Human Y chromosome undergoes purifying selection

A somewhat technical yet interesting study on Y chromosome evolution in humans:

Melissa A. Wilson Sayres et al., Natural Selection Reduced Diversity on Human Y Chromosomes. PLoS ONE 2014. Open access → LINK [doi:10.1371/journal.pgen.1004064]

Abstract


The human Y chromosome exhibits surprisingly low levels of genetic diversity. This could result from neutral processes if the effective population size of males is reduced relative to females due to a higher variance in the number of offspring from males than from females. Alternatively, selection acting on new mutations, and affecting linked neutral sites, could reduce variability on the Y chromosome. Here, using genome-wide analyses of X, Y, autosomal and mitochondrial DNA, in combination with extensive population genetic simulations, we show that low observed Y chromosome variability is not consistent with a purely neutral model. Instead, we show that models of purifying selection are consistent with observed Y diversity. Further, the number of sites estimated to be under purifying selection greatly exceeds the number of Y-linked coding sites, suggesting the importance of the highly repetitive ampliconic regions. While we show that purifying selection removing deleterious mutations can explain the low diversity on the Y chromosome, we cannot exclude the possibility that positive selection acting on beneficial mutations could have also reduced diversity in linked neutral regions, and may have contributed to lowering human Y chromosome diversity. Because the functional significance of the ampliconic regions is poorly understood, our findings should motivate future research in this area.

Positive selection (or directional selection) happens when a variant gets so good that everything else becomes bad by comparison. This may be just because an environmental change, possibly caused by migration (or whatever other reason) substantially alters the rules of the game. Much more rarely a novel mutation (or accumulation of several of them) may happen to generate a phenotype that is much more fit even for pre-existent conditions. As I understand it, positive selection does happen only rarely (but spectacularly). An example in humans is the selection of whiter skin shades in latitudes far away from the tropics (because of the “photosynthesis” of vitamin D in the skin, crucial for early brain development), another more generalized one is the selection for improved brains (not necessarily just bigger), able to face changing conditions more dynamically and develop more efficient tools and weapons.

Purifying selection (or negative selection) is quite different and surely much more common. As novel mutations arise randomly, in at least many cases, the vast majority I dare say, they happen to be harmful for a previously well-tuned genotype (and its derived phenotype). As result, the carriers have decreased opportunities for reproduction, when they don’t just die right away. Natural selection acts mostly this way and in many cases the types can become very stable for this reason, as happens with genera that have been successful on this planet since long before humankind arose, such as sharks or crocodiles.

This last is what seems to be happening to the human Y chromosome: novel mutations are at least quite often harmful (maybe they cause sterility or whatever other traits in the male that cause decreased reproductive efficiency) and they are regularly pruned off the tree by natural selection. 

Purifying selection slows down the effective mutation rate

Interestingly the authors mention that:

… if purifying selection is the dominant force on the Y chromosome, the topology of the tree should remain intact, but the coalescent times are expected to be reduced.

That would be, I understand, because the observed mutation rate has little relation with the actual accumulated (effective) mutation rate, which is much slower because of the continuous pruning of the negative selection.

Purifying selection has also been observed in the mitochondrial DNA, having the same kind of slowing impact on the “molecular clock”.

 

Plants do use epigenetics to adapt to diverse environments

If you’ve ever grown plants that come from a distant land, you may be familiar with the fact that you may need an adaptive process of one or more generations to get the best of them. Oddly enough this time is often too short for genetic adaption to happen and sweep over, especially as most of the ill-adapted plants don’t really die nor fail to reproduce (i.e. they are not too aggressively selected against). How does it happen then? Epigenetics may have the answer.

Robert J. Schmidt et al., Patterns of population epigenomic diversity. Nature 2013. Open access → LINK [doi:10.1038/nature11968]

Abstract


Natural epigenetic variation provides a source for the generation of phenotypic diversity, but to understand its contribution to such diversity, its interaction with genetic variation requires further investigation. Here we report population-wide DNA sequencing of genomes, transcriptomes and methylomes of wild Arabidopsis thaliana accessions. Single cytosine methylation polymorphisms are not linked to genotype. However, the rate of linkage disequilibrium decay amongst differentially methylated regions targeted by RNA-directed DNA methylation is similar to the rate for single nucleotide polymorphisms. Association analyses of these RNA-directed DNA methylation regions with genetic variants identified thousands of methylation quantitative trait loci, which revealed the population estimate of genetically dependent methylation variation. Analysis of invariably methylated transposons and genes across this population indicates that loci targeted by RNA-directed DNA methylation are epigenetically activated in pollen and seeds, which facilitates proper development of these structures.

From the body of the article:

Epiallele formation in the absence of genetic variation can result in
phenotypic variation, which is most evident in the plant kingdom, as
exemplified by the peloric and colorless non-ripening variants from Linaria vulgaris and Solanum lycopersicum, respectively^{6, 7}. Although rates of spontaneous variation in DNA methylation and mutation can be decoupled in the laboratory^{8, 9, 10, 11},
in natural settings, these two features of genomes co-evolve to create
phenotypic diversity on which natural selection can act.

…

Similarly to the limited examples of pure epialleles (methylation
variants that form independent of genetic variation), few examples of
DNA methylation variants linked to genetic variants are known^{15, 16, 17}.

And the ‘Conclusion remarks’ (emphasis is mine):

Natural epigenomic variation is widespread within A. thaliana,
and the population-based epigenomics presented here has uncovered
features of the DNA methylome that are not linked to underlying genetic
variation, such as all forms of SMPs and CG-DMRs. However, C-DMRs have
positional association decay patterns similar to linkage disequilibrium
decay patterns for SNPs and in some cases are associated with genetic
variants, but the majority of C-DMRs were not tested by association
mapping due to low allele frequencies and could result from rare
sequence variants. Our combined analyses of genetic and methylation
variation did not uncover a correlation between major effect mutations
and genes silenced by RdDM, suggesting that this pathway may target
these genes for another purpose. This purpose could be to restrict
expression from vegetative tissues similarly to transposons. Another
possible purpose of being targeted by RdDM could be to coordinate
expression specifically in pollen and in seed to ensure proper
gametophytic and embryonic development. Animals also use small
RNA-directed DNA methylation and heterochromatin formation mechanisms to
maintain the epigenome of the germ line through the use of
Piwi-interacting RNAs³⁶.
In both plants and animals these small RNAs are derived from the genome
of companion cells, which are terminal in nature and can afford
widespread reactivation of transposon and repeat sequences as they are
not passed on to the next generation. Our study provides evidence that
RdDM-targeted genes may have co-opted this transposon silencing
mechanism to maintain their silenced state in vegetative tissues and
transgenerationally, as well as to ensure proper expression important
for pollen, seed and germ line development.

 

Puctuated equilibrium, speciation and everything else

I believe it is worth recommending the reading of this new review paper which discusses the various evolutionary theories en vogue, with emphasis in punctuated equilibrium, which is surely a very realistic model:

Jaroslav Fregg, Microevolutionary, macroevolutionary, ecological and taxonomical implications of punctuational theories of adaptive evolution. Biology Direct 2013. Open access → LINK [doi:10.1186/1745-6150-8-1]

Abstract


Punctuational theories of evolution suggest that adaptive evolution proceeds mostly, or even entirely, in the distinct periods of existence of a particular species. The mechanisms of this punctuated nature of evolution suggested by the various theories differ. Therefore the predictions of particular theories concerning various evolutionary phenomena also differ.


Punctuational theories can be subdivided into five classes, which differ in their mechanism and their evolutionary and ecological implications. For example, the transilience model of Templeton (class III), genetic revolution model of Mayr (class IV) or the frozen plasticity theory of Flegr (class V), suggests that adaptive evolution in sexual species is operative shortly after the emergence of a species by peripatric speciation — while it is evolutionary plastic. To a major degree, i.e. throughout 98-99% of their existence, sexual species are evolutionarily frozen (class III) or elastic (class IV and V) on a microevolutionary time scale and evolutionarily frozen on a macroevolutionary time scale and can only wait for extinction, or the highly improbable return of a population segment to the plastic state due to peripatric speciation.


The punctuational theories have many evolutionary and ecological implications. Most of these predictions could be tested empirically, and should be analyzed in greater depth theoretically. The punctuational theories offer many new predictions that need to be tested, but also provide explanations for a much broader spectrum of known biological phenomena than classical gradualistic evolutionary theories.

I don’t dare to evaluate the paper but I do recommend reading it because it can help us to better understand what is going on when we talk of speciation, competition, evolution, dynamic equilibrium, etc. I picked up this quote:

Approximately 35% of the substitutions (20-70%, depending on the studied taxon) was shown to occur in brief periods of speciation. It is worth mentioning that we are not aware of how many speciation events actually occur in the studied, seemingly unbranched lineages. Therefore, the published estimates of speciation associated substitution rates represent only the lower margin of the real figures.

And the only figure, which illustrates how a highly diverse population/species can be stable and how evolution can happen and often does in bottlenecks instead:

Most punctuational theories of evolution, including the evolutionary conceptions of Wright, Mayr, Carson, Templeton and Flegr (for comparison see Table 1), suggest that sexually reproducing species respond evolutionarily to selection (are evolutionarily plastic) only during speciation. The mechanisms of this type of evolutionary behavior of sexual species suggested by the various theories differ, for a review see [1]. For example, the genetic revolution model [2] implicitly and the frozen plasticity theory explicitly [3] suggest that a species is evolutionary plastic when its members are genetically uniform, i.e. only after a portion of the original species has split off, skirted extinction for several generations, and then undergone rapid multiplication (Figure 1).

The paper uses the “open review” format, including commentaries from the reviewers and the replies by the author – this I find an interesting novelty which adds some value to the paper by pointing possible avenues for discussion or further research.

 

Adaptionism (humor)

From the often great comic strip (cum video theater) Saturday Morning Breakfast Cereal:

 

Complex speciation process of polar and brown bears?

Actual modern hybrid

According to new research, polar and brown bears could have diverged as long ago as 4-5 million years but have been hybridizing intermittently since then, specially as ice sheets receded in interglacial periods as today’s.

In fact we know that they do it nowadays.

While some clades of brown bear, notably the Admiralty Islands (but also French ones) are more closely related to polar bear by mitochondrial DNA,  by overall nuclear DNA they fall wholly within the brown bear clade. That’s because, mtDNA-wise polar bears are a subset of brown bears, while by nuclear DNA they are more clearly distinct.

The authors propose that this implies mtDNA introgression from brown bear into polar bears, up to the point of total displacement of the native polar bear lineages, but of course it may also be that some of their calculations are totally wrong. After all molecular-clock-o-logy is not rocket science, not at all and a total lineage replacement by just occasional inter-breeding seems a most unlikely event with the laws of probability in hand.

My impression is in fact the opposite: that the nuclear differentiation should have happened after that of the mtDNA but that molecular-clock speculations obscure this fact. But whatever. I may also be wrong, of course but I just can’t accept molecular-clock-o-logy as evidence of anything – doing that is pseudoscience.

Ref. Webb Miller et al. Polar and brown bear genomes reveal ancient admixture and demographic footprints of past climate change. PNAS 2012. Open access. [Early edition link, DOI: 10.1073/pnas.121050610] 

See also: Buffalo University press release, Science Daily.

Phylogenetic labyrinth… or molecular-clock fanaticism?

Update: PConroy mentions (see comments) a previous study (Current Biology 2011, Science Now article), which states that there is even closer mtDNA affinity between extinct Irish brown bears and modern polar bears than these have with the Alaskan ABC islander ones.

 

The ultimate anti-creationist argument

Or rather why would you bother debating creationism, evolution, tectonics, the Big Bang… when you can directly discuss God and demonstrate its falsehood in such a simple, elegant and bullet-proof way as Carl Sagan did. 

Just replace the word God by dragon.

Jesus taught (?) with parables, Sagan did the same. The improbable (lit. not provable) dragon of which no evidence exists and which nobody (but apparently the mischievous side of Carl Sagan) believes in (logically) is exactly like God. Why would anyone believe in something of which no evidence whatsoever exists? Dragon or God is the same.

Ok, where’s the dragon… or where is God?

 

Complexity arose from protein "weakness"

I find this twist on our understanding of evolution as quite interesting. It may still be true that only the fittest survive but fit means whatever actually works, not strongest or otherwise simplistically, linearly more.

If the weakest works best for whatever reason, then the weakest survive.

In this case we are before a case of proteins that work worse… and by working worse, they begin to interact and therefore create complexity.

That is what, for researchers Ariel Fernández and Michael Lynch, caused the rise of biological complexity: the evolution from prokaryote to eukaryote and so on: errors in proteins, weaker proteins… which eventually caused protein binding and compelxity.

Ariel Fernández and Michael Lynch, Non-adaptive origins of interactome complexity. Nature 2011. Freely accessible.

Story at Science Daily.

 

News May 20

A hyper quick review of some news that I may not have time (or even knowledge) to discuss in further depth:

Biology and genetics

• Human RNA often does not match DNA to the letter. Why? We do not know yet. -> SD
• Packing and unpacking DNA -> SD
• Did smell lead to larger brains in mammals -> SD

Archaeology and prehistory

• Niaosung culture (1400-550 BCE) findings in Taiwan -> The China Post

 

Evolution news: punctuated speciation and the fittest wins only sometimes

We all (except a handful of fanatics) agree that evolution happens. What is not fully clear are the details of how it happens. These days two new researches challenge some conceptualizations and support others instead.

Evolution is not constant but punctual.

That is what Stephen A. Smith (left) and colleagues have discovered when analyzing the phylogeny of angiosperms (flowering plants). They found that the conceptualization of evolution as punctuated rather than constant seems to be correct, and also that the characteristics of a new taxon evolve in a single population or root species before diversification (radiation) occurs.

The research has been published in the American Journal of Botany (open access) and a synthesis appears at Science Daily.

Perfectly fit? Maybe not needed.

A simplistic school promotes the idea that given enough evolutionary time in a simple ecological niche only one competitor will survive: the fittest one.

However this does not seem to be the case. Research by Robert E. Beardmore and colleagues, published in Nature (ppv), vindicates previous research in which optimal efficiency coexists with suboptimal one:

The fit use food well but they aren’t resilient to mutations, whereas the less efficient, unfit consumers are maintained by their resilience to mutation. If there’s a low mutation rate, survival of the fittest rules, but if not, lots of diversity can be maintained.

Full story at Science Daily.