Hybridization and convergent evolution are phenomena of broad interest in evolutionary biology, but their occurrence poses challenges for reconstructing evolutionary affinities among affected taxa. Sticklebacks in the genus Pungitius are a case in point: evolutionary relationships and taxonomic validity of different species and populations in this circumpolarly distributed species complex remain contentious due to convergent evolution of traits regarded as diagnostic in their taxonomy, and possibly also due to frequent hybridization among taxa. To clarify the evolutionary relationships among different Pungitius species and populations globally, as well as to study the prevalence and extent of introgression among recognized species, genomic data sets of both reference genome‐anchored single nucleotide polymorphisms and de novo assembled RAD‐tag loci were constructed with RAD‐seq data. Both data sets yielded topologically identical and well‐supported species trees. Incongruence between nuclear and mitochondrial DNA‐based trees was found and suggested possibly frequent hybridization and mitogenome capture during the evolution of Pungitius sticklebacks. Further analyses revealed evidence for frequent nuclear genetic introgression among Pungitius species, although the estimated proportions of autosomal introgression were low. Apart from providing evidence for frequent hybridization, the results challenge earlier mitochondrial and morphology‐based hypotheses regarding the number of species and their affinities in this genus: at least seven extant species can be recognized on the basis of genetic data. The results also shed new light on the biogeographical history of the Pungitius‐complex, including suggestion of several trans‐Arctic invasions of Europe from the Northern Pacific. The well‐resolved phylogeny should facilitate the utility of this genus as a model system for future comparative evolutionary studies.
Aim Stickleback fish exhibit considerable morphological variation within and between species, and similar armour phenotypes are often found in different taxonomic groups. Although several Pungitius species and subspecies have been recognized, their evolutionary history and relationships remain poorly known. We investigated the phylogenetic relationships and phenotypic divergence in this genus with a particular focus on P. pungitius and P. laevis.Location Northern Hemisphere.Methods Nucleotide variation was analysed in five mitochondrial regions (control region, cytochrome b, ATPase 6, 12S rRNA and 16S rRNA) covering a total of 3236 bp in 194 individuals from five recognized species (P. pungitius, P. laevis, P. platygaster, P. tymensis and P. kaibarae).Results Six highly divergent lineages were identified, including those corresponding to P. pungitius, P. platygaster, P. tymensis and P. kaibarae. However, P. laevis was found to be polyphyletic, consisting of three divergent lineages. Two of them were independent monophyletic groups, whereas the third one clustered together with P. pungitius. All of the P. laevis lineages, as well as one P. pungitius lineage, were found in the central and southern parts of France. Divergence within this genus was indicated to have begun about 4.4 Ma in the Pliocene epoch. All divergences in the Western Palaearctic were estimated to have occurred during the Pleistocene (≤ 2.6 Ma). No correspondence was found between the molecular phylogeny and the occurrence of distinct armour phenotypes within this genus. Main conclusionsThe results suggest that glacial events during the Pleistocene are likely to have strongly impacted the diversification of this genus in the Western Palaearctic, implying that the central and southern parts of France were important glacial refugia for the ancestral Pungitius fish. It also appears that similar armour phenotypes have evolved independently in different Pungitius lineages, questioning the utility of these traits as diagnostic taxonomic characters.
To elucidate the genes involved in the formation of white and black plumage in ducks, RNA from white and black feather bulbs of an F2 population were analyzed using RNA-Seq. A total of 2,642 expressed sequence tags showed significant differential expression between white and black feather bulbs. Among these tags, 186 matched 133 annotated genes that grouped into 94 pathways. A number of genes controlling melanogenesis showed differential expression between the two types of feather bulbs. This differential expression was confirmed by qPCR analysis and demonstrated that Tyr (Tyrosinase) and Tyrp1 (Tyrosinase-related protein-1) were expressed not in W-W (white feather bulb from white dorsal plumage) and W-WB (white feather bulb from white-black dorsal plumage) but in B-B (black feather bulb from black dorsal plumage) and B-WB (black feather bulb from white-black dorsal plumage) feather bulbs. Tyrp2 (Tyrosinase-related protein-2) gene did not show expression in the four types of feather bulbs but expressed in retina. C-kit (The tyrosine kinase receptor) expressed in all of the samples but the relative mRNA expression in B-B or B-WB was approximately 10 fold higher than that in W-W or W-WB. Additionally, only one of the two Mitf isoforms was associated with plumage color determination. Downregulation of c-Kit and Mitf in feather bulbs may be the cause of white plumage in the duck.
Astroviral infection is considered to be one of the causes of mammalian diarrheal diseases. It has been shown that astrovirus infections cause varying degrees of diarrhea in turkeys and mice. However, the pathogenesis of porcine astrovirus is unknown. In this study, the virulence of a cytopathic porcine astrovirus (PAstV) strain (PAstV1-GX1) isolated from the PK-15 cell line was tested using seven-day-old nursing piglets. The results showed that PAstV1-GX1 infection could cause mild diarrhea, growth retardation, and damage of the villi of the small intestinal mucosa. However, all the above symptoms could be restored within 7 to 10days post inoculation (dpi). To evaluate the innate immunity response of PAstV in vivo, the alteration of inflammatory cytokine expression in piglets infected with PAstV1-GX1 was determined using quantitative real-time reverse transcription polymerase chain reaction (qRT-PCR). The mRNA expression levels of the IFNβ and ISG54 were found to be significantly elevated in virus-infected piglets. In contrast, expression of IFNλ was downregulated in piglets infected with PAstV1-GX1. In addition, the mRNA expression of the tight junction protein 1 and 2 and zonula occludin 1, which are associated with the intestinal barrier permeability, were affected after PAstV1 infection. The present study adds to our understanding of the pathogenic mechanism of PAstV and has established an animal model for further study of pig astrovirus infection.
Pleistocene glaciations have strongly affected the biogeography of many species residing in periglacial and previously glaciated regions. Smoothtail nine-spined sticklebacks (Pungitius laevis) have three highly divergent mitochondrial lineages in France, one of which shares the same mitochondrial cluster with a congener P. pungitius. To understand if interspecific introgression has happened between the two species, we carried out phylogeographic and population genetic analyses using mitochondrial and nuclear gene sequences. Our results indicated asymmetric mitochondrial introgression from P. pungitius to P. laevis and genetic admixture of these species in one of the P. laevis lineages, suggesting historical hybridization.Deep intraspecific mitochondrial divergence within P. laevis in central and southern France mostly coinciding with major drainages suggests that these areas were important glacial refugia for the species explaining the observed intraspecific divergence. The historical hybridization between P. laevis and P. pungitius likely occurred in a refugium at central France, and the newly formed P. laevis lineage spread northward during postglacial recolonization. The study adds to the long list of species showing complete mitogenome capture owing to historical hybridizations, and highlights the reticulate nature of population differentiation in taxa subject to postglacial range-expansions.
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