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I looked up haplotype blocks in Google Scholar, and the results returned seemed to show that almost all the relevant articles were published between 2001 and 2009, with almost nothing since 2010.

Why has interest in haplotype blocks apparently waned over the last decade? Has the concept been discredited?

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    $\begingroup$ Please check out this post at academia stackexchange and maybe edit your question to include representative trend. The top most articles found by google scholar search are not a random sample of all articles found. I don't know exact google algorithm but my guess is it puts highly cited articles near the top. Older articles had more time to accumulate citations. $\endgroup$ – BagiM Jul 23 at 8:02
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    $\begingroup$ can you confirm that the language hasn't just changed? i believe that many people will just write "haplotypes" these days and may omit the word "blocks". Has there been a meaningful decrease in the word "haplotypes"? $\endgroup$ – Maximilian Press Jul 23 at 17:28
  • $\begingroup$ also, just posting screenshots of unsorted google scholar hits is not convincing that what you say is true. can you actually quantify the usage of the relevant terms in a time-sorted fashion? $\endgroup$ – Maximilian Press Jul 23 at 17:32
  • $\begingroup$ @David yes, I actually would like to ask if the concept of haplotype blocks (or as someone likes to call it, haplotypes) has been discredited $\endgroup$ – cienhundred100 Jul 24 at 10:17
  • $\begingroup$ I have edited your question, taking the emphasis away from the Google Scholar Search and towards the validity of the concept. As your inference from the search is clearly wrong, I cut two of your graphics which I hope you will agree are displensible. $\endgroup$ – David Sep 7 at 18:25
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Has interest in haplotype blocks waned over the decade?

No.

You can set a time range on Google Scholar, which the screenshot shows was not done. I did that and:

  • A search for ‘haplotype block’ from 2000 to 2009 gives 22,000 hits.

  • A search for ‘haplotype block’ from 2000 to 2009 gives 25,700 hits.

Haplotype block hits over the century

(The term haploblock is now often used as an abbreviation, but it turns out that haplotype block is still much more frequent.)

So I have to conclude there must have been something wrong with the approach adopted by the poster. It is worth mentioning, however, that a Google Books ngram analysis of haplotype block shows first usage in 2000, a peak at 2007 dropping to a approx. 30% of the maximum in 2019. This may just reflect an rush to publish books on a new topic that has subsided, although the rate of publication in journals has been more constant.

What are haplotype blocks, why are they interesting, and how do they differ from haplotypes?

This is illustrated by an interesting paper in a recent (2020) issue of Nature that comes from the work of a large consortium addressing the question of the adaptation of sunflowers to different ecological niches. This involves the evolution of so-called ecotypes, differing in properties such as flowering time and ability to grow on sand dunes.

The problem is that these adaptations involve many different genes (and hence alleles) which means they involve different haplotypes, according to the definition in Wikipedia:

A haplotype (haploid genotype) is a group of alleles in an organism that are inherited together from a single parent.

However these different sunflower ecotypes are not physically separated from others, so that one would expect hybridization between them to occur, resulting in the loss of the haplotype and the adaptation. As the paper points out, this problem is actually a reformulation of criticisms of Darwin’s theories by his contemporaries:

Romanes, G. J. “Physiological selection; an additional suggestion on the origin of species.” Zool. J. Linn. Soc. 19, 337–411 (1886).

(although I must admit not to have read the original.)

The fact that this does not happen is because the alleles constituting the haplotype exist in non-recombing blocks — haplotype blocks.

A haplotype block is a region of an organism’s genome in which there is little evidence of a history of genetic recombination, and which contain only a small number of distinct haplotypes.

What prevents the recombination of such blocks? It appears that the most come explanation is that rearrangement of the regions containing the haplotype blocks occurs, preventing recombination. One of the easiest rearrangement to understand is simple inversion, two large blocks of which were found on chromosome 5.

The studies in the paper started with two haplotype blocks which had been shown to be involved in the ecotypes shown, and which were found to contain genes previously implicated in these processes, such as FLOWERING LOCUS T and HEAT-INTOLERANT 1. By genome-wide association studies they identified a total of 37 haplotype blocks on the basis of linkage disequilibrium. A diagram of some of these blocks in different sunflower species may wet the reader’s appetite:

Haplotype blocks in the sunflower

So, in answer to the poster’s specific query: The concept of haplotype blocks is very much alive!

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