Reproductive dynamics shapes genomotype composition in an allopolyploid complex.

Hybrid complexes are composed of organisms with multiple combinations of parental genomes (genomotypes) that interconnect through nets of crosses. Although several such complexes are well established without speciation or extinction, mechanisms shaping their dynamics remain poorly understood. In this study, we quantified the reproductive success of the allopolyploid Iberian fish Squalius alburnoides in experimental free-access and directional crosses involving the most common genomotypes. Specifically, we analysed the paternity of the offspring produced when females had free access to male genomotypes and quantified variations in egg allocation, fertilization rate, and offspring survival among crosses involving each male genomotype. The composition of the offspring produced from free-access crosses varied significantly from that expected from random mating, suggesting that offspring production and viability are not independent of parental male genomotype. Moreover, directional crosses producing the genomotype most commonly found in wild populations appeared to be the most successful, with females laying more eggs, and fertilization rate and offspring survival being the highest. These results suggest that reproductive dynamics plays a relevant role in structuring the genomotype composition of populations and opens a path to future research on the ecology and evolutionary biology of allopolyploids and their multiplicity of possible evolutionary pathways.

Introgressive hybridization as a promoter of genome reshuffling in natural homoploid fish hybrids (Cyprinidae, Leuciscinae).

Understanding the mechanisms underlying diversification and speciation by introgressive hybridization is currently one of the major challenges in evolutionary biology. Here, the analysis of hybridization between two pairs of Iberian Leuciscinae provided new data on independent hybrid zones involving Achondrostoma oligolepis (AOL) and Pseudochondrostoma duriense (PDU), and confirmed the occurrence of hybrids between AOL and Pseudochondrostoma polylepis (PPO). A multilevel survey combining morphological, genetic and cytogenomic markers on a vast population screening successfully sorted the selected fishes as admixed. Results were similar in both AOL × PDU and AOL × PPO systems. Overall, hybrid morphotypes, cytogenomic data and genetic profiling indicated preferential backcrossing and suggested AOL as a major genomic contributor. Moreover, results implied AOL as more permissive to introgression than PDU or PPO. Although PDU- and PPO-like individuals appeared more resilient to genome modifications, AOL appeared to be more involved and affected by the ongoing hybridization events, as chromosomal translocations were only found in AOL-like individuals. All hybrids analysed evidenced extensive ribosomal DNA (rDNA) polymorphism that was not found in parental species, but usually seen falling within the range of possible parental combinations. Yet, transgressive phenotypes that cannot be explained by normal recombination, including more rDNA clusters than expected or the occurrence of syntenic rDNAs, were also detected. Present results proved rapid genomic evolution providing the genetic novelty for species to persist. In addition, although the ultimate consequences of such apparently extensive and recurrent events remain unknown, modern genome-wide methodologies are of great promise towards answering questions concerning the causes, dynamics and impacts of hybridization.

Chromosomes of Iberian Leuciscinae (Cyprinidae) revisited: Evidence of genome restructuring in homoploid hybrids using dual-color FISH and CGH.

Iberian Leuciscinae have been used in many studies as models to explore topics such as hybridization, allopolyploidy, modes of reproduction, and evolution. This article focuses on the contribution of cytogenomics to foster research in this group of cyprinid fish. Conventional and molecular banding results were reviewed, facilitating comparative analysis between nase and chub taxa inhabiting Portuguese freshwaters. Hybridization is known to occur within both Chondrostoma s.l. and Squalius genera although polyploidy has only been reported in the latter; the reasons behind such differential genome flexibility remain unidentified. FISH tools allowed recognizing additional chromosome markers, confirming NOR polymorphism and distinguishing species and their hybrids. Recombination and genome instability were detected in homoploid and polyploid hybrid genomes supporting active NOR transposition. However, the multiplication of rDNAs in these species does not seem to be associated with Rex3 retroelement, though hybrids were not surveyed. CGH and GISH allowed reaffirming the hybrid origin of S. alburnoides and confirming that the conservative karyotype patterns within Iberian leuciscines are restricted to the macrostructure. Current data also support the usefulness of mapping repetitive DNAs, especially for nonmodel compact genomes with less variable karyotypes and sequence data resources unavailable, like in many cyprinid lineages.

Natural pathways towards polyploidy in animals: the Squalius alburnoides fish complex as a model system to study genome size and genome reorganization in polyploids.

When comparing the known picture of polyploidy in animals and in plants, it is possible to recognize some similarities, namely: (i) multiple and recurrent origins in several well-established taxonomic groups; (ii) a strong and regular association with hybridization events; (iii) the production of genotypic diversity; (iv) a rapid genomic reshuffling; (v) a very active role of transposable elements in allopolyploids; (vi) a comparatively privileged occurrence in harsher environments when compared with their diploid relatives, and (vii) gene silencing and divergence of duplicated genes without disruption of duplicated loci. Research on polyploidy was highly biased towards plants during the last century because polyploidy in animals was for long time considered rare, occasional and irrelevant from an evolutionary perspective. However, as empirically observed in plants, genome rediploidization starts in polyploid organisms immediately after the polyploid shock. Given the speed and dynamicity of this process, evidence of genome multiplication is completely erased over time, and hence, only the most recent events are likely to be acknowledged. Although varying in expression between and within taxonomic groups, polyploidy and hybridization are ubiquitous in animals and may be recurrent, fostering evolution. Since evolutionary allopolyploid genomes behave as biologically diploid, zoologists have to challenge the old paradigm of an irrelevant evolutionary role in animals using current genomic and cytogenomic tools. These methods are most likely to reveal the role of polyploid mechanisms in producing evolutionary novelties. Nonsexual complexes are the perfect models to bridge the gap between empirical and theoretical research, while the evolutionary process is in action. Such animal complexes represent a transient stage that, in general, moves towards a polyploid stage, where bisexuality might be recovered, ultimately giving rise to a new gonochoric species. These pathways are herein illustrated by the Iberian allopolyploid Squalius alburnoides. Some general aspects on this fish's complex are updated and reviewed, namely the reproductive modes of the distinct genomotypes, since variable ploidies and genomic combinations occur in natural populations. Most recent data on the mechanisms of gene expression regulation and the importance of the genomic context in driving allelic expression are also included. It was first demonstrated that a regulatory mechanism involving dosage compensation by gene-copy silencing exists in allotriploid females and that allelic expression patterns differed either between genomically equivalent individuals or within the same individual (between tissues and genes). Thus, instead of a whole haplome inactivation, a biased silencing towards repression of a specific allele was observed as well as a reduction of the transcript levels to the diploid state. See also sister article focusing on plants by Tayalé and Parisod in this themed issue.

Synaptonemal complexes in the hybridogenetic Squalius alburnoides fish complex: new insights on the gametogenesis of allopolyploids.

In the Squalius alburnoides fish complex, allotriploid females (3n = 75) reproduce mostly by meiotic hybridogenesis, producing haploid gametes by means of the elimination of the heterospecific chromosome set and recombination between the 2 homospecific genomes. A synaptonemal complexes (SCs) analysis was performed in specimens from a confined southern population (Quarteira, Portugal) to understand chromosome dynamics during gametogenesis. The comparative study between hybrid females with QAA genome composition and the parental bisexual species Squalius aradensis (2n = 50, QQ genome) evidenced: (i) that allotriploid meiocytes comprise the complete chromosome set (75 chromosomes) in prophase I, proving the heterospecific genome (Q) is only excluded after pachytene stage, and (ii) a 2-phase synaptic process where initially, exclusively homologous SCs form and the unmatched univalents remain in a bouquet conformation, followed by the establishment of extensive non-homologous SCs with multivalent associations among the later. These findings disagree with most literature concerning the meiotic process in allotriploid vertebrates, since the most accountable mechanisms (premeiotic exclusion of the unmatched chromosome set and whole genome endoduplication) were not observed.

Life-history variability of non-native centrarchids in regulated river systems of the lower River Guadiana drainage (south-west Iberian Peninsula).

Life-history variability of two non-native centrarchids, pumpkinseed Lepomis gibbosus and largemouth bass Micropterus salmoides, was evaluated in three stream stretches of the lower River Guadiana drainage (south-west Iberian Peninsula) with different degrees of regulated flows. Abundance, condition and population structure differed among populations for both species, but invasion success was lower in the least regulated river. Lepomis gibbosus were abundant and had multiple age classes in the three river sites, whereas M. salmoides were less abundant and mainly represented by young-of-the-year fish. Juvenile growth in L. gibbosus was similar in all three populations, though longevity was slightly greater in the population from the River Guadiana mainstream. Lepomis gibbosus exhibited a long reproductive season, but the duration of season, size at maturity and reproductive effort varied among populations. The life-history differences found demonstrate the importance of species adaptation to local conditions which might favour their invasion success. Lepomis gibbosus were more adaptable and resilient to local conditions, whereas M. salmoides seemed dependent on reservoirs and large rivers for maintenance of riverine populations.

Reconfirming the hybrid origin and generic status of the Iberian cyprinid complex Squalius alburnoides.

The recent allocation of the cyprinid complex Squalius alburnoides to the genus Iberocypris in the Handbook of European Freshwater Fishes is refuted by confirming evidence of a close relationship with the genus Squalius. Squalius alburnoides is here defined as a complex based on the existence of a hybrid form with distinct genome combinations and ploidies and of a reconstituted nuclear non-hybrid male form also with hybrid origin.

Evidence for hermaphroditism in the Squalius alburnoides allopolyploid fish complex.

Fish show an amazing variety of mechanisms of sex determination and modes of reproduction. Of these, simultaneous hermaphroditism has rarely been described. Here, we report a novel case of this phenomenon in adults of the Squalius alburnoides allopolyploid cyprinid complex. We found evidence for the simultaneous presence of mature male and female gonads on the basis of gonad gross morphology and histological analyses. Different stages of male and female germ cell maturation were identified, including motile spermatocytes. We hypothesize on the genetic and/or environmental causes of this phenomenon.

Scaleprinting: individual identification based on scale patterns.

A non-intrusive method for individual identification of Iberian cyprinid complex Squalius alburnoides is presented, with possible application to other fish complexes and species. The proposed methodology is based on scale patterns that vary greatly between individuals.

Reading the history of a hybrid fish complex from its molecular record.

Squalius alburnoides is a widely distributed intergeneric hybrid complex with fish of both sexes, varying ploidy levels and proportions of the parental genomes. Its dispersal routes were here delineated and framed by the reconstruction of the phylogeny and phylogeography of other Squalius with which it hybridizes, based on the available data on the paleohydrographical history of the Iberian Peninsula. Results based on sequences of cytochrome b and beta-actin genes showed that: proto-Squalius pyrenaicus originated at least five species as it dispersed throughout the Iberian Peninsula in the Mio-Pliocene; the S. alburnoides complex likely had a single origin in the bulk of Iberia, in the Upper Tagus/Guadiana area, when hydrographical rearrangements allowed the contact between its ancestors (around 700,000 years ago); interspecific crosses allowed the introgression of mitochondrial and nuclear genes of S. alburnoides in allopatric species/populations of other Squalius and vice-versa; and reconstituted S. alburnoides non-hybrid males may contribute to the replacement of the typical mtDNA of the complex (in the populations where they occur, crosses with females of other Squalius seem to have been especially frequent). A number of dispersal events and colonization routes are proposed.

Lack of correspondence between CMA3-, Ag-positive signals and 28S rDNA loci in two Iberian minnows (Teleostei, Cyprinidae) evidenced by sequential banding.

Despite the growing outcome of results that put doubt upon the reliability of silver (Ag) staining and chromomycin A3 (CMA3) fluorescent banding in the detection of major ribosomal gene sites (NORs), these methods have been widely used, especially in fishes. In order to clarify the previous patterns obtained with those techniques, we performed fluorescence in situ hybridisation (FISH) with 28S rDNA probe followed by sequential CMA3 and Ag staining in diploid non-hybrid males of the Squalius alburnoides complex and in Squalius pyrenaicus. The results from all the studied specimens revealed a lack of correlation between classical and molecular techniques. Not just some other regions besides NORs were stained with CMA3 and Ag, but also the majority of the 28S rDNA sites were not detected. Care should then be taken in considering CMA3- and Ag-stained sites as NORs since their accuracy for that purpose may not always correspond to the expectations.

Cytogenetic variability in genus odontocheila (Coleoptera, Cicindelidae): karyotypes, C-banding, NORs and localisation of ribosomal genes of O. confusa and O. nodicornis.

Two species of Odontocheila, O. confusa and O. nodicornis, from the Neotropical Region were studied regarding their karyotypes, localisation and activity of ribosomal genes and C-banding. The species, although belonging to the same genus, have quite distinct karyotypes. O. confusa has 10 pairs of autosomes and a single sex chromosome mechanism of the XY/XX type, thus a diploid value of 2n = 22 in males and females. One aneuploid male with a diploid number of 2n = 20 and one male with three B chromosomes were found in a total of eight males studied. O. nodicornis has 17 autosomal pairs and also a single chromosome system but of the X0/XX type, thus a diploid value of 2n = 35 in males and 2n = 36 in females. Fluorescence in situ hybridisation (FISH) revealed the presence of rDNA clusters in two autosomes in both species in mitotic and meiotic figures. Silver staining of male interphase nuclei confirmed the FISH results and showed that all rDNA genes were active. C-banding analysis revealed the presence of constitutive heterochromatin in the centromeres of all chromosomes in the two species plus two pairs in O. nodicornis with terminal positive C-bands. These results are discussed from the cytogenetic and evolutionary point of view.

Mitochondrial DNA variation in the highly endangered cyprinid fish Anaecypris hispanica: importance for conservation.

Anaecypris hispanica is a cyprinid fish which is endemic to the Guadiana River basin in the Iberian Peninsula, and whose abundance and geographical range have contracted considerably during the last 20 years. We investigated mitochondrial DNA cytochrome b and control region variation among specimens representative of nine tributaries, using direct sequencing and diagnostic restriction fragment length polymorphism. The samples from the Caia, Degebe, Ardila, and Odeleite rivers exhibited haplotypes that differed by a large number of site differences, which may be indicative of population bottlenecks that have caused stochastic extinction of haplotypes. In contrast, the populations from the Xévora, Chança, Carreiras, Vascão and Foupana rivers exhibited low levels of nucleotide diversity, which together with high haplotype diversity may also be indicative of genetic bottleneck events, with subsequent population expansion. Phylogenetic analyses, a minimum spanning network, and an analysis of molecular variance revealed geographical structuring, suggesting limited or no gene flow between populations. The populations from extreme southern rivers (Foupana and Odeleite) are monophyletic entities, suggesting that they have been isolated, probably as a consequence of brackish water upstream of their confluence with the Guadiana. The results suggest that the Foupana and the Odeleite populations, and the remaining northern populations altogether should be managed as three distinct Evolutionary Significant Units (ESUs). Within the northern ESU, four Management Units (MUs) should be considered.

Response of antioxidant enzymes in freshwater fish populations (Leuciscus alburnoides complex) to inorganic pollutants exposure.

Evidence is accumulating indicating the importance of antioxidant enzyme activity measurements in eco-toxicological studies, as they may constitute markers for exposure to a large variety of pollutants. Variation of antioxidant enzymes, superoxide dismutase (SOD) and glutathione S-transferases (GST) and the effect of heavy metals and selenium exposure on these enzymes were investigated in the livers of Iberian endemic minnows (Leuciscus alburnoides complex) captured in a copper (Cu) mining area. Higher hepatic levels of copper and selenium were always observed in fish captured at the polluted site relative to the reference area population, reflecting the environmental monitoring results. A seasonal fluctuation in zinc and selenium levels for both populations was also observed which could be related to gonad maturation. The activity of SOD did not show significant regional alterations, but a seasonal variation occurred presumably associated with the Leuciscus life cycle. The GST activity was higher in the fish population from the polluted area (except in spring) and GST variability was associated with selenium and copper levels when both regions were compared. The increased GST activity was probably a metabolic adaptation to the continuous exposure to higher levels of those elements.

Evolution in action through hybridisation and polyploidy in an Iberian freshwater fish: a genetic review.

The Iberian minnow Leuciscus alburnoides represents a complex of diploid and polyploid forms with altered modes of reproduction. In the present paper, we review the recent data on the origin, reproductive modes, and inter-relationships of the various forms of the complex, in order to predict its evolutionary potential. The complex follows the hybrid-origin model suggested for most other asexual vertebrates. Diploid and triploid females from the southern river basins exhibit reproductive modes that cannot be conveniently placed into the categories generally recognised for these vertebrate complexes, which imply continuous shifting between forms, where genomes derived from both parental ancestors are cyclically lost, gained or replaced. Replacement of nuclear genomes allow the introduction of novel genetic material, that may compensate for the disadvantages of asexual reproduction. Contrasting with most other vertebrate complexes, L. alburnoides males are fertile and play an important role in the dynamics of the complex. Moreover, diploid hybrid males may have initiated a tetraploidization process, when a diploid clonal sperm fertilised a diploid egg. This direct route to tetraploidy by originating fish with the right constitution for normal meiosis (symmetric), may eventually lead to a new sexually reproducing polyploid species. This case-study reinforces the significance of hybridisation and polyploidy in evolution and diversification of vertebrates.

Production of fertile unreduced sperm by hybrid males of the Rutilus alburnoides complex (Teleostei, cyprinidae). An alternative route to genome tetraploidization in unisexuals.

The hybrid minnow Rutilus alburnoides comprises diploid and polyploid females and males. Previous studies revealed that diploid and triploid females exhibit altered oogenesis that does not involve random segregation and recombination of the genomes of the two ancestors, constituting unisexual lineages. In the present study, we investigated the reproductive mode of hybrid males from the Tejo basin, using experimental crosses and flow cytometric analysis of blood and sperm. The results suggest that diploid hybrids produced fertile unreduced sperm, transmitting their hybrid genome intact to offspring. Triploid hybrids also produced unreduced sperm, but it was not possible to obtain data concerning their fertility. Finally, tetraploid hybrids produced fertile diploid sperm, which exhibited Mendelian segregation. Tetraploid R. alburnoides may reestablish biparental reproduction, as individuals of both sexes with the appropriate constitution for normal meiosis (two haploid genomes from each parental species) are likely to occur in natural populations. Tetraploids probably have arisen from syngamy of diploid eggs and diploid sperm produced by diploid hybrid males. Diploid hybrid males may therefore play a significant role in the dynamics of the complex, starting the evolutionary process that may ultimately lead to a new sexually reproducing species.

NOR polymorphism in the Iberian species Chondrostoma lusitanicum (Pisces: Cyprinidae)--re-examination by FISH.

Chromosomal polymorphism regarding the number of chromosomal NOR sites in the cyprinid fish Chondrostoma lusitanicum reported previously (Rodrigues & Collares-Pereira, 1996) was re-examined using fluorescence in situ hybridization (FISH) with a ribosomal DNA (rDNA) probe. All positive CMA3-bands contained ribosomal DNA documented by either two or four FISH positive signals in the respective karyotypes. This polymorphism suggests the occurrence of structural rearrangements of translocation type in rDNA region from one ancestral NOR-bearing chromosome pair ubiquitous among leuciscine cyprinid fishes to another pair. The absence of individuals heterozygous for this polymorphism is discussed.

MATERNAL ANCESTRY OF THE RUTILUS ALBURNOIDES COMPLEX (TELEOSTEI, CYPRINIDAE) AS DETERMINED BY ANALYSIS OF CYTOCHROME b SEQUENCES.

Cytochrome b (cyt b) sequences from specimens of the Rutilus alburnoides unisexual complex and five bisexual species were compared to examine hypotheses regarding the origin and maternal ancestry of this complex. Phylogenetic analysis revealed a monophyletic relationship among unisexuals and Leuciscus pyrenaicus, clearly identifying this species as the maternal ancestor. Considerable mtDNA diversity exists among R. alburnoides populations, with many localities exhibiting unique haplotypes. The topology recovered from analysis of cyt b variation among populations suggested that R. alburnoides is polyphyletically derived from their sympatric L. pyrenaicus populations, indicating that unisexual lineages have been generated through multiple hybridization events. Although much less abundant, R. alburnoides is present outside the range of L. pyrenaicus, suggesting that it may have dispersed from the Tejo drainage into the northern basins. In this region, Leuciscus carolitertii is most likely the sexual host for the unisexual complex.

Karyological analysis of Cylindera trisignata (Latreille & Dejean, 1822) from Portugal (Coleoptera, Cicindelidae).

Cellular suspensions of germinal tissues of Cylindera trisignata provided the definition of its karyotype: 2n = 23 and 2n = 26 for the males and females respectively. This Palearctic species has a sex chromosome system of the X1X2X3X4Y/X1X1X2X2X3X3X4X4 type, only found until now in Cicindela maroccana pseudomaroccana. The heterosomes are not well-differentiated from the general morphological standpoint. To explain the origin of the 4X condition, a mechanism of dissociation of the X chromosomes rather than an incorporation of autosomal segments is proposed. However, based on the occurrence of distinct ploidy levels, both in male and female cells, with a relatively high incidence for the tetraploid condition with regular autosomal bivalents, the hypothesis of a possible evolutionary role of polyploidy is suggested.