Tuesday, 6 February 2018

Mites Evolving All Around Us

A scanning electron microscope image of an American house dust mite, Dermatophagoides farinae.
Image credit: Ellen Foot Perkowski
House dust mites evolved a new way to protect their genome | University of Michigan News

Unless you have a microscope or exceptionally good eyesight you are never likely to see one but you are living now with millions of them in your carpets, furniture and beds. They are of course the ubiquitous house dust mites, and they have an interesting and unusual evolutionary history.

This history in turn is probably responsible for a unique solution to a common problem faced by all organisms - how to cope with those pieces of non-coding DNA called transposons, part of the junk DNA, that can randomly relocate themselves within a genome, causing mutations and diseases. Transposons behave a little like independent strands of DNA with evolutionary pressures to survive despite evolutionary pressure on their 'hosts' to control them.

The house dust mites' unusual history is that they are a rare example of a former parasite that has reverted to a free-living existence. A parasitic lifestyle very often produces a genetic crisis as the parasite combats attempts by the host to resist it, so this intense selection pressure can lead to some extreme solutions to problems. For example very many parasites undergo a great reduction of complexity as they come to depend on the host for many functions. This is, of course, contrary to what creationists often tell their dupes - that evolution always involves an increase in complexity. It doesn't. Evolution does not have a direction or obey rules, least of all so creationists can pretend evolution requires something rendered impossible by some mysterious effect of the Second Law of Thermodynamics.

Converting back to a non-parasitic life-style is also a major change for the organism which can produce another genetic crisis, as it now needs to protect itself from a new range of threats, so house dust mites seem to have undergone two such crises in their evolution.

The evolutionary arms race between transposons and almost all organisms, has evolved multiple mechanism, one of which involves RNA interference (RNAi). An investigation of the genome of house dust mites has failed to find a major pathway in this mechanism; instead they seem to have evolved a novel solution. Since the pathway is found in other related members of the Acari class, this is believed to have been a fairly recent event.

The findings of the team from the Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan, USA and the Department of Biological Sciences, University of Southern Mississippi, Hattiesburg, Mississippi, USA, published their finding in an open access paper in PLOS Genetics a few days ago. They suggest that it was two genetic crises in the evolution fort to a parasitic life-syle and then back again that caused this 'rewiring' of the mechanism for dealing with the transposon problem.

Abstract
House dust mites are common pests with an unusual evolutionary history, being descendants of a parasitic ancestor. Transition to parasitism is frequently accompanied by genome rearrangements, possibly to accommodate the genetic change needed to access new ecology. Transposable element (TE) activity is a source of genomic instability that can trigger large-scale genomic alterations. Eukaryotes have multiple transposon control mechanisms, one of which is RNA interference (RNAi). Investigation of the dust mite genome failed to identify a major RNAi pathway: the Piwi-associated RNA (piRNA) pathway, which has been replaced by a novel small-interfering RNAs (siRNAs)-like pathway. Co-opting of piRNA function by dust mite siRNAs is extensive, including establishment of TE control master loci that produce siRNAs. Interestingly, other members of the Acari have piRNAs indicating loss of this mechanism in dust mites is a recent event. Flux of RNAi-mediated control of TEs highlights the unusual arc of dust mite evolution.

Author summary
Investigation of small RNA populations in dust mites revealed absence of the piwi-associated RNA (piRNA) pathway. Apart from several nematode and platyhelminths lineages, piRNAs are an essential component of animal genome surveillance, actively targeting and silencing transposable elements. In dust mites, expansion of Dicer produced small-interfering RNA (siRNA) biology compensates for loss of piRNAs. The dramatic difference we find in dust mites is likely a consequence of their evolutionary history, which is marked by descent from a parasite to the current free-living form. Our study highlights a correlation between perturbation of transposon surveillance and shifts in ecology.

Mondal M, Klimov P, Flynt AS (2018)
Rewired RNAi-mediated genome surveillance in house dust mites.
PLoS Genet 14(1): e1007183. https://doi.org/10.1371/journal.pgen.1007183

Copyright: © 2018 The authors.
Published open access
Reprinted under the terms of a Creative Commons Attribution 4.0 International license (CC BY 4.0)

So how does this fit with creationism's recent lab-coated version, intelligent (sic) design?

It doesn't of course. Everything about the evolution of house dust mites refutes the idea of any intelligence being involved.

Firstly, we have the problem of bits of non-coding junk DNA being able to relocate randomly withing the genome. What was non-coding junk DNA doing there in the first place and for what purpose is it able to randomly relocate, causing mutations and disease? Whatever it was, looked at it from an intelligent (sic) design perspective, the solution to this apparently pointless problem is a hugely complex system for controlling it and minimising its effects. Meanwhile, the problem seems to have been repetitively 'redesigned' to overcome the solutions, so there are no multiple solutions.

Then we have the apparent abandonment of these solutions in just one member of a class of arthropods and it's replacement with a different solution, while all other members and almost all other eukaryote species, have the old solutions. Is this what an intelligent designer does, especially one which will know inerrently in advance whether its new solution is better or worse than it's old ones so has no need to experiment?

And all this to allow a species that started off free-living, to became a parasite and then in a design volte-face become free-living again when humans provided lots of nice places for it to live and a plentiful supply of skin scales for food.

It anyone can discern any semblance of intelligence in this, please tell me where it is. Whatever it was that led to this situation, the word 'intelligent' seems singularly inapt. Seeing this as intelligent probably says all that need be said about the person calling it intelligent. but then, these are people who can't understand a simple process like evolution so think it must be magic.

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