Case study on using genomic analyses for research and conservation of endangered Knipowitschia and Orsinigobius species
Fishes of the genera Knipowitschia and Orsinigobius are target species of this investigation, since they present an excellent case study for scientific investigation of evolutionary histories, pathways and adaptations, as well as demonstrating possibilities and benefits of employment reference genomes and analyses based on the whole-genome sequencing datasets for practical conservation of endemic and endangered species. They have very small distribution ranges and small population sizes, but high importance in ecosystem structure and functions. Due to their small sizes, restricted distributed areas and no commercial value, there is a serious lack of data even on their taxonomical status, but also on their local adaptations, population structures and diversities and all other aspects of their biology. Moreover, previously conducted investigations that included these species and were based on single-gene analyses failed to resolve their taxonomic position or phylogenetic relationships faithfully. Unfortunately, these species have been neglected also in a conservative sense. Their endangerment states have been estimated based solely on their distribution ranges (whose determination is questionable due to taxonomic uncertainties and lack of recent field investigation) and habitat conditions, so it is likely that they do not reflect the real states of populations. Due to the lack of scientific data and conservational interest, some of this endemic species have not been included in the Annexes of the Habitats Directive, and thereafter, have not been recognized as Natura 2000 species and monitoring on the states of their conservational elements have not been foreseen so far. As a consequence, practical conservation of endemic Knipowitschia and Orsinigobius species is almost non-existent. Thereafter, performance of comprehensive genomic investigation and combination of their results with habitat and threats analyses, as well as stakeholder's involvement activities, was identified as a possibility to obtain important scientific data on the populations of the endemic and endangered fish species, their evolutions and adaptations, but also to motivate and foster their practical conservation. Moreover, all the mentioned data about Knipowitschia and related genera made them a good test case for BGE to show how reference-based genomics can support description and protection of overlooked freshwater biodiversity.