dispersability. First, we confirm the genetic origin of S. skyense. Second, we show that S. venustum is a haploid species genetically distinct from morphologically similar species. Lastly, S. nitidulum was found to have a distinct haplotype, but cannot be genetically separated from other red Acutifolia species. We also found high genetic variation within red Acutifolia specimens, indicating the need of further morphological examination and possibly taxonomic revision.Until then, our results have shown that genetic data can aid in prioritizing targets of conservation efforts when taxonomy is unresolved. All three taxa should be further searched for by field biologists to increase knowledge about their distribution ranges.

Pelophylax esculentus is an interspecific hybrid which reproduces hemiclonally by crossing with the parental species (P. ridibundus or P. lessonae). The structure of hemiclonal population systems is of great interest. The majority of investigations into populations of water frogs deal with samples of mature animals, while subadults are less studied. We collected a random sample of 73 small water frogs from three localities in the Siverskyi Donets River floodplain. All frogs were measured, injected with colchicines and killed after anesthesia. We determined the species specifity, sex, age and ploidy of every individual. In addition, we measured testis length and studied the germ cells of all males by means of karyological analysis. We calculated the portion of triploids in the largest subsample from the vicinity of the Biological Station of V.N. Karazin Kharkiv National University and carried out a meta-analysis of previous publications dealing with composition of green frog samples from this locality. The proportion of triploids in our sample appeared to be approximately the same as 12 years ago. However, this proportion in our sample differed significantly from that obtained in recent samples of green frogs belonging to other age groups (adults and metamorphs) from the same locality. The share of triploids of P. esculentus is the lowest in the sample of metamorphs. This proportion increases in froglets because of early death of representatives of parental species which originated from hybrid-hybrid crossing. Then the number of triploids among adult P. esculentus individuals declines again probably because of their lower viability compared to diploids. We have revealed that subadult diploids have erythrocytes smaller than 28 microns, while triploids’ erythrocytes exceed 27 microns. Therefore, in borderline cases true ploidy could be determined only by the karyological technique. The average ratio between testis length and body length appeared to be larger in the parental species than in both diploid and triploid hybrids. Karyological analysis has revealed that P. esculentus had significantly lower portions of spermatocytes I with normal karyotype (13 bivalents) in the testis in comparison with P. ridibundus, but this value increases in adult hybrids. We suggest that increasing of spermatogenesis stability in adult frogs as opposed to subadults might be the consequence of both selection of germ cell lines in the testis and more frequent survival of individuals with stable gametogenesis.