Towards retrieving the Promethean treasure: a first molecular assessment of the freshwater fish diversity of Georgia

Ponticolaalasanicus sp. n. (Gobiiformes, Gobiidae) from the Alazani River Basin, Georgia

Background

The South Caucasus Region and Georgia, in particular, is a biodiversity hotspot and characterised by high diversity of landscapes and ecosystems, as well as high levels of endemism. At the same time, diversity of freshwater organisms in the region remains poorly studied, including fishes. The freshwater fish fauna of the South Caucasus Region consists of 119 fish species, of which 13 species belong to the order Gobiiformes. It should be noted that gobies are amongst the poorly studied taxa in Georgia and probably unknown/undescribed species still living in the Georgian freshwater ecosystems which requires further research.

New information

Ponticolaalasanicus, a new species is described from the Alazani River, western Caspian Sea Basin, Georgia. It is distinguished from its congeners in the Caspian and Black Sea Basins by having the following features: dorsal fin with VI-VII spines and 15½-16½ branched rays, anal fin with 10½-12½ branched rays; lateral line with 48-55 scales; laterally compressed body with dark brown and black blotches - scales ctenoid; first and second dorsal fins almost touching with dorsal fins bases; head large, depressed, wider than deep, its length approaches almost 3.4th of standard length; nape scaled completely; cycloid scales cover upper part of opercle, cheeks noticeably swollen; snout longer than eye, eye diameter 4.5 times its head length; lower jaw slightly protruding; upper lip is uniform; pelvic disc short, elongated and flat, not reaching the anus; the pectoral fins extends vertically through first branched dorsal fin; caudal fin rounded. Ponticolaalasanicus sp. n. belongs to P.syrman group and it is separated by a minimum Kimura 2-parameter distance of 3.5, 3.6 and 4.8% from P.syrman, P.iranicus and P.patimari, respectively.

Risk of invasiveness of non-native fishes in the South Caucasus biodiversity and geopolitical hotspot

Aquatic invasions are one of the major threats for freshwater ecosystems. However, in developing countries, knowledge of biological invasions, essential for the implementation of appropriate legislation, is often limited if not entirely lacking. In this regard, the identification of potentially invasive non-native species by risk screening, followed by a full risk assessment of the species ranked as higher risk, enables decision-makers to be informed about the extent of the threats posed to the recipient (risk assessment) area. In this study, 32 non-native extant and horizon fish species were screened for their risk of invasiveness under current and predicted climate conditions for the South Caucasus – a biodiversity and geopolitical hotspot that includes the countries of Armenia, Azerbaijan and Georgia. Overall, the number of very high-risk species increased from four (12.5%) under current climate conditions to 12 (37.5%) under predicted climate conditions. The highest-risk species under both conditions included the already established gibel carp Carassius gibelio and topmouth gudgeon Pseudorasbora parva, the locally translocated pikeperch Sander lucioperca and the horizon North African catfish Clarias gariepinus. Under predicted climate conditions, a very high risk of invasiveness was predicted also for the translocated three-spined stickleback Gasterosteus aculeatus and Eurasian perch Perca fluviatilis, for the already established eastern mosquitofish Gambusia holbrooki, ruffe Gymnocephalus cernua, sharpbelly Hemiculter leucisculus and Nile tilapia Orechromis niloticus, and for the horizon pumpkinseed Lepomis gibbosus and largemouth bass Micropterus salmoides. Future research on the non-native species in the South Caucasus should be conducted both country- and region-wide and should account not only for the high biodiversity, but also for the critical geopolitical situation affecting the study area.

Species diversity and DNA barcode library of freshwater Molluscs of South Caucasus

This study provides the first attempt to investigate the molecular diversity of South Caucasian freshwater molluscs (Mollusca, Gastropoda) and lay down the first bricks to build up a DNA-barcode library. In total, 289 COI barcode sequences were obtained from 33 morpho-species belonging to 24 molluscan genera and 10 families that represent nearly 30% of known freshwater molluscan diversity of the South Caucasus region. DNA barcodes were analysed by means of the Barcode Index Number (BIN) and the other tools available in BOLD Systems. Results showed that the knowledge of freshwater molluscs diversity in the South Caucasus is far from comprehensive. For the studied 33 morpho-species, 289 barcodes were clustered into 40 BINs, from which unique BINs were defined for 12 species and five species were characterised with more than a single BIN. From the studied taxa, 60% were characterised larger than 2.2% sequence divergence indicating high genetic variation or cryptic diversity. Within our limited taxonomic coverage, we found one new species for the Republic of Georgia (Galbaschirazensis) and at least three undescribed species belonging to the genera Stagnicola, Segmentina and Anisus. Uniqueness and high molecular diversity of the studied species emphasise the need for further intensive morphological and molecular investigations of the South Caucasian freshwater molluscan fauna.

DNA barcoding and species delimitation of the genus Oxynoemacheilus (Teleostei: Nemacheilidae) in Anatolia

The DNA barcoding approach was used for the determination of evolutionary relationships and species delimitation of the genus Oxynoemacheilus (Teleostei: Nemacheilidae). The COI barcode region (615 bp amplicon) was used to barcode 444 individuals from 64 morphologically identified species in the genus Oxynoemacheilus and 189 haplotypes were identified. The average of the interspecific p distance (9.59%) was about 21-fold higher than the average intraspecific distance (0.44%). A general genetic threshold of 1.46% sequence divergence was defined for species delimitation. The multiple species delimitation methods (BCM, GMYC, bPTP and TCS) revealed a total of 62 molecular operational taxonomic units for 64 morphospecies with a new loach species from the BuyukMelen River. Neighbour-joining, maximum likelihood and Bayesian inference analyses indicated that all haplotypes were clustered into 62 clades, which corresponded to Oxynoemacheilus species, with strong bootstrap support (≥95%). Furthermore, all samples grouped in concurrence with the taxonomic status of the species except for species groups (O. germencicus-O. cinicus-O. mesudae and O. leontinae-O. namiri) that were showed intraspecific overlap in genetic diversity for COI-based barcodes. In conclusion, our analyses indicate that COI-based barcodes provide reliable species discrimination. Therefore, we currently recommend COI barcodes as the suitable barcode for genus Oxynoemacheilus.

A practical approach to revise the Oxynoemacheilus bergianus species group (Teleostei: Nemacheilidae)

The Oxynoemacheilus bergianus species group is revised based on tree topology (ML, NJ, MP), distance (K2P and ASAP) and Poisson tree process analyses of DNA barcode data tested against morphometric and morphological characters including colour patterns. The O. bergianus species group is distinguished from other Oxynoemacheilus groups based on morphological characters: its constituent species have a slender caudal peduncle, a suborbital flap in the male, a mottled or blotched colour pattern, and lack bold, black spots on the caudal-fin base. It is also supported as a monophyletic unit in our molecular analysis.                 The O. bergianus group includes 10 molecular clades following congruently well-supported NJ, MP and ML based entities. Species described as O. bergianus, O. banarescui, O. erdali, O. fatsaensis, O. samanticus, and O. simavicus from Turkey, O. lenkoranensis from Azerbaijan, and O. longipinnis and O. parvinae from Iran belong to this species group. The group includes also four unnamed molecular clades. We were unable to detect external differences between any of the molecular clades in colour pattern or any morphometric or morphological characters examined. In the 10 molecular clades in the O. bergianus species group, the intraclade K2P distance ranges from 0.0–1.8% while the distances between molecular clades ranges from 0.6–5.9%. To resolve the species diversity of this group, we also analysed the intraspecific and interspecific variability in the K2P distance of DNA barcode data from 53 other Oxynoemacheilus species. Here, the intraspecific variability ranges from 0.0–2.4% while the interspecific K2P distance ranges from 1.2–20.8%. In the O. bergianus species group, only four groups are detected by the mPTP species delimitation approach distinguished by a K2P distance of 2.9% or more. We treat these four groups as valid species, corresponding to O. banarescui, O. bergianus, O. fatsaensis, and O. simavicus. Oxynoemacheilus samanticus from the Kızılırmak and Seyhan drainages, O. lenkoranensis from the Caspian basin, O. erdali from the Euphrates, and O. longipinnis and O. parvinae from the Tigris drainage are treated as synonyms of O. bergianus. Fishes from an unnamed molecular clade from the upper Tigris, and from a second unnamed clade from the upper Euphrates, are both identified as O. bergianus. Oxynoemacheilus bergianus might be a junior synonym of O. bergi from the Kura. The distribution range of O. simavicus, described from the Simav drainage in the Marmara basin, is expanded to the east and two molecularly differentiated population groups occur in the Sakarya drainage, the Büyük Melen River and potentially in other adjacent coastal streams. Oxynoemacheilus fatsaensis, described from the coastal stream Elekçi in northern Anatolia, is also widespread in the Yeşilırmak drainage. Morphological characters proposed to distinguish O. fatsaensis from the other species of the O. bergianus group could not be confirmed by our data on fishes from the Yeşilırmak. This study also discusses the theoretical background, our reasons for conducting this revision in the way we did, and what the alternatives would be.  

Aquatic Organisms Research with DNA Barcodes

Since their inception, DNA barcodes have become a powerful tool for understanding the biodiversity and biology of aquatic species, with multiple applications in diverse fields such as food security, fisheries, environmental DNA, conservation, and exotic species detection. Nevertheless, most aquatic ecosystems, from marine to freshwater, are understudied, with many species disappearing due to environmental stress, mostly caused by human activities. Here we highlight the progress that has been made in studying aquatic organisms with DNA barcodes, and encourage its further development in assisting sustainable use of aquatic resources and conservation.

A genomic perspective on an old question: Salmo trouts or Salmo trutta (Teleostei: Salmonidae)?

There are particular challenges in defining the taxonomic status of recently radiated groups due to the low level of phylogenetic signal. Members of the Salmo trutta species-complex, which mostly evolved during and following the Pleistocene, show high morphological and ecological diversity that, along with their very wide geographic distribution, have led to morphological description of 47 extant nominal species. However, many of these species have not been supported by previous phylogenetic studies, which could be partly due to lack of significant genetic differences among them, the limited resolution offered by molecular methods previously used, as well as the often local scale of these studies. The development of next-generation sequencing (NGS) and related analytical tools have enhanced our ability to address such challenging questions. In this study, Genotyping-by-Sequencing (GBS) of 15,169 filtered SNPs and mitochondrial DNA (mtDNA) D-loop sequences were combined to assess the phylogenetic relationships among 166 brown trouts representing 21 described species and three undescribed groups collected from 84 localities throughout their natural distribution in Europe, west Asia, and North Africa. The data were analysed using different clustering algorithms (admixture analysis and discriminant analysis of principal components-DAPC), a Bayes Factor Delimitation (BFD) test, species tree reconstruction, gene flow tests (three- and four-population tests), and Rogue taxa identification tests. Genomic contributions of the Atlantic lineage brown trout were found in all major sea basins excluding the North African and Aral Sea basins, suggesting introgressive hybridization of native brown trouts driven by stocking using strains of the Atlantic lineage. After removing the phylogenetic noise caused by the Atlantic brown trout, admixture clusters and DAPC clustering based on GBS data, respectively, resolved 11 and 13 clusters among the previously described brown trout species, which were also supported by BFD test results. Our results suggest that natural hybridization between different brown trout lineages has probably played an important role in the origin of several of the putative species, including S. marmoratus, S. carpio, S. farioides, S. pellegrini, S. caspius (in the Kura River drainage) and Salmo sp. in the Danube River basin. Overall, our results support a multi-species taxonomy for brown trouts. They also resolve some species in the Adriatic-Mediterranean and Black Sea drainages as members of very closely related genomic clusters that may need taxonomic revision. However, any final conclusions pertaining to the taxonomy of the brown trout complex should be based on an integrative approach combining genomic, morphological, and ecological data. To avoid challenges in taxonomy and conservation of species complexes like brown trouts, it is suggested to describe species based on genomic clusters of populations instead of describing species based only on morphologically differentiated single type populations.