Land-bridge calibration of molecular clocks and the post-glacial colonization of Scandinavia by the Eurasian field vole microtus agrestis

Phylogeography interprets molecular genetic variation in a spatial and temporal context. Molecular clocks are frequently used to calibrate phylogeographic analyses, however there is mounting evidence that molecular rates decay over the relevant timescales. It is therefore essential that an appropriate rate is determined, consistent with the temporal scale of the specific analysis. This can be achieved by using temporally spaced data such as ancient DNA or by relating the divergence of lineages directly to contemporaneous external events of known time. Here we calibrate a Eurasian field vole (Microtus agrestis) mitochondrial genealogy from the well-established series of post-glacial geophysical changes that led to the formation of the Baltic Sea and the separation of the Scandinavian peninsula from the central European mainland. The field vole exhibits the common phylogeographic pattern of Scandinavian colonization from both the north and the south, however the southernmost of the two relevant lineages appears to have originated in situ on the Scandinavian peninsula, or possibly in the adjacent island of Zealand, around the close of the Younger Dryas. The mitochondrial substitution rate and the timescale for the genealogy are closely consistent with those obtained with a previous calibration, based on the separation of the British Isles from mainland Europe. However the result here is arguably more certain, given the level of confidence that can be placed in one of the central assumptions of the calibration, that field voles could not survive the last glaciation of the southern part of the Scandinavian peninsula. Furthermore, the similarity between the molecular clock rate estimated here and those obtained by sampling heterochronous (ancient) DNA (including that of a congeneric species) suggest that there is little disparity between the measured genetic divergence and the population divergence that is implicit in our land-bridge calibration

Speciation in the house mouse, Mus musculus - mechanisms of isolation

Speciation, the formation of species, is a central problem in evolutionary biology. The genetic basis and evolution of reproductive isolation between taxa is a key for understanding speciation. The house mouse Mus musculus is an excellent model for the study of reproductive isolation. Two subspecies, M. m. musculus and M. m. domesticus that diverged from each other approximately between 1,000,000-350,000 years ago, form a narrow hybrid zone that extends across Europe. The standard chromosome complement of this species consists of 40 acrocentric chromosomes. However, in M. m. domesticus there are many local karyotypic races that are characterised by different sets of acrocentrics and metacentrics. Accumulation of chromosomal rearrangements may lead to reproductive isolation between populations. The first theoretical model of this process was postulated by Dobzhansky (1937) and Muller (1942). They expressed the idea that speciation is a by-product of independent divergence between populations. The hybrid zone between sister mouse taxa can be used to identify genomic regions underlying reproductive isolation. Variation in the degree of gene flow across the hybrid zone is measured using molecular markers. Thus, mice offer a unique opportunity to study relationships between genotype and phenotype

Times to most recent common mitochondrial ancestor (tMRCAs).

<p>Time to most recent common mitochondrial ancestor (tMRCA) for whole field vole population and the six clades. Median and 95% highest posterior density (HPD) range of times, obtained with Bayesian genealogy sampling, calibrated with possible times of origin of whole species and clade from southern Scandinavian peninsula.</p

Stages of land connectivity relating to mammal colonization of Scandinavia.

<p>Based on reconstructions in Björck <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0103949#pone.0103949-Bjrck1" target="_blank">[30]</a>, <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0103949#pone.0103949-Bjrck2" target="_blank">[31]</a>; see text for detail. Dates in ka BP, defined as thousand years before AD 1950, calibrated using IntCal04 and IntCal09 curves <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0103949#pone.0103949-Reimer1" target="_blank">[32]</a>, <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0103949#pone.0103949-Reimer2" target="_blank">[33]</a>. Fennoscandian ice sheet - light gray, land - green, open water - light blue, modern coastline - black outline. <b>a:</b> Deglaciation of Scandinavian peninsula, until 13.1 ka BP (with dotted lines showing successive positions of ice sheet edge during late glacial retreat); <b>b:</b> First land bridge, 13.1-12.7 ka BP; <b>c:</b> Younger Dryas glacial re-advance and re-opening of Øresund channel, 12.7-12.1 ka BP; <b>d:</b> Second land bridge, 12.1-10.3 ka BP; <b>e:</b> Separation of Scandinavian peninsula by Dana River and then formation of Baltic Sea, 10.3-9.2 ka BP.</p

Geographical locations of samples from each clade.

<p>Closely adjacent localities assigned to same map location.</p

Bayesian skyline plots showing effective female population size.

<p>Effective female population size (<i>N_ef</i>), in thousands, multiplied by mean generation time (<i>T</i>), in years. Heavy line is median and lighter lines are 95% highest posterior density (HPD) limits. <i>N_ef x T</i> plotted on log scale for clarity and truncated to median estimate of tMRCA.</p

Genetic variation in the six mitochondrial lineages.

<p>Nucleotide diversity (<i>π</i>) with standard error estimated from 1 000 bootstrap replicates. Neutrality test statistics (Tajima's <i>D</i> and Fu's <i>F_S</i>) with significance derived from 10 000 coalescent simulations.</p