Inferences on the evolutionary history of the Drosophila americana polymorphic X/4 fusion from patterns of polymorphism at the X-linked paralytic and elav genes

Chromosomal Rearrangements and Satellite DNAs: Extensive Chromosome Reshuffling and the Evolution of Neo-Sex Chromosomes in the Genus Pyrrhulina (Teleostei; Characiformes)

Chromosomal rearrangements play a significant role in the evolution of fish genomes, being important forces in the rise of multiple sex chromosomes and in speciation events. Repetitive DNAs constitute a major component of the genome and are frequently found in heterochromatic regions, where satellite DNA sequences (satDNAs) usually represent their main components. In this work, we investigated the association of satDNAs with chromosome-shuffling events, as well as their potential relevance in both sex and karyotype evolution, using the well-known Pyrrhulina fish model. Pyrrhulina species have a conserved karyotype dominated by acrocentric chromosomes present in all examined species up to date. However, two species, namely P. marilynae and P. semifasciata, stand out for exhibiting unique traits that distinguish them from others in this group. The first shows a reduced diploid number (with 2n = 32), while the latter has a well-differentiated multiple X1X2Y sex chromosome system. In addition to isolating and characterizing the full collection of satDNAs (satellitomes) of both species, we also in situ mapped these sequences in the chromosomes of both species. Moreover, the satDNAs that displayed signals on the sex chromosomes of P. semifasciata were also mapped in some phylogenetically related species to estimate their potential accumulation on proto-sex chromosomes. Thus, a large collection of satDNAs for both species, with several classes being shared between them, was characterized for the first time. In addition, the possible involvement of these satellites in the karyotype evolution of P. marilynae and P. semifasciata, especially sex-chromosome formation and karyotype reduction in P. marilynae, could be shown.

Integrating Cytogenetics and Population Genomics: Allopatry and Neo-Sex Chromosomes May Have Shaped the Genetic Divergence in the Erythrinus erythrinus Species Complex (Teleostei, Characiformes)

Simple Summary

Fish present astonishing diversity, comprising more species than the combined total of all other vertebrates. Here, we integrated cytogenetic and genomic data to investigate how the evolution of multiple sex chromosomes together with allopatry is linked to genetic diversity and speciation in the fish species Erythrinus erythrinus. We hypothesized that the presence of multiple sex chromosomes has contributed to the genetic differentiation of populations, which could have potentially accelerated speciation.

Abstract

Diversity found in Neotropical freshwater fish is remarkable. It can even hinder a proper delimitation of many species, with the wolf fish Erythrinus erythrinus (Teleostei, Characiformes) being a notable example. This nominal species shows remarkable intra-specific variation, with extensive karyotype diversity found among populations in terms of different diploid chromosome numbers (2n), karyotype compositions and sex chromosome systems. Here, we analyzed three distinct populations (one of them cytogenetically investigated for the first time) that differed in terms of their chromosomal features (termed karyomorphs) and by the presence or absence of heteromorphic sex chromosomes. We combined cytogenetics with genomic approaches to investigate how the evolution of multiple sex chromosomes together with allopatry is linked to genetic diversity and speciation. The results indicated the presence of high genetic differentiation among populations both from cytogenetic and genomic aspects, with long-distance allopatry potentially being the main agent of genetic divergence. One population showed a neo-X₁X₂Y sexual chromosome system and we hypothesize that this system is associated with enhanced inter-population genetic differentiation which could have potentially accelerated speciation compared to the effect of allopatry alone.

Shared evolutionary trajectories of three independent neo-sex chromosomes in Drosophila

Dosage compensation (DC) on the X Chromosome counteracts the deleterious effects of gene loss on the Y Chromosome. However, DC is not efficient if the X Chromosome also degenerates. This indeed occurs in Drosophila miranda, in which both the neo-Y and the neo-X are under accelerated pseudogenization. To examine the generality of this pattern, we investigated the evolution of two additional neo-sex chromosomes that emerged independently in D. albomicans and D. americana and reanalyzed neo-sex chromosome evolution in D. miranda. Comparative genomic and transcriptomic analyses revealed that the pseudogenization rate on the neo-X is also accelerated in D. albomicans and D. americana although to a lesser extent than in D. miranda. In males, neo-X-linked genes whose neo-Y-linked homologs are pseudogenized tended to be up-regulated more than those whose neo-Y-linked homologs remain functional. Moreover, genes under strong functional constraint and genes highly expressed in the testis tended to remain functional on the neo-X and neo-Y, respectively. Focusing on the D. miranda and D. albomicans neo-sex chromosomes that emerged independently from the same autosome, we further found that the same genes tend to become pseudogenized in parallel on the neo-Y. These genes include Idgf6 and JhI-26, which may be unnecessary or even harmful in males. Our results indicate that neo-sex chromosomes in Drosophila share a common evolutionary trajectory after their emergence, which may prevent sex chromosomes from being an evolutionary dead end.

Genomic organization of repetitive DNAs and its implications for male karyotype and the neo-Y chromosome differentiation in Erythrinus erythrinus (Characiformes, Erythrinidae)

Studies have demonstrated the effective participation of repetitive DNA sequences in the origin and differentiation of the sex chromosomes in some biological groups. In this study several microsatellites and retrotranposable sequences were cytogenetically mapped in the Erythrinus erythrinus (Bloch & Schneider, 1801) male genome (karyomorph C), focusing on the distribution of these sequences in the sex chromosomes and in the evolutionary processes related to their differentiation. Males of E. erythrinus - karyomorph C - present 2n = 51 chromosomes (7m + 2sm + 6st + 36a), including the X1X2Y sex chromosomes. The C-positive heterochromatin has a predominant localization on the centromeric region of most chromosome pairs, but also in some telomeric regions. The 5S rDNA sites are located in the centromeric region of 27 chromosomes, including 26 acrocentric ones and the metacentric Y chromosome. The retrotransposons Rex 1 and Rex 6 show a dispersed pattern in the karyotype, contrasting with the Rex 3 distribution which is clearly co-localized with all the 27 5S rDNA sites. The microsatellite sequences show a differential distribution, some of them restricted to telomeric and/or interstitial regions and others with a scattered distribution on the chromosomes. However, no preferential accumulation of these elements were observed in the neo-Y chromosome, in contrast to what usually occurs in simple sex chromosome systems.

Drosophila americana as a model species for comparative studies on the molecular basis of phenotypic variation

Understanding the molecular basis of within and between species phenotypic variation is one of the main goals of Biology. In Drosophila, most of the work regarding this issue has been performed in D. melanogaster, but other distantly related species must also be studied to verify the generality of the findings obtained for this species. Here, we make the case for D. americana, a species of the virilis group of Drosophila that has been diverging from the model species, D. melanogaster, for approximately 40 Myr. To determine the suitability of this species for such studies, polymorphism and recombination estimates are presented for D. americana based on the largest nucleotide sequence polymorphism data set so far analyzed (more than 100 data sets) for this species. The polymorphism estimates are also compared with those obtained from the comparison of the genome assembly of two D. americana strains (H5 and W11) here reported. As an example of the general utility of these resources, we perform a preliminary study on the molecular basis of lifespan differences in D. americana. First, we show that there are lifespan differences between D. americana populations from different regions of the distribution range. Then, we perform five F2 association experiments using markers for 21 candidate genes previously identified in D. melanogaster. Significant associations are found between polymorphism at two genes (hep and Lim3) and lifespan. For the F2 association study involving the two sequenced strains (H5 and W11), we identify amino acid differences at Lim3 and Hep that could be responsible for the observed changes in lifespan. For both genes, no large gene expression differences were observed between the two strains.

Chromosomal mapping of microsatellite repeats in the rock bream fish Oplegnathus fasciatus, with emphasis of their distribution in the neo-Y chromosome

Despite the theoretical and experimental progress, our understanding on sex chromosome differentiation is still diagrammatic. The accumulation of repetitive DNA sequences is believed to occur in early stages of such differentiation. As fish species present a wide range of sex chromosome systems they are excellent models to examine the differentiation of these chromosomes. In the present study, the chromosomal distribution of 9 mono-, di- and tri-nucleotide microsatellites were analyzed using fluorescence in situ hybrization (FISH) in rock bream fish (Oplegnathus fasciatus), which is characterized by an X1X2Y sex chromosome system. Generally, the males and females exhibited the same autosomal pattern of distribution for a specific microsatellite probe. The male specific Y chromosome displays a specific amount of distinct microsatellites repeats along both arms. However, the accumulation of these repetitive sequences was not accompanied by a huge heterochromatinization process. The present data provide new insights into the chromosomal constitution of the multiple sex chromosomes and allow further investigations on the true role of the microsatellite repeats in the differentiation process of this sex system.

Progressive recombination suppression and differentiation in recently evolved neo-sex chromosomes

Recombination suppression leads to the structural and functional differentiation of sex chromosomes and is thus a crucial step in the process of sex chromosome evolution. Despite extensive theoretical work, the exact processes and mechanisms of recombination suppression and differentiation are not well understood. In threespine sticklebacks (Gasterosteus aculeatus), a different sex chromosome system has recently evolved by a fusion between the Y chromosome and an autosome in the Japan Sea lineage, which diverged from the ancestor of other lineages approximately 2 Ma. We investigated the evolutionary dynamics and differentiation processes of sex chromosomes based on comparative analyses of these divergent lineages using 63 microsatellite loci. Both chromosome-wide differentiation patterns and phylogenetic inferences with X and Y alleles indicated that the ancestral sex chromosomes were extensively differentiated before the divergence of these lineages. In contrast, genetic differentiation appeared to have proceeded only in a small region of the neo-sex chromosomes. The recombination maps constructed for the Japan Sea lineage indicated that recombination has been suppressed or reduced over a large region spanning the ancestral and neo-sex chromosomes. Chromosomal regions exhibiting genetic differentiation and suppressed or reduced recombination were detected continuously and sequentially in the neo-sex chromosomes, suggesting that differentiation has gradually spread from the fusion point following the extension of recombination suppression. Our study illustrates an ongoing process of sex chromosome differentiation, providing empirical support for the theoretical model postulating that recombination suppression and differentiation proceed in a gradual manner in the very early stage of sex chromosome evolution.

The contrasting role of heterochromatin in the differentiation of sex chromosomes: an overview from Neotropical fishes

During the evolutionary process of the sex chromosomes, a general principle that arises is that cessation or a partial restriction of recombination between the sex chromosome pair is necessary. Data from phylogenetically distinct organisms reveal that this phenomenon is frequently associated with the accumulation of heterochromatin in the sex chromosomes. Fish species emerge as excellent models to study this phenomenon because they have much younger sex chromosomes compared to higher vertebrates and many other organisms making it possible to follow their steps of differentiation. In several Neotropical fish species, the heterochromatinization, accompanied by amplification of tandem repeats, represents an important step in the morphological differentiation of simple sex chromosome systems, especially in the ZZ/ZW sex systems. In contrast, multiple sex chromosome systems have no additional increase of heterochromatin in the chromosomes. Thus, the initial stage of differentiation of the multiple sex chromosome systems seems to be associated with proper chromosomal rearrangements, whereas the simple sex chromosome systems have an accumulation of heterochromatin. In this review, attention has been drawn to this contrasting role of heterochromatin in the differentiation of simple and multiple sex chromosomes of Neotropical fishes, highlighting their surprising evolutionary dynamism.

Cross-species chromosome painting tracks the independent origin of multiple sex chromosomes in two cofamiliar Erythrinidae fishes

Background

The Erythrinidae fish family is characterized by a large variation with respect to diploid chromosome numbers and sex-determining systems among its species, including two multiple X₁X₂Y sex systems in Hoplias malabaricus and Erythrinus erythrinus. At first, the occurrence of a same sex chromosome system within a family suggests that the sex chromosomes are correlated and originated from ancestral XY chromosomes that were either homomorphic or at an early stage of differentiation. To identify the origin and evolution of these X₁X₂Y sex chromosomes, we performed reciprocal cross-species FISH experiments with two sex-chromosome-specific probes designed from microdissected X₁ and Y chromosomes of H. malabaricus and E. erythrinus, respectively.

Results

Our results yield valuable information regarding the origin and evolution of these sex chromosome systems. Our data indicate that these sex chromosomes evolved independently in these two closed related Erythrinidae species. Different autosomes were first converted into a poorly differentiated XY sex pair in each species, and additional chromosomal rearrangements produced both X₁X₂Y sex systems that are currently present.

Conclusions

Our data provide new insights into the origin and evolution of sex chromosomes, which increases our knowledge about fish sex chromosome evolution.

Resolving the phylogenetic relationships and evolutionary history of the Drosophila virilis group using multilocus data

The Drosophila virilis group is one of the major lineages of Drosophila previously recognised and it has been used as a model for different types of studies. It comprises 13 species whose phylogenetic relationships are not well resolved. In the present study, six nuclear genes (Adh, fused, Gpdh, NonA, CG9631 and CG7219) and the mitochondrial ribosomal RNA genes (12S-16S) have been used to estimate the evolutionary tree of the group using different methods of phylogenetic reconstruction. Different competing evolutionary hypotheses have also been compared using the Approximately Unbiased test to further evaluate the robustness of the inferred trees. Results are, in general, consistent with previous studies in recovering the four major lineages of the group (D. virilis phylad, Drosophila montana subphylad, Drosophila kanekoi subphylad and Drosophila littoralis subphylad), although D. kanekoi, D. littoralis and Drosophila ezoana are here inferred to be more closely related to the D. virilis phylad than to the D. montana subphylad. The age of the crown group, estimated with a Bayesian method that assumes a relaxed molecular clock, is placed in the late Miocene (∼ 10 Mya). The oldest lineages also appeared during this period (∼ 7.5 to ∼ 8.9 Mya), while the ages of the basal nodes of the montana subphylad and the virilis phylad are located in the early Pliocene (∼ 4.9 and ∼ 4.1 Mya). Major cladogenesis events correlate to geological and palaeoclimatic occurrences that most likely affected the freshwater and deciduous forests where these species are found. The inferred biogeographical history of the group, based on the statistical dispersal-vicariance analysis, indicates that the last common ancestor of the group had a Holarctic distribution from which the North American and the Eurasian lineages evolved as a result of a vicariant event.

Local adaptation for body color in Drosophila americana

Pigmentation is one of the most variable traits within and between Drosophila species. Much of this diversity appears to be adaptive, with environmental factors often invoked as selective forces. Here, we describe the geographic structure of pigmentation in Drosophila americana and evaluate the hypothesis that it is a locally adapted trait. Body pigmentation was quantified using digital images and spectrometry in up to 10 flies from each of 93 isofemale lines collected from 17 locations across the United States and found to correlate most strongly with longitude. Sequence variation at putatively neutral loci showed no evidence of population structure and was inconsistent with an isolation-by-distance model, suggesting that the pigmentation cline exists despite extensive gene flow throughout the species range, and is most likely the product of natural selection. In all other Drosophila species examined to date, dark pigmentation is associated with arid habitats; however, in D. americana, the darkest flies were collected from the most humid regions. To investigate this relationship further, we examined desiccation resistance attributable to an allele that darkens pigmentation in D. americana. We found no significant effect of pigmentation on desiccation resistance in this experiment, suggesting that pigmentation and desiccation resistance are not unequivocally linked in all Drosophila species.

Intraspecific polymorphism to interspecific divergence: genetics of pigmentation in Drosophila

Genetic changes contributing to phenotypic differences within or between species have been identified for a handful of traits, but the relationship between alleles underlying intraspecific polymorphism and interspecific divergence is largely unknown. We found that noncoding changes in the tan gene, as well as changes linked to the ebony gene, contribute to pigmentation divergence between closely related Drosophila species. Moreover, we found that alleles linked to tan and ebony fixed in one Drosophila species also contribute to variation within another species, and that multiple genotypes underlie similar phenotypes even within the same population. These alleles appear to predate speciation, which suggests that standing genetic variation present in the common ancestor gave rise to both intraspecific polymorphism and interspecific divergence.

An old bilbo-like non-LTR retroelement insertion provides insight into the relationship of species of the virilis group

In Drosophila, at the population and species level, fixation of a TE insertion is an unlikely fate. Of the few reported fixations at the species level most involve non-LTR retroelements. In this work we report the fixation of a non-LTR retroelement in five species (Drosophila littoralis, Drosophila virilis, Drosophila lummei, Drosophila americana and Drosophila novamexicana) of the virilis group of Drosophila. In most species, this TE insertion is being lost through the accumulation of small deletions, but there is also evidence for the accumulation of large deletions. In the americana lineage an insertion of about 900 bp of the non-LTR retroelement is a marker for the Xc inversion. This insertion is, at most, 80 kb away from the basal Xc inversion breakpoint. The presence of a bilbo-like element in D. littoralis but not in D. kanekoi, suggests that D. littoralis is more closely related to species of the virilis phylad than to species of the montana phylad, which is in contrast with the traditional view. Nevertheless, the phylogenetic analyses here performed using a 7 gene dataset suggest that D. littoralis is indeed more closely related to species of the virilis phylad than to species of the montana phylad. The re-evaluation of the phylogenetic relationship of the species of the virilis group, under the assumption of a relaxed molecular clock, results in an estimated age of the bilbo-like element insertion of at least 7.5 Mya.

Inferring the evolutionary history of Drosophila americana and Drosophila novamexicana using a multilocus approach and the influence of chromosomal rearrangements in single gene analyses

The evolutionary history of closely related organisms can prove sometimes difficult to infer. Hybridization and incomplete lineage sorting are the main concerns; however, genome rearrangements can also influence the outcome of analyses based on nuclear sequences. In the present study, DNA sequences from 12 nuclear genes, for which the approximate chromosomal locations are known, have been used to estimate the evolutionary history of two forms of Drosophila americana (Drosophila americana americana and Drosophila americana texana) and Drosophila novamexicana (virilis group of species). The phylogenetic analysis of the combined data set resulted in a phylogeny showing reciprocal monophyly for D. novamexicana and D. americana. Single gene analyses, however, resulted in incongruent phylogenies influenced by chromosomal rearrangements. Genetic differentiation estimates indicated a significant differentiation between the two species for all genes. Within D. americana, however, there is no evidence for differentiation between the chromosomal forms except at genes located near the X/4 fusion and Xc inversion breakpoint. Thus, the specific status of D. americana and D. novamexicana is confirmed, but there is no overall evidence for genetic differentiation between D. a. americana and D. a. texana, not supporting a subspecific status. Based on levels of allele and nucleotide diversity found in the strains used, it is proposed that D. americana has had a stable, large population during the recent past while D. novamexicana has speciated from a peripheral southwestern population having had an ancestral small effective population size. The influence of chromosomal rearrangements in single gene analyses is also examined.

Patterns of molecular variation and evolution in Drosophila americana and its relatives

We present the results of a survey of DNA sequence variability at X-linked and autosomal loci in Drosophila americana and of patterns of DNA sequence evolution among D. americana and four other related species in the virilis group of Drosophila. D. americana shows a typical level of silent polymorphism for a Drosophila species, but has an unusually low ratio of nonsynonymous to silent variation. Both D. virilis and D. americana also show a low ratio of nonsynonymous to synonymous substitutions along their respective lineages since the split from their common ancestor. The proportion of amino acid substitutions between D. americana and its relatives that are caused by positive selection, as estimated by extensions of the McDonald-Kreitman test, appears to be unusually high. We cannot, however, exclude the possibility that this reflects a recent increase in the intensity of selection on nonsynonymous mutations in D. americana and D. virilis. We also find that base composition at neutral sites appears to be in overall equilibrium among these species, but there is evidence for departure from equilibrium for codon usage in some lineages.

Patterns of microsatellite variation through a transition zone of a chromosomal cline in Drosophila americana

Chromosomal rearrangements have been considered as important barriers to gene flow and were often used in the delineation of species. The original taxonomic designation of Drosophila americana americana and Drosophila americana texana is based on the presence/absence of a centric fusion between the X- and fourth chromosomes. D. a. americana presents the derived fused state, whereas Drosophila a. texana presents the freely segregating ancestral state. The degree of genetic separation between the two chromosomal forms is still controversial, with different genetic markers yielding contrasting results even when the same populations were analyzed. Using 27 polymorphic microsatellites, we re-evaluated patterns of genetic differentiation between six D. americana populations sampled through a transition zone of both chromosomal forms in the central United States. Our results clearly reject a scenario of two differentiated species forming a hybrid zone in a region of parapatry and indicate that gene flow minimizes genome-wide differentiation associated with the two chromosomal arrangements.

Steps in the evolution of heteromorphic sex chromosomes

We review some recently published results on sex chromosomes in a diversity of species. We focus on several fish and some plants whose sex chromosomes appear to be 'young', as only parts of the chromosome are nonrecombining, while the rest is pseudoautosomal. However, the age of these systems is not yet very clear. Even without knowing what proportions of their genes are genetically degenerate, these cases are of great interest, as they may offer opportunities to study in detail how sex chromosomes evolve. In particular, we review evidence that recombination suppression occurs progressively in evolutionarily independent cases, suggesting that selection drives loss of recombination over increasingly large regions. We discuss how selection during the period when a chromosome is adapting to its role as a Y chromosome might drive such a process.

Evidence for introgression in differentiated North-American and Finnish Drosophila montana populations

The virilis group species Drosophila montana is widely distributed around the northern hemisphere. Here we show that it consists of at least two well differentiated populations (Finnish and North-American populations) that have been diverging for the last 0.55-0.95 My. These populations show significant chromosomal, behavioural and morphological differences, but no apparent postzygotic isolation. Evidence for introgression is found for both Finnish and North-American populations at two out of the three X-linked genes (fused, elav and su(s)) studied here. In the light of these findings, previously reported evidence for selective sweeps in D. montana populations is re-evaluated.

A multilocus microsatellite phylogeny of the Drosophila virilis group

We used a set of 48 polymorphic microsatellites derived from Drosophila virilis to infer phylogenetic relationships in the D. virilis clade. Consistent with previous studies, D. virilis and D. lummei were the most basal species of the group. Within the D. montana phylad, the phylogenetic relationship could not be resolved. Special attention was given to the differentiation between D. americana texana, D. americana americana and D. novamexicana. Significant differences between these three groups were detected by F(ST) analyses. Similarly, a model-based clustering method for multilocus genotype data also provided strong support for the presence of three differentiated groups. This genome-wide differentiation between D. americana texana and D. americana americana contrasts with previous analyses based on DNA sequence data.