Molecular phylogeny of two lineages of Leuciscinae cyprinids (Telestes and Scardinius) from the peri-Mediterranean area based on cytochrome b data

We examined phylogenetic relationships in two lineages of Leuciscinae cyprinid fishes based on the sequence data of the complete mitochondrial DNA region coding for the cytochrome b gene (1140 bp). Telestes includes obligate riverine, moderately cold water-adapted species whereas Scardinius comprises warm-adapted species living in lowland lakes and still waters of rivers and streams. We also analysed selected representatives of Leuciscus and Phoxinellus because the taxonomic status of some species belonging to these genera is dubious and they could be placed in the genus Telestes. The study includes 18 species, 43 populations, and 111 individuals from 9 of the 14 peri-Mediterranean ichthyogeographic districts. Clades recovered from the phylogenetic analyses do not support previous taxonomic assumptions based on morphology. Telestes, Leuciscus, and Phoxinellus do not form monophyletic assemblages; phylogenetic analyses suggest that L. polylepis, L. turskyi, P. croaticus, and P. metohiensis should be included in Telestes. Similarly, populations of Scardinius erythrophthalmus do not cluster together and the endangered S. scardafa, endemic to central Italy and surviving in a single locality, is nested within them. The radiations of Telestes and Scardinius occurred in different time periods. A major diversification of Telestes is consistent with a sea dispersal during the freshwater Messinian "Lago Mare" phase of the Mediterranean Sea. Cladogenetic events within Scardinius are likely related to the extension and confluence of river drainages in lowlands following multiple lowering of the sea level during the Quaternary glaciations.     

On the populations of roach (Rutilus rutilus), rudd (Scardinius erythrophthalmus), and their hybriin Esthwaite Water, with notes on the distinctions between them

Samples of cyprinid fishes from Esthwaite Water, Westmorland, have been examined and identified as roach ( Rutilus rutilus ), rudd ( Scardinius erythrophthalmus ), with a high degree (37%) of hybridization between these species. The distinguishing features of roach and rudd are discussed in the light of the difficulty of distinguishing the roach x rudd hybrid from the roach. It is concluded that the only reliable characters are the number and external morphology of the pharyngeal teeth.     

A molecular approach to detect hybridization between bream Abramis brama, roach Rutlius rutilus and rudd Scardinius erythrophthalmus

Hybridization between roach Rutilus rutilus , bream Abramis brama and rudd Scardinius erythrophthalmus was investigated using morphological and genetic analysis employing both nuclear (ITS1) and mitochondrial (cytochrome b ) markers. Allele-specific amplification (ASA) reactions for both markers were developed and ITS1 sequence data for all three species are presented. Sequencing detected two ITS1 haplotypes within both roach and bream which most likely evolved in isolation and were subsequently brought together as a result of restocking by anglers. Analysis of cloned hybrid nuclear ribosomal DNA revealed evidence of recombination between parental ITS1 sequences. ASA proved to be an effective method for identifying hybrids and detected multiple ITS1 copies in fishes identified as purebred by morphological analysis. In addition this suggests post-F1 hybridization and introgression may be occurring between roach and bream, and rudd and bream, although some barriers appear to be suppressing backcrosses within the hybrid population. Analysis of the hybrid population demonstrated that hybridization has occurred in both directions.     

Some morphological characteristics of Acipenserid fishes: considerations of their variability and utility in taxonomy

The use of traditionally utilized morphological characteristics as diagnostic tools in tetraploid and octaploid sturgeons assumes that they are heterogenous in nature. Octoploid species are supposed to be of independent origin through multiple events of polyploidization and through interspecific hybridization among tetraploid species. In this study probable relationships between tetraploid and octoploid species are suggested by morphological characteristica. The genus Acipenser should include both former genus Acipenser and Huso and this seems to be the only realistic deduction that can be concluded from morphological features.     

Feeding ofScardinius acarnanicus Stephanidis, 1939 (Pisces: Cyprinidae) from Lakes Lysimachia and Trichonis, Greece

The feeding of the endemic freshwater fish Scardinius acarnanicus Stephanidis, 1939 has been studied from the content of its intestine and from the results of feeding experiments in the laboratory. This species appears to be phytoplanktophagous when young, whereas as an adult, it becomes macrophytophagous. No difference was observed in the diet of males and females.     

Comparative Analysis of Feeding and Schooling Behaviour of the Cyprinidae Alburnus alburnus (L., 1758), Rutilus rutilus (L., 1758), and Scardinius erythrophthalmus (L., 1758) in a Backwater of the Danube near Vienna

Underwater observations of the three common fish species Alburnus alburnus (L., 1758), Rutilus rutilus (L., 1758) and Scardinius erythrophthalmus (L., 1758) in a small part of the Danube flood area near Vienna have been made from June to October 1985 and 1986. Particular emphasis has been laid on the partitioning of feeding resources and habitat. It has been established that these species prefer different water zones. Alburnus a. and Scardinius e. are “obligate” schoolers (BREDER, 1967) whereas Rutilus r. is a facultative schooler. While feeding Rutilus r. and Scardinius e. form “aggregations” (BREDER, 1959) and both adopt equivalent feeding techniques. Furthermore Alburnus a. is a quick moving species living near the surface and chasing mostly in schools. While inter- and intraspecific aggression is rarely observed for Rutilus r. and Scardinius e., Alburnus a. often show interspecific actions.     

Hybridization between two parapatric ranid frog species in the northern Sierra Nevada,California, USA

Contact zones between species provide a unique opportunity to test whether taxa can hybridize or not. Cross‐breeding or hybridization between closely related taxa can promote gene flow (introgression) between species, adaptation, or even speciation. Though hybridization events may be short‐lived and difficult to detect in the field, genetic data can provide information about the level of introgression between closely related taxa. Hybridization can promote introgression between species, which may be an important evolutionary mechanism for either homogenization (reversing initial divergence between species) or reproductive isolation (potentially leading to speciation). Here, we used thousands of genetic markers from nuclear DNA to detect hybridization between two parapatric frog species (Rana boylii and Rana sierrae) in the Sierra Nevada of California. Based on principal components analysis, admixture, and analysis of heterozygosity at species diagnostic SNPs, we detected two F1 hybrid individuals in the Feather River basin, as well as a weak signal of introgression and gene flow between the frog species compared with frog populations from two other adjacent watersheds. This study provides the first documentation of hybridization and introgression between these two species, which are of conservation concern.     

Life history traits of Scardinius acarnanicus (Economidis, 1991) (Pisces: Cyprinidae) in two Greek lakes (Lysimachia and Trichonis)

Age, growth, reproduction and mortality of Scardinius acarnanicus, an endemic cyprinid fish from central and western Greece, were investigated in two contrasting environments, the eutrophic Lake Lysimachia and the oligotrophic to mesotrophic Lake Trichonis. Maximum ages observed were 7+ for males and 10+ for females in Lake Lysimachia and 8+ for males and females in Lake Trichonis. Scardinius acarnanicus grew allometrically (slope of fork length–somatic weight regressions >3) and relatively rapidly until age 2 or 3 years, then slowed at a time coincident with maturation. Total instantaneous mortality rates of fish from Lake Trichonis were higher than in Lake Lysimachia. Scardinius acarnanicus is a multiple spawner; monthly values of the gonadosomatic index (GSI) indicated that spawning occurred mainly in April. Mean egg diameter in Lake Lysimachia was 1.54 ± 0.2 and 1.28 ± 0.16 mm in Lake Thrichonis. In Lake Lysimachia, the population sex ratio departed markedly from 1 : 1; females were more abundant at ages >3 and the overall male : female ratio was 1 : 1.47. In Lake Trichonis, females were more abundant at ages >6; the overall male : female ratio was 1 : 1.16, not significantly different from a 1 : 1 ratio.     

Length–weight relationships of three fish species from Trasimeno Lake,Italy

Length–weight relationships for Alburnus arborella, Esox cisalpinus and Scardinius hesperidicus from Trasimeno Lake are provided. A total of 4,205 specimens were collected for examination from 2008 to 2014 throughout the lake by means of electrofishing and nets. For all species the value of b ranged from 2.887 for Esox cisalpinus males to 3.115 for Scardinius hesperidicus. The study provides the first reference of length–weight relationships for the three species. A new maximum total length is also reported for E. cisalpinus.     

Hybrids of Abramis brama with Scardinius erythrophthalmus and Rutilus rutilus from Lake Volvi, Macedonia, Greece

Two specimens of the hybrid Abramis brama × Scardinius erythrophthalmus and a single specimen of the hybrid A. brama × Rutilus rutilus are reported and described from Lake Volvi, Macedonia, Greece. This is the first occurrence of either hybrid in Greek fresh waters.     

Coalescent histories on phylogenetic networks and detection of hybridization despite incomplete lineage sorting

Analyses of the increasingly available genomic data continue to reveal the extent of hybridization and its role in the evolutionary diversification of various groups of species. We show, through extensive coalescent-based simulations of multilocus data sets on phylogenetic networks, how divergence times before and after hybridization events can result in incomplete lineage sorting with gene tree incongruence signatures identical to those exhibited by hybridization. Evolutionary analysis of such data under the assumption of a species tree model can miss all hybridization events, whereas analysis under the assumption of a species network model would grossly overestimate hybridization events. These issues necessitate a paradigm shift in evolutionary analysis under these scenarios, from a model that assumes a priori a single source of gene tree incongruence to one that integrates multiple sources in a unifying framework. We propose a framework of coalescence within the branches of a phylogenetic network and show how this framework can be used to detect hybridization despite incomplete lineage sorting. We apply the model to simulated data and show that the signature of hybridization can be revealed as long as the interval between the divergence times of the species involved in hybridization is not too small. We reanalyze a data set of 106 loci from 7 in-group Saccharomyces species for which a species tree with no hybridization has been reported in the literature. Our analysis supports the hypothesis that hybridization occurred during the evolution of this group, explaining a large amount of the incongruence in the data. Our findings show that an integrative approach to gene tree incongruence and its reconciliation is needed. Our framework will help in systematically analyzing genomic data for the occurrence of hybridization and elucidating its evolutionary role.     

Discovery and characterization of a large number of diagnostic markers to discriminate Oncorhynchus mykiss and O. clarkii

Hybridization of cutthroat trout and steelhead/rainbow trout is ubiquitous where they are sympatric, either naturally or owing to introductions. The ability to detect hybridization and introgression between the two species would be greatly improved by the development of more diagnostic markers validated across the two species' many phylogenetic lineages. Here, we describe 81 novel genetic markers and associated assays for discriminating the genomes of these sister species. These diagnostic nucleotide polymorphisms were discovered by sequencing of rainbow trout expressed sequence tags (ESTs) in a diverse panel of both cutthroat trout and steelhead/rainbow trout. The resulting markers were validated in a large number of lineages of both species, including all extant subspecies of cutthroat trout and most of the lineages of rainbow trout that are found in natural sympatry with cutthroat trout or used in stocking practices. Most of these markers (79%) distinguish genomic regions for all lineages of the two species, but a small number do not reliably diagnose coastal, westslope and/or other subspecies of cutthroat trout. Surveys of natural populations and hatchery strains of trout and steelhead found rare occurrences of the alternative allele, which may be due to either previous introgression or shared polymorphism. The availability of a large number of genetic markers for distinguishing genomic regions originating in these sister species will allow the detection of both recent and more distant hybridization events, facilitate the study of the evolutionary dynamics of hybridization and provide a powerful set of tools for the conservation and management of both species.     

European mink-polecat hybridization events: hazards from natural process?

Determining the significance of hybridization events raises essential issues both in conservation and in evolutionary biology. Here, we report a genetic investigation of sympatric polecat and endangered European mink populations. Although the two species were morphologically very similar, the European mink and the polecat were easily discriminated from allozymes and microsatellites and showed a high level of private alleles (effective number of alleles: mink=1.45 and polecat=3.09). Nevertheless, the allozymic polymorphism remained lower in the European mink (4 loci, 10.5%) than in polecat (9 loci, 23.7%). Similarly, from microsatellite data, the polymorphism only reached 36% at 0.99 in the European mink; whereas in the polecat, the polymorphism reached 82% at 0.99. Natural hybridization events between two native species were detected. Because of the low fertility of hybrids, interbreeding could be regarded as producing "hybrid sink" that leads to a progressive assimilation of mink by polecat. Nonetheless, pure mink populations inhabited streams in western France, and hybridization events were only detected in areas where mink were rare and now presumed disappeared. Rather than revealing the poor efficiency of the specific recognition system, our results suggest that hybridization is associated with the scarcity of mating partners.     

Clinical application of array-based comparative genomic hybridization for the identification of prognostically important genetic alterations in chronic lymphocytic leukemia

Genomic aberrations have increasingly gained attention as prognostic markers in B-cell chronic lymphocytic leukemia (CLL). Fluorescence in situ hybridization (FISH) has improved the detection rate of genomic alterations in CLL from approximately 50% using conventional cytogenetics to greater than 80%. More recently, array comparative genomic hybridization (CGH) has gained popularity as a clinical tool that can be applied to detect genomic gains and losses of prognostic importance in CLL. Array CGH and FISH are particularly useful in CLL because genomic gains and losses are key events with both biologic and prognostic significance, while balanced translocations have limited prognostic value. Although FISH has a higher technical sensitivity, it requires separate, targeted hybridizations for the detection of alterations at genomic loci of interest. Array CGH, on the other hand, has the ability to provide a genome-wide survey of genomic aberrations with a single hybridization reaction. Array CGH is expanding the known genomic regions of importance in CLL and allows these regions to be evaluated in the context of a genome-wide perspective. Ongoing clinical trials are evaluating the use of genomic aberrations as tools for risk-stratifying patients for therapy, thus increasing the need for reliable and high-yield methods to detect these genomic changes. In this review, we consider the use of array CGH as a clinical tool for the identification of genomic alterations with prognostic significance in CLL, and suggest ways to integrate this test into the clinical molecular diagnostic laboratory work flow.     

The demonstration of natural hybridization between two swallowtail species Parnassius nomion and Parnassius bremeri (Lepidoptera, Papilionidae) using RAPD-PCR technique]

Genetic evidence for interspecific hybridization between Parnassius nomion and Parnassius bremeri in nature is presented. To demonstrate hybridization between these species, RAPD analysis was used. By testing 25 decamer primers, three and two diagnostic markers were revealed for P. nomion and P. bremeri, respectively. Out of 28 animals examined, 4 were shown to be interspecific hybrids. According to the distribution of diagnostic markers, the interspecific hybrids were intermediate with regard to the parental species. Ecological and biological characteristics of two swallowtail species that promote their hybridization in nature are discussed.     

Phylogeography and introgressive hybridization: chipmunks (genus Tamias) in the northern Rocky Mountains

Abstract. If phylogeographic studies are to be broadly used for assessing population-level processes relevant to speciation and systematics, the ability to identify and incorporate instances of hybridization into the analytical framework is essential. Here, we examine the evolutionary history of two chipmunk species, Tamias ruficaudus and Tamias amoenus , in the northern Rocky Mountains by integrating multivariate morphometrics of bacular (os penis) variation, phylogenetic estimation, and nested clade analysis with regional biogeography. Our results indicate multiple examples of mitochondrial DNA introgression layered within the evolutionary history of these nonsister species. Three of these events are most consistent with recent and/or ongoing asymmetric introgression of mitochondrial DNA across morphologically defined secondary contact zones. In addition, we find preliminary evidence where a fourth instance of nonconcordant characters may represent complete fixation of introgressed mitochondrial DNA via a more ancient hybridization event, although alternative explanations of convergence or incomplete sorting of ancestral polymorphisms cannot be dismissed with these data. The demonstration of hybridization among chipmunks with strongly differentiated bacular morphology contradicts long-standing assumptions that variation within this character is diagnostic of complete reproductive isolation within Tamias . Our results illustrate the utility of phylogeographic analyses for detecting instances of reticulate evolution and for incorporating this and other information in the inference of the evolutionary history of species.     

Sequence polymorphism-based identification and quantification of Vibrio nigripulchritudo at the species and subspecies level targeting an emerging pathogen for cultured shrimp in New Caledonia

In a previous study, we demonstrated the existence of an emerging cluster of Vibrio nigripulchritudo that proved to be associated with shrimp mortality events in New Caledonia. Using sequence polymorphisms evidenced in this previous MultiLocus Sequence Typing study, we developed two new quantitative PCR assays permitting the detection and quantification of V. nigripulchritudo at the genospecies level using SYBR Green I chemistry and at the emerging cluster level using Fluorescence Resonance Energy Transfer technology with hybridization probes. The use of this molecular diagnostic tool evidenced the colonization of the shrimp pond ecosystem by the pathogenic cluster at least at the onset of the disease. This new tool will allow better investigation of the dynamics of this bacterial pathogen in the shrimp farm ecosystem.     

Hybridization masks speciation in the evolutionary history of the Galápagos marine iguana

The effects of the direct interaction between hybridization and speciation—two major contrasting evolutionary processes—are poorly understood. We present here the evolutionary history of the Galápagos marine iguana (Amblyrhynchus cristatus) and reveal a case of incipient within-island speciation, which is paralleled by between-island hybridization. In-depth genome-wide analyses suggest that Amblyrhynchus diverged from its sister group, the Galápagos land iguanas, around 4.5 million years ago (Ma), but divergence among extant populations is exceedingly young (less than 50 000 years). Despite Amblyrhynchus appearing as a single long-branch species phylogenetically, we find strong population structure between islands, and one case of incipient speciation of sister lineages within the same island—ostensibly initiated by volcanic events. Hybridization between both lineages is exceedingly rare, yet frequent hybridization with migrants from nearby islands is evident. The contemporary snapshot provided by highly variable markers indicates that speciation events may have occurred throughout the evolutionary history of marine iguanas, though these events are not visible in the deeper phylogenetic trees. We hypothesize that the observed interplay of speciation and hybridization might be a mechanism by which local adaptations, generated by incipient speciation, can be absorbed into a common gene pool, thereby enhancing the evolutionary potential of the species as a whole.     

Nucleic acid hybridization: from research tool to routine diagnostic method

The nucleic acid hybridization reaction is extremely specific and thus a valuable tool for the identification of genes or organism of interest. The increasing use of nucleic acid hybridization in applied fields like diagnostic medicine has led to the development of more convenient hybridization assays than those originally used in basic research. In conventional nucleic acid hybridization methods immobilized nucleic acids are detected on a filter by a radiolabelled probe. Sandwich hybridization is a simple test format for the analysis of unpurified biological material, but has the disadvantage of a slow reaction rate. Solution hybridization methods are fast and easy to perform provided that a method to separate the formed hybrids from the reaction mixture is available. In non-isotopic detection the nucleic acid probe is modified with a chemical group, which is identified with a labelled detector molecule after hybridization. The low sensitivity of detection is the main problem in nucleic acid hybridization methods. Procedures to amplify the detectable signal or the amount of detectable nucleic acid sequences are potential solutions to this problem. The new hybridization methods have successfully been used for some applications, but still need to be combined into well performing tests to be applicable to any desired purpose.     

Frequent mitochondrial gene introgression among high elevation Tibetan megophryid frogs revealed by conflicting gene genealogies

Historical mitochondrial introgression causes differences between a species' mitochondrial gene genealogy and its nuclear gene genealogy, making tree-based species delineation ambiguous. Using sequence data from one mitochondrial gene (cytochrome b ) and three nuclear genes (introns), we examined the evolutionary history of four high elevation Tibetan megophryid frog species, Scutiger boulengeri , Scutiger glandulatus , Scutiger mammatus and Scutiger tuberculatus . The three nuclear genes shared a similar history but the mitochondrial gene tree suggested a drastically different evolutionary scenario. The conflicts between them were explained by multiple episodes of mitochondrial introgression events via historical interspecific hybridization. 'Foreign' mitochondrial genomes might have been fixed in populations and extended through a large portion of the species' distribution. Some hybridization events were probably as old as 10 Myr, while others were recent. An F₁ hybrid was also identified. Historical hybridization events among the four species appeared to be persistent and were not restricted to the period of Pleistocene glaciation, as in several other well-studied cases. Furthermore, hybridization involved several species and occurred in multiple directions, and there was no indication of one mitochondrial genome being superior to others. In addition, incomplete lineage sorting resulting from budding speciation may have also explained some discrepancies between the mitochondrial DNA and nuclear gene trees. Combining all evidences, the former ' Scutiger mammatus ' appeared to be two species, including a new species. With the availability of a wide range of highly variable nuclear gene markers, we recommend using a combination of mitochondrial gene and multiple nuclear genes to reveal a complete species history.