Alexandros Triantafyllidis

Genetic Identification and Phylogeny of Three Species of the Genus Trachurus Based on Mitochondrial DNA Analysis

The genetic identification and the phylogenetic relationships of 3 European species of the genus Trachurus (T. trachurus, T. mediterraneus, and T. picturatus) across their geographical distribution, have been investigated by mitochondrial DNA analysis. Both cytochrome b and 16S ribosomal DNA sequence analysis revealed the existence of several species-specific positions that distinguish the 3 studied species. Genetic distances between the species indicated that T. mediterraneus and T. picturatus are more closely related than T. trachurus. Similar topologies have been produced by neighbor-joining, maximum-likelihood, and maximum-parsimony trees, and they were in accordance with previous taxonomic classification. Internucleotide and intranucleotide diversity of T. picturatus was 2 times higher than that of T. mediterraneus and T. trachurus, possibly owing to the low levels of fishing pressure for T. picturatus. This is the first report of the phylogenetic relationships of the 3 Trachurus species and provides a possible scenario of the time of divergence related to the closure of the Gibraltar Straits. In addition, the present results can be used for genetic identification of the 3 species, even from the early stage of eggs, and for detection of commercial fraud.

DNA barcoding analysis of fish species diversity in four north Greek lakes

Materials and methods: The present study is the first to apply DNA barcoding on identifying 37 freshwater fish species from the rich Balkan ichthyofauna. Results: The results are highly successful since in most cases barcodes cluster according to species, in agreement with morphological taxonomic studies. This is also evident based on mean conspecific and congeneric Kimura two-parameter distance values. The 5.6-fold difference between these values is lower than previous barcoding studies, possibly due to the restricted samplings and the recent taxonomy reevaluation for several species. A number of species were identified, where future work is needed: For the species Scardinius erythrophthalmus, Perca fluviatilis, and Rutilus rutilus, the divergence values found among conspecific populations could warrant their placement into different species; for Barbus and Rhodeus populations, the reported interspecific distances found were lower than expected; and for Cobitis species, the application of barcoding seems problematic, due to their complicated reproduction. Conclusion: The extension of this work to other Greek or even Balkan freshwater systems should clarify the situation.

Sub-arctic populations of European lobster, Homarus gammarus, in northern Norway

The European lobster is distributed throughout the south and western regions of the Norwegian coast. A previous lobster allozyme investigation (1993) in the Tysfjord region, north of the Arctic Circle demonstrated that the lobster population from this region was genetically different from lobster samples collected in other parts of Norway. More detailed investigation including supplementary extensive sampling and additional allozyme, microsatellite and mtDNA analyses are reported here. This investigation supports the genetic distinctness of the Tysfjord population and shows that this is mainly due to a reduction (60–70%) in gene diversity (observed heterozygosities and number of alleles) compared with lobsters from more southern regions. In addition to the Tysfjord region, the comprehensive sampling also included lobsters found in the adjacent Nordfolda fjord system. Genetic analyses provided evidence for significant differences between the lobster populations of Tysfjord and Nordfolda, even though they are separated by a coastal distance of only 142 km. The two populations were also different with regards to several biological characteristics such as body size. The genetic difference between these two geographically close populations is likely to be due to the local hydrological conditions, preventing larval dispersal between the fjord systems. Assessment of lobster abundance in the north-west region suggests that the sub-arctic lobster populations are geographically isolated.

Mislabeling of Two Commercial North American Hake Species Suggests Underreported Exploitation of Offshore Hake

Abstract Mislabeling of North American merlucciid hakes in stock surveys and commercial market samples was detected by employing nuclear 5S ribosomal DNA (rDNA) and mitochondrial cytochrome b variation as molecular markers. Results showed that offshore hake Merluccius albidus is sold in European markets but is labeled as the morphologically similar silver hake M. bilinearis, which is the target species of the fishery. This suggests that offshore hake may be inadvertently included within silver hake landings, as the two species overlap in the southern area of silver hake distribution (approximately 41°-35°N latitude near North American coasts). An inexpensive and technically easy technique based on polymerase chain reaction (PCR) amplification of a fragment of 5S rDNA and visualization of PCR products in agarose gels is recommended for routine species assignation in landings for purposes of exploitation estimates and for authentication of commercial hake species.

Development of Mitochondrial DNA Primers for Use with Homarid Lobsters

AbstractDNA primer sets were developed for the amplification of complete mitochondrial genomes for both European and American lobsters in 4 suitable-sized segments. Optimal conditions for polymerase chain reaction routine screening were established. The 4 segments were screened with 24 restriction endonucleases in a test population sample, covering the whole distribution of the European lobster, and restriction patterns of each enzyme were revealed. A segment of 3000 bp comprising part of cytochrome oxidase I gene, the genes cytochrome oxidase II and III, subunits 6 and 8 of ATPase, subunit 3 of the NAD dehydrogenase, and various transfer RNAs, was found to be the most polymorphic. A number of enzyme patterns in each segment differentiated European and American lobsters. Extra bands were observed, indicating heteroplasmy phenomena, which were verified with various approaches. Furthermore, a primer set that enables 1-step ampli- fication of the complete mitochondrial genome of the European lobster was established.

Genetic characterization of common carp (Cyprinus carpio) populations from Greece using mitochondrial DNA sequences

Wild common carp from two lakes and two rivers in Greece were genetically characterized with sequencing analysis of two mitochondrial DNA segments: cytochrome b (1119 bp) and D-loop (646 bp). A total of 9 variable singleton sites and 7 unique haplotypes were detected. A common haplotype was found in three out of the four populations examined, which seems to be the ancestral one and represents the European origin of common carp from Greece. This haplotype could be also justified by the introductions reported with individuals belonging to the Central European race, into many natural habitats in Greece. Limited genetic variation — in Evros and Aliakmonas populations — could be due to bottleneck effects and small effective population sizes, whereas the different haplotypes found in Lake Volvi could represent different common carp stocks. Values of sequence divergence among Greek haplotypes ranged from 0.0006 to 0.0023. The Neighbour-Joining (NJ) phylogenetic tree constructed based on the combined sequences, reveals that the populations of common carp from Greece belong to the European group of populations — which is highly divergent from the South East-Asia cluster — and to the subspecies Cyprinus carpio carpio.

TRES: Identification of Discriminatory and Informative SNPs from Population Genomic Data

The advent of high-throughput genomic technologies is enabling analyses on thousands or even millions of single-nucleotide polymorphisms (SNPs). At the same time, the selection of a minimum number of SNPs with the maximum information content is becoming increasingly problematic. Available locus ranking programs have been accused of providing upwardly biased results (concerning the predicted accuracy of the chosen set of markers for population assignment), cannot handle high-dimensional datasets, and some of them are computationally intensive. The toolbox for ranking and evaluation of SNPs (TRES) is a collection of algorithms built in a user-friendly and computationally efficient software that can manipulate and analyze datasets even in the order of millions of genotypes in a matter of seconds. It offers a variety of established methods for evaluating and ranking SNPs on user defined groups of populations and produces a set of predefined number of top ranked loci. Moreover, dataset manipulation algorithms enable users to convert datasets in different file formats, split the initial datasets into train and test sets, and finally create datasets containing only selected SNPs occurring from the SNP selection analysis for later on evaluation in dedicated software such as GENECLASS. This application can aid biologists to select loci with maximum power for optimization of cost-effective panels with applications related to e.g. species identification, wildlife management, and forensic problems. TRES is available for all operating systems at http://mlkd.csd.auth.gr/bio/tres.

Life History Traits of Ylikiensis Roach (Rutilus ylikiensis) in Two Greek Lakes of Different Trophic State

ABSTRACT The possible influence of trophic state on the life traits of a Greek endemic cyprinid fish (Rutilus ylikiensis) was investigated in two contrasting lakes. Lysimachia Lake is a eutrophic and very polluted shallow lake, while Trichonis Lake is an oligotrophic to mesotrophic, clearer, and deeper lake. Significant differences between the lakes were found in relation to the life history traits of the fish. In the eutrophic lake, fish achieved higher age and spawned more but smaller eggs than in the oligotrophic lake. In the eutrophic lake, females achieved higher age than males and the overall sex ratio of males: females was 1:3.42. The extrapolated mortality rate for females was significantly lower than that for males. Females were significantly heavier than males of the same length. In contrast to the above, no such differences between sexes were found in the oligotrophic lake.

Threatened fishes of the world: Silurus aristotelis (Agassiz 1856) (Siluridae)

Common names: Aristotle’s catfish (E), glanidi (G), Aristotelis derived from the ancient Greek philosopher Aristotle (384 – 322 BCE) who was the first described the reproductive strategy and parental care of the species. Conservation status: Listed as endangered in the EU Habitat Directive 92/43/EEC (Annexes II, IV). Strictly protected by the Bern Convention (Appendix II). Protected by Presidential Decree No. 67/1981 of the Greek State. Identification:D 3, A 73 (70 – 74), C 17, P l, 12 (10 – 13), V 10 Vertebrae 56. The hard ray of the pectoral fin has 12 – 14 serrations, males have wider ray with more serrations than females. Body elongate, cylindrical anteriorly, compressed posteriorly, males are more slender than females. Head large and depressed, two pairs of barbells, one in each maxilla, the maxillary pair are especially long. Gape very wide, the lower maxilla is prolonged. The dorsal fin is very small, caudal fin is distinct from the anal fin, anal fin-base very long. Colouration variable; usually fairly dark, the upper side dark brown olive-green to blue-black and the flanks paler. Underside, especially the belly, pale to white. Upon this ground colour are imposed cloudy or spotted marblings. The skin is scaleless, max TL=40 cm, maximum age 10 years. Distribution: Endemic to the lower Acheloos River system (W Greece) which includes the lakes Trichonis, Lysimachia, Ozeros, Amvrakia. Two nonnative populations where established by translocation of fish from Trichonis Lake to Pamvotis Lake (NW Greece) and Volvi Lake (N Greece) between 1950 and 1955 (Leonardos 1996). Abundance: Was originally abundant in the distribution area. In recent years most populations exhibit tendencies to decline due to high mortalities occurring from the pollution and fishing pressure. Healthy populations in the Lysimachia and Pamvotis Lakes, small populations in Trichonis and Amvrakia Lakes, and very rare in Volvi Lake. Habitat and Ecology: Occurs in the slow flowing reaches of rivers with turbid water, streams and canals, in lakes especially with dense weed-bed and muddy bottoms. It feeds at night predominantly on fish live and dead, and secondarily on crustaceans, gastropods, aquatic insects, small frogs and snakes (lliadou & Ondrias 1986). Reproduction: Females mature at 2 – 3 year, extended breeding period with ripe gonads from April to July (lliadou & Ondrias 1986). Eggs are laid near the shore in nest-building with pieces of aquatic plants, part of woods. Artificially fertilized eggs have diameter around 2.7 mm, and hatch after 5 days at 23 C. The newly hatched larvae have 7 mm NL (Economou et al.1994). Threats: Major threats are connected with habitat loss or degradation caused by human activities. The main threats are habitat degradation (Pamvotis Lake, Volvi Lake), runoffs from agricultural (Amvrakia, Ozeros, Lysimachia), municipal effluences (Lysimachia and Pamvotis Lakes), water level fluctuations (Amvrakia, Pamvotis). Over fishing and use of illegal fishing methods is widely practiced in Trichonis Lake. Conservation action: At present, no actions are implemented for the conservation of the species. Conservation recommendations: Pollution from agricultural and sewage effluent should be reduced. The ecology and life traits of S. aristotelis need to be further studied so as to quantify the impact of habitat loss and fragmentation on its survival. The reproductive biology and the artificial reproduction of the fish must be studied with an emphasis in reintroduction programs wherever the species is extinct or rare. Remarks: Genetic (mitochondrial and microsatellite DNA) analyses revealed the clear differentiation of the native Trichonis and Amvrakia populations. (Triantafyllidis et al. 2002). Consequently, populations should be managed and conserved separately. Enhancement stockings, with translocations of individuals from one site to another, are not recommended. Although the introduction of S. aristotelis in the Lake Volvi is considered successful based on genetic (microsatellite) variability estimates (Triantafyllidis et al. 2002).

Ensemble Feature Selection using Rank Aggregation Methods for Population Genomic Data

Single Nucleotide Polymorphisms (SNPs) constitute important genetic markers with numerous medical and biological applications of high scientific and economic interest. SNP datasets are typically high dimensional, containing up to million features. Reasons originating from both biology and machine learning, dictate to perform feature selection which is mainly performed after feature evaluation. In this paper we present methods for SNP evaluation and eventually selection, based on combining results obtained from established genetic marker evaluation methods originating from the field of population genetics. To achieve this we have formulated the feature selection task as a ranking aggregation problem, which is a classical problem in social choice and voting theory.