Alignment and Phylogenetic Trees

The Alignment consists of the masked 42,626 16SrDNA sequences sampled from Genbank Gammaproteobacteria as well as all known endosymbionts from lice including the newly sequenced taxa for this study: KX146199-KX146216. The tree files consists of 6 phylogenetic trees taken from different samples of the 42,626 taxa. The reduced trees are consensus trees of sampled sequence from a clustering algorithm, selected to represent sequence diversity. Numbers on the names of these datasets indicate the stringency of clustering. For example Ribo.70.con.tre indicates the sequences were selected from clusters were each sequence in the cluster had to be at least 70% or more similar to each other. Ribo.80.con.tre means the tree was built from sequences clustered with 80% similarity or more. Finally Ribo.100.con.tre indicates 100% of the sequences were used in this tree

MasterMSATmegacephalusOrderedLoci_11B

Microsatellite data for Microdipodops megacephlaus - 11 loci, 4 population

MasterMSATpallidusOrderLoci_11B

Microdipodops pallidus raw microsatellite data - 10 loci, 2 populations

Maximum likelihood phylogram representing phylogenetic relationships of <i>Riesia</i> p-endosymbionts.

<p>Numbers above the node represent divergence dates (in millions of years) whereas numbers below the nodes are bootstrap support values (only numbers greater then 60 are shown). The divergence date calibration point of 9.42–17.38 My is indicated with an asterisk.</p

Maximum likelihood phylogram representing phylogenetic relationships of louse p-endosymbionts, common insect p-endosymbionts, and closely related taxa as determined from a BLAST search of each louse endosymbiont sequence.

<p>Numbers at nodes indicate maximum likelihood support values greater than 60. Gray lines indicate louse p-endosymbionts. The p-endosymbiont from <i>Pedicinus badii</i> (the louse that parasitizes Red Colobus monkeys) is shown in red demonstrating that it does not group with the <i>Riesia</i> p-endosymbionts. There are now at least six distinct clades of p-endosymbionts sampled from sucking lice.</p

Percent sequence divergence and rate of nucleotide substitution of the <i>16S rDNA</i> of <i>Riesia</i> the p-endosymbiont from anthropoid primate lice calibrated at 9.42 and 17.38 My.

<p>Percent sequence divergence and rate of nucleotide substitution of the <i>16S rDNA</i> of <i>Riesia</i> the p-endosymbiont from anthropoid primate lice calibrated at 9.42 and 17.38 My.</p

Bacteria taxa, their hosts, and GenBank accession numbers used in the phylogenetic analysis presented in Figure 1.

<p>Some bacteria lack a species name because they have not been characterized completely. Secondary rather than primary endosymbionts are indicated with an asterisk. Free-living bacteria have no associated host.</p

Reduced major axis regression of the log transformed data from Figure 3.

<p>The age of the association is on the x-axis and the rate of nucleotide evolution is on the y-axis. 78% of the variation in rate of nucleotide evolution can be explained by the age of the association suggesting that the rate of nucleotide evolution does decrease over time in p-endosymbionts of insects.</p

Primary endosymbiont nucleotide substitution rates as a function of the age of insect/p-endosymbiont association.

<p>Ages and rates were retrieved from the literature or were calculated from pairwise sequence divergences and are shown as percent per 50 My. Point estimates (diamonds) represent the median value between the upper and lower estimates (bars show the full range of dates). The dotted line indicates a rate of 2% per 50 My. It has been suggested that the tse-tse fly and aphid p-endosymbionts (<i>Wigglesworthia</i> and <i>Buchnera</i>, respectively) are closely related to each other and are the result of a more ancient endosymbiosis event than represented here <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0004969#pone.0004969-Lerat1" target="_blank">[68]</a>, <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0004969#pone.0004969-Canback1" target="_blank">[69]</a>. Using an older date to calculate rates, however, does not change the results (data available upon request).</p

TickDrag

Off-host tick dat