Thursday, August 27, 2015

Protein evolution in Arachnids

Opiliones (Cosmetidae) | by Sidclay Dias
Just at the conference last week it was announced that BOLD, the world's workbench for DNA Barcode data, surpassed the 500 000 species mark. Some 420 000 of those are animal species. With so much information now available for a single gene region (cytochrome c oxidase 1 or COI) we are in a very good position to probe patterns of mitochondrial evolution.

Colleagues here at BIO (Monica Young and Paul Hebert) did just that. In their brand new study they examined levels of amino acid substitution and the frequency of indels in COI from 4177 species of arachnids. 

Arachnids are the second most diverse group of arthropods with about 100 000 described species but there are colleagues that estimate the real diversity of the group to be at least ten times larger. Certainly a large group to tackle but the with representatives from all 16 orders and 43% of its families (267/625) the dataset studied is equally impressive. 

The colleagues examined divergences at three taxonomic levels—among members of each order to an outgroup, among families in each order and among BINs, a species proxy, in each family. Order Distances vary fourfold (0.10–0.39), while the mean of the Family Distances for the ten orders ranges fivefold (0.07–0.35). BIN Distances show great variation, ranging from 0.01 or less in 12 families to more than 0.25 in eight families. Patterns of amino acid substitution in COI are generally congruent with previously reported variation in nucleotide substitution rates in arachnids, but provide some new insights, such as clear rate acceleration in the Opiliones. By revealing a strong association between elevated rates of nucleotide and amino acid substitution, this study builds evidence for the selective importance of the rate variation among arachnid lineages. Moreover, it establishes that groups whose COI genes have elevated levels of amino acid substitution also regularly possess indels, a dramatic form of protein reconfiguration.

Indels are an interesting phenomenon especially in animal COI, where they seldom occur.Even more interesting is the relationship between a higher substitution rate and the occurrence of indels and other dramatic changes such as genomic rearrangements. Earlier work has shown that mitochondrial strand-specific nucleotide composition bias in some arachnid groups was among other things caused by an inversion of a fragment containing the COI gene. 

Overall, this study suggests that the mitochondrial genome of some arachnid groups is dynamic with high rates of amino acid substitution and frequent indels, while it is ‘locked down’ in others. Dynamic genomes are most prevalent in arachnids with short generation times, but the possible impact of breeding system deserves investigation since many of the rapidly evolving lineages reproduce by haplodiploidy, a mode of reproduction absent in ‘locked down’ taxa.

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