The Origin and Evolution of Chromosomal Reciprocal Translocation in Quasipaa boulengeri (Anura, Dicroglossidae)

Chromosomal rearrangements have long fascinated evolutionary biologists for being widely implicated in causing genetic differentiation. Suppressed recombination has been demonstrated in various species with inversion; however, there is controversy over whether such recombination suppression would facilitate divergence in reciprocal translocation with reduced fitness. In this study, we used the spiny frog, Quasipaa boulengeri, whose western Sichuan Basin populations exhibit translocation polymorphisms, to test whether the genetic markers on translocated (rearranged) or normal chromosomes have driven this genetic differentiation. We also investigated its overall genetic structure and the possibility of chromosomal fixation. Whole-chromosome painting and genetic structure clustering suggested a single origin of the translocation polymorphisms, and high-throughput sequencing of rearranged chromosomes isolated many markers with known localizations on chromosomes. Using these markers, distinct patterns of gene flow were found between rearranged and normal chromosomes. Genetic differentiation was only found in the translocated chromosomes, not in normal chromosomes or the mitochondrial genome. Hybrid unfitness cannot explain the genetic differentiation, as then the differentiation would be observed throughout the whole genome. Our results suggest that suppressed recombination drives genetic differentiation into a balanced chromosomal polymorphism. Mapping to a reference genome, we found that the region of genetic differentiation covered a wide range of translocated chromosomes, not only in the vicinity of chromosomal breakpoints. Our results imply that the suppressed recombination region could be extended by accumulation of repetitive sequences or capture of alleles that are adapted to the local environment, following the spread and/or fixation of chromosomal rearrangement.

Host plant-related genomic differentiation in the European cherry fruit fly, Rhagoletis cerasi

Elucidating the mechanisms and conditions facilitating the formation of biodiversity are central topics in evolutionary biology. A growing number of studies imply that divergent ecological selection may often play a critical role in speciation by counteracting the homogenising effects of gene flow. Several examples involve phytophagous insects, where divergent selection pressures associated with host plant shifts may generate reproductive isolation, promoting speciation. Here, we use ddRADseq to assess the population structure and to test for host‐related genomic differentiation in the European cherry fruit fly, Rhagoletis cerasi (L., 1758) (Diptera: Tephritidae). This tephritid is distributed throughout Europe and western Asia, and has adapted to two different genera of host plants, Prunus spp. (cherries) and Lonicera spp. (honeysuckle). Our data imply that geographic distance and geomorphic barriers serve as the primary factors shaping genetic population structure across the species range. Locally, however, flies genetically cluster according to host plant, with consistent allele frequency differences displayed by a subset of loci between Prunus and Lonicera flies across four sites surveyed in Germany and Norway. These 17 loci display significantly higher F_ST values between host plants than others. They also showed high levels of linkage disequilibrium within and between Prunus and Lonicera flies, supporting host‐related selection and reduced gene flow. Our findings support the existence of sympatric host races in R. cerasi embedded within broader patterns of geographic variation in the fly, similar to the related apple maggot, Rhagoletis pomonella, in North America.

An ancient hybridization event reconciles mito-nuclear discordance among spiral-horned antelopes

The spiral-horned antelopes (genus Tragelaphus) are among the most phenotypically diverse of all large mammals, and evolved in Africa during an adaptive radiation that began in the late Miocene, around 6 million years ago. Tragelaphus was able to exploit the habitat heterogeneity created by Plio-Pleistocene paleoclimatic fluctuations and tectonic processes to eventually occupy almost every habitat type in present day sub-Saharan Africa. The smallest of the spiral-horned antelopes, the bushbuck (T. scriptus), is also widely distributed across Africa, but is genetically divided into polyphyletic Scriptus and Sylvaticus mitochondrial (mt)DNA superlineages that inhabit opposite halves of the continent, suggesting the convergent evolution of independent bushbuck species. In this study, we provide a species tree reconstruction for the genus Tragelaphus and show that Scriptus and Sylvaticus are reciprocally monophyletic at nuclear DNA loci, comprising a single species across its African range. Given that mtDNA will sort into species-specific lineages more quickly than nuclear DNA, only an ancient interspecific hybridization event between a female from a now-extinct Tragelaphus species and a proto-Scriptus bushbuck male can reconcile the mito-nuclear incongruence. This extinct species diverged from the nyala (T. angasii) in the Pliocene about 4.1 million years ago. This study adds to an increasing body of evidence that suggests interspecific hybridization may be more common than previously thought.

Heterogeneous rates of genome rearrangement contributed to the disparity of species richness in Ascomycota

Background

Chromosomal rearrangements have been shown to facilitate speciation through creating a barrier of gene flow. However, it is not known whether heterogeneous rates of chromosomal rearrangement at the genome scale contributed to the huge disparity of species richness among different groups of organisms, which is one of the most remarkable and pervasive patterns on Earth. The largest fungal phylum Ascomycota is an ideal study system to address this question because it comprises three subphyla (Saccharomycotina, Taphrinomycotina, and Pezizomycotina) whose species numbers differ by two orders of magnitude (59,000, 1000, and 150 respectively).

Results

We quantified rates of genome rearrangement for 71 Ascomycota species that have well-assembled genomes. The rates of inter-species genome rearrangement, which were inferred based on the divergence rates of gene order, are positively correlated with species richness at both ranks of subphylum and class in Ascomycota. This finding is further supported by our quantification of intra-species rearrangement rates based on paired-end genome sequencing data of 216 strains from three representative species, suggesting a difference of intrinsic genome instability among Ascomycota lineages. Our data also show that different rates of imbalanced rearrangements, such as deletions, are a major contributor to the heterogenous rearrangement rates.

Conclusions

Various lines of evidence in this study support that a higher rate of rearrangement at the genome scale might have accelerated the speciation process and increased species richness during the evolution of Ascomycota species. Our findings provide a plausible explanation for the species disparity among Ascomycota lineages, which will be valuable to unravel the underlying causes for the huge disparity of species richness in various taxonomic groups.

Electronic supplementary material

The online version of this article (10.1186/s12864-018-4683-0) contains supplementary material, which is available to authorized users.

Semi-permeable species boundaries in Iberian barbels (Barbus and Luciobarbus, Cyprinidae)

BACKGROUND

The evolution of species boundaries and the relative impact of selection and gene flow on genomic divergence are best studied in populations and species pairs exhibiting various levels of divergence along the speciation continuum. We studied species boundaries in Iberian barbels, Barbus and Luciobarbus, a system of populations and species spanning a wide degree of genetic relatedness, as well as geographic distribution and range overlap. We jointly analyze multiple types of molecular markers and morphological traits to gain a comprehensive perspective on the nature of species boundaries in these cyprinid fishes.

RESULTS

Intraspecific molecular and morphological differentiation is visible among many populations. Genomes of all sympatric species studied are porous to gene flow, even if they are not sister species. Compared to their allopatric counterparts, sympatric representatives of different species share alleles and show an increase in all measures of nucleotide polymorphism (S, Hd, K, π and θ). High molecular diversity is particularly striking in L. steindachneri from the Tejo and Guadiana rivers, which co-varies with other sympatric species. Interestingly, different nuclear markers introgress across species boundaries at various levels, with distinct impacts on population trees. As such, some loci exhibit limited introgression and population trees resemble the presumed species tree, while alleles at other loci introgress more freely and population trees reflect geographic affinities and interspecific gene flow. Additionally, extent of introgression decreases with increasing genetic divergence in hybridizing species pairs.

CONCLUSIONS

We show that reproductive isolation in Iberian Barbus and Luciobarbus is not complete and species boundaries are semi-permeable to (some) gene flow, as different species (including non-sister) are exchanging genes in areas of sympatry. Our results support a speciation-with-gene-flow scenario with heterogeneous barriers to gene flow across the genome, strengthening with genetic divergence. This is consistent with observations coming from other systems and supports the notion that speciation is not instantaneous but a gradual process, during which different species are still able to exchange some genes, while selection prevents gene flow at other loci. We also provide evidence for a hybrid origin of a barbel ecotype, L. steindachneri, suggesting that ecology plays a key role in species coexistence and hybridization in Iberian barbels. This ecotype with intermediate, yet variable, molecular, morphological, trophic and ecological characteristics is the local product of introgressive hybridization of L. comizo with up to three different species (with L. bocagei in the Tejo, with L. microcephalus and L. sclateri in the Guadiana). In spite of the homogenizing effects of ongoing gene flow, species can still be discriminated using a combination of morphological and molecular markers. Iberian barbels are thus an ideal system for the study of species boundaries, since they span a wide range of genetic divergences, with diverse ecologies and degrees of sympatry.

Dynamic karyotype evolution and unique sex determination systems in Leptidea wood white butterflies

Background

Chromosomal rearrangements have the potential to limit the rate and pattern of gene flow within and between species and thus play a direct role in promoting and maintaining speciation. Wood white butterflies of the genus Leptidea are excellent models to study the role of chromosome rearrangements in speciation because they show karyotype variability not only among but also within species. In this work, we investigated genome architecture of three cryptic Leptidea species (L. juvernica, L. sinapis and L. reali) by standard and molecular cytogenetic techniques in order to reveal causes of the karyotype variability.

Results

Chromosome numbers ranged from 2n = 85 to 91 in L. juvernica and 2n = 69 to 73 in L. sinapis (both from Czech populations) to 2n = 51 to 55 in L. reali (Spanish population). We observed significant differences in chromosome numbers and localization of cytogenetic markers (rDNA and H3 histone genes) within the offspring of individual females. Using FISH with the (TTAGG)_n telomeric probe we also documented the presence of multiple chromosome fusions and/or fissions and other complex rearrangements. Thus, the intraspecific karyotype variability is likely due to irregular chromosome segregation of multivalent meiotic configurations. The analysis of female meiotic chromosomes by GISH and CGH revealed multiple sex chromosomes: W₁W₂W₃Z₁Z₂Z₃Z₄ in L. juvernica, W₁W₂W₃Z₁Z₂Z₃ in L. sinapis and W₁W₂W₃W₄Z₁Z₂Z₃Z₄ in L. reali.

Conclusions

Our results suggest a dynamic karyotype evolution and point to the role of chromosomal rearrangements in the speciation of Leptidea butterflies. Moreover, our study revealed a curious sex determination system with 3–4 W and 3–4 Z chromosomes, which is unique in the Lepidoptera and which could also have played a role in the speciation process of the three Leptidea species.

Electronic supplementary material

The online version of this article (doi:10.1186/s12862-015-0375-4) contains supplementary material, which is available to authorized users.

Reduced recombination patterns in Robertsonian hybrids between chromosomal races of the house mouse: chiasma analyses

The recombination suppression models of chromosomal speciation posit that chromosomal rearrangements act as partial barriers to gene flow allowing these regions to accumulate genetic incompatibilities, thus contributing to the divergence of populations. Empirical and theoretical studies exploring the requirements of these models have mostly focused on the role of inversions. Here, the recombination landscape of heterozygosity for Robertsonian (Rb) fusions is investigated in the house mouse. Laboratory-bred F1 males and females between highly differentiated races from Tunisia (Rb: 2n=22, Standard, St: 2n=40) were produced in which all Rb fusions are present as trivalents in meiosis. Recombination patterns were determined by the analysis of chiasmata and compared with previous data on the Tunisian parental mice. A comparative analysis was performed on wild-caught male mice spanning the hybrid zone between two Italian races (2n=40, 2n=22). The results showed that the chiasma characteristics of both male and female Tunisian F1 and Italian hybrids clearly differed from those of Rb and St mice. Not only was the mean chiasma number (CN) intermediate between those of the parental mice in both geographic samples, but the distribution of chiasmata along the chromosomal arms of the F1 showed a distinct mosaic pattern. In short, the proximal region in the F1 exhibited a reduced CN similar to that observed in homozygous Rb, whereas distal regions more closely matched those in St mice. These results suggest that Rb rearrangements (homozygous or heterozygous) reduce recombination in the proximal regions of the chromosomes supporting their potential role in recombination-mediated speciation models.

Phylogeny of the Centaurea group (Centaurea, Compositae) - geography is a better predictor than morphology

The Centaurea group is part of the Circum-Mediterranean Clade (CMC) of genus Centaurea subgenus Centaurea, a mainly Mediterranean plant group with more than 200 described species. The group is traditionally split on morphological basis into three sections: Centaurea, Phalolepis and Willkommia. This division, however, is doubtful, especially in light of molecular approaches. In this study we try to resolve this phylogenetic problem and to consolidate the circumscription and delimitation of the entire group against other closely related groups. We analyzed nuclear (internal transcribed spacer of the ribosomal genes) and chloroplast (rpl32-trnL intergenic spacer) DNA regions for most of the described species of the Centaurea group using phylogenetic and network approaches, and we checked the data for recombination. Phylogeny was used to reconstruct the evolution of the lacerate-membranaceous bract appendages using parsimony. The magnitude of incomplete lineage sorting was tested estimating the effective population sizes. Molecular dating was performed using a Bayesian approach, and the ancestral area reconstruction was conducted using the Dispersal-Extinction-Cladogenesis method. Monophyly of the Centaurea group is confirmed if a few species are removed. Our results do not support the traditional sectional division. There is a high incongruence between the two markers and between genetic data and morphology. However, there is a clear relation between geography and the structure of the molecular data. Diversification in the Centaurea group mainly took place during the Pliocene and Pleistocene. The ancestral area infered for the Circum-Mediterranean Clade of Centaurea is the Eastern Mediterranean, whereas for the Centaurea group it is most likely NW-Africa. The large incongruencies, which hamper phylogenetic reconstruction, are probably the result of introgression, even though the presence of incomplete lineage sorting as an additional factor cannot be ruled out. Convergent evolution of morphological traits may have led to incongruence between morphology-based, traditional systematics and molecular results. Our results also cast major doubts about current species delimitation.

Phenotypic variation across chromosomal hybrid zones of the common shrew (Sorex araneus) indicates reduced gene flow

Sorex araneus, the Common shrew, is a species with more than 70 karyotypic races, many of which form parapatric hybrid zones, making it a model for studying chromosomal speciation. Hybrids between races have reduced fitness, but microsatellite markers have demonstrated considerable gene flow between them, calling into question whether the chromosomal barriers actually do contribute to genetic divergence. We studied phenotypic clines across two hybrid zones with especially complex heterozygotes. Hybrids between the Novosibirsk and Tomsk races produce chains of nine and three chromosomes at meiosis, and hybrids between the Moscow and Seliger races produce chains of eleven. Our goal was to determine whether phenotypes show evidence of reduced gene flow at hybrid zones. We used maximum likelihood to fit tanh cline models to geometric shape data and found that phenotypic clines in skulls and mandibles across these zones had similar centers and widths as chromosomal clines. The amount of phenotypic differentiation across the zones is greater than expected if it were dissipating due to unrestricted gene flow given the amount of time since contact, but it is less than expected to have accumulated from drift during allopatric separation in glacial refugia. Only if heritability is very low, Ne very high, and the time spent in allopatry very short, will the differences we observe be large enough to match the expectation of drift. Our results therefore suggest that phenotypic differentiation has been lost through gene flow since post-glacial secondary contact, but not as quickly as would be expected if there was free gene flow across the hybrid zones. The chromosomal tension zones are confirmed to be partial barriers that prevent differentiated races from becoming phenotypically homogenous.

A new form of the mole vole Ellobius tancrei Blasius, 1884 (Mammalia, Rodentia) with the lowest chromosome number

The subterranean mole vole, Ellobius tancrei, with aspecific variability in autosomes (2n = 31-54) and unusual sex chromosomes (XX in males and females), represents an amazing model for studying the role of chromosome changes in speciation. New materials from the upper reaches of the Surkhob River in the Pamiro-Alay mountains resulted in the discovery of a new form with 2n = 30. The application of Zoo-FISH and G-banding methods allowed the detection of 13 pairs of autosomes as Robertsonian metacentrics originated after fusions of acrocentrics of an assumed ancestral karyotype of Ellobius tancrei with 2n = 54. The sex chromosomes (XX, in both sexes) and one pair of acrocentric autosomes are the only acrocentrics in this karyotype, and the set with 2n = 30 possesses the lowest possible chromosome number among populations of Ellobius tancrei.

Understanding the basis of diminished gene flow between hybridizing chromosome races of the house mouse

Speciation may be promoted in hybrid zones if there is an interruption to gene flow between the hybridizing forms. For hybridizing chromosome races of the house mouse in Valtellina (Italy), distinguished by whole-arm chromosomal rearrangements, previous studies have shown that there is greater interruption to gene flow at the centromeres of chromosomes that differ between the races than at distal regions of the same chromosome or at the centromeres of other chromosomes. Here, by increasing the number of markers along race-specific chromosomes, we reveal a decay in between-race genetic differentiation from the centromere to the distal telomere. For the first time, we use simulation models to investigate the possible role of recombination suppression and hybrid breakdown in generating this pattern. We also consider epistasis and selective sweeps as explanations for isolated chromosomal regions away from the centromere showing differentiation between the races. Hybrid breakdown alone is the simplest explanation for the decay in genetic differentiation with distance from the centromere. Robertsonian fusions/whole-arm reciprocal translocations are common chromosomal rearrangements characterizing both closely related species and races within species, and this fine-scale empirical analysis suggests that the unfitness associated with these rearrangements in the heterozygous state may contribute to the speciation process.

Chromosomal rearrangements do not seem to affect the gene flow in hybrid zones between karyotypic races of the common shrew (Sorex araneus)

Chromosomal rearrangements are proposed to promote genetic differentiation between chromosomally differentiated taxa and therefore promote speciation. Due to their remarkable karyotypic polymorphism, the shrews of the Sorex araneus group were used to investigate the impact of chromosomal rearrangements on gene flow. Five intraspecific chromosomal hybrid zones characterized by different levels of karyotypic complexity were studied using 16 microsatellites markers. We observed low levels of genetic differentiation even in the hybrid zones with the highest karyotypic complexity. No evidence of restricted gene flow between differently rearranged chromosomes was observed. Contrary to what was observed at the interspecific level, the effect of chromosomal rearrangements on gene flow was undetectable within the S. araneus species.

Natural hybridization between extremely divergent chromosomal races of the common shrew (Sorex araneus, Soricidae, Soricomorpha): hybrid zone in Siberia

Chromosomal races of the common shrew differ in sets of metacentric chromosomes and on contact may produce hybrids with extraordinarily complex configurations at meiosis I that are associated with reduced fertility. There is an expectation that these may be some of the most extreme tension zones available for study and therefore are of interest as potential sites for reproductive isolation. Here, we analyse one of these zones, between the Novosibirsk race (characterized by metacentrics go, hn, ik, jl, mp and qr) and the Tomsk race (metacentrics gk, hi, jl and mn and acrocentrics o, p, q and r), which form hybrids with a chain-of-nine (CIX) and a chain-of-three (CIII) configuration at meiosis I. At the Novosibirsk-Tomsk hybrid zone, the CIX chromosomes form clines of 8.53 km standardized width on average, whereas the cline for the CIII chromosomes was 52.83 km wide. The difference in these cline widths fits with the difference in meiotic errors expected with the CIX and CIII configuration, and we produce estimates of selection against hybrids with these types of configurations, which we relate to dispersal and age of the hybrid zone. The hybrid zone is located at the isocline at 200 m altitude above sea level; this relationship between the races and altitude is suggested at both coarse and fine scales. This indicates adaptive differences between the races that may in turn have been promoted by the chromosome differences. Thus, the extreme chromosomal divergence between the Novosibirsk and Tomsk may be associated with genic differentiation, but it is still striking that, despite the large chromosomal differences, reproductive isolation between the Novosibirsk and Tomsk races has not occurred.

Unprecedented within-species chromosome number cline in the Wood White butterfly Leptidea sinapis and its significance for karyotype evolution and speciation

Background

Species generally have a fixed number of chromosomes in the cell nuclei while between-species differences are common and often pronounced. These differences could have evolved through multiple speciation events, each involving the fixation of a single chromosomal rearrangement. Alternatively, marked changes in the karyotype may be the consequence of within-species accumulation of multiple chromosomal fissions/fusions, resulting in highly polymorphic systems with the subsequent extinction of intermediate karyomorphs. Although this mechanism of chromosome number evolution is possible in theory, it has not been well documented.

Results

We present the discovery of exceptional intraspecific variability in the karyotype of the widespread Eurasian butterfly Leptidea sinapis. We show that within this species the diploid chromosome number gradually decreases from 2n = 106 in Spain to 2n = 56 in eastern Kazakhstan, resulting in a 6000 km-wide cline that originated recently (8,500 to 31,000 years ago). Remarkably, intrapopulational chromosome number polymorphism exists, the chromosome number range overlaps between some populations separated by hundreds of kilometers, and chromosomal heterozygotes are abundant. We demonstrate that this karyotypic variability is intraspecific because in L. sinapis a broad geographical distribution is coupled with a homogenous morphological and genetic structure.

Conclusions

The discovered system represents the first clearly documented case of explosive chromosome number evolution through intraspecific and intrapopulation accumulation of multiple chromosomal changes. Leptidea sinapis may be used as a model system for studying speciation by means of chromosomally-based suppressed recombination mechanisms, as well as clinal speciation, a process that is theoretically possible but difficult to document. The discovered cline seems to represent a narrow time-window of the very first steps of species formation linked to multiple chromosomal changes that have occurred explosively. This case offers a rare opportunity to study this process before drift, dispersal, selection, extinction and speciation erase the traces of microevolutionary events and just leave the final picture of a pronounced interspecific chromosomal difference.

Chromosomal Speciation Revisited: Modes of Diversification in Australian Morabine Grasshoppers (Vandiemenella, viatica Species Group)

Chromosomal rearrangements can alter the rate and patterns of gene flow within or between species through a reduction in the fitness of chromosomal hybrids or by reducing recombination rates in rearranged areas of the genome. This concept, together with the observation that many species have structural variation in chromosomes, has led to the theory that the rearrangements may play a direct role in promoting speciation. Australian morabine grasshoppers (genus Vandiemenella, viatica species group) are an excellent model for studying the role of chromosomal rearrangement in speciation because they show extensive chromosomal variation, parapatric distribution patterns, and narrow hybrid zones at their boundaries. This species group stimulated development of one of the classic chromosomal speciation models, the stasipatric speciation model proposed by White in 1968. Our population genetic and phylogeographic analyses revealed extensive non-monophyly of chromosomal races along with historical and on-going gene introgression between them. These findings suggest that geographical isolation leading to the fixation of chromosomal variants in different geographic regions, followed by secondary contact, resulted in the present day parapatric distributions of chromosomal races. The significance of chromosomal rearrangements in the diversification of the viatica species group can be explored by comparing patterns of genetic differentiation between rearranged and co-linear parts of the genome.

Natural hybridization between extremely divergent chromosomal races of the common shrew (Sorex araneus, Soricidae, Soricomorpha): hybrid zone in European Russia

The Moscow and Seliger chromosomal races of the common shrew differ by Robertsonian fusions and possibly whole-arm reciprocal translocations (WARTs) such that their F₁ hybrids produce a chain-of-eleven configuration at meiosis I and are expected to suffer substantial infertility. Of numerous hybrid zones that have been described in the common shrew, those between the Moscow and Seliger races involve the greatest chromosomal difference. We collected 211 individuals from this zone to generate a total dataset of 298 individuals from 187 unique global positioning system (GPS) locations within the vicinity of interracial contact. We used a geographic information system (GIS) to map the location of the hybrid zone, which follows a direct route between two lakes, as would be anticipated from tension zone theory. Even within the central area of the hybrid zone, there is a much higher frequency of pure race individuals than hybrid, making this a clear example of a bimodal zone in the sense of Jiggins & Mallet (2000). The zone runs through good habitat for common shrews, but nevertheless it is very narrow (standard cline widths: 3-4 km), as would be anticipated from low hybrid fitness. There is clear potential for an interruption to gene flow and build-up of reproductive isolation. As found in some other hybrid zones, there is a high frequency of novel genetic variants, in this case, new chromosomal rearrangements. Here, we report a de novo Robertsonian fission and a de novo reciprocal translocation, both for the first time in the common shrew. There is an extraordinarily high frequency of de novo mutations recorded in F₁ hybrids in the zone and we discuss how chromosomal instability may be associated with such hybrids. The occurrence of a de novo Robertsonian fission is of considerable significance because it provides missing evidence that fissions are the basis of the novel acrocentric forms found and apparently selected for in certain common shrew hybrid zones.

Chromosomes tell half of the story: the correlation between karyotype rearrangements and genetic diversity in sedges, a group with holocentric chromosomes

Chromosome rearrangements may affect the rate and patterns of gene flow within species, through reduced fitness of structural heterozygotes or by reducing recombination rates in rearranged areas of the genome. While the effects of chromosome rearrangements on gene flow have been studied in a wide range of organisms with monocentric chromosomes, the effects of rearrangements in holocentric chromosomes--chromosomes in which centromeric activity is distributed along the length of the chromosome--have not. We collected chromosome number and molecular genetic data in Carex scoparia, an eastern North American plant species with holocentric chromosomes and highly variable karyotype (2n = 56-70). There are no deep genetic breaks within C. scoparia that would suggest cryptic species differentiation. However, genetic distance between individuals is positively correlated with chromosome number difference and geographic distance. A positive correlation is also found between chromosome number and genetic distance in the western North American C. pachystachya (2n = 74-81). These findings suggest that geographic distance and the number of karyotype rearrangements separating populations affect the rate of gene flow between those populations. This is the first study to quantify the effects of holocentric chromosome rearrangements on the partitioning of intraspecific genetic variance.

No evidence for Z-chromosome rearrangements between the pied flycatcher and the collared flycatcher as judged by gene-based comparative genetic maps

Revealing the genetic basis of reproductive isolation is fundamental for understanding the speciation process. Chromosome speciation models propose a role for chromosomal rearrangements in promoting the build up of reproductive isolation between diverging populations and empirical data from several animal and plant taxa support these models. The pied flycatcher and the collared flycatcher are two closely related species that probably evolved reproductive isolation during geographical separation in Pleistocene glaciation refugia. Despite the short divergence time and current hybridization, these two species demonstrate a high degree of intrinsic post-zygotic isolation and previous studies have shown that traits involved in mate choice and hybrid viability map to the Z-chromosome. Could rearrangements of the Z-chromosome between the species explain their reproductive isolation? We developed high coverage Z-chromosome linkage maps for both species, using gene-based markers and large-scale SNP genotyping. Best order maps contained 57-62 gene markers with an estimated average density of one every 1-1.5 Mb. We estimated the recombination rates in flycatcher Z-chromosomes to 1.1-1.3 cM/Mb. A comparison of the maps of the two species revealed extensive co-linearity with no strong evidence for chromosomal rearrangements. This study does therefore not provide support the idea that sex chromosome rearrangements have caused the relatively strong post-zygotic reproductive isolation between these two Ficedula species.

Staggered chromosomal hybrid zones in the house mouse: relevance to reticulate evolution and speciation

In the house mouse there are numerous chromosomal races distinguished by different combinations of metacentric chromosomes. These may come into contact with each other and with the ancestral all-acrocentric race, and form hybrid zones. The chromosomal clines that make up these hybrid zones may be coincident or separated from each other (staggered). Such staggered hybrid zones are interesting because they may include populations of individuals homozygous for a mix of features of the hybridising races. We review the characteristics of four staggered hybrid zones in the house mouse and discuss whether they are examples of primary or secondary contact and whether they represent reticulate evolution or not. However, the most important aspect of staggered hybrid zones is that the homozygous populations within the zones have the potential to expand their distributions and become new races (a process termed 'zonal raciation'). In this way they can add to the total 'stock' of chromosomal races in the species concerned. Speciation is an infrequent phenomenon that may involve an unusual set of circumstances. Each one of the products of zonal raciation has the potential to become a new species and by having more races increases the chance of a speciation event.

Reduced gene flow at pericentromeric loci in a hybrid zone involving chromosomal races of the house mouse Mus musculus domesticus

The West European house mouse, Mus musculus domesticus, is a particularly suitable model to investigate the role of chromosomal rearrangements in reproductive isolation. In fact, it exhibits a broad range of chromosomal polymorphism due to Robertsonian (Rb) fusions leading to various types of contact zones between different chromosomal races. In the present study, we analyzed a parapatric contact in central Italy between the Cittaducale chromosomal race (CD: 2n= 22) and the surrounding populations with standard karyotype (2n= 40) to understand if Rb fusions play a causative role in speciation. One hundred forty-seven mice from 17 localities were genotyped by means of 12 microsatellite loci. A telomeric and a pericentromeric locus situated on six chromosome arms (four Rbs and one telocentric) were selected to detect differences in the amount of gene flow for each locus in different chromosomal positions. The analyses performed on the two subsets of loci show differences in the level of gene flow, which is more restricted near the centromeres of Rb chromosomes. This effect is less pronounced in the homozygotes populations settled at the border of the hybrid zone. We discuss the possible cause of the differential porosity of gene flow in Rbs considering "hybrid dysfunctions" and "suppressed recombination" models.

Islands of speciation or mirages in the desert? Examining the role of restricted recombination in maintaining species

Over the past decade, many studies documented high genetic divergence between closely related species in genomic regions experiencing restricted recombination in hybrids, such as within chromosomal rearrangements or areas adjacent to centromeres. Such regions have been called 'islands of speciation' because of their presumed role in maintaining the integrity of species despite gene flow elsewhere in the genome. Here, we review alternative explanations for such patterns. Segregation of ancestral variation or artifacts of nucleotide diversity within species can readily lead to higher F(ST) in regions of restricted recombination than other parts of the genome, even in the complete absence of interspecies gene flow, and thereby cause investigators to erroneously conclude that islands of speciation exist. We conclude by discussing strengths and weaknesses of various means for testing the role of restricted recombination in maintaining species.

Genomic patterns of adaptive divergence between chromosomally differentiated sunflower species

Understanding the genetic mechanisms of speciation and basis of species differences is among the most important challenges in evolutionary biology. Two questions of particular interest are what roles divergent selection and chromosomal differentiation play in these processes. A number of recently proposed theories argue that chromosomal rearrangements can facilitate the development and maintenance of reproductive isolation and species differences by suppressing recombination within rearranged regions. Reduced recombination permits the accumulation of alleles contributing to isolation and adaptive differentiation and protects existing differences from the homogenizing effects of introgression between incipient species. Here, we examine patterns of genetic diversity and divergence in rearranged versus collinear regions in two widespread, extensively hybridizing sunflower species, Helianthus annuus and Helianthus petiolaris, using sequence data from 77 loci distributed throughout the genomes of the two species. We find weak evidence for increased genetic divergence near chromosomal break points but not within rearranged regions overall. We find no evidence for increased rates of adaptive divergence on rearranged chromosomes; in fact, collinear chromosomes show a far greater excess of fixed amino acid differences between the two species. A comparison with a third sunflower species indicates that much of the nonsynonymous divergence between H. annuus and H. petiolaris probably occurred during or soon after their formation. Our results suggest a limited role for chromosomal rearrangements in genetic divergence, but they do document substantial adaptive divergence and provide further evidence of how species integrity and genetic identity can be maintained at many loci in the face of extensive hybridization and gene flow.

Chromosomal rearrangements and gene flow over time in an inter-specific hybrid zone of the Sorex araneus group

Most hybrid zones have existed for hundreds or thousands of years but have generally been observed for only a short time period. Studies extending over periods long enough to track evolutionary changes in the zones or assess the ultimate outcome of hybridization are scarce. Here, we describe the evolution over time of the level of genetic isolation between two karyotypically different species of shrews (Sorex araneus and Sorex antinorii) at a hybrid zone located in the Swiss Alps. We first evaluated hybrid zone movement by contrasting patterns of gene flow and changes in cline parameters (centre and width) using 24 microsatellite loci, between two periods separated by 10 years apart. Additionally, we tested the role of chromosomal rearrangements on gene flow by analysing microsatellite loci located on both rearranged and common chromosomes to both species. We did not detect any movement of the hybrid zone during the period analysed, suggesting that the zone is a typical tension zone. However, the gene flow was significantly lower among the rearranged than the common chromosomes for the second period, whereas the difference was only marginally significant for the first period. This further supports the role of chromosomal rearrangements on gene flow between these taxa.

The conservation status of the tuco-tucos, genus Ctenomys (Rodentia: Ctenomyidae), in southern Brazil

The goal of conservation biology should be related to the preservation of species and also to the evolutionary and ecological processes that were responsible to form them and that are still acting. We review the conservation status of the species of tuco-tuco (Ctenomys torquatus, C. lami, C. minutus, and C. flamarioni) from southern Brazil, and relate these data to the geological history of a particular area in that region, the Coastal Plain of the States of Rio Grande do Sul and Santa Catarina. The implications of the data on these species from the Southeastern Brazil are also discussed in relation to the evolution and risk of extinction of these subterranean rodents.

Divergence between the Drosophila pseudoobscura and D. persimilis genome sequences in relation to chromosomal inversions

As whole-genome sequence assemblies accumulate, a challenge is to determine how these can be used to address fundamental evolutionary questions, such as inferring the process of speciation. Here, we use the sequence assemblies of Drosophila pseudoobscura and D. persimilis to test hypotheses regarding divergence with gene flow. We observe low differentiation between the two genome sequences in pericentromeric and peritelomeric regions. We interpret this result as primarily a remnant of the correlation between levels of variation and local recombination rate observed within populations. However, we also observe lower differentiation far from the fixed chromosomal inversions distinguishing these species and greater differentiation within and near these inversions. This finding is consistent with models suggesting that chromosomal inversions facilitate species divergence despite interspecies gene flow. We also document heterogeneity among the inverted regions in their degree of differentiation, suggesting temporal differences in the origin of each inverted region consistent with the inversions arising during a process of divergence with gene flow. While this study provides insights into the speciation process using two single-genome sequences, it was informed by lower throughput but more rigorous examinations of polymorphism and divergence. This reliance highlights the need for complementary genomic and population genetic approaches for tackling fundamental evolutionary questions such as speciation.

Chromosomal rearrangements and genetic structure at different evolutionary levels of the Sorex araneus group

Robertsonian (Rb) fusions received large theoretical support for their role in speciation, but empirical evidence is often lacking. Here, we address the role of Rb rearrangements on the genetic differentiation of the karyotypically diversified group of shrews, Sorex araneus. We compared genetic structure between 'rearranged' and 'common' chromosomes in pairwise comparisons of five karyotypic taxa of the group. Considering all possible comparisons, we found a significantly greater differentiation at rearranged chromosomes, supporting the role of chromosomal rearrangements in the general genetic diversification of this group. Intertaxa structure and distance were larger across rearranged chromosomes for most of the comparisons, although these differences were not significant. This last result could be explained by the large variance observed among microsatellite-based estimates. The differences observed among the pairs of taxa analysed support the role of both the hybrid karyotypic complexity and the level of evolutionary divergence.

Recombination map of the common shrew, Sorex araneus (Eulipotyphla, Mammalia)

The Eurasian common shrew (Sorex araneus L.) is characterized by spectacular chromosomal variation, both autosomal variation of the Robertsonian type and an XX/XY(1)Y(2) system of sex determination. It is an important mammalian model of chromosomal and genome evolution as it is one of the few species with a complete genome sequence. Here we generate a high-precision cytological recombination map for the species, the third such map produced in mammals, following those for humans and house mice. We prepared synaptonemal complex (SC) spreads of meiotic chromosomes from 638 spermatocytes of 22 males of nine different Robertsonian karyotypes, identifying each autosome arm by differential DAPI staining. Altogether we mapped 13,983 recombination sites along 7095 individual autosomes, using immunolocalization of MLH1, a mismatch repair protein marking recombination sites. We estimated the total recombination length of the shrew genome as 1145 cM. The majority of bivalents showed a high recombination frequency near the telomeres and a low frequency near the centromeres. The distances between MLH1 foci were consistent with crossover interference both within chromosome arms and across the centromere in metacentric bivalents. The pattern of recombination along a chromosome arm was a function of its length, interference, and centromere and telomere effects. The specific DNA sequence must also be important because chromosome arms of the same length differed substantially in their recombination pattern. These features of recombination show great similarity with humans and mice and suggest generality among mammals. However, contrary to a widespread perception, the metacentric bivalent tu usually lacked an MLH1 focus on one of its chromosome arms, arguing against a minimum requirement of one chiasma per chromosome arm for correct segregation. With regard to autosomal chromosomal variation, the chromosomes showing Robertsonian polymorphism display MLH1 foci that become increasingly distal when comparing acrocentric homozygotes, heterozygotes, and metacentric homozygotes. Within the sex trivalent XY(1)Y(2), the autosomal part of the complex behaves similarly to other autosomes.

Reproductive isolation between chromosomal races of the house mouse Mus musculus domesticus in a parapatric contact area revealed by an analysis of multiple unlinked loci

The house mouse, Mus musculus domesticus, exhibits a high level of chromosomal polymorphism because of the occurrence and fast fixation of Robertsonian fusions between telocentric chromosomes. For this reason, it has been considered a classical speciation model to analyse the role of the chromosomal changes in reproductive isolation. In this study, we analysed a parapatric contact area between two metacentric races in central Italy, the Cittaducale race (CD: 2n = 22) and the Ancarano race (ACR: 2n = 24), to estimate gene flow at the boundary. Hybrids between these two races show high levels of structural heterozygosity and are expected to be highly infertile. A sample of 88 mice from 14 sites was used. The mice were genotyped by means of eight microsatellite loci mapped in four different autosomal arms. The results show clear genetic differentiation between the CD and ACR races, as revealed by differences in allele frequencies, factorial correspondence analysis and indexes of genetic population (e.g. F(ST) and R(ST)) along the contact zone. The genetic differentiation between the races was further highlighted by assignation and clustering analyses, in which all the individuals were correctly assigned by their genotypes to the source chromosomal race. This result is particularly interesting in view of the absence of any geographical or ecological barrier in the parapatric contact zone, which occurs within a village. In these conditions, the observed genetic separation suggests an absence of gene flow between the races. The CD-ACR contact area is a rare example of a final stage of speciation between chromosomal races of rodents because of their chromosomal incompatibility.

Genetic diversity and population size: island populations of the common shrew, Sorex araneus

Populations of many species are currently being fragmented and reduced by human interactions. These processes will tend to reduce genetic diversity within populations and reduce individual heterozygosities because of genetic drift, inbreeding and reduced migration. Conservation biologists need to know the effect of population size on genetic diversity, as this is likely to influence a population's ability to persist. Island populations represent an ideal natural experiment with which to study this problem. In a study of common shrews (Sorex araneus) on offshore Scottish islands, 497 individuals from 13 islands of different sizes and 6 regions on the mainland were trapped and genotyped at eight microsatellite loci. Previous genetic work had revealed that most of the islands in this study were highly genetically divergent from one another and the mainland. We found that most of the islands exhibited lower genetic diversity than the mainland populations. In the island populations, mean expected heterozygosity, mean observed heterozygosity and mean allelic richness were significantly positively correlated with log island size and log population size, which were estimated using habitat population density data and application of a Geographic Information System.

Nonuniform processes of chromosome evolution in sedges (Carex: Cyperaceae)

Holocentric chromosomes-chromosomes that lack localized centromeres-occur in numerous unrelated clades of insects, flatworms, and angiosperms. Chromosome number changes in such organisms often result from fission and fusion events rather than polyploidy. In this study, I test the hypothesis that chromosome number evolves according to a uniform process in Carex section Ovales (Cyperaceae), the largest New World section of an angiosperm genus renowned for its chromosomal variability and species richness. I evaluate alternative models of chromosome evolution that allow for shifts in both stochastic and deterministic evolutionary processes and that quantify the rate of evolution and heritability/phylogenetic dependence of chromosome number. Estimates of Ornstein-Uhlenbeck model parameters and tree-scaling parameters in a generalized least squares framework demonstrate that (1) chromosome numbers evolve rapidly toward clade-specific stationary distributions that cannot be explained by constant variance (Brownian motion) evolutionary models, (2) chromosome evolution in the section is rapid and exhibits little phylogenetic inertia, and (3) explaining the phylogenetic pattern of chromosome numbers in the section entails inferring a shift in evolutionary dynamics at the root of a derived clade. The finding that chromosome evolution is not a uniform process in sedges provides a novel example of karyotypic orthoselection in an organism with holocentric chromosomes.

Using a Bayesian method to assign individuals to karyotypic taxa in shrew hybrid zones

Individuals sampled in hybrid zones are usually analysed according to their sampling locality, morphology, behaviour or karyotype. But the increasing availability of genetic information more and more favours its use for individual sorting purposes and numerous assignment methods based on the genetic composition of individuals have been developed. The shrews of the Sorex araneus group offer good opportunities to test the genetic assignment on individuals identified by their karyotype. Here we explored the potential and efficiency of a Bayesian assignment method combined or not with a reference dataset to study admixture and individual assignment in the difficult context of two hybrid zones between karyotypic species of the Sorex araneus group. As a whole, we assigned more than 80% of the individuals to their respective karyotypic categories (i.e. 'pure' species or hybrids). This assignment level is comparable to what was obtained for the same species away from hybrid zones. Additionally, we showed that the assignment result for several individuals was strongly affected by the inclusion or not of a reference dataset. This highlights the importance of such comparisons when analysing hybrid zones. Finally, differences between the admixture levels detected in both hybrid zones support the hypothesis of an impact of chromosomal rearrangements on gene flow.