Massive Evolutionary Reduction in Genome Size

A Chilean cicada, which hosts particularly unusual symbiotic bacteria.

Photo credit: Piotr Lukasik

UM Publishes Research on Unusual Gene Evolution in Bacteria - UM News - University Of Montana:

Hopefully getting back to blogging again after spending time on another book, it's a pleasure coming back with details of two papers published by the same team a few days ago that shatter so many creationist dogmas, it's hard to keep count.

Creationists will tell you, for example, that evolution involves an increase in complexity and therefore an increase in information in the genome, and that this is impossible because of some mysterious application of the Second Law of Thermodynamics which ignore the fact that an organism, Earth, and even the solar system are not closed systems. Never-the-less, they'll confidently assure you that in this way science has proved evolution can't happen, it's just that millions of working biologists never got the memo and have been mistaking the observed instances of not evolution for examples of... well... evolution.

During the past 70 million years, the bacteria underwent extreme adaptations to live within the insects’ bodies, losing between an estimated 95 to 97 percent of their genes and resulting in some of the smallest genomes known to any organisms. In the process, they lost the ability to live anywhere outside of cicadas.

“Cicada symbiotic complexes are very different from any other known organism, said Matt Campbell, a UM graduate student who studies cicadas in UM biology Associate Professor John McCutcheon’s lab, based in the Division of Biological Sciences.

UM Publishes Research on Unusual Gene Evolution in Bacteria, January 05, 2018

It's nonsense, of course, and contradicts what we can observe, but even if this mysterious prediction of the Second Law were true, it ignores the fact that evolution does not essentially involve an increase in complexity. There are literally millions of parasitic and symbiotic species, both single-celled and multicellular, that have evolved from free-living species and in doing so have lost not only major organs such as digestive systems, but a large part of their genome.

In the case of symbiotic species, especially where there is mutual dependence, one species might almost have become an integral part of the host cell - mitochondria and chloroplasts for example, some of their genes having migrated into the cell nucleus.

These two papers describe a bacterial endosymbiont in species of cicada which has taken this process to extremes, not only with a highly reduced genome but with several genome lines of the same original bacteria (Hodgkinia) present in the same cells and each mutually dependent on the other as each carries out part of an essential process. Cicada's, like many single food source species, are dependent on endosymbiotic species to supplement essential nutrients missing from the food source. Cicadas' symbiotic bacteria produce amino acids and vitamins.

Significance
Highly reduced genomes from bacteria that are long-term beneficial endosymbionts of insects often show remarkable structural stability. Endosymbionts in insects diverged by tens or hundreds of millions of years often have genomes almost completely conserved in gene order and content. Here, we show that an endosymbiont in some cicadas has repeatedly and independently fractured into complexes of distinct genomic and cellular lineages present in the same host. Individual endosymbiont lineages, having lost many of the essential ancestral genes, rely on each other for basic function and together seem to provide the same nutritional benefits as the ancestral single symbiont. These cicada endosymbionts show genomic parallels to mitochondria and provide another example of how normally stable genomes can lose structural stability.

Abstract
Bacterial endosymbionts that provide nutrients to hosts often have genomes that are extremely stable in structure and gene content. In contrast, the genome of the endosymbiont Hodgkinia cicadicola has fractured into multiple distinct lineages in some species of the cicada genus Tettigades. To better understand the frequency, timing, and outcomes of Hodgkinia lineage splitting throughout this cicada genus, we sampled cicadas over three field seasons in Chile and performed genomics and microscopy on representative samples. We found that a single ancestral Hodgkinia lineage has split at least six independent times in Tettigades over the last 4 million years, resulting in complexes of between two and six distinct Hodgkinia lineages per host. Individual genomes in these symbiotic complexes differ dramatically in relative abundance, genome size, organization, and gene content. Each Hodgkinia lineage retains a small set of core genes involved in genetic information processing, but the high level of gene loss experienced by all genomes suggests that extensive sharing of gene products among symbiont cells must occur. In total, Hodgkinia complexes that consist of multiple lineages encode nearly complete sets of genes present on the ancestral single lineage and presumably perform the same functions as symbionts that have not undergone splitting. However, differences in the timing of the splits, along with dissimilar gene loss patterns on the resulting genomes, have led to very different outcomes of lineage splitting in extant cicadas.

Piotr Łukasik, Katherine Nazario, James T. Van Leuven, Matthew A. Campbell, Mariah Meyer, Anna Michalik, Pablo Pessacq, Chris Simon, Claudio Veloso, John P. McCutcheon.
Multiple origins of interdependent endosymbiotic complexes in a genus of cicadas.
Proceedings of the National Academy of Sciences, 2017; 201712321 DOI: 10.1073/pnas.1712321115

The second paper, published in Current Biology is behind a paywall and the copyright holders want £22 to reproduce even the abstract. (Matthew A. Campbell, Piotr Łukasik, Chris Simon, John P. McCutcheon; Idiosyncratic Genome Degradation in a Bacterial Endosymbiont of Periodical Cicadas; Current Biology , Volume 27 , Issue 22 , 3568 - 3575.e3. DOI: http://dx.doi.org/10.1016/j.cub.2017.10.008) This paper shows that there are up to twenty circular molecules of Hodgkinia DNA which together contain much of the ancestral Hodgkinia genome. The 'dose' of Hodgkinia genome varies widely in different cicada species.

Cicadas are know for their long life cycle, often spending many years as underground nymphs before emerging to become become short-lived breeding adults. The cicadas with the longest life-cycles appear to have the most complex arrangement with their symbiotic bacteria. It is believed this arrangement evolved by accident as there is no obvious adaptive advantage for the cicadas so long as they continue to get their food supplements.

There is, as we might expect, no intelligent reason why a bacterial genome should become fragmented in this way either or why, for that matter, an insect like a cicada should be designed so its needs symbiotic bacteria resident within it in order to survive because the food source it is 'designed' to exploit isn't entirely adequate.

Maybe a a creationist can offer an explanation as well as explaining how evolution has apparently proceeded by a huge reduction on genome size.

But I doubt it. These things are best ignored.

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