Reconstructing the Evolutionary History of Chromosomal Races on Islands: A Genome-Wide Analysis of Natural House Mouse Populations.

Chromosomal evolution is widely considered to be an important driver of speciation, as karyotypic reorganization can bring about the establishment of reproductive barriers between incipient species. One textbook example for genetic mechanisms of speciation are large-scale chromosomal rearrangements such as Robertsonian (Rb) fusions, a common class of structural variants that can drastically change the recombination landscape by suppressing crossing-over and influence gene expression by altering regulatory networks. Here, we explore the population structure and demographic patterns of a well-known house mouse Rb system in the Aeolian archipelago in Southern Italy using genome-wide data. By analyzing chromosomal regions characterized by different levels of recombination, we trace the evolutionary history of a set of Rb chromosomes occurring in different geographical locations and test whether chromosomal fusions have a single shared origin or occurred multiple times. Using a combination of phylogenetic and population genetic approaches, we find support for multiple, independent origins of three focal Rb chromosomes. The elucidation of the demographic patterns of the mouse populations within the Aeolian archipelago shows that an interplay between fixation of newly formed Rb chromosomes and hybridization events has contributed to shaping their current karyotypic distribution. Overall, our results illustrate that chromosome structure is much more dynamic than anticipated and emphasize the importance of large-scale chromosomal translocations in speciation.

Detection of cryptic diversity in lizards (Squamata) from two Biosphere Reserves in Mesoamerica.

A combined approach based on karyology and DNA taxonomy allowed us to characterize the taxonomic peculiarities in 10 Mesoamerican lizard species, belonging to six genera and five families, inhabiting two Biosphere Reserve in Chiapas, Mexico: La Sepultura Biosphere Reserve, and Montes Azules Biosphere. The karyotypes of four species, Phyllodactylus sp. 3 (P. tuberculosus species group) (2n = 38), Holcosus festivus (Lichtenstein et von Martens, 1856) (2n = 50), Anolis lemurinus Cope, 1861 (2n = 40), and A. uniformis Cope, 1885 (2n = 29-30) are described for the first time, the last one showing a particular X1X1X2X2/X1X2Y condition. In Aspidoscelis deppii (Wiegmann, 1834) (2n = 50) and Anolis capito Peters, 1863 (2n = 42), we found a different karyotype from the ones previously reported for these species. Moreover, in A. capito, the cytogenetic observation is concurrent with a considerable genetic divergence (9%) at the studied mtDNA marker (MT-ND2), which is indicative of a putative new cryptic species. The skink Scincella cherriei (Cope, 1893), showed high values of genetic divergence (5.2% at 16S gene) between the specimens from Montes Azules and those from Costa Rica and Nicaragua, comparable to the values typical of sister species in skinks. A lower level of genetic divergence, compatible with an intraspecific phylogeographic structure, has been identified in Lepidophyma flavimaculatum Duméril, 1851. These new data identify taxa that urgently require more in-depth taxonomic studies especially in these areas where habitat alteration is proceeding at an alarming rate.

Phylogeographic structure and ecological niche modelling reveal signals of isolation and postglacial colonisation in the European stag beetle.

Lucanus cervus (L.), the stag beetle, is a saproxylic beetle species distributed widely across Europe. Throughout its distribution the species has exhibited pronounced declines and is widely considered threatened. Conservation efforts may be hindered by the lack of population genetic data and understanding of the spatial scale of population connectivity. To address this knowledge gap this research details the first broad scale phylogeographic study of L. cervus based on mitochondrial DNA (mtDNA) sequencing and microsatellite analysis of samples collected from 121 localities across Europe. Genetic data were complemented by palaeo-distribution models of spatial occupancy during the Last Glacial Maximum to strengthen inferences of refugial areas. A salient feature of the mtDNA was the identification of two lineages. Lineage I was widespread across Europe while lineage II was confined to Greece. Microsatellites supported the differentiation of the Greek samples and alongside palaeo-distribution models indicated this area was a glacial refuge. The genetic endemism of the Greek samples, and demographic results compatible with no signatures of spatial expansion likely reflects restricted dispersal into and out of the area. Lineage I exhibited a shallow star like phylogeny compatible with rapid population expansion across Europe. Demographic analysis indicated such expansions occurred after the Last Glacial Maximum. Nuclear diversity and hindcast species distribution models indicated a central Italian refuge for lineage I. Palaeo-distribution modelling results also suggested a western refuge in northern Iberia and south-west France. In conclusion the results provide evidence of glacial divergence in stag beetle while also suggesting high, at least on evolutionary timescales, gene flow across most of Europe. The data also provide a neutral genetic framework against which patterns of phenotypic variation may be assessed.

Meiotic behavior of a complex hexavalent in heterozygous mice for Robertsonian translocations: insights for synapsis dynamics.

Natural populations of the house mouse Mus musculus domesticus show great diversity in chromosomal number due to the presence of chromosomal rearrangements, mainly Robertsonian translocations. Breeding between two populations with different chromosomal configurations generates subfertile or sterile hybrid individuals due to impaired meiotic development. In this study, we have analyzed prophase-I spermatocytes of hybrids formed by crossing mice from Vulcano and Lipari island populations. Both populations have a 2n = 26 karyotype but different combinations of Robertsonian translocations. We studied the progress of synapsis, recombination, and meiotic silencing of unsynapsed chromosomes during prophase-I through the immunolocalization of the proteins SYCP3, SYCP1, γH2AX, RAD51, and MLH1. In these hybrids, a hexavalent is formed that, depending on the degree of synapsis between chromosomes, can adopt an open chain, a ring, or a closed configuration. The frequency of these configurations varies throughout meiosis, with the maximum degree of synapsis occurring at mid pachytene. In addition, we observed the appearance of heterologous synapsis between telocentric and metacentric chromosomes; however, this synapsis seems to be transient and unstable and unsynapsed regions are frequently observed in mid-late pachytene. Interestingly, we found that chiasmata are frequently located at the boundaries of unsynapsed chromosomal regions in the hexavalent during late pachytene. These results provide new clues about synapsis dynamics during meiosis. We propose that mechanical forces generated along chromosomes may induce premature desynapsis, which, in turn, might be counteracted by the location of chiasmata. Despite these and additional meiotic features, such as the accumulation of γH2AX on unsynapsed chromosome regions, we observed a large number of cells that progressed to late stages of prophase-I, indicating that synapsis defects may not trigger a meiotic crisis in these hybrids.

Asymmetric hybridization in Cordulegaster (Odonata: Cordulegastridae): Secondary postglacial contact and the possible role of mechanical constraints.

Two Cordulegaster dragonflies present in Italy, the Palaearctic and northern distributed Cordulegaster boltonii and the endemic to the south of the peninsula Cordulegaster trinacriae, meet in central Italy and give rise to individuals of intermediate morphology. By means of mitochondrial and nuclear markers and of Geometric Morphometrics applied to sexual appendages, we defined i) the geographical boundaries between the two species in Italy and ii) we determined the presence, the extent, and the genetic characteristics of the hybridization. Genetic data evidenced asymmetric hybridization with the males of C. trinacriae able to mate both interspecifically and intraspecifically. The results contrast with expectations under neutral gene introgression and sexual selection. This data, along with the morphological evidence of significant differences in size and shape of sexual appendages between the males of the two species, seem indicative of the role of mechanical constraints in intraspecific matings. The origin of the two species is dated about to 1.32 Mya and the hybridization resulted related to range expansion of the two species after Last Glacial Maximum and this led to the secondary contact between the two taxa in central Italy. At last, our results indicate that the range of C. trinacriae, a threatened and protected species, has been moving northward probably driven by climate changes. As a result, the latter species is currently intruding into the range of C. boltonii. The hybrid area is quite extended and the hybrids seem well adapted to the environment. From a conservation point of view, even if C. trinacriae has a strong genetic identity, the discovery of hybridization between the two species should be considered in a future species management.

Arthropods and associated pathogens from native and introduced rodents in Northeastern Italy.

Introduced Siberian chipmunks Eutamias sibiricus have been reported to be important reservoirs for human Lyme disease, as they may host high numbers of hard ticks carrying Borrelia spp. and other pathogens. In the present study, we assessed the prevalence of Borrelia spp. and other pathogenic bacteria in ectoparasite arthropod species infesting Siberian chipmunks and coexisting native small rodents. Small rodents were trapped with Sherman traps in Veneto (NE Italy), where the largest Italian populations of chipmunks occur. A total of 14 individual ticks were found on 223 rodents, with 6 more ticks obtained from stored dead chipmunks from the same study area. Ectoparasites were screened for pathogens by molecular analyses including species-specific PCR amplifications. Rickettsia monacensis, Borrelia lusitaniae, and Anaplasma platys were present in the parasites of both native rodents and introduced chipmunks. The present findings suggest a role for the invasive species E. sibiricus in the maintenance of the Ixodes ricinus life cycle, which may result in the modification of the transmission dynamics of tick-borne pathogens. Moreover, the presence of Rickettsia in urban populations of chipmunks may represent a serious risk for human health and should be investigated further.

Hexavalents in spermatocytes of Robertsonian heterozygotes between Mus m. domesticus 2n=26 from the Vulcano and Lipari Islands (Aeolian Archipelago, Italy).

The size and shape of the chromosomes, as well as the chromosomal domains that compose them, are determinants in the distribution and interaction between the bivalents within the nucleus of spermatocytes in prophase I of meiosis. Thus the nuclear architecture characteristic of the karyotype of a species can be modified by chromosomal changes such as Rb chromosomes. In this study we analysed the meiotic prophase nuclear organization of the heterozygous spermatocytes from Mus musculus domesticus 2n=26, and the synaptic configuration of the hexavalent formed by the dependent Rb chromosomes Rbs 6.16, 16.10, 10.15, 15.17 and the telocentric chromosomes 6 and 17. Spreads of 88 pachytene spermatocytes from two males were studied and in all of them five metacentric bivalents, four telocentric bivalents, one hexavalent and the XY bivalent were observed. About 48% of the hexavalents formed a chain or a ring of synapsed chromosomes, the latter closed by synapsis between the short arms of telocentric chromosomes 6 and 17.  About 52% of hexavalents formed an open chain of 10 synapsed chromosomal arms belonging to 6 chromosomes.  In about half of the unsynapsed hexavalents one of the telocentric chromosome short arms appears associated with the X chromosome single axis, which was otherwise normally paired with the Y chromosome.  The cluster of pericentromeric heterochromatin mostly determines the hexavalent's nuclear configuration, dragging the centromeric regions and all the chromosomes towards the nuclear envelope similar to an association of five telocentric bivalents. These reiterated encounters between these chromosomes restrict the interactions with other chromosomal domains and might favour eventual rearrangements within the metacentric, telocentric or hexavalent chromosome subsets. The unsynapsed short arms of telocentric chromosomes frequently bound to the single axis of the X chromosome could further complicate the already complex segregation of hexavalent chromosomes.

R2d2 Drives Selfish Sweeps in the House Mouse.

A selective sweep is the result of strong positive selection driving newly occurring or standing genetic variants to fixation, and can dramatically alter the pattern and distribution of allelic diversity in a population. Population-level sequencing data have enabled discoveries of selective sweeps associated with genes involved in recent adaptations in many species. In contrast, much debate but little evidence addresses whether "selfish" genes are capable of fixation-thereby leaving signatures identical to classical selective sweeps-despite being neutral or deleterious to organismal fitness. We previously described R2d2, a large copy-number variant that causes nonrandom segregation of mouse Chromosome 2 in females due to meiotic drive. Here we show population-genetic data consistent with a selfish sweep driven by alleles of R2d2 with high copy number (R2d2(HC)) in natural populations. We replicate this finding in multiple closed breeding populations from six outbred backgrounds segregating for R2d2 alleles. We find that R2d2(HC) rapidly increases in frequency, and in most cases becomes fixed in significantly fewer generations than can be explained by genetic drift. R2d2(HC) is also associated with significantly reduced litter sizes in heterozygous mothers, making it a true selfish allele. Our data provide direct evidence of populations actively undergoing selfish sweeps, and demonstrate that meiotic drive can rapidly alter the genomic landscape in favor of mutations with neutral or even negative effects on overall Darwinian fitness. Further study will reveal the incidence of selfish sweeps, and will elucidate the relative contributions of selfish genes, adaptation and genetic drift to evolution.

New Metacentric Populations and Phylogenetic Hypotheses Involving Whole-Arm Reciprocal Translocation in Mus musculus domesticus from Sicily, Southern Italy.

The house mouse Mus musculus domesticus is characterized by more than 100 metacentric populations, due to the occurrence of Robertsonian (Rb) fusions, together with the standard all-telocentric karyotype (2n = 40). We examined G-banded karyotypes of 18 mice from 10 localities in Sicily and describe 3 new metacentric populations: 'Ragusa Ibla' (IRAG), 2n = 33-36, Rb(2.4), Rb(5.6), Rb(9.16), Rb(13.17); 'Piana degli Albanesi' (IPIA), 2n = 23, Rb(1.18), Rb(2.15), Rb(3.5), Rb(4.12), Rb(6.11), Rb(7.8), Rb(9.16), Rb(10.14), Rb(13.17); 'Trapani' (ITRA), 2n = 22, Rb(1.18), Rb(2.15), Rb(3.7), Rb(4.12), Rb(5.9), Rb(6.11), Rb(8.16), Rb(10.14), Rb(13.17). Three mice belonged to the previously reported 'Castelbuono' race (ICAS), 2n = 24, which is very similar to the nearby 'Palermo' (IPAL) race, 2n = 26. Three Rb fusions not yet observed in wild mouse populations were identified: Rb(3.5), Rb(3.7) and Rb(5.9). Rb fusions shared among 4 races (IPIA, IRAG, ICAS, and IPAL) allowed us to describe their potential phylogenetic relationships. We obtained 2 alternative phylogenetic trees. The differences between them are mainly due to various modes of formation of IPIA and ITRA. In the first hypothesis, the specific Rb fusions occurred independently. In the second, those of IRAG originated from those of IPIA via whole-arm reciprocal translocations.

Cryptic speciation and chromosomal repatterning in the South African climbing mice Dendromus (Rodentia, Nesomyidae).

We evaluate the intra- and interspecific diversity in the four South African rodent species of the genus Dendromus. The molecular phylogenetic analysis on twenty-three individuals have been conducted on a combined dataset of nuclear and mitochondrial markers. Moreover, the extent and processes underlying chromosomal variation, have been investigated on three species by mean of G-, C-bands, NORs and Zoo-FISH analysis. The molecular analysis shows the presence of six monophyletic lineages corresponding to D. mesomelas, D. mystacalis and four lineages within D. cfr. melanotis with high divergence values (ranges: 10.6% - 18.3%) that raises the question of the possible presence of cryptic species. The first description of the karyotype for D. mesomelas and D. mystacalis and C- and G- banding for one lineage of D. cfr. melanotis are reported highlighting an extended karyotype reorganization in the genus. Furthermore, the G-banding and Zoo-FISH evidenced an autosome-sex chromosome translocation characterizing all the species and our timing estimates this mutation date back 7.4 mya (Late Miocene). Finally, the molecular clock suggests that cladogenesis took place since the end of Miocene to Plio-Pleistocene, probably due to ecological factors, isolation in refugia followed by differential adaptation to the mesic or dry habitat.

Testing the performance of a fragment of the COI gene to identify western Palaearctic stag beetle species (Coleoptera, Lucanidae).

THE TAXONOMY OF STAG BEETLES (COLEOPTERA: Lucanidae) remains challenging, mainly due to the sexual dimorphism and the strong allometry in males. Such conjecture confounds taxonomic based conservation efforts that are urgently needed due to numerous threats to stag beetle biodiversity. Molecular tools could help solve the problem of identification of the different recognized taxa in the "Lucanus cervus complex" and in some related Palaearctic species. We investigated the potential use of a 670 bp region at the 3' end of the mitochondrial cytochrome c oxidase subunit I gene (COI) for barcoding purposes (different from the standard COI barcoding region). Well resolved species and subspecies were L. tetraodon, L. cervusakbesianus, L. c. laticornis, as well as the two eastern Asian outgroup taxa L. formosanus and L. hermani. Conversely, certain taxa could not be distinguished from each other based on K2P-distances and tree topologies: L. c. fabiani / L. (P.) barbarossa, L. c. judaicus / an unknown Lucanus species, L. c. cervus / L. c. turcicus / L. c. pentaphyllus / L. (P.) macrophyllus / L. ibericus. The relative roles of phenotypic plasticity, recurrent hybridisation and incomplete lineage sorting underlying taxonomic and phylogenetic discordances are discussed.

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.

A new chromosomal race of the house mouse, Mus musculus domesticus, in the Vulcano Island-Aeolian Archipelago, Italy.

In this paper we describe a new Robertsonian (Rb) race of the house mouse from Vulcano (Aeolian archipelago) through the identification of the metacentric chromosomes. We analysed fifteen mice. All the specimens were found to have the same karyotype 2n=26. This karyotype is characterized by Rb(1.2), Rb(3.9), Rb(4.13), Rb(5.14), Rb(8.12), Rb(10.16) and Rb(15.17). The differences between the race of Vulcano and the races in a neighbour island (Lipari) consist in the presence of Rb(10.16) and Rb(15.17) in the former and Rb(6.16) and Rb(10.15) in the latter. We discuss the possible hypotheses regarding the origin between these two races including the possible occurrence of a whole arm reciprocal translocation (WART) on the Vulcano island.