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Gyrodactylid parasites were observed on non-native populations of North-American freshwater catfishes, Ameiurus nebulosus and Ameiurus melas (Siluriformes: Ictaluridae), at several sites in the Elbe River basin, Czech Republic, Europe. Using a combination of morphological and genetic analyses, the parasites infecting A. nebulosus were determined to be Gyrodactylus nebulosus, a North American parasite co-introduced to Europe along with its Ameiurus fish hosts. Subtle morphometrical differences, as well as seasonal variations, were observed among parasites collected from A. nebulosus and A. melas. The host-related variation was further supported through genetic analysis of the partial 18S rDNA, ITS1-5.8S-ITS2 and COI, showing 0.2, 3.0 and 4.8% divergence, respectively. Consistent genetic differences indicated there were two distinct genotypes. Subtle morphological differences associated with the shape of sickle toe, anchor root and ventral bar membrane, according to host species, also supported the description of a new cryptic species, Gyrodactylus melas n. sp., infecting A. melas. Multivariate morphometrical analysis of haptoral hard parts showed significant differences between the anchor lengths of G. nebulosus and G. melas n. sp. However, the measurements of the haptoral hard structures partially overlapped between species, limiting the usage of these parameters for species delineation.

Aim: Grammomys are mostly arboreal rodents occurring in forests, woodlands and thickets throughout sub-Saharan Africa. We investigated whether the divergence events within the genus follow the existing evolutionary scenario for the development of African forests since the late Miocene. Location: Sub-Saharan African forests and woodlands. Methods: We inferred the molecular phylogeny of Grammomys using Bayesian and maximum likelihood methods and DNA sequences of 351 specimens collected from across the distribution of the genus. We mapped the genetic diversity, estimated the divergence times by a relaxed clock model and compared evolution of the genus with forest history. Results: Phylogenetic analysis confirms the monophyly of Grammomys and reveals five main Grammomys lineages with mainly parapatric distributions: (1) the poensis group in Guineo-Congolese forests; (2) the selousi group with a distribution mainly in coastal forests of southern and eastern Africa; (3) the dolichurus group restricted to the easternmost part of South Africa; (4) the macmillani group in the northern part of eastern and Central Africa with one isolated species in Guiñean forests; and (5) the surdaster group, widely distributed in eastern Africa south of the equator. Every group contains well supported sublineages suggesting the existence of undescribed species. The earliest split within the genus (groups 1 vs. 2-5) occurred in the late Miocene and coincides with the formation of the Rift Valley which resulted in the east-west division of the initially pan-African forest. The subsequent separation between groups (2 vs. 3-5) also dates to the end of the Miocene and suggests the split between Grammomys from coastal to upland forests in eastern Africa followed by a single dispersal event into western Africa during the Pleistocene. Conclusions: The evolutionary history of the genus Grammomys closely reflects the accepted scenario of major historical changes in the distribution of tropical African forests since the late Miocene.

The Afar Triangle in easternmost Africa is one of biogeographically important regions, whose recent biota is virtually unknown. Here we evaluated the level of evolutionary uniqueness of biodiversity of this region in a wide regional and continental biogeographical context, using rodents as a model group. By combining our recent collections with historical records, and based on genetic data and phylogenetic approaches, we specifically tested whether and to what extent the geographical isolation of the Afar Depression is reflected in allopatric diversification of arid-adapted mammals. We documented the presence of 16 rodent species (four are reported for the first time in Ethiopia and one rediscovered there after more than 100 years) and eight additional species are likely present based on literature data. Comparative phylogeographic analysis suggests that the Afar Triangle can be considered as a part of a larger Somalian biogeographical region, but its fauna is genetically distinct, including the presence of narrow Afar endemics. To a lesser extent, there are taxa with evolutionary affinities to the eastern Sahara–Sahelian region and to the southern Arabian Peninsula. Compared to the Ethiopian Highlands, the rodent fauna of Afar is relatively poor. However, similarly to highlands, the evolutionary distinctiveness of mammals in the Afar Triangle is very high and it can be considered a unique centre of endemism. Our first comprehensive summary of Afar rodents significantly fills the gap in the knowledge of the mammalian fauna of arid regions in Ethiopia and the Horn of Africa in general and highlights the significance of the region for nature conservation.

The house mouse, Mus musculus , is a widely used animal model in biomedical research, with classical laboratory strains (CLS) being the most frequently employed. However, the limited genetic variability in CLS hinders their applicability in evolutionary studies. Wild-derived strains (WDS), on the other hand, provide a suitable resource for such investigations. This study quantifies genetic and phenotypic data of 101 WDS representing 5 species, 3 subspecies, and 8 natural Y consomic strains and compares them with CLS. Genetic variability was estimated using whole mtDNA sequences, the Prdm9 gene, and copy number variation at two sex chromosome-linked genes. WDS exhibit a large natural variation with up to 2173 polymorphic sites in mitogenomes, whereas CLS display 92 sites. Moreover, while CLS have two Prdm9 alleles, WDS harbour 46 different alleles. Although CLS resemble M. m. domesticus and M. m. musculus WDS, they differ from them in 10 and 14 out of 16 phenotypic traits, respectively. The results suggest that WDS can be a useful tool in evolutionary and biomedical studies with great potential for medical applications.

Polymorphism of the major histocompatibility complex (MHC), DAB1 gene was characterized for the first time in the European bitterling (Rhodeus amarus), a freshwater fish employed in studies of host-parasite coevolution and mate choice, taking advantage of newly designed primers coupled with high-throughput amplicon sequencing. Across 221 genotyped individuals, we detected 1–4 variants per fish, with 28% individuals possessing 3–4 variants. We identified 36 DAB1 variants, and they showed high sequence diversity mostly located within predicted antigen-binding sites, and both global and codon-specific excess of non-synonymous mutations. Despite deep divergence between two major allelic lineages, functional diversity was surprisingly low (3 supertypes). Overall, these findings suggest the role of positive and balancing selection in promotion and long-time maintenance of DAB1 polymorphism. Further investigations will clarify the role of pathogen-mediated selection to drive the evolution of DAB1 variation.

Bacteriophages are abundant components of vertebrate gut microbial communities, impacting bacteriome dynamics, evolution, and directly interacting with the superhost. However, knowledge about gut phageomes and their interaction with bacteriomes in vertebrates under natural conditions is limited to humans and non-human primates. Widely used specific-pathogen-free (SPF) mouse models of host-microbiota interactions have altered gut bacteriomes compared to wild mice, and data on phageomes from wild or other non-SPF mice are lacking. We demonstrate divergent gut phageomes and bacteriomes in wild and captive non-SPF mice, with wild mice phageomes exhibiting higher alpha-diversity and interindividual variability. In both groups, phageome and bacteriome structuring mirrored each other, correlating at the individual level. Re-analysis of previous data from phageomes of SPF mice revealed their enrichment in Suoliviridae crAss-like phages compared to our non-SPF mice. Disrupted bacteriomes in mouse models can be treated by transplanting healthy phageomes, but the effects of phageome transplants on healthy adult gut microbiota are still unknown. We show that experimental transplantation of phageomes from wild to captive mice did not cause major shifts in recipient phageomes. However, the convergence of recipient-to-donor phageomes confirmed that wild phages can integrate into recipient communities. The differences in the subset of integrated phages between the two recipient mouse strains illustrate the context-dependent effects of phage transplantation. The transplantation did not impact recipient gut bacteriomes. This resilience of healthy adult gut microbiomes to the intervention has implications for phage allotransplantation safety.

Immune genes show remarkable levels of adaptive variation shaped by pathogen-mediated selection. Compared to humans, however, population polymorphism in animals has been understudied. To provide an insight into immunogenetic diversity in birds, we sequenced complete protein-coding regions of all Toll-like receptor ( TLR ) genes with direct orthology between mammals and birds ( TLR3 , TLR4 , TLR5 and TLR7 ) in 110 domestic chickens from 25 breeds and compared their variability with a corresponding human dataset. Chicken TLRs ( chTLRs ) exhibit on average nine-times higher nucleotide diversity than human TLRs ( hTLRs ). Increased potentially functional non-synonymous variability is found in chTLR ligand-binding ectodomains. While we identified seven sites in chTLRs under positive selection and found evidence for convergence between alleles, no selection or convergence was detected in hTLRs . Up to six-times more alleles were identified in fowl (70 chTLR4 alleles vs. 11 hTLR4 alleles). In chTLRs , high numbers of alleles are shared between the breeds and the allelic frequencies are more equal than in hTLRs . These differences may have an important impact on infectious disease resistance and host-parasite co-evolution. Though adaptation through high genetic variation is typical for acquired immunity (e.g. MHC ), our results show striking levels of intraspecific polymorphism also in poultry innate immune receptors.

Good genes models of mate choice predict additive genetic benefits of choice whereas the compatibility hypothesis predicts nonadditive fitness benefits. Here the Chinese rose bitterling, Rhodeus ocellatus, a freshwater fish with a resource-based mating system, was used to separate additive and nonadditive genetic benefits of female mate choice. A sequential blocked mating design was used to test female mate preferences, and a cross-classified breeding design coupled with in vitro fertilizations for fitness benefits of mate choice. In addition, the offspring produced by the pairing of preferred and nonpreferred males were reared to maturity and their fitness traits were compared. Finally, the MHC DAB1 gene was typed and male MHC genotypes were correlated with female mate choice. Females showed significant mate preferences but preferences were not congruent among females. There was a significant interaction of male and female genotype on offspring survival, rate of development, growth rate, and body size. No significant male additive effects on offspring fitness were observed. Female mate preferences corresponded with male genetic compatibility, which correlated with MHC dissimilarity. It is proposed that in the rose bitterling genetic compatibility is the mechanism by which females obtain a fitness benefit through mate choice and that male MHC dissimilarity, likely mediated by odor cues, indicates genetic compatibility.

Genomic analysis of hybrid zones offers unique insights into emerging reproductive isolation and the dynamics of introgression. Because hybrid genomes consist of blocks inherited from one or the other parental taxon, linkage information is essential. In most cases, the spectrum of local ancestry tracts can be efficiently uncovered from dense linkage maps. Here, we report the development of such a map for the hybridizing toads, Bombina bombina and Bombina variegata (Anura: Bombinatoridae). Faced with the challenge of a large (7–10 Gb), repetitive genome, we set out to identify a large number of Mendelian markers in the nonrepetitive portion of the genome that report B. bombina vs B. variegata ancestry with appropriately quantified statistical support. Bait sequences for targeted enrichment were selected from a draft genome assembly, after filtering highly repetitive sequences. We developed a novel approach to infer the most likely diplotype per sample and locus from the raw read mapping data, which is robust to over-merging and obviates arbitrary filtering thresholds. Validation of the resulting map with 4755 markers underscored the large-scale synteny between Bombina and Xenopus tropicalis. By assessing the sex of late-stage F2 tadpoles from histological sections, we identified the sex-determining region in the Bombina genome to 7 cM on LG5, which is homologous to X. tropicalis chromosome 5, and inferred male heterogamety. Interestingly, chromosome 5 has been repeatedly recruited as a sex chromosome in anurans with XY sex determination.

Among bird species, the most studied major histocompatibility complex (MHC) is the chicken MHC. Although the number of studies on MHC in free-ranging species is increasing, the knowledge on MHC variation in species closely related to chicken is required to understand the peculiarities of bird MHC evolution. Here we describe the variation of MHC class IIB (MHCIIB) exon 2 in a population of the Grey partridge (Perdix perdix), a species of high conservation concern throughout Europe and an emerging galliform model in studies of sexual selection. We found 12 alleles in 108 individuals, but in comparison to other birds surprisingly many sites show signatures of historical positive selection. Individuals displayed between two to four alleles both on genomic and complementary DNA, suggesting the presence of two functional MHCIIB loci. Recombination and gene conversion appear to be involved in generating MHCIIB diversity in the Grey partridge; two recombination breakpoints and several gene conversion events were detected. In phylogenetic analysis of galliform MHCIIB, the Grey partridge alleles do not cluster together, but are scattered through the tree instead. Thus, our results indicate that the Grey partridge MHCIIB is comparable to most other galliforms in terms of copy number and population polymorphism.