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Trophic specialization plays a major role in ecological speciation. Multiple adaptive radiations among cyprinid fish of the genus Labeobarbus were recently discovered in riverine environments of the Ethiopian Highlands, East Africa. These radiations contain parallel diversifications of trophic morphology, including thick-lipped or ‘rubberlip’ phenotype, whose trophic function remains largely unexplored. To test the adaptive value of thickened lips, to identify the ecological niche of the thick-lipped ecomorphs, and to test of these ecomorphs are the products of speciation we studied six sympatric pairs of ecomorphs with hypertrophied lips and the normal lip structure from different riverine basins. Trophic morphology, diet, stable isotope (15N and 13C) signatures as well as mtDNA markers and genome-wide SNP variation were analyzed. Our results show that thick-lipped ecomorphs partition trophic resources with generalized ecomorphs in only one half of the examined sympatric pairs despite the pronounced divergence in lip structure. In these thick-lipped ecomorphs that were trophically diverged, the data on their diet along with the elevated 15N values suggest an insectivorous specialization different from the basal omnivorous-detritivouros feeding mode of generalized ecomorphs. Genetic data confirmed an independent and parallel origin of all six lipped ecomorphs. Yet, only one of those six thick-lipped ecomorphs had a notable genetic divergence with sympatric non-lipped ecomorphs based on nuclear SNPs data (FST = 0.21). Sympatric pairs can be sorted by combinations of phenotypic, ecological, and genetic divergence within the speciation continuum from an ecologically non-functional mouth polymorphism via ecologically functional polymorphism to completed speciation via divergent evolution.

Influenced by rapid changes in climate and landscape features since the Miocene, widely distributed species provide suitable models to study the environmental impact on their evolution and current genetic diversity. The dice snake Natrix tessellata, widely distributed in the Western Palearctic is one such species. We aimed to resolve a detailed phylogeography of N. tessellata with a focus on the Central Asian clade with 4 and the Anatolia clade with 3 mitochondrial lineages, trace their origin, and correlate the environmental changes that affected their distribution through time. The expected time of divergence of both clades began at 3.7 Mya in the Pliocene, reaching lineage differentiation approximately 1 million years later. The genetic diversity in both clades is rich, suggesting different ancestral areas, glacial refugia, demographic changes, and colonization routes. The Caspian lineage is the most widespread lineage in Central Asia, distributed around the Caspian Sea and reaching the foothills of the Hindu Kush Mountains in Afghanistan, and Eastern European lowlands in the west. Its distribution is limited by deserts, mountains, and cold steppe environments. Similarly, Kazakhstan and Uzbekistan lineages followed the Amu Darya and the Syr Darya water systems in Central Asia, with ranges delimited by the large Kyzylkum and Karakum deserts. On the western side, there are several lineages within the Anatolia clade that converged in the central part of the peninsula with 2 being endemic to Western Asia. The distribution of both main clades was affected by expansion from their Pleistocene glacial refugia around the Caspian Sea and in the valleys of Central Asia as well as by environmental changes, mostly through aridification.

Adaptive radiation of freshwater fishes was long thought to be possible only in lacustrine environments. Recently, several studies have shown that riverine and stream environments also provide the ecological opportunity for adaptive radiation. In this study, we report on a riverine adaptive radiation of six ecomorphs of cyprinid hillstream fishes of the genus Garra in a river located in the Ethiopian Highlands in East Africa. Garra are predominantly highly specialized algae-scrapers with a wide distribution ranging from Southeast Asia to West Africa. However, adaptive phenotypic diversification in mouth type, sucking disc morphology, gut length and body shape have probably been found among these ecomorphs in a single Ethiopian river. Moreover, we found two novel phenotypes of Garra ("thick-lipped" and "predatory") that had not been discovered before in this species-rich genus (>160 species). Mitochondrial and genome-wide data suggest monophyletic, intrabasin evolution of Garra phenotypic diversity with signatures of gene flow from other local populations. Although sympatric ecomorphs are genetically distinct and can be considered to being young species as suggested by genome-wide single nucleotide polymorphism data, mitochondrial DNA was unable to identify any genetic structure suggesting recent and rapid speciation events. Some data suggest a hybrid origin of the novel "thick-lipped" ecomorph. Here we highlight how, driven by ecological opportunity, an ancestral trophically highly specialized lineage is likely to have rapidly radiated in a riverine environment promoted by the evolution of novel feeding strategies. published

This paper presents the current state of research on the intestinal microbiota of fish of different ecological groups from water bodies of West and East Siberia. The present study focused on the gut bacterial diversity of 16 species/forms of fish (due to intricate taxonomical position of whitefish from Teletskoye Lake) inhabiting Chany Lake (Novosibirsk oblast), Teletskoye Lake (Altai Republic), Baikal Lake and other water bodies of East Siberia using molecular genetic methods. The analysis of the conducted studies shows the main features of gut bacterial communities in the digestive tract of fish and to better understand the features of the functioning of aquatic ecosystems in Siberia. In all studied fish (except for Lena grayling and Baikal omul), regardless of their habitat, taxonomy, digestive system structure (presence or absence of stomach and pyloric caeca) and feeding habits, bacteria of all four phyla (Proteobacteria, Bacteroidetes, Firmicutes, and Actinobacteria) were found among the dominants. Such differences can also be explained by sample preparation techniques before sequencing that researchers may apply. Also, the uncultivated microbiota such as Pseudoalteromonadaceae (Lake Chany), Comamonadaceae and Bacillaceae (whitefish from Lake Teletskoye) and Rhodobacteraceae (Baikal omul and whitefish) were often found among the dominant bacterial taxa in the digestive tract of the most studied fish. Moreover, the data focused on the structure of gut bacterial community of fish will be useful for the development of aquaculture industry in the region, since the information makes it possible to identify pathogenic, opportunistic, and probiotic bacteria in aquatic ecosystems.

The impact of parasites on gut microbiota of the host is well documented, but the role of the relationship between the parasite and the host in the formation of the microbiota is poorly understood. Using 16S amplicon sequencing and newly developed methodological approaches, we characterize the gut microbiota of the sympatric pair of whitefish Coregonus lavaretus complex and the associated microbiota of cestodes parasitizing their intestine. The essence of the proposed approaches is, firstly, to use the method of successive washes of the microbiota from the cestode’s surfaces to analyze the degree of bacterial association to the tegument of the parasite. Secondly, to use a method combining the sampling of intestinal content and mucosa with the wash-out procedure from the mucosa to understand the real structure of the fish gut microbiota. Our results demonstrate that the trophic diversification of a sympatric pair of whitefish predetermines a segregation by ecological niches of their respective microbial communities within their intestine. Additional environmental niches for settlement of bacteria in the intestine are formed by the parasitic helminths that caused the restructuring of the bacterial community in infected fish compared to those uninfected. Using the desorption method in Ringer’s solution, we have demonstrated that Proteocephalus sp. cestodes possess their own microbial community which is put together from “surface” bacteria received from the host, bacteria which are weakly and strongly associated with the tegument, and microbiota obtained after removal of the tegument from the cestodes.

Ranaviruses are a group of double-strand DNA viruses that infect fish, amphibians and reptiles. These viruses are responsible for mass fish and amphibian mortality events worldwide, both in the wild and at the fish and amphibian farms. The number of detected epizootics has grown significantly in recent years. In Eastern Europe and Northern Asia, including Russia, very few ranavirosis monitoring studies have been conducted, in contrast with Western Europe and America. In the present work, we used a qPCR assay to survey for the first time the amphibian populations of West Siberia (Russia) for the presence of ranaviruses. In total, we studied 252 tissue samples from six amphibian species, collected across West Siberia from the south to the Arctic regions. We report a single infected sample: a common toad (Bufo bufo) captured near Tyumen city. The phylogenetic analysis showed that the detected virus strain belongs to the CMTV lineage. This is only the second observation of Ranavirus in Russia.

Heteromorphic W and Y sex chromosomes often experience gene loss and heterochromatinization, which is frequently viewed as their “degeneration”. However, the evolutionary trajectories of the heterochromosomes are in fact more complex since they may not only lose but also acquire new sequences. Previously, we found that the heterochromatic W chromosome of a lizard Eremias velox (Lacertidae) is decondensed and thus transcriptionally active during the lampbrush stage. To determine possible sources of this transcription, we sequenced DNA from a microdissected W chromosome sample and a total female DNA sample and analyzed the results of reference-based and de novo assembly. We found a new repetitive sequence, consisting of fragments of an autosomal protein-coding gene ATF7IP2, several SINE elements, and sequences of unknown origin. This repetitive element is distributed across the whole length of the W chromosome, except the centromeric region. Since it retained only 3 out of 10 original ATF7IP2 exons, it remains unclear whether it is able to produce a protein product. Subsequent studies are required to test the presence of this element in other species of Lacertidae and possible functionality. Our results provide further evidence for the view of W and Y chromosomes as not just “degraded” copies of Z and X chromosomes but independent genomic segments in which novel genetic elements may arise.

Simple Summary With the increase in global population the production of animal proteins becomes increasingly crucial. Aquaculture is the first animal protein supply industry for human consumption. Intensive farming techniques are employed to increase productivity, but these may cause stressful conditions for fish, resulting in impaired growth and poor health conditions. Intestinal inflammation is one of the most common diseases of fish in intensive farming. Intestinal inflammation is usually accompanied by an alteration of the microbiota or dysbiosis. Inflammation and dysbiosis are so tightly intertwined that inflammation may contribute to or result from dysregulation of gut microbiota. Natural substances of plant origin rich in bioactive molecules or more simply phytochemicals, have been proved to be able to reduce inflammation and improve the general health status in various commercially relevant species. In this study, we evaluated the effect of tannins, a class of polyphenols, the most abundant phytochemicals, on intestinal inflammation and microbiota in zebrafish (Danio rerio), a small freshwater fish become an attractive biomedicine and aquaculture animal model during the last decades. The zebrafish has been employed in a vast array of studies aiming at investigating the essential processes underlying intestinal inflammation and injury due to its conservative gut morphology and functions. In this study, we administered a diet enriched with chestnut shell extract rich in tannins to a zebrafish model of intestinal inflammation. The treatment ameliorated the damaged intestinal morphophysiology and the microbiota asset. Our results sustain that products of natural origin with low environmental impact and low cost, such as tannins, may help to ease some of the critical issues affecting the aquaculture sector. Abstract The aim of the present study was to test the possible ameliorative efficacy of phytochemicals such as tannins on intestinal inflammation and dysbiosis. The effect of a chestnut shell (Castanea sativa) extract (CSE) rich in polyphenols, mainly represented by tannins, on k-carrageenan-induced intestinal inflammation in adult zebrafish (Danio rerio) was tested in a feeding trial. Intestinal inflammation was induced by 0.1% k-carrageenan added to the diet for 10 days. CSE was administered for 10 days after k-carrageenan induced inflammation. The intestinal morphology and histopathology, cytokine expression, and microbiota were analyzed. The k-carrageenan treatment led to gut lumen expansion, reduction of intestinal folds, and increase of the goblet cells number, accompanied by the upregulation of pro-inflammatory factors (TNFα, COX2) and alteration in the number and ratio of taxonomic groups of bacteria. CSE counteracted the inflammatory status enhancing the growth of health helpful bacteria (Enterobacteriaceae and Pseudomonas), decreasing the pro-inflammatory factors, and activating the anti-inflammatory cytokine IL-10. In conclusion, CSE acted as a prebiotic on zebrafish gut microbiota, sustaining the use of tannins as food additives to ameliorate the intestinal inflammation. Our results may be relevant for both aquaculture and medical clinic fields.

Adaptive radiation of fishes was long thought to be possible only in lacustrine environments. Recently, several studies have shown that also riverine and stream environments provide the ecological opportunity for adaptive radiation. In this study, we report on a riverine adaptive radiation of six ecomorphs of cyprinid hillstream fishes of the genus Garra in a river located in the Ethiopian Highlands in East Africa. Garra are predominantly highly specialized algae-scrapers with a wide distribution ranging from Southeastern Asia to Western Africa. However, adaptive phenotypic diversification in mouth type, sucking disc morphology, gut length and body shape have been found among these new species in a single Ethiopian river. Moreover, we found two novel phenotypes of Garra (‘thick-lipped’ and ‘predatory’) that were not described before in this species-rich genus (>160 species). Mitochondrial and genome-wide data suggest monophyletic, intra-basin evolution of Garra phenotypic diversity with signatures of gene flow from other local populations. Although sympatric ecomorphs are genetically distinct and can be considered to being young species as suggested by genome-wide SNP data, mtDNA was unable to identify any genetic structure suggesting a recent and rapid speciation event. Furthermore, we found evidence for a hybrid origin of the novel ‘thick-lipped’ phenotype, as being the result of the hybridization of two other sympatrically occurring species. Here we highlight how, driven by ecological opportunity, an ancestral trophically highly specialized lineage is likely to have rapidly adaptively radiated in a riverine environment, and that this radiation was promoted by the evolution of novel feeding strategies.

Heteromorphic W and Y sex chromosomes often experience gene loss and heterochromatinization, which is frequently viewed as their “degeneration”. However, the evolutionary trajectories of the heterochromosomes are in fact more complex since they may not only lose but also acquire new sequences. Previously, we found that the heterochromatic W chromosome of a lizard Eremias velox (Lacertidae) is decondensed and thus transcriptionally active during the lampbrush stage. To determine possible sources of this transcription, we sequenced DNA from a microdissected W chromosome sample and a total female DNA sample and analyzed the results of reference-based and de novo assembly. We found a new repetitive sequence, consisting of fragments of an autosomal protein-coding gene ATF7IP2, several SINE elements, and sequences of unknown origin. This repetitive element is distributed across the whole length of the W chromosome, except the centromeric region. Since it retained only 3 out of 10 original ATF7IP2 exons, it remains unclear whether it is able to produce a protein product. Subsequent studies are required to test the presence of this element in other species of Lacertidae and possible functionality. Our results provide further evidence for the view of W and Y chromosomes as not just “degraded” copies of Z and X chromosomes but independent genomic segments in which novel genetic elements may arise.

Aims. The aim of the study was to investigate the skin microbiota of Prussian carp infested by ectoparasites from the genus Argulus and Lernaea. Methods and Results. Associated microbiota of skin of Prussian carp and ectoparasites were investigated by sequencing of the V3, V4 hypervariable regions of 16S rRNA using Illumina MiSeq sequencing platform. Conclusions. According to the Spearman rank correlation test, the increasing load of ulcerations of the skin of Prussian carp was weakly negative correlated with reduction in the abundance of the following taxa: Acrobacter, bacteria C39 (Rhodocyclaceae), Rheinheimera, Comamonadaceae, Helicobacteraceae, and Vogesella. In the present study, the microbiota of ectoparasites from genus Lernaea and Argulus were characterized for the first time. The microbiota associated with L. cyprinacea was significantly different from microbial communities of intact skin mucosa of both infested and uninfested fish and skin ulcers (ADONIS, p≤0.05). The microbiota associated with parasitic crustaceans L. cyprinacea were dominated by unclassified bacteria from Comamonadaceae, Aeromonadaceae families, and Vogesella. The dominant microbiota of A. foliaceus were represented by Flavobacterium, Corynebacterium, and unclassified Comamonadaceae. Significance and Impact of Study. Results from these studies indicate that ectoparasites have the potential to alter skin microbiota, which can play a possible role in transmission of secondary bacterial infection in fish, caused by pathogenic bacteria. info:eu-repo/semantics/acceptedVersion

Herein, data on rainbow trout infections with the copepod Caligus lacustris in cage aquaculture on Lake Ladoga is presented. Caligus lacustris (n = 127 ex.) were collected from a farm in Lake Ladoga housing cage-reared rainbow trout to describe the size–age and sex structure of the copepod population. Morphological features of the copepods were evaluated according to 10 characters with terminology proposed by Kabata and Gusev (J Linn Soc (Zool) 46(309):155–207, 1966). To determine the phylogenetic position of C. lacustris within the genus Caligus, fragments of the cytochrome c oxidase subunit 1 mitochondrial gene (COI, 645 bp) and 18S rRNA gene (1617 bp) were sequenced. An increase of parasite prevalence was observed as the lake was warming up from July to September. The morphological features of the crustacean’s larval and adult stages, characterized by specific parameters of quantitative traits, are described. Three COI haplotypes and only one 18S rRNA haplotype of C. lacustris were identified among five samples. Based on 18S rRNA analysis (resolution of the COI tree was poor), we can conclude that the clade containing C. lacustris, and the aforementioned sister species, appears as an early radiation of the genus Caligus. The development of freshwater aquaculture contributes to the transfer of the native parasite C. lacustris to farmed rainbow trout. info:eu-repo/semantics/acceptedVersion

Herein, data on rainbow trout infections with the copepod Caligus lacustris in cage aquaculture on Lake Ladoga is presented. Caligus lacustris (n = 127 ex.) were collected from a farm in Lake Ladoga housing cage-reared rainbow trout to describe the size-age and sex structure of the copepod population. Morphological features of the copepods were evaluated according to 10 characters with terminology proposed by Kabata and Gusev (J Linn Soc (Zool) 46(309):155-207, 1966). To determine the phylogenetic position of C. lacustris within the genus Caligus, fragments of the cytochrome c oxidase subunit 1 mitochondrial gene (COI, 645 bp) and 18S rRNA gene (1617 bp) were sequenced. An increase of parasite prevalence was observed as the lake was warming up from July to September. The morphological features of the crustacean's larval and adult stages, characterized by specific parameters of quantitative traits, are described. Three COI haplotypes and only one 18S rRNA haplotype of C. lacustris were identified among five samples. Based on 18S rRNA analysis (resolution of the COI tree was poor), we can conclude that the clade containing C. lacustris, and the aforementioned sister species, appears as an early radiation of the genus Caligus. The development of freshwater aquaculture contributes to the transfer of the native parasite C. lacustris to farmed rainbow trout.

Multiple repeated patterns of adaptive radiation were revealed in cyprinid fish inhabiting the compact geographic region of the Ethiopian Highlands. We found four independently evolved radiations in the evolutionary hexaploid (2n = 150) Labeobarbus lineage based on matrilineal relationships of >800 individuals. Each radiation displayed similar patterns of mouth phenotype diversification, and included ecomorphs/species of the generalized, lipped, scraping (one or two), and large-mouthed (one to three) types. All radiations were detected in geographically isolated rivers, and originated from different ancestral populations. This is the first documented case in which numerous parallel radiations of fishes occurred–via different ways–in a riverine environment. Some radiations are very recent and monophyletic, while others are older and include ecomorphs that originated in separate mini flocks and later combined into one. The diversification bursts among Ethiopian Labeobarbus were detected in the mid-upper reaches of rivers (1050-1550 m above sea level), which likely offer ecological opportunities that include diverse habitats yet poor fauna (i.e. lower competition and relaxed selection). This promising example of parallel evolution of adaptive radiation warrants further investigation.

Five ecologically and phenotypically divergent ecomorphs of the genus Salmo are known from a landlocked alpine lake in the Caucasus, Lake Sevan. It is an example of sympatric diversification within a species-rich lineage with predominate mode of speciation being allopatric. The diversification of Sevan trouts was accompanied by spawning resource partitioning. Four lacustrine ecomorphs with different temporal-spatial spawning strategies and divergent morphology and coloration evolved along with a fifth ecomorph, brook trout, inhabiting the tributaries. Unfortunately, the Sevan trout diversity was almost destroyed by human activity, with two ecomorphs becoming extinct in the 1980s. We performed reconstruction of the evolutionary history of Sevan trouts based on high-throughput sequencing of both contemporary and historical DNA (∼ 50 y.o.) of all Sevan trout ecomorphs. Our study of complete mitogenomes along with genome-wide SNP data revealed the monophyly of four lacustrine ecomorphs and local brook trout, all derived from the anadromous form Caspian salmon, S. caspius. The species tree suggests a scenario of stepwise evolution from riverine to lacustrine spawning. Three genomic clusters were revealed, of which two refer to the riverine and lacustrine spawners within the flock of Sevan trouts (with FST value = 0.069). A few SNP outliers under selection were discovered that could be responsible for assortative mating based on visual recognition. The Holocene climatic oscillations and the desiccation of tributaries could have played an important role in the origin of lacustrine spawning. The relationships between lacustrine ecomorphs were not yet fully resolved. This radiation warrants further investigation.

Little ground squirrel (Spermophilus pygmaeus) is a polytypic species with a wide geographic range, divided by a number of large rivers (Don, Volga, and Ural rivers). Preliminary analysis of the mtDNA control region revealed substantial genetic differentiation (7%) between populations of little ground squirrel inhabiting the right and left banks of the Volga River, suggesting that large rivers act as geographic barriers for this species. Here, we present the results of the genetic diversity analysis of little ground squirrel (52 individuals from 35 localities) across the species range. The Don and Ural rivers, unlike the Volga River, had no considerable effect on the phylogeographic structure of little ground squirrel. Geographic subdivision found in ground squirrels living to the east of the Volga River could be explained by the influence of a large paleo-river flowing along the Turgai valley during glacial periods. The Volga River divides the species into two major groups (western and eastern), both with a high level of haplotype diversity. The genetic variability indices are almost twofold higher in the western clade. The results ​​of neutrality and isolation by distance tests support a relatively recent range expansion of the eastern clade. In overall, the observed structure of genetic diversity supports the hypothesis on the European origin of S. pygmaeus with the center of species origin on the territory of Caucasian geographic region. The division of little ground squirrels into western and eastern phylogenetic lineages probably occurred under the influence of fluctuations of the Caspian Sea level, due to the formation of temporary migration corridors during the regression periods.

Aims The aim of this work was to study the gut microbial diversity from eight species of wild fish with different feeding habits, digestive physiology (gastric vs agastric) and provide comparative structural analysis of the microbial communities within their environment (food items, water, sediments and macrophytes). Methods and Results The microbiota of fish gut and their prey items were studied using next generation high‐throughput sequencing of the 16S ribosomal RNA genes. A scatter plot based on PCoA scores demonstrated the microbiota formed three groups: (i) stomach and intestinal mucosa (IM), (ii) stomach and intestinal content (IC), and (iii) prey and environment. Comparisons using ANOSIM showed significant differences among IC of omnivorous, zoobenthivorous, zooplanktivorous‐piscivorous fishes (P ≤ 0·1). No significant difference was detected for mucosa from the same groups (P > 0·1). Conclusions Neither the interspecies differences in fish diet nor their phylogenetic position had any effect on the microbiome of the IM, but diet did influence the composition of the microbiota of the IC. Significance and Impact of the Study The data demonstrate that fish harboured specific groups of bacteria that do not completely reflect the microbiota of the environment or prey. info:eu-repo/semantics/acceptedVersion

Sevan trout, Salmo ischchan, dwelling in the mountain Lake Sevan (Caucasus) is a unique species complex. Four sympatric forms of Sevan trout were divergent in both their phenotypes and ecologies. Three forms were lacustrine spawners but were unique in their spawning times and the type of substrate. The fish community of Lake Sevan was strongly impacted by human activity in twentieth century. Two forms of Sevan trout went extinct in the 1980s and the other two forms are at the brink of extinction. The present study demonstrated that archived/historical scales of extinct forms stored at room temperature for up to 44 years are a suitable source of DNA for high-throughput sequencing and for the reconstruction of mitochondrial genomes. In addition, we obtained the mitochondrial genomes of the extant forms for comparison to the extinct forms and reconstruction of a mitogenomic phylogeny of all forms of Sevan trout. The mitogenome gene arrangement was identical in all individuals studied with structure similar to other Salmo spp. The nucleotide sequence divergence between sympatric forms was shallow (P-distance = 0.0003–0.0012). A phylogenetic tree based on mitogenomes confirmed sister position of Sevan trout to the Caspian trout, Salmo trutta caspius (P-distance = 0.0049).

The results of analysis of the variability of body shape of different Daphnia galeata morphs from geographically distinct populations—Lake Glubokoe (Moscow oblast) and Lake Chany (Novosibirsk oblast) are given. The morphological analysis was combined with the analysis of the variability of fragments of the 16S and 12S genes of the mitochondrial DNA (mtDNA) and the internal transcribed spacer 2 (ITS2) of the nuclear DNA. A reconstruction of the phylogenetic relationships between species of the genus Daphnia has been performed using a combined fragment of the 16S and 12S genes of the mtDNA. An inconsistency in the distribution of the 12S- and ITS2-haplotypes for the species D. galeata has been revealed, which indicates the introgression of mtDNA in the Lake Chany population.

Long-tailed ground squirrel (Urocitellus undulatus) is a polytypic species with a wide distribution from the Tien Shan to the Amur River region. Previously, considerable genetic differentiation between eastern and western populations of this species was demonstrated. Moreover, the greatest differences were observed in the western part of the range located in Central Asia, the region that was subjected to repeated glaciations in the past and represents one of the centers of the ground squirrel secondary diversification. The analysis of polymorphism of the mitochondrial DNA control region was carried out on long-tailed ground squirrels living in the northern part of Central Asia, on the territory of the Altai Mountains (45 individuals from 23 localities). The presence of two genetically differentiated (7.7% differences) and geographically separated lineages (western and eastern) was revealed. The data obtained disprove the hypothesis on unidirectional, from west to east, colonization of the Altai Mountains after the end of the last glacial maximum and show the two pathways of the ground squirrel colonization of the Altai, from both western and eastern refugia.

The radiation of Palearctic green toads (Bufotes) holds great potential to evaluate the role of hybridization in phylogeography at multiple stages along the speciation continuum. With fifteen species representing three ploidy levels, this model system is particularly attractive to examine the causes and consequences of allopolyploidization, a prevalent yet enigmatic pathway towards hybrid speciation. Despite substantial efforts, the evolutionary history of this species complex remains largely blurred by the lack of consistency among the corresponding literature. To get a fresh, comprehensive view on Bufotes phylogeography, here we combined genome-wide multilocus analyses (RAD-seq) with an extensive compilation of mitochondrial, genome size, niche modelling, distribution and phenotypic (bioacoustics, morphometrics, toxin composition) datasets, representing hundreds of populations throughout Eurasia. We provide a fully resolved nuclear phylogeny for Bufotes and highlight exceptional cyto-nuclear discordances characteristic of complete mtDNA replacement (in 20% of species), mitochondrial surfing during post-glacial expansions, and the formation of homoploid hybrid populations. Moreover, we traced the origin of several allopolyploids down to species level, showing that all were exclusively fathered by the West Himalayan B. latastii but mothered by several diploid forms inhabiting Central Asian lowlands, an asymmetry consistent with hypotheses on mate choice and Dobzhansky-Muller incompatibilities. Their intermediate call phenotypes potentially allowed for rapid reproductive isolation, while toxin compositions converged towards the ecologically-closest parent. Across the radiation, we pinpoint a stepwise progression of reproductive isolation through time, with a threshold below which hybridizability is irrespective of divergence (15My). Finally, we clarified the taxonomy of Bufotes (including genetic analyses of type series) and formally described two new species, B. cypriensis sp. nov. (endemic to Cyprus) and B. perrini sp. nov. (endemic to Central Asia). Embracing the genomic age, our framework marks the advent of a new exciting era for evolutionary research in these iconic amphibians. ispartof: MOLECULAR PHYLOGENETICS AND EVOLUTION vol:141 ispartof: location:United States status: published

[EN] Large African barbs of the genus Labeobarbus constitute a hexaploid lineage (2n = 150). This group is widely distributed in African freshwaters, and exhibits profound phenotypic variation that could be a prerequisite for adaptive radiation. Using morphological, molecular, and stable isotope analyses, we investigated whether an adaptive radiation has occurred in a riverine assemblage of the Labeobarbus gananensis complex. This complex is composed of six phenotypically distinct sympatric forms inhabiting the Genale River (Ethiopian highlands, East Africa) in the Juba and Wabe¿Shebelle drainages (Indian Ocean basin). Of the six forms, five were divergent in their mouth morphology, corresponding to generalised, lipped, scraping (two forms), and large¿mouthed phenotypes. One form had no mouth specialisation, but differed from the others in body shape (short and deep body; short form). Stable isotope analysis revealed differences in 15N among these forms, representing different foraging strategies (omnivorous, scraping, and piscivorous). Phylogenetic analysis of two mitochondrial DNA markers confirmed the monophyly of L. gananensis, suggesting an intra¿riverine radiation. However, the Genale assemblage appears to have originated through a combination of allopatric and sympatric events. Some of the specialised forms within the Juba and Wabe¿Shebelle drainage originated independently from the local generalised forms in three different river regions. Each of these cases could be considered as a small species flock composed of two or three sympatric forms. Our study shows that adaptive radiation in rivers can be enhanced by a combination of sympatric speciation and temporal geographic isolation, leading to local sympatric speciation followed by migration.

Alburnoides holciki was described from the Hari River basin, which was the only basin it was known from. Populations from the Amu Darya basin were previously recognized as A. eichwaldii or Alburnoides sp. Our study recognized specimens of Alburnoides from the Amu Darya basin as A. holciki based on morphological data and the COI barcode gene. The population from the Zeravshan basin showed some morphological differences compared to others but were similar in the COI gene and needs further investigation. New results extend the range of A. holciki for almost 1000 km ­from the Hari River to the upper Amu Darya tributaries in Tajikistan. The intraspecific genetic similarity in the COI gene between populations in the Hari and Amu Darya rivers supports the geographical hypothesis of a recent connection of these rivers.

Using the approach of sequencing the V3‐V4 region of the 16S rRNA gene, we have analysed the bacterial diversity associated with the distinct compartments of the gastrointestinal tract of perch (Perca fluviatilis) and cestodes (Proteocephalus sp.) parasitizing their digestive tract. The dominant microbiota associated with cestodes (Proteocephalus sp.) was represented by bacteria from the genera Serratia, Pseudomonas and Mycoplasma. By comparing the associated microbiota of perch and cestodes, a clear difference in bacterial composition and diversity was revealed between the community from the stomach content and other parts of the gastrointestinal tract of fish. Microbiota associated with cestodes was not significantly different in comparison with microbiota of different subcompartments of perch (mucosa and content of intestine and pyloric caeca) (ADONIS, p > .05) excluding microbiota of stomach content (ADONIS, p ≤ .05). PICRUSt‐based functional assessments of the microbial communities of perch and cestodes indicated that they mainly linked in terms of metabolism and environmental information processing and could play an important role in the nutrition and health of host. info:eu-repo/semantics/acceptedVersion

Aims The aim of the present study was to investigate the composition of the intestinal microbiota during the acute stage of a bacterial infection to understand how dysbiosis of the gut may influence overall taxonomic hierarchy and diversity, and determine if there exists a bacterial taxon(s) that serve as markers for healthy or diseased rainbow trout (Oncorhynchus mykiss). Methods and Results From July to September 2015 29 specimens of three‐year‐old (an average weight from 240.9±37.7 to 850.7±70.1 g) rainbow trout Oncorhynchus mykiss were studied. Next‐generation high‐throughput sequencing of the 16S ribosomal RNA genes was applied to stomach and intestinal samples to compare the impact of infection status on the microbiota of rainbow trout Oncorhynchus mykiss (Walbaum) from the northwest part of Eurasia (Karelian region, Russia). The alpha diversity (Chao1, Simpson and Shannon index) of the microbial community of healthy rainbow trout was significantly higher than in unhealthy fish. The greatest contribution to the gut microbial composition of healthy fish was made by OTU's belonging to Bacillus, Serratia, Pseudomonas, Cetobacterium, and Lactobacillus. Microbiota of unhealthy fish in most cases was represented by the genera Serratia, Bacillus, and Pseudomonas. In microbiota of unhealthy fish there were also registered unique taxa such as bacteria from the family Mycoplasmataceae and Renibacterium. Analysis of similarities (ANOSIM test) revealed the significant dissimilarity between the microbiota of stomach and intestine (p≤0.05). Conclusions A substantial finding was the absence of differences between microbial communities of the stomach and intestine in the unhealthy groups if compared with healthy fish. Significance and Impact of Study These results demonstrated alterations of the gut microbiota of farmed rainbow trout, O. mykiss during co‐infections and can be useful for the development of new strategies for disease control programs. info:eu-repo/semantics/acceptedVersion

It has been generally acknowledged that glacial climates at the time of the Pleistocene altered the patterns of species distributions, prompting latitudinal and altitudinal distribution shifts in several species, including poikilothermic species commonly known for their thermal sensitivity. However, the historical phylogeographic patterns of such species have remained largely unknown. Here, we present the historical biogeographic, phylogenetic, and phylogeographic relationships of the Caucasian pit viper, G. h. caucasicus, based on two mtDNA (cyt b and ND4) and one nDNA (c-mos) genes. This pit viper represents the westernmost member of the Crotalinae subfamily in the Palearctic and occurs in a variety of habitats, from 30 m to 3,000 m above sea level. In Iran, it is distributed on the northern and southern slopes of the Alborz Mountains, rendering it a target for phylogenetic and phylogeographic studies of a terrestrial poikilothermic animal. Our study identified four Iranian lineages of G. h. caucasicus along the northeastern to northwestern slopes of the Alborz Mountains and southern Azerbaijan (Talysh Mountains). Diversification of the Iranian lineages highlights population expansion and subsequent isolation into four plausible refugial areas during the Quaternary paleo-climatic oscillations, confirmed by our molecular dating and historical biogeographic analyses. The results of coalescence-based simulations support the incursion of the species from northeastern Iran to the western end of the Alborz, and then toward Transcaucasia via two directions: northern and southern slopes of the Alborz Mountains. Furthermore, our results clearly implied that G. h. caucasicus should be elevated to species rank and further referred to as G. caucasicus (Nikolsky, 1916).

Large African barbs of the genusLabeobarbusare widely distributed in African freshwaters, and exhibit profound phenotypic plasticity that could be a prerequisite for adaptive radiation. Using morphological, molecular, and stable isotope analyses, we investigated whether an adaptive radiation has occurred in a riverine assemblage of theL. gananensiscomplex. This complex is composed of six phenotypically distinct sympatric forms inhabiting the Genale River (Ethiopian highlands, East Africa). Of the six forms, five were divergent in their mouth morphology, corresponding to ‘generalized’, ‘lipped’, ‘scraping’ (two forms) and ‘large-mouthed’ phenotypes. Stable isotope analysis revealed differences in 15N and 13C among these forms, representing different foraging strategies (omnivorous, scraping and piscivorous). Phylogenetic analysis of two mtDNA markers confirmed the monophyly ofL. gananensis, suggesting an intra-riverine radiation. However, the Genale assemblage appears to have originated through a combination of allopatric and sympatric events. Some of the specialized forms within this drainage originated independently from the local generalized forms in three different river regions within local ‘mini-flocks’ composed of two to three sympatric forms. Our study shows that adaptive radiation in rivers can be enhanced by a combination of sympatric speciation and temporal geographic isolation, leading to local sympatric speciation followed by migration.

Species with large geographic distributions present a challenge for phylogeographic studies due to the logistic difficulties of obtaining adequate samples. Daphnia O.F. Müller (Anomopoda: Daphniidae) is a model genus for evolutionary biology and ecology, but many regions such as the remote areas of Siberia, remain poorly studied. Here we examined genetic polymorphism in the ribosomal 12S and the protein-coding ND2 mitochondrial genes of three closely related taxa of the Daphnia (Daphnia) longispina complex, namely D. galeata Sars, D. longispina O.F. Müller and D. dentifera Forbes. We estimated the phylogenetic relationships among these taxa based on a concatenated alignment of these two genes. Using sequences from the present study and those available in GenBank, we investigated the geographic distributions of the mitochondrial haplotypes of these species and proposed an evolutionary scenario for each taxon. Network structures, haplotype distribution patterns, and FST values indicated significant differences in the evolutionary history of the examined species. Our analysis of D. galeata populations confirmed its recent and fast expansion, without a previous phase of a strong population disconnection. In contrast, the high haplotype diversity in D. dentifera and D. longispina could be explained by the survival of different phylogroups in several glacial refugia located in different geographic regions. For all studied species, maximum haplotype diversity was recorded in the remote regions of Siberia-lakes of the Yenisei River and Transbaikalia. Our study is an important step in our understanding of the evolutionary history of the Daphnia longispina group and provides further evidence of the biogeographic significance of Siberia for freshwater taxa.

During a scientific field expedition to the Alai-Pamir range five specimens of the genus Gloydius have been collected in the larger Alai. A morphological and genetical examination of the specimens has shown that they are part of the G. halys complex, but represent a new taxon which is characterized by the following unique character combination: It is a slender and moderately stout small snake, up to 479 mm total length. The head has nine symmetrical plates on the upper head, 7 supralabial and 8-9 infralabial scales. Body scales in 20-22 rows around midbody, 143-156 ventral and 35-45 usually paired subcaudal scales. The cloacal plate not divided. The general coloration consists of various different tones of olive, tan and brown, having a distinct head, but an indistinct body pattern with, excluding the tail, 26-29 transverse crossbands, which are not extending to the sides of the body. The haplotype network shows the new species within the G. halys complex and close related to both, G. h. halys and G. h. caraganus. So far the new described species is only known from the Alai range. However, various Gloydius specimens are found in Kyrgyzstan and because of the complicated taxonomy those specimens have to re-identified to clarify their status and the status of the new species.

Aims The aim of this study was to evaluate, via various molecular methods, the possible correlations between microbial community structure of Prussian carp and the environmental compartments of their habitat. Methods and Results Microbial communities in the intestine and environmental compartments were studied using PCR-screening, cloning and next-generation high-throughput sequencing of the 16S ribosomal RNA genes. The 16S rDNA metagenomic sequencing showed higher bacterial diversity in comparison with clone libraries, while group-specific PCR showed positive detection of nine bacteria phyla. Proteobacteria, Bacteroidetes, Firmicutes, Cyanobacteria and Actinobacteria were most abundant both in the intestine and habitat environments. The comparative analyses reveal that the bacterial community in the Prussian carp intestine is most similar to that identified from the chironomid. Conclusions This study demonstrated some differences between molecular methods and showed advantages and limitations associated with them. These differences have the potential to reduce bias in results obtained from analysis of the community structure. The advantages of each molecular technique can be used for a better understanding of microbial diversity. The microbiota of Prussian carp intestine is most similar to those from the chironomids. Significance and Impact of the Study We investigated the diversity of the intestinal microbiota in an economically important aquaculture species, the Prussian carp (Carassius gibelio). The results provide significant information to discuss possible functions of these bacteria for further understanding of Prussian carp health.

In contrast to the abundant fossil record of arctic ground squirrels, Urocitellus parryii, from eastern Beringia, only a limited number of fossils is known from its western part. In 1946, unnamed GULAG prisoners discovered a nest with three mummified carcasses of arctic ground squirrels in the permafrost sediments of the El’ga river, Yakutia, Russia, that were later attributed to a new species, Citellus (Urocitellus) glacialis Vinogr. To verify this assignment and to explore phylogenetic relationships between ancient and present-day arctic ground squirrels, we performed 14C dating and ancient DNA analyses of one of the El’ga mummies and four contemporaneous fossils from Duvanny Yar, northeastern Yakutia. Phylogenetic reconstructions, based on complete cytochrome b gene sequences of five Late Pleistocene arctic ground squirrels and those of modern U. parryii from 21 locations across western Beringia, provided no support for earlier proposals that ancient arctic ground squirrels from Siberia constitute a distinct species. In fact, we observed genetic continuity of the glacialis mitochondrial DNA lineage in modern U. parryii of the Kamchatka peninsula. When viewed in a broader geographic perspective, our findings provide new insights into the genetic history of U. parryii in Late Pleistocene Beringia.