Many genes in fish have species-specific asymmetric rates of molecular evolution

BACKGROUND: Gene and genome duplication events increase the amount of genetic material that might then contribute to an increase in the genomic and phenotypic complexity of organisms during evolution. Thus, it has been argued that there is a relationship between gene copy number and morphological complexity and/or species diversity. This hypothesis implies that duplicated genes have subdivided or evolved novel functions compared to their pre-duplication proto-orthologs. Such a functional divergence might be caused by an increase in evolutionary rates in one ortholog, by changes in expression, regulatory evolution, insertion of repetitive elements, or due to positive Darwinian selection in one copy. We studied a set of 2466 genes that were present in Danio rerio, Takifugu rubripes, Tetraodon nigroviridis and Oryzias latipes to test (i) for forces of positive Darwinian selection; (ii) how frequently duplicated genes are retained, and (iii) whether novel gene functions might have evolved. RESULTS: 25% (610) of all investigated genes show significantly smaller or higher genetic distances in the genomes of particular fish species compared to their human ortholog than their orthologs in other fish according to relative rate tests. We identified 49 new paralogous pairs of duplicated genes in fish, in which one of the paralogs is under positive Darwinian selection and shows a significantly higher rate of molecular evolution in one of the four fish species, whereas the other copy apparently did not undergo adaptive changes since it retained the original rate of evolution. Among the genes under positive Darwinian selection, we found a surprisingly high number of ATP binding proteins and transcription factors. CONCLUSION: The significant rate difference suggests that the function of these rate-changed genes might be essential for the respective fish species. We demonstrate that the measurement of positive selection is a powerful tool to identify divergence rates of duplicated genes and that this method has the capacity to identify potentially interesting candidates for adaptive gene evolution

Three rounds (1R/2R/3R) of genome duplications and the evolution of the glycolytic pathway in vertebrates

BACKGROUND: Evolution of the deuterostome lineage was accompanied by an increase in systematic complexity especially with regard to highly specialized tissues and organs. Based on the observation of an increased number of paralogous genes in vertebrates compared with invertebrates, two entire genome duplications (2R) were proposed during the early evolution of vertebrates. Most glycolytic enzymes occur as several copies in vertebrate genomes, which are specifically expressed in certain tissues. Therefore, the glycolytic pathway is particularly suitable for testing theories of the involvement of gene/genome duplications in enzyme evolution. RESULTS: We assembled datasets from genomic databases of at least nine vertebrate species and at least three outgroups (one deuterostome and two protostomes), and used maximum likelihood and Bayesian methods to construct phylogenies of the 10 enzymes of the glycolytic pathway. Through this approach, we intended to gain insights into the vertebrate specific evolution of enzymes of the glycolytic pathway. Many of the obtained gene trees generally reflect the history of two rounds of duplication during vertebrate evolution, and were in agreement with the hypothesis of an additional duplication event within the lineage of teleost fish. The retention of paralogs differed greatly between genes, and no direct link to the multimeric structure of the active enzyme was found. CONCLUSION: The glycolytic pathway has subsequently evolved by gene duplication and divergence of each constituent enzyme with taxon-specific individual gene losses or lineage-specific duplications. The tissue-specific expression might have led to an increased retention for some genes since paralogs can subdivide the ancestral expression domain or find new functions, which are not necessarily related to the original function

Why do snails have hairs? A Bayesian inference of character evolution

BACKGROUND: Costly structures need to represent an adaptive advantage in order to be maintained over evolutionary times. Contrary to many other conspicuous shell ornamentations of gastropods, the haired shells of several Stylommatophoran land snails still lack a convincing adaptive explanation. In the present study, we analysed the correlation between the presence/absence of hairs and habitat conditions in the genus Trochulus in a Bayesian framework of character evolution. RESULTS: Haired shells appeared to be the ancestral character state, a feature most probably lost three times independently. These losses were correlated with a shift from humid to dry habitats, indicating an adaptive function of hairs in moist environments. It had been previously hypothesised that these costly protein structures of the outer shell layer facilitate the locomotion in moist habitats. Our experiments, on the contrary, showed an increased adherence of haired shells to wet surfaces. CONCLUSION: We propose the hypothesis that the possession of hairs facilitates the adherence of the snails to their herbaceous food plants during foraging when humidity levels are high. The absence of hairs in some Trochulus species could thus be explained as a loss of the potential adaptive function linked to habitat shifts

Barcoding Nemo: DNA-Based Identifications for the Ornamental Fish Trade

BACKGROUND:Trade in ornamental fishes represents, by far, the largest route for the importation of exotic vertebrates. There is growing pressure to regulate this trade with the goal of ensuring that species are sustainably harvested and that their point of origin is accurately reported. One important element of such regulation involves easy access to specimen identifications, a task that is currently difficult for all but specialists because of the large number of species involved. The present study represents an important first step in making identifications more accessible by assembling a DNA barcode reference sequence library for nearly half of the ornamental fish species imported into North America. METHODOLOGY/PRINCIPAL FINDINGS:Analysis of the cytochrome c oxidase subunit I (COI) gene from 391 species from 8 coral reef locations revealed that 98% of these species exhibit distinct barcode clusters, allowing their unambiguous identification. Most species showed little intra-specific variation (adjusted mean = 0.21%), but nine species included two or three lineages showing much more divergence (2.19-6.52%) and likely represent overlooked species complexes. By contrast, three genera contained a species pair or triad that lacked barcode divergence, cases that may reflect hybridization, young taxa or taxonomic over-splitting. CONCLUSIONS/SIGNIFICANCE:Although incomplete, this barcode library already provides a new species identification tool for the ornamental fish industry, opening a realm of applications linked to collection practices, regulatory control and conservation

First Molecular Evidence for Underestimated Biodiversity of Rhachotropis (Crustacea, Amphipoda), with Description of a New Species

The crustacean genus Rhachotropis has a worldwide distribution and amongst the largest bathymetric range known from any amphipod genus. DNA barcoding of new material from around New Zealand and the Ross Sea indicated depth-related biogeographic patterns. New Zealand Rhachotropis do not form a monophyletic clade. Species from bathyal depths on the Chatham Rise, east of New Zealand, show lower sequence divergence to bathyal species from California and the Arctic than to abyssal New Zealand species. Species sampled in the Kermadec Trench, north of New Zealand below 5000 m, seem to be more closely related to Ross Sea abyssal species than to the New Zealand shelf species. The worldwide geographic and bathymetric distribution for all Rhachotropis species is presented here. Depth may have a greater influence on phylogeny than geographic distance. Molecular and morphological investigations of Rhachotropis specimens from the Chatham Rise, New Zealand revealed a species new to science which is described in detail, including scanning electron microscopy. This increases the number of described species of Rhachotropis to 60 worldwide

A workflow for accurate metabarcoding using nanopore MinION sequencing

1. Metabarcoding has become a common approach to the rapid identification of the species composition in a mixed sample. The majority of studies use established short‐read high‐throughput sequencing platforms. The Oxford Nanopore MinION™, a portable sequencing platform, represents a low‐cost alternative allowing researchers to generate sequence data in the field. However, a major drawback is the high raw read error rate that can range from 10% to 22%. 2. To test if the MinION™ represents a viable alternative to other sequencing platforms we used rolling circle amplification (RCA) to generate full‐length consensus DNA barcodes for a bulk mock sample of 50 aquatic invertebrate species with at least 15% genetic distance to each other. By applying two different laboratory protocols, we generated two MinION™ runs that were used to build error‐corrected consensus sequences. A newly developed Python pipeline, ASHURE, was used for data processing, consensus building, clustering, and taxonomic assignment of the resulting reads. 3. Our pipeline achieved median accuracies of up to 99.3% for long concatemeric reads (>45 barcodes) and successfully identified all 50 species in the mock community. The use of RCA was integral for increasing consensus accuracy but was also the most time‐consuming step of the laboratory workflow. Most concatemeric reads were skewed towards a shorter read length range with a median read length of up to 1262bp. 4. Our study demonstrates that Nanopore sequencing can be used for metabarcoding, but exploration of other isothermal amplification procedures to improve consensus accuracy is recommended

Fresh Waters and Fish Diversity: Distribution, Protection and Disturbance in Tropical Australia

Background: Given the globally poor protection of fresh waters for their intrinsic ecological values, assessments are needed to determine how well fresh waters and supported fish species are incidentally protected within existing terrestrial protected-area networks, and to identify their vulnerability to human-induced disturbances. To date, gaps in data have severely constrained any attempt to explore the representation of fresh waters in tropical regions.\ud \ud Methodology and Results: We determined the distribution of fresh waters and fish diversity in the Wet Tropics of Queensland, Australia. We then used distribution data of fresh waters, fish species, human-induced disturbances, and the terrestrial protected-area network to assess the effectiveness of terrestrial protected areas for fresh waters and fish species. We also identified human-induced disturbances likely to influence the effectiveness of freshwater protection and evaluated the vulnerability of fresh waters to these disturbances within and outside protected areas. The representation of fresh waters and fish species in the protected areas of the Wet Tropics is poor: 83% of stream types defined by order, 75% of wetland types, and 89% of fish species have less than 20% of their total Wet Tropics length, area or distribution completely within IUCN category II protected areas. Numerous disturbances affect fresh waters both within and outside of protected areas despite the high level of protection afforded to terrestrial areas in the Wet Tropics (>60% of the region). High-order streams and associated wetlands are influenced by the greatest number of human-induced disturbances and are also the least protected. Thirty-two percent of stream length upstream of protected areas has at least one human-induced disturbance present.\ud \ud Conclusions/Significance: We demonstrate the need for greater consideration of explicit protection and off-reserve management for fresh waters and supported biodiversity by showing that, even in a region where terrestrial protection is high, it does not adequately capture fresh waters

Unexpected high genetic diversity at the extreme Northern geographic limit of Taurulus bubalis (Euphrasen, 1786)

The longspined bullhead (Taurulus bubalis, Euphrasen 1786) belongs to the family Cottidae and is a rocky shore species that inhabits the intertidal zones of the Eastern Atlantic since Iceland, southward to Portugal and also the North Sea and Baltic, northward to the Gulf of Finland, with some occurrences in the northern Mediterranean coasts eastward to the Gulf of Genoa. We analysed the phylogeographic patterns of this species using mitochondrial and nuclear markers in populations throughout most of its distributional range in west Europe. We found that T. bubalis has a relatively shallow genealogy with some differentiation between Atlantic and North Sea. Genetic diversity was homogeneous across all populations studied. The possibility of a glacial refugium near the North Sea is discussed. In many, but not all, marine temperate organisms, patterns of diversity are similar across the species range. If this phenomenon proves to be most common in cold adapted species, it may reflect the availability of glacial refugia not far from their present-day northern limits

DNA Analysis of Traded Shark Fins and Mobulid Gill Plates Reveals a High Proportion of Species of Conservation Concern

Continuously increasing demand for plant and animal products causes unsustainable depletion of biological resources. It is estimated that one-quarter of sharks and rays are threatened worldwide and although the global fin trade is widely recognized as a major driver, demand for meat, liver oil, and gill plates also represents a significant threat. This study used DNA barcoding and 16 S rRNA sequencing as a method to identify shark and ray species from dried fins and gill plates, obtained in Canada, China, and Sri Lanka. 129 fins and gill plates were analysed and searches on BOLD produced matches to 20 species of sharks and five species of rays or – in two cases – to a species pair. Twelve of the species found are listed or have been approved for listing in 2017 in the appendices of the Convention on International Trade in Endangered Species of Fauna and Flora (CITES), including the whale shark (Rhincodon typus), which was surprisingly found among both shark fin and gill plate samples. More than half of identified species fall under the IUCN Red List categories ‘Endangered’ and ‘Vulnerable’, raising further concerns about the impacts of this trade on the sustainability of these low productivity species