Recoding of Translation in Turtle Mitochondrial Genomes: Programmed Frameshift Mutations and Evidence of a Modified Genetic Code

A +1 frameshift insertion has been documented in the mitochondrial gene nad3 in some birds and reptiles. By sequencing polyadenylated mRNA of the chicken (Gallus gallus), we have shown that the extra nucleotide is transcribed and is present in mature mRNA. Evidence from other animal mitochondrial genomes has led us to hypothesize that certain mitochondrial translation systems have the ability to tolerate frameshift insertions using programmed translational frameshifting. To investigate this, we sequenced the mitochondrial genome of the red-eared slider turtle (Trachemys scripta), where both the widespread nad3 frameshift insertion and a novel site in nad4l were found. Sequencing the region surrounding the insertion in nad3 in a number of other turtles and tortoises reveal general mitochondrial +1 programmed frameshift site features as well as the apparent redefinition of a stop codon in Parker’s snake-neck turtle (Chelodina parkeri), the first known example of this in vertebrate mitochondria

Evidence from mitochondrial genomics on interordinal relationships in insects

Mitochondrial (mt) genomes are the largest molecular data source for deep level insect phylogenetics that is also obtainable in a reasonable timeframe and for a reasonable cost. Over 100 insect mt genomes have been sequenced, representing 29 of the 30 orders, multiple suborders for a third of the orders, and many representatives of the mega-diverse orders. Genome rearrangements have been found in a third of the insect orders however these rearrangements diagnose groups of ordinal or lower rank. Sequence based phylogenetic hypotheses utilizing mt genomic data are a promising source of data on interordinal relationships however these studies are hampered by base compositional biases, unequal rates of nucleotide substitution across groups and other long-branch effects. Available data from the field of insect mitogenomic phylogenetics is reviewed and future directions in this research outlined

Evolutionary transitions of complex labile traits: silk weaving and arboreal nesting in Polyrhachis ants

Understanding the maintenance and evolution of complex group behavioural systems has broad significance to our understanding of social evolution, yet we have little insight into how these systems have evolved. Nest-weaving, a rare group behaviour considered a pinnacle of cooperative action in social insects, involves the coordination of workers and larvae by incorporating larval silk into the nest structure. To investigate the evolution of this complex behaviour in the ant genus Polyrhachis, we used comparative analysis and an inferred molecular phylogeny based on three mitochondrial genes COI, COII and CytB, and three nuclear genes EF1 a-F2, Wg and Tf. Our results showed that arboreality and nest-weaving are closely associated, but in contrast to the previous hypotheses, represent the ancestral state in the monophyletic genus. Nest-weaving within the genus, moreover, is remarkably labile. Arboreality and nest-weaving have been lost and partially regained on at least two occasions: two non-weaving subterranean species (sister taxa likely reflecting a single evolutionary event) have reverted to arboreal nesting habits without regaining the use of silk nests, while a third subterranean species has transitioned to nesting in silk nests on the sides of rocks, obtaining silk from spiders and not their own larvae. The loss of larval cocoons, which is correlated with the most complex form of nest-weaving behavior as typified in Oecophylla, has occurred independently on at least two occasions within Polyrhachis. The repeated loss of nest-weaving behaviour and its partial regaining within the genus provides the first example of a complex group-level trait that did not arise through behavioural progression from simple to complex states. The evolution and loss of complex group-level traits may be more evolutionarily labile than previously appreciated

PGDnointrons_alnFLYTREE

Alignment of dipteran PGD gene sequences from the FLYTREE project in fasta format