A multilocus assessment of nuclear and mitochondrial sequence data elucidates phylogenetic relationships among European spirlins (Alburnoides, Cyprinidae)

DNA barcoding of the genus Alburnoides Jeitteles, 1861 (Actinopterygii, Cyprinidae) from Anatolia, Turkey

The present study investigated the ability of DNA barcoding to reliably identify the endemic freshwater species in Turkey, known as biodiversity hotspots. The barcode region (652 bp) of the mitochondrial cytochrome c oxidase subunit I (COI) was used to barcode 153 individuals from 13 morphologically identified species of the genus Alburnoides. Based on the Kimura two-parameter (K2P) evolution model, the average interspecific distance (0.0595) was 31-fold higher than the average intraspecific distance (0.0019). There was a clear-cut barcode gap (0.0158–0.0187) between maximum intraspecific distance (A. tzanevi and A. velioglui) and minimum nearest-neighbour distance (A. freyhofi and A. kurui) for Anatolian Alburnoides species and a common genetic threshold of 0.0158 sequence divergence was defined for species delimitation. The multiple species delimitation methods (ABGD, ASAP, GMYC and bPTP) revealed a total of 11 molecular operational taxonomic units (MOTUs) for 13 morphospecies. Neighbour-joining (NJ), Maximum Likelihood (ML) and Bayesian Inference (BI) tree analysis indicated that all haplotypes were clustered into two major clades, which corresponded to eleven Alburnoides species clusters, with strong bootstrap support. Furthermore, all the specimens clustered in concurrence with the morpho-taxonomic status of the species, except for two species (A. coskuncelebii and A. emineae) that were morphologically differentiated, but showed overlap in variation for COI-based DNA barcode data with other species. Overall, present results identified that COI-based DNA barcoding is effective for species identification and cataloguing of genus Alburnoides in Turkey.

Evolutionary history of the Pelasgus minnows (Teleostei: Leuciscidae), an ancient endemic genus from the Balkan Peninsula

The Balkans are one of the European biodiversity hotspots, hosting outstandingly rich, yet threatened, flora and fauna. This region hosts one of the richest endemic freshwater ichthyofauna in Europe, including several genera occurring exclusively here. One of these is the genus of the primary freshwater minnows Pelasgus, which was designated only in 2007. The genus is one of the most ancient genera of the family Leuciscidae and comprises seven small-bodied species, inhabiting slower, well-vegetated courses of rivers. This work is the first molecular multilocus phylogeny of the genus, based on one mitochondrial and three nuclear markers. In total, 305 individuals across almost entire distribution range of the genus were analysed. We inferred the evolutionary history of the species by comparing the results of our calibrated multilocus coalescent species-tree to palaeogeological events. The diversification of the genus started in the early Miocene and continued through to the beginning of Pleistocene. We identified the regions of the oldest colonization by Pelasgus, the drainages of the ancient lakes Ohrid and Prespa, and the southernmost part of the Peloponnese, hosting Pelasgus minutus, P. prespensis and P. laconicus, respectively. We showed that P. prespensis is not endemic to Lake Prespa, as previously thought; it occurs also in the Albanian River Devoll. This corroborates the emerging opinion that the endemic taxa of ancient lakes evolved within larger-scale historic drainages and not only within the lakes. Our results showed that the species with the most recent common ancestor of the early Pliocene origin, P. thesproticus, P. epiroticus, P. stymphalicus and P. marathonicus, have neighbouring distribution ranges. Pelasgus epiroticus is especially interesting, not only for its pronounced genetic diversity with a geographic pattern, but also for being found at three localities within the native distribution range of P. stymphalicus as a result of a translocation. At two of these localities, we identified hybrids between the two species, and at one of them, the genetically pure native species was not found at all. This points to a threat of the loss of the native ichthyofauna due to unintentional translocations.

Increased spatial resolution of sampling in the Carpathian basin helps to understand the phylogeny of central European stream-dwelling gudgeons

Background

Phylogenetic studies of widespread European fish species often do not completely cover their entire distribution area, and some areas are often excluded from analyses than others. For example, Carpathian stocks are often omitted from these surveys or are under-represented in the samples. However, this area served as an extra-Mediterranean refugia for many species; therefore, it is assumed that fish stocks here may show special phylogenetic features. For this reason, increased spatial resolution of sampling, namely revealing genetic information from unexamined Carpathian areas within the range of doubtful taxa, may help us better understand their phylogenetic features. To test this hypothesis, a phylogenetic investigation using a partial mtCR sequence data was conducted on 56 stream-dwelling freshwater fish (Gobio spp.) individuals collected from 11 rivers of the data-deficient Southeastern Carpathian area. Moreover, we revieved the available phylogenetic data of Middle-Danubian stream-dwelling gudgeon lineages to delineate their distribution in the area.

Results

Seven out of the nine detected haplotypes were newly described, suggesting the studied area hosts distinct and diverse Gobio stocks. Two valid species (G. obtusirostris, G. gobio), and a haplogroup with doubtful phylogenetic position” G. sp. 1" were detected in the area, showing a specific spatial distribution pattern. The distribution of the detected lineages in the Middle-Danubian area correspond with recent and paleo hydrogeographic features, at the same time mainly on their bordering areas show considerable overlap.

Conclusions

Despite the relatively limited geographic range of the study, our results provide important information which contributes to a better understanding of the phylogenetic, taxonomic and distribution features of Central European gudgeons. The genetically confirmed distribution data of the indicated lineages corresponds well with the recent and near-recent hydrogeographic features of the area, and assumes several hybrid zones in the Carpathian Basin. Additionally, the results show that the middle and lower Danubian watershed cannot be excluded from the range of G. gobio. Moreover, the” G. sp. 1", is slightly differentiated but phylogenetically distinct entity, and is the only Gobio taxa thus far detected in the middle and lower Tisza-basin. However, further investigations are necessary to clarify the taxonomic position of this group.

Uncovering the diversity of monogeneans (Platyhelminthes) on endemic cypriniform fishes of the Balkan Peninsula: new species of Dactylogyrus and comments on their phylogeny and host-parasite associations in a biogeographic context

Seven new species of Dactylogyrus Diesing, 1850 (Dactylogyridae) are described from the gills of seven endemic species of cyprinoids (Cyprinidae, Leuciscidae) inhabiting the Balkan Peninsula: Dactylogyrus romuli n. sp. from Luciobarbus albanicus (Greece), Dactylogyrus remi n. sp. from Luciobarbus graecus (Greece), Dactylogyrus recisus n. sp. from Pachychilon macedonicum (Greece), Dactylogyrus octopus n. sp. from Tropidophoxinellus spartiaticus (Greece), Dactylogyrus vukicae n. sp. from Delminichthys adspersus (Bosnia and Herzegovina), Dactylogyrus leptus n. sp. from Chondrostoma knerii (Bosnia and Herzegovina), and Dactylogyrus sandai n. sp. from Telestes karsticus (Croatia). To delineate species boundaries, we used an integrative taxonomic approach combining morphological and genetic data. With these tools, we illustrate that some species of monogeneans considered as cryptic might be designated as pseudocryptic (morphologically similar, not easily differentiated) after a posteriori detailed morphological examination, as happened with D. romuli n. sp. and D. remi n. sp. Thus, for accurate species characterization, it is particularly important to acquire both morphological and molecular data from the same individual specimens, ideally along with illustrations of taxonomically important structures directly taken from hologenophores. Using phylogenetic reconstruction, we investigated the phylogenetic position of newly described Dactylogyrus species within Dactylogyrus species from Balkan cyprinoids with regard to morphological characteristics, host range, and geographical distribution.

High diversity of fish ectoparasitic monogeneans (Dactylogyrus) in the Iberian Peninsula: a case of adaptive radiation?

The epicontinental fauna of the Iberian Peninsula is strongly influenced by its geographical history. As the possibilities for dispersion of organisms into and from this region were (and still are) limited, the local fauna consists almost exclusively of endemic species. Almost all Iberian freshwater fishes of the families Leuciscidae and Cyprinidae are endemic and on-going research on these taxa continually uncovers new species. Nevertheless, information on their host-specific parasites remains scarce. In this study, we investigate the diversity and phylogenetic relationships in monogeneans of the genus Dactylogyrus (gill ectoparasites specific to cyprinoid fish) in the Iberian Peninsula. Twenty-two species were collected and identified from 19 host species belonging to Cyprinidae and Leuciscidae. A high degree of endemism was observed, with 21 Dactylogyrus species reported from Iberia only and a single species, D. borealis, also reported from other European regions. Phylogenetic analysis split the endemic Iberian Dactylogyrus into two well-supported clades, the first encompassing Dactylogyrus parasitizing endemic Luciobarbus spp. only, and the second including all Dactylogyrus species of endemic leuciscids and four species of endemic cyprinids. Species delimitation analysis suggests a remarkable diversity and existence of a multitude of cryptic Dactylogyrus species parasitizing endemic leuciscids (Squalius spp. and representatives of Chondrostoma s.l.). These results suggest a rapid adaptive radiation of Dactylogyrus in this geographically isolated region, closely associated with their cyprinoid hosts. Moreover, phylogenetic analysis supports that Dactylogyrus parasites colonized the Iberian Peninsula through multiple dispersion events.

New data on the western Balkan leuciscids Alburnoides and Alburnus (Teleostei, Leuciscidae) from the Vjosa River, Albania

The first voucher-confirmed record of Alburnus scoranza and the first morphological description of Alburnoides for the Vjosa River system in Albania are reported with a brief discussion of the diagnostic morphological traits and taxonomic assignment of both species.

High cryptic diversity of bitterling fish in the southern West Palearctic

South-east Europe, along with the adjacent region of south-west Asia, is an important biodiversity hotspot with high local endemism largely contributed by contemporary continental lineages that retreated to southern refugia during colder Quaternary periods. We investigated the genetic diversity of the European bitterling fish (Rhodeus amarus) species complex (Cyprinidae) across its range in the western Palearctic, but with a particular emphasis in the region of Balkan, Pontic and Caspian refugia. We genotyped 12 polymorphic microsatellite loci and a partial sequence of mitochondrial gene cytochrome b (CYTB) for a set of 1,038 individuals from 60 populations. We used mtDNA sequences to infer phylogenetic relationships and historical demography, and microsatellite markers to describe fine-scale genetic variability and structure. Our mtDNA analysis revealed six well-supported lineages, with limited local co-occurrence. Two lineages are distributed throughout central and western Europe (lineages "A" and "B"), with two zones of secondary contact. Another two lineages were restricted to the Ponto-Aegean region of Greece (lineages "C" and "D") and the final two lineages were restricted south of the Caucasus mountains (lineage "E" from the Black Sea watershed and lineage "F" from the Caspian watershed). A signal of recent expansion was revealed in the two widespread lineages and the Ponto-Aegean lineage "C". The geographic distribution of clusters detected by nuclear microsatellites corresponded well with mitochondrial lineages and demonstrated finely sub-structured populations. A profound population structure suggested a significant role of genetic drift in differentiation among lineages. Lineage divergence in the Ponto-Aegean and Caspian regions are substantial, supporting the validity of two described endemic species (Rhodeus meridionalis as lineage "D" and Rhodeus colchicus as lineage "E") and invite taxonomic evaluation of the other two southern lineages (Thracean "C" and Caspian "F").

The phylogenetic relationships and species richness of host-specific Dactylogyrus parasites shaped by the biogeography of Balkan cyprinids

Parasites exhibiting a high degree of host specificity are expected to be intimately associated with their hosts. Therefore, the evolution of host-specific parasites is at least partially shaped by the evolutionary history and distribution of such hosts. Gill ectoparasites of Dactylogyrus (Monogenea) are specific to cyprinid fish. In the present study, we investigated the evolutionary history of 47 Dactylogyrus species from the Balkan Peninsula, the Mediteranean region exhibiting the highest cyprinid diversity in Europe, and from central European cyprinids. Phylogenetic analyses revealed four well-supported clades of endemic and non-endemic Dactylogyrus spp. with four basal taxa. Endemic cyprinids with a limited distribution range were parasitized by endemic Dactylogyrus species, but some of them shared several Dactylogyrus species with central European cyprinids. Species delimitation analyses based on molecular data suggest that Dactylogyrus diversity is higher than that defined from morphology. Some endemic cyprinid species harboured Dactylogyrus species of different origins, this probably resulting from multiple host switching. Our results support the view that the evolution of Dactylogyrus in the Balkans has been influenced not only by the historical dispersion and distribution of their cyprinid hosts, but also by recent contacts of non-native cyprinid species with endemic cyprinid fauna in this region.

Phylogenetic relationships and classification of the Holarctic family Leuciscidae (Cypriniformes: Cyprinoidei)

The phylogenetic relationships and classification of the freshwater fish order Cypriniformes, like many other species-rich groups of vertebrates, has evolved over time with some consistency and inconsistencies of relationships across various studies. Within Cypriniformes, the Holarctic family Leuciscidae is one of the most widely distributed and highly diverse monophyletic groups of cyprinoids. Despite several studies conducted on this group, alternative hypotheses exist as to the composition and relationships within Leuciscidae. Here we assess the extent, composition, phylogenetic relationships, and taxonomy of this highly diverse group of fishes, using multiple mitochondrial and nuclear loci and a comprehensive and dense taxonomic sampling. Analyses of 418 specimens (410 species) resolve a well-supported Leuciscidae including 362 specimens (358 taxa) in six well-supported subfamilies/major clades: Pseudaspininae/Far East Asian clade (FEA); Laviniinae/North American Western clade (WC); Plagopterinae/North American Creek Chub-Plagopterin clade (CC-P); Leuciscinae/Eurasian Old World clade (OW) (minus Phoxinus) plus North American Notemigonus; Phoxininae/Eurasian Phoxinus clade (PHX); and Pogonichthyinae/North American clade (NA) including all remaining leuciscids. Within Leuciscidae, neither the traditional phoxinins (Phoxinus, FEA, Nearctic genera) nor all Nearctic genera (minus Notemigonus) are resolved as monophyletic; whereas the WC and CC-P form two independent lineages from remaining North American cyprinoids. A close relationship exists between Eurasian Phoxinus, NA, and OW clades, while FEA is the sister group to all remaining Leuciscidae. Major lineages resolved within these six subfamilies are mostly congruent with some previous studies. Our results suggests a complex evolutionary history of this diverse and widespread group of fishes.

The phylogenetic position of the enigmatic Balkan Aulopyge huegelii (Teleostei: Cyprinidae) from the perspective of host-specific Dactylogyrus parasites (Monogenea), with a description of Dactylogyrus omenti n. sp

BACKGROUND

The host specificity of fish parasites is considered a useful parasite characteristic with respect to understanding the biogeography of their fish hosts. Dactylogyrus Diesing, 1850 (Monogenea) includes common parasites of cyprinids exhibiting different degrees of host specificity, i.e. from strict specialism to generalism. The phylogenetic relationships and historical dispersions of several cyprinid lineages, including Aulopyge huegelii Heckel, 1843, are still unclear. Therefore, the aims of our study were to investigate (i) the Dactylogyrus spp. parasites of A. huegelii, and (ii) the phylogenetic relationships of Dactylogyrus spp. parasitizing A. huegelii as a possible tool for understanding the phylogenetic position of this fish species within the Cyprininae lineage.

RESULTS

Two species of Dactylogyrus, D. vastator Nybelin, 1924 and D. omenti n. sp., were collected from 14 specimens of A. huegelii from the Šujica River (Bosnia and Herzegovina). While D. vastator is a typical species parasitizing Carassius spp. and Cyprinus carpio L, D. omenti n. sp. is, according to phylogenetic reconstruction, closely related to Dactylogyrus species infecting European species of Barbus and Luciobarbus. The genetic distance revealed that the sequence for D. vastator from A. huegelii is identical with that for D. vastator from Barbus plebejus Bonaparte, 1839 (Italy) and Carassius gibelio (Bloch, 1782) (Croatia). Dactylogyrus omenti n. sp. was described as a species new to science.

CONCLUSIONS

Our findings support the phylogenetic position of A. huegelii within the Cyprininae lineage and suggest that A. huegelii is phylogenetically closely related to Barbus and Luciobarbus species. The morphological similarity between D. omenti n. sp. and Dactylogyrus species of Middle Eastern Barbus suggests historical contact between cyprinid species recently living in allopatry and the possible diversification of A. huegelii from a common ancestor in this area. On other hand, the genetic similarity between D. vastator ex A. huegelii and D. vastator ex C. gibelio collected in Balkan Peninsula suggests that A. huegelii was secondarily parasitized by D. vastator, originating from C. gibelio after introduction of this fish species from Asia to Europe.

DNA barcoding of the fishes of the genus Alburnoides (Actinopterygii, Cyprinidae) from Caucasus

Spirlins of the genus Alburnoides are widespread fishes, which taxonomy has been rapidly developing in recent years. Mitochondrial cytochrome c oxidase subunit I (COI) was used as DNA barcode marker to create a reference dataset of Caucasian Alburnoides and to test its barcoding efficiency. All four previously known Caucasian species of Alburnoides were confirmed as valid species with high genetic distances to sister species as well confirmed as Caucasian endemics. Alburnoides samiii, previously known from Sefidroud basin (Iran), was discovered in Transcaucasia. The accuracy of species identification of Ponto-Caspian Alburnoides by DNA barcodes was 100%. In addition, one potentially new species within A. gmelini was revealed. Despite the limited ability of COI to infer phylogenetic relationships, study provided evidence that Ponto-Caspian lineage of Alburnoides includes significantly larger number of species from Caspian Sea basin and inland basins of Central Asia.

A molecular approach to the genus Alburnoides using COI sequences data set and the description of a new species, A. damghani, from the Damghan River system (the Dasht-e Kavir Basin, Iran) (Actinopterygii, Cyprinidae)

The molecular status of nine species of the genus Alburnoides from different river drainages in Iran and additionally by seven species from Europe was assessed. mtDNA COI gene sequences from freshly collected specimens and available NCBI data revealed four major phylogenetic lineages. Based on the results, a distinct taxon from the Cheshmeh Ali (Ali Spring), a Damghan River tributary in the endorheic Dasht-e Kavir basin, northern Iran, which is the closest sister to Alburnoides namaki (Namak Lake basin) + Alburnoides coadi (Nam River in the endorheic Dasht-e Kavir basin) is considered as a new species, Alburnoides damghani sp. n. It is distinguished from other Alburnoides species in Iran by a combination of character states including: a weakly-developed, variably-scaled, ventral keel from completely scaleless to completely scaled, a short snout with the tip of the mouth cleft on a level with the lower margin of the pupil or slightly lower, a small eye (eye horizontal diameter slightly to markedly less than interorbital width), commonly 8½ branched dorsal-fin rays, commonly 11-12½ branched anal-fin rays, 40-46(47) total lateral-line scales, 2.5-4.2 or 2.5-4.1 pharyngeal teeth, gill rakers short and widely spaced, 6-8 in total, 39-41 (commonly 40), total vertebrae, (19)20(21) abdominal vertebrae, 19-21 (most commonly 20) caudal vertebrae, abdominal vertebral region most commonly equal to or longer than caudal region, and most common vertebral formulae 20+20 and 21+19.