Cryptic speciation in the field vole: a multilocus approach confirms three highly divergent lineages in Eurasia.

Species are generally described from morphological features, but there is growing recognition of sister forms that show substantial genetic differentiation without obvious morphological variation and may therefore be considered 'cryptic species'. Here, we investigate the field vole (Microtus agrestis), a Eurasian mammal with little apparent morphological differentiation but which, on the basis of previous sex-linked nuclear and mitochondrial DNA (mtDNA) analyses, is subdivided into a Northern and a Southern lineage, sufficiently divergent that they may represent two cryptic species. These earlier studies also provided limited evidence for two major mtDNA lineages within Iberia. In our present study, we extend these findings through a multilocus approach. We sampled 163 individuals from 46 localities, mainly in Iberia, and sequenced seven loci, maternally, paternally and biparentally inherited. Our results show that the mtDNA lineage identified in Portugal is indeed a distinct third lineage on the basis of other markers as well. In fact, multilocus coalescent-based methods clearly support three separate evolutionary units that may represent cryptic species: Northern, Southern and Portuguese. Divergence among these units was inferred to have occurred during the last glacial period; the Portuguese lineage split occurred first (estimated at c. 70 000 bp), and the Northern and Southern lineages separated at around the last glacial maximum (estimated at c. 18 500 bp). Such recent formation of evolutionary units that might be considered species has repercussions in terms of understanding evolutionary processes and the diversity of small mammals in a European context.

Asymmetric and differential gene introgression at a contact zone between two highly divergent lineages of field voles (Microtus agrestis).

Secondary contact zones have the potential to shed light on the mode and rate at which reproductive isolation accumulates during allopatric speciation. We investigated the population genetics of a contact zone between two highly divergent lineages of field voles (Microtus agrestis) in the Swiss Jura mountains. To shed light on the processes underlying introgression, we used maternally, paternally, and bi-parentally inherited markers. Though the two lineages maintained a strong genetic structure, we found some hybrids and evidence of gene flow. The extent of introgression varied with the mode of inheritance, being highest for mtDNA and absent for the Y chromosome. In addition, introgression was asymmetric, occurring only from the Northern to the Southern lineage. Both patterns seem parsimoniously explained by neutral processes linked to differences in effective sizes and sex-biased dispersal rates. The lineage with lower effective population size was also the more introgressed, and the mode-of-inheritance effect correlated with the male-biased dispersal rate of microtine rodents. We cannot exclude, however, that Haldane's effect contributed to the latter, as we found a marginally significant deficit in males (the heterogametic sex) among hybrids. We propose a possible demographic scenario to account for the patterns documented, and empirical extensions to further investigate this contact zone.

A highly divergent mitochondrial DNA lineage of Microtus agrestis in southern Europe.

The Mediterranean peninsulas constitute important areas for endemism and intraspecific variation, and are likely places for cryptic biodiversity. We assessed the phylogeographic pattern of field voles (Microtus agrestis) in southern and central Europe by sequence analysis of a 385-bp fragment of the mitochondrial cytochrome b gene in 74 specimens from 44 localities. The majority of samples consisted of skulls collected from owl pellets. The data revealed a highly distinct cytochrome b lineage in an area ranging from Portugal to Hungary. This southern field vole phylogroup differed by a sequence divergence of 5.6-7.1% from the remaining haplotypes, a level of divergence comparable to that found between known Microtus sibling species. However, this ancient phylogeographic break that dates back many glacial cycles has not been recognised previously by either morphology or karyotype. The southern cytochrome b lineage was further divided into two well-defined sublineages that appear to have derived from different glacial refugia in the Iberian Peninsula.

Holarctic phylogeography of the root vole (Microtus oeconomus): implications for late Quaternary biogeography of high latitudes.

A species-wide phylogeographical study of the root vole (Microtus oeconomus) was performed using the whole 1140 base pair mitochondrial (mt) cytochrome b gene. We examined 83 specimens from 52 localities resulting in 65 unique haplotypes. Our results demonstrate that the root vole is divided into four main mtDNA phylogenetic lineages that seem to have largely allopatric distributions. Net divergence estimates (2.0-3.5%) between phylogroups, as well as relatively high nucleotide diversity estimates within phylogroups, indicate that the distinct phylogeographical structure was initiated by historical events that predated the latest glaciation. European root voles are divided into a Northern and a Central mtDNA phylogroup. The mtDNA data in concert with fossil records imply that root voles remained north of the classical refugial areas in southern Europe during the last glacial period. The currently fragmented populations in central Europe belong to a single mtDNA phylogroup. The Central Asian and the North European lineages are separated by the Ural Mountains, a phylogeographical split also found in collared lemmings (Dicrostonyx) and the common vole (M. arvalis). The Beringian lineage occurs from eastern Russia through Alaska to northwestern Canada. This distribution is congruent with the traditional boundaries of the Beringian refugium and with phylogeographical work on other organisms. In conclusion, similarities between the phylogeographical patterns in the root vole and other rodents, such as Arctic and subarctic lemmings, as well as more temperate vole species, indicate that late Quaternary geological and climatic events played a strong role in structuring northern biotic communities.

Phylogeography of lemmings (Lemmus): no evidence for postglacial colonization of Arctic from the Beringian refugium.

Beringia is considered as an important glacial refugium that served as the main source for colonization of formerly glaciated Arctic regions. To obtain high resolution views of Arctic refugial history, we examined mitochondrial cytochrome b phylogeography in the northern genus of rodents, Lemmus (true lemmings), sampled across its circumpolar distribution. Strong phylogeographical structure suggests vicariant separation over several glacial-interglacial periods and does not provide evidence supporting the importance of Beringia for extensive colonization of formerly glaciated regions. Rather than a source of postglacial colonization, Beringia represents an area of intraspecific endemism previously undetected by biogeographical analysis. Existing phylogeographical structure suggests that vicariant separation by glacial barriers was an important factor generating genetic divergence and, thus, increasing genetic diversity in lemmings on continental and circumpolar scales. However, there is little evidence for the direct effect of the last glaciation on the level of genetic variation and allele genealogy in lemmings on a regional geographical scale. This finding implies that the population genetic models of postglacial colonization suggested for temperate taxa might have limited applicability for Arctic species.

Direct evidence for suppression of recombination within two pericentric inversions in humans: a new sperm-FISH technique.

Crossover within a pericentric inversion produces reciprocal recombinant chromosomes that are duplicated/deficient for all chromatin distal to the breakpoints. In view of this fact, a new technique is presented for estimating the frequency of recombination within pericentric inversions. YAC probes were selected from within the q- and p-arm flanking regions of two human inversions, and two-color FISH analysis was performed on sperm from heterozygous inversion carriers. A total of 6,006 sperm were analyzed for chromosome 1 inversion (p31q12), and 3,168 were analyzed for chromosome 8 inversion (p23q22). Both inversions displayed suppression of crossing-over, although the amount of suppression differed between the two inversions. The recombination frequency of 13.1% recorded for chromosome 8 inversion was similar to the frequency of 11.4% previously estimated by the human/hamster-fusion method. For chromosome 1 inversion, the recombination frequency of 0. 4% reported here was below the limits of detection of the fusion technique. The simplicity of the FISH technique and the ease of scoring facilitate analysis of a sample-population size much larger than previously had been possible.

The mouse H19 locus mediates a transition between imprinted and non-imprinted DNA replication patterns.

Genes subject to genomic imprinting generally occur in clusters of hundreds of kilobases. These domains exhibit several gamete of origin-dependent manifestations, including a pattern of asynchronous replication when studied by fluorescence in situ hybridization (FISH). We find a transition from asynchronous replication at the imprinted mouse H19 gene to synchronous replication at the downstream Rpl23 gene, the human homologue of which appears to be non-imprinted. Two-colour FISH demonstrates that this transition is due solely to a difference in replication timing between the upstream and downstream chromatin on the later-replicating (maternal) chromosome. This difference is lost in mice deleted for the H19 gene body and 9.9 kb of upstream DNA when this deletion is maternally inherited, with synchronous replication patterns extending over 110 kb upstream from the deleted area. No effect is seen when the deletion is paternally inherited. The presence of a boundary element in this region has been suggested by observations of position-independent expression of H19 -containing transgenes and the blocking of accessibility of downstream enhancers to the upstream Igf2 and Ins2 genes on the maternal chromosome. The FISH studies presented here demonstrate the insulation of replication patterns within the imprinted domain from downstream, non-imprinted chromatin, mediated by an element at the H19 locus which is subject to genomic imprinting.

The occurrence of mountain hare mitochondrial DNA in wild brown hares.

If interspecific hybrids are fertile and backcross to either parental species, transmission of mitochondrial DNA over the species barrier can occur. To investigate if such transmission has occurred between the brown hare Lepus europeus Pall and the mountain hare L. timidus L. in Scandinavia, an analysis of genetic variation in mitochondrial DNA from 36 hares, collected from 15 localities, was performed. Sequence divergence of mtDNA between species was estimated at 8 +/- 1% (SD). Intraspecific mtDNA sequence divergence varied between 0.09 and 0.38% in brown hares and 0.10 and 1.44% in mountain hares. In six out of 18 brown hares examined, two different haplotypes of mountain hare origin were detected, demonstrating a transmission of mtDNA haplotypes from mountain hares to brown hares. The results indicate that interspecific hybridization between the two species occurs in wild populations.

The origin and distribution of the Lund Y chromosome in Microtus agrestis (Rodentia, Mammalia).

The Lund Y (Lu-Y) chromosome of the field vole (Microtus agrestis) is distinguished from the standard Y (St-Y) by its much longer short arm. G-banding revealed that the Lu-Y originated by a pericentric inversion in the St-Y. Chromosome analysis of 297 male field voles from 92 localities in Fennoscandia. Germany, and England, in addition to data from the literature, made it possible to map the distribution area of the Lu-Y. It is restricted to the south-western parts of Sweden. The question of when and where the Lund Y population originated is discussed. Adding data from a hybrid zone (Jaarola et al. 1997) and from females, totally 491 specimens from 120 localities were analyzed without detecting any variation in chromosome number and autosome morphology. Other cases of intraspecific Y chromosome polymorphism in mammals, and the use of Y chromosome variants as population genetic markers, are discussed.

Distribution and genetic heterogeneity of Puumala virus in Sweden.

Small mammals trapped in Sweden were analysed for specific antibody responses against three hantavirus serotypes and for the presence of viral antigen. To determine the genetic identity of viral RNA in lungs of seropositive bank voles (Clethrionomys glareolus), polymerase chain reactions and subsequent partial sequencing of both the M and S segments were employed. The sequences obtained were all identified as Puumala (PUU) virus, with a high degree of heterogeneity between the different geographical localities. Alignment of nucleotide and deduced amino acid sequences, together with phylogenetic analysis, showed that PUU viruses circulating in central Sweden were distinct from those in the northern region. The localization of the two distinct PUU virus genotypes was shown to correlate with the postglacial recolonization of Sweden by bank voles.

Colonization history of north European field voles (Microtus agrestis) revealed by mitochondrial DNA.

The genetic structure of field vole (Microtus agrestis) populations from northern Europe was examined by restriction fragment length polymorphisms of mitochondrial DNA (mtDNA) in 150 individuals from 67 localities. A total of 83 haplotypes was observed, most of which were rare and highly localized geographically. Overall nucleotide diversity was high (1.34%), but showed a tendency to decrease with higher latitude. Two major mtDNA lineages differing by 2% in nucleotide sequence were identified. A southern mtDNA lineage was observed in field voles from Britain, Denmark and southern and central Sweden, whereas voles from Finland and northern Sweden belonged to a northern lineage. The strict phylogeographic pattern suggests that the present population genetic structure in field voles reflects glacial history: the two groups are derived from different glacial refugia, and recolonized Fennoscandia from two directions. A 150-200-km-wide secondary contact zone between the two mtDNA groups was found in northern Sweden. Distinct phylogeographic substructuring was observed within both major mtDNA groups.

The behavior during pachynema of a normal and an inverted Y chromosome in Microtus agrestis.

The pachytene behavior of the chromosomes of Microtus agrestis (L.) (Rodentia, Arvicolidae) males carrying either the standard, or the pericentrically inverted Lund Y chromosome have been examined by electron microscopy of microspread spermatocytes. There is no synapsis between the X and either the standard or the Lund Y chromosomes during any substage of pachynema. Since synapsis is generally considered a prerequisite for crossing over, there appears to be no opportunity for crossover or chiasma formation between the X and Y in this species. The G-, C- and NOR-banded mitotic karyotypes of animals carrying the standard and Lund Y are also presented.

Absence of synapsis during pachynema of the normal sized sex chromosomes of Microtus arvalis.

The pachytene behavior of the chromosomes of males of Microtus arvalis (Pall.) (Rodentia, Arvicolidae) was examined by electron microscopy in microspread preparations of spermatocytes. There was no synapsis between the axes of these two chromosomes during this period. Since synapsis is universally considered a prerequisite for crossing over and chiasmata formation, disjunction of the sex chromosomes in this species prerequisite for crossing over and chiasmata formation, disjunction of the sex chromosomes in this species must be presumed to be achiasmatic. Unlike previously examined species with no synapsis or crossing over between the X and Y, the sex chromosomes of M. arvalis are of normal size: the X chromosome is of an "original" X size and the Y is a small acrocentric. C-band studies of M. arvalis mitotic metaphase reveal no blocks of heterochromatin on the sex chromosomes. The implications of these findings are discussed.

Genetic divergence in mitochondrial DNA between the wood mouse (Apodemus sylvaticus) and the yellow necked mouse (A. flavicollis).

Genetic variability and the relationships between clones of mitochondrial DNA (mtDNA) provide data which can be used to construct hypotheses about the biogeographical and postglacial colonization history of Fennoscandian species. We have investigated fragment differences in mtDNA among 24 Wood mice (Apodemus sylvaticus) from 8 localities, and 9 Yellow necked mice (A. flavicollis) from four North European localities. The greatest intraspecific sequence divergence found between mtDNA clones was 1.40% within A. sylvaticus and 1.00% within A. flavicollis. The mean pairwise divergence in samples from a local population (n = 14) of A. sylvaticus was only 0.003%. Interspecific fragment comparison of mtDNA from A. sylvaticus and A. flavicollis give a sequence divergence close to 10%. However, comparison of genetic distances based on mtDNA between the two Apodemus species shows that they are more distantly related than suggested by nuclear distances. The observed discrepancy between distances estimated from mitochondrial and nuclear DNA suggests that mtDNA divergence predated divergence in nuclear genes or that there was an influx of nuclear variation during the speciation process or in connection with the expansion and contractions of populations during interglacial and glacial periods.

Concordant divergence in proteins and mitochondrial DNA between two vole species in the genus Clethrionomys.

The bank vole (Clethrionomys glareolus) and the northern red-backed vole (C. rutilus) are two closely related species where interspecific crosses result in fertile female but sterile male offspring. Mitochondrial DNA (mtDNA) from C. rutilus has passed the species barrier and is found in C. glareolus from northern Fennoscandia. The present report shows that the genetic distance between the two species, calculated from enzyme data (Nei's D), is 0.64. Isoelectric focusing of muscle proteins resolved around 55 bands, of which each species had 6 or 7 bands not present in the other species. Sequence divergence of mtDNA from the two species is 13.9%. A comparison between protein and mtDNA distances in other species pairs reveals a high correlation between the two measures, indicating that differences in mtDNA between taxa are not random when compared to divergence in protein-coding nuclear genes. The relationship between genetic divergence in proteins and that in mtDNA between Clethrionomys glareolus and C. rutilus is similar to that found in other species pairs. It is also shown that despite large differences on the protein level it is still, in some cases, possible for species pairs to produce fertile hybrid females.