Jan 162010
 

One of the most talked about ideas in genetic studies of asexual reproduction has been that of extreme Allelic Sequence Divergence (ASD), often called the “Meselson effect” after Matthew Meselson who is usually credited with this idea. In obligatory asexuals (apomicts), which never have the opportunity to recombine during meiosis, the once homologous chromosome pairs are now independent of each other. Their gene copies (previously normal alleles) can accumulate independent mutations, be subject to different types and intensities of selection, and diverge in structure and function without recombination bringing them back together again. Since homologous chromosomes contain the maternal and paternal alleles in meiotic (sexual) species these will in effect become independent genetic loci when meiosis is abandoned, much like gene duplicates elsewhere in the genome. Although they will start out as very similar, once meiosis stops they will start to diverge along independent trajectories and the prediction is that in ancient asexuals they will become very divergent indeed. There are some unusual phylogenetic relationships between apomict “alleles” too.Just like with gene duplicates there will be three broad classes of outcome.

  1. One copy may accumulate debilitating mutations and become a pseudogene
  2. Purifying selection may prevent the accumulation of many non-synonymous substitutions and the copies may continue to fulfill the same functional role.
  3. They may diverge in function and become members of a gene family.

An interesting question is whether these apomicts can suffer from haploinsufficiency effects. Polyploid apomicts are more common, probably due to hybridization being a common way to originate apomixis, but do diploids apomicts suffer when option 1 or 3 (above) occur? Is 2 just a method of maintaining the di-allelic buffer that normal sexual diploids have?

I was reading MJD White (1945) “Animal Cytology and Evolution” last year and was struck by the similarity there to current ideas of extreme ASD.

“If we suppose an ameiotic form evolving for a very long period of time we might imagine its two chromosome sets becoming completely unlike, so that it could no longer be considered as a diploid either in a genetical or cytological sense.” (p283)

The divergence of chromosomes as described by White 65 years ago is, just like gene sequence divergence, continuous. I like this quote as a different perspective on modern ideas of extreme ASD in ameiotic species (Meselson effect). Did these ideas originate with White? Some of them it seems, but as always, its probably more complex than that. I would like to see a real review of the history of studies of asexual reproduction. I sometimes joke that if there is any doubt evolutionary ideas should just be assumed to originate with Haldane until there is evidence to the contrary.

The figure is taken from: Lunt, D.H. (2008) BMC Evolutionary Biology 2008, 8:194

Jul 072008
 

I’ve just had a manuscript published at BMC Evolutionary Biology so thought I’d share a synopsis.
I’ve been interested in root knot nematodes for a while as they are a powerful system for evolutionary genetics and amazingly successful parasites of plants- especially crop plants. Trudgill and Blok (2001) estimate that they “have host ranges that encompass the majority of flowering plants” and that Meloidogyne incognita “is possibly the single most damaging crop pathogen in the world”.
Interestingly, the 3 most damaging species are obligatory asexual mitotic parthenogens (apomicts), which is perhaps counter intuitive given the ongoing arms race between plants and nematode. Root Knot Nematodes have previously been suggested to be ancient asexuals, and I’m interested in the consequences of asexuality for the genome, and the phylogenetic pattern of genetic diversity. In this work I sequenced a number of nuclear protein-coding genes to test the predictions of ancient asexuality (in terms of allelic sequence divergence and phylogenetic clustering of alleles within morphological species). I also sequenced a sperm-specific gene to look for evidence of pseudogene formation and changes in evolutionary rate with respect to their sexual (meiotically-reproducing) close relatives. This work provides evidence that the signatures of ancient asexuality that were recovered are actually the product of a reasonably recent interspecific hybridization event.

This manuscript is free to download at the BMC site (although the correctly formatted version isn’t available yet).

Genetic tests of ancient asexuality in Root Knot Nematodes reveal recent hybrid origins

David H Lunt

BMC Evolutionary Biology 2008, 8:194
doi:10.1186/1471-2148-8-194
Published: 7 July 2008

Abstract

Background
The existence of “ancient asexuals”, taxa that have persisted for long periods of evolutionary history without sexual recombination, is both controversial and important for our understanding of the evolution and maintenance of sexual reproduction. A lack of sex has consequences not only for the ecology of the asexual organism but also for its genome. Several genetic signatures are predicted from long-term asexual (apomictic) reproduction including (i) large “allelic” sequence divergence (ii) lack of phylogenetic clustering of “alleles” within morphological species and (iii) decay and loss of genes specific to meiosis and sexual reproduction. These genetic signatures can be difficult to assess since it is difficult to demonstrate the allelic nature of very divergent sequences, divergence levels may be complicated by processes such as inter-specific hybridization, and genes may have secondary roles unrelated to sexual reproduction. Apomictic species of Meloidogyne root knot nematodes have been suggested previously to be ancient asexuals. Their relatives reproduce by meiotic parthenogenesis or facultative sexuality, which in combination with the abundance of nematode genomic sequence data, makes them a powerful system in which to study the consequences of reproductive mode on genomic divergence.

Results
Here, sequences from nuclear protein-coding genes are used to demonstrate that the first two predictions of ancient asexuality are found within the apomictic root knot nematodes. Alleles are more divergent in the apomictic taxa than in those species exhibiting recombination and do not group phylogenetically according to recognized species. In contrast some nuclear alleles, and mtDNA, are almost identical across species. Sequencing of Major Sperm Protein, a gamete-specific gene, from both meiotic and ameiotic species reveals no increase in evolutionary rate nor change in substitution pattern in the apomictic taxa, indicating that the locus has been maintained by selection.

Conclusions
The data strongly suggests the tropical root knot nematode apomicts have a recent origin and are not anciently asexual. The results support that interspecific hybridization has been involved in the origin of this asexual group and has played a role in shaping the patterns of genetic diversity observed. This study suggests that genetic signatures of ancient asexuality must be taken with caution due to the confounding effect of interspecific hybridization, which has long been implicated in the origins of apomictic species.

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Trudgill, DL and Blok, VC (2001) Apomictic, polyphagous root-knot nematodes: exceptionally successful and damaging biotrophic root pathogens. Annu Rev Phytopathol 39:53-77