Genetic diversity of modern horses

Genetic diversity of modern horses

Some very distinctive groupings of modern breeds emerge in this survey of modern horse breed genetic variation, and some of these groups have clear geographical associations.

Horses are very mobile, and can also be traded; much of their existing variation may also be the result of artificial breeding which might have included both selection for particular desirable traits as well as mixing different populations.

Now that there is a fairly clear picture of modern variation, it will be useful to explore how this has emerged over time. It'll be interesting to see how ancient horses fit into the modern picture: will they prove ancestral to those living in the same regions, or is there a process of continuous renewal, with multiple episodes of turnover, as good breeds emerge somewhere across the geographical range of the animal, and quickly replace less advantageous ones?

PLoS ONE 8(1): e54997. doi:10.1371/journal.pone.0054997

Genetic Diversity in the Modern Horse Illustrated from Genome-Wide SNP Data

Jessica L. Petersen et al.

Horses were domesticated from the Eurasian steppes 5,000–6,000 years ago. Since then, the use of horses for transportation, warfare, and agriculture, as well as selection for desired traits and fitness, has resulted in diverse populations distributed across the world, many of which have become or are in the process of becoming formally organized into closed, breeding populations (breeds). This report describes the use of a genome-wide set of autosomal SNPs and 814 horses from 36 breeds to provide the first detailed description of equine breed diversity. FST calculations, parsimony, and distance analysis demonstrated relationships among the breeds that largely reflect geographic origins and known breed histories. Low levels of population divergence were observed between breeds that are relatively early on in the process of breed development, and between those with high levels of within-breed diversity, whether due to large population size, ongoing outcrossing, or large within-breed phenotypic diversity. Populations with low within-breed diversity included those which have experienced population bottlenecks, have been under intense selective pressure, or are closed populations with long breed histories. These results provide new insights into the relationships among and the diversity within breeds of horses. In addition these results will facilitate future genome-wide association studies and investigations into genomic targets of selection.

Link

Y chromosome and mtDNA study of modern Middle Eastern populations (Badro et al. 2013)

Y chromosome and mtDNA study of modern Middle Eastern populations (Badro et al. 2013)

I will just briefly comment on the occurrence of L3* mtDNA in the Near East. This is a critical haplogroup because of its age of ~70ky. If all L3* in the Near East represents African migrants, then only the M and N macrogroups appeared in Eurasia, and a good case can be made for a "late" OoA event.

On the other hand, it is quite possible that some of the L3* in the Near East does not represent recent admixture, but rather native forms of L3 with deep ancestry in the region. If that is the case, then the Near East will emerge as the origin of L3, with M, N representing Out-of-Near East-into-Eurasia founders, and the various L3*(xM, N) representing Out-of-Near East-into-Africa founders.

It is difficult to say at present what will turn out to be the case. Ancient DNA has the potential of resolving this issue, because if L3*(xM, N) in Eurasia is really recent (e.g., associated with Islamic/Arab dispersals spanning Africa and Eurasia), then it ought to be missing from the earliest genetic layers.

Also of interest the geographical distribution of Y-haplogroups; nothing much new here, but still useful as a reference:

PLoS ONE 8(1): e54616. doi:10.1371/journal.pone.0054616

Y-Chromosome and mtDNA Genetics Reveal Significant Contrasts in Affinities of Modern Middle Eastern Populations with European and African Populations 

Danielle A. Badro et al.

The Middle East was a funnel of human expansion out of Africa, a staging area for the Neolithic Agricultural Revolution, and the home to some of the earliest world empires. Post LGM expansions into the region and subsequent population movements created a striking genetic mosaic with distinct sex-based genetic differentiation. While prior studies have examined the mtDNA and Y-chromosome contrast in focal populations in the Middle East, none have undertaken a broad-spectrum survey including North and sub-Saharan Africa, Europe, and Middle Eastern populations. In this study 5,174 mtDNA and 4,658 Y-chromosome samples were investigated using PCA, MDS, mean-linkage clustering, AMOVA, and Fisher exact tests of FST's, RST's, and haplogroup frequencies. Geographic differentiation in affinities of Middle Eastern populations with Africa and Europe showed distinct contrasts between mtDNA and Y-chromosome data. Specifically, Lebanon's mtDNA shows a very strong association to Europe, while Yemen shows very strong affinity with Egypt and North and East Africa. Previous Y-chromosome results showed a Levantine coastal-inland contrast marked by J1 and J2, and a very strong North African component was evident throughout the Middle East. Neither of these patterns were observed in the mtDNA. While J2 has penetrated into Europe, the pattern of Y-chromosome diversity in Lebanon does not show the widespread affinities with Europe indicated by the mtDNA data. Lastly, while each population shows evidence of connections with expansions that now define the Middle East, Africa, and Europe, many of the populations in the Middle East show distinctive mtDNA and Y-haplogroup characteristics that indicate long standing settlement with relatively little impact from and movement into other populations.

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Breeding a (part-/quasi-) Neandertal the old-fashioned way

Breeding a (part-/quasi-) Neandertal the old-fashioned way

Razib has an interesting suggestion about how one could breed a Neandertal:

The most humane and viable manner in which you might do this is simply start a religion in a Bene Gesserit fashion where the prophesied Kwisatz Haderach is a Neandertal. Over the generations by selecting individuals within the population (which could draw in converts) enriched for Neandertal ancestry to mate assortatively one could slowly increase the proportion of that ancestral component. 

The idea is simple: if you mate two persons with x% and y% Neandertal ancestry, you will get (in the expected sense) a baby with 0.5(x+y)% Neandertal ancestry. In actuality the baby's Neandertal ancestry will be a random variable z with mean 0.5(x+y) and some variation around that mean.

Now, if x and y are very different from each other (e.g., at the limit you had crossed a full Neandertal with x=100% and a full sapiens with y=0%), then z will always be in-between x and y.

But, if x and y are fairly close to each other, it's possible that thanks to the wonders of recombination it will happen that z will be greater than both x and y, because the offspring might actually happen -by chance- to inherit many Neandertal alleles from both mom and dad.

Project the above procedure over the millennia, and it's easy to see how one might incrementally increase the proportion of Neandertal ancestry in the gene pool to an arbitrary degree: individuals might start with, say, 2% Neandertal ancestry, and given enough crossings per generation (so that enough individuals with >2% Neandertal ancestry will be produced), and enough generations, the number will inch along, and converge to 100%.

But, actually, reaching a 100% Neandertal might be impossible. To see why, consider that while many Neandertal alleles introgressed into the modern human population a few tens of thousands of years ago, surviving down to the present, some of them did not introgress and some that did were culled away by either drift or natural selection. 

Moreover, we might not be able to utilize all extant Neandertal alleles because we can mostly identify Neandertal-ness with respect to ancient DNA samples.

In other words, the modern human gene pool has a lot of Neandertal alleles floating around, but some of these don't look like Neandertal alleles (because we didn't find them in any ancient specimen yet), while others are simply long gone.

Such a breeding program would therefore not produce a Neandertal in the end, for the same reason that you cannot produce a grey hue by mixing different shades of red and blue: you also need some yellow. The modern human gene pool may have lots of Neandertal alleles but it may not have enough.

In any case, it would still be possible to create a, say, 50% Neandertal, or whatever the proportion of Neandertal alleles still in existence is. But, will such an individual be a Neandertal in the physical sense?

Which were the alleles that conferred Neandertal-ness to their bearers? We don't know, but this property may very well have involved both (i) combinations of alleles that exist in modern humans, and, (ii) alleles we no longer possess.

As an analogy, imagine that in the future, polar bears are extinct, but some of their DNA introgressed into other bear populations. Future zoologists might breed specimens that have a lot of polar bear alleles, but will lack the alleles conferring white coat color. Such a hypothetical breed of bear might possess a high degree of genome-wide similarity to actual polar bears, but it won't be the same where it counts.

Thus, it may very well be possible to create individuals from extinct human populations (be they archaic hominins such as Neandertals, or even admixed modern humans such as Tainos), but one might not get a 100% replica of such populations by breeding alone. Even if one was able to reconstruct a great part of such creatures' genome, the most important portions might still be missing.

Facial shape uncorrelated with aggression

Facial shape uncorrelated with aggression

Of interest is the calculation of sexual dimorphism for a variety of indices in different datasets (Figure 1; left). The figure caption:

Box and whisker plots of global sexual dimorphism computed across the different databases. Indices that differed significantly among sexes (after t-test for independent samples) are shown in solid grey. A) Howells database; b) Pucciarelli database, c) 2D Geometric Morphometric database, d) 3D Geometric Morphometric database, e) Patagonian groups database. Square: median; box: 25%–75%; whisker: minimum-maximum values.

Also of interest Figure S1 (bottom right), which breaks down the sexual dimorphism in different populations. The caption reads:

Box and whisker plots of fWHR depicting inter-sexual differences across the populations of each database. a) Howells database; b) Pucciarelli database, c) 2D Geometric Morphometric database, d) 3D Geometric Morphometric database, e) Patagonian groups database. Square: median; box: 25%–75%; whisker: minimum-maximum values. Orange: females, blue: males. Populations showing significantly greater male fWHR (after t-test for independent samples) are marked with grey boxes.

It would be nice if more anthropometric datasets were publicly available. Perhaps some of the above-mentioned are, but I didn't see any mention of how to obtain them in the paper itself.


PLoS ONE 8(1): e52317. doi:10.1371/journal.pone.0052317

Lack of Support for the Association between Facial Shape and Aggression: A Reappraisal Based on a Worldwide Population Genetics Perspective

Jorge Gómez-Valdés et al.

Antisocial and criminal behaviors are multifactorial traits whose interpretation relies on multiple disciplines. Since these interpretations may have social, moral and legal implications, a constant review of the evidence is necessary before any scientific claim is considered as truth. A recent study proposed that men with wider faces relative to facial height (fWHR) are more likely to develop unethical behaviour mediated by a psychological sense of power. This research was based on reports suggesting that sexual dimorphism and selection would be responsible for a correlation between fWHR and aggression. Here we show that 4,960 individuals from 94 modern human populations belonging to a vast array of genetic and cultural contexts do not display significant amounts of fWHR sexual dimorphism. Further analyses using populations with associated ethnographical records as well as samples of male prisoners of the Mexico City Federal Penitentiary condemned by crimes of variable level of inter-personal aggression (homicide, robbery, and minor faults) did not show significant evidence, suggesting that populations/individuals with higher levels of bellicosity, aggressive behaviour, or power-mediated behaviour display greater fWHR. Finally, a regression analysis of fWHR on individual's fitness showed no significant correlation between this facial trait and reproductive success. Overall, our results suggest that facial attributes are poor predictors of aggressive behaviour, or at least, that sexual selection was weak enough to leave a signal on patterns of between- and within-sex and population facial variation.

Link

Ancestry Composition to be fixed

Ancestry Composition to be fixed

From the explanation at the relevant thread:

Ancestry Composition (AC) works by learning (training) a set of useful features from reference individuals with known ancestry (the training set) and then using these features to predict the ancestry of our customers.

Our set of reference individuals consists in part of customers who reported their 4 grandparents were born in the same country. Remember that we also remove the outliers, or people whose genetic ancestry doesn't match their survey answers. From this set, AC learns to associate certain haplotypes with their geographical origin. AC is then able to recognize similar haplotypes and thus to predict the ancestry of other customers.

However, when predicting the ancestry of reference individuals, AC suffers from overfitting, a problem common to many supervised learning methods. As a consequence, AC predicts the ancestry of most reference individuals as being 100% from their grandparents’ birthplace.

We addressed this issue using a method inspired from cross-validation. We divided the training set into 5 folds, each containing 20% of the reference individuals. We then trained 5 AC models in which each fold in turn is excluded from the set of reference individuals. So each of these models is learned using 80% of the reference individuals. Additionally, we retain the model that was trained using all the reference individuals. From this process, we end up with 6 different models from which we can predict the ancestry of our customers.

Now, when predicting the ancestry of a customer, we start by figuring out if he/she is a reference individual. If yes, we identify the fold in which the customer belongs, and we use the corresponding model for prediction. If not, we use the fold containing all of the reference data. This way, we ensure that AC was never trained using the haplotypes of the individual it tries to predict.

I had proposed basically the same solution about a month ago, and it's great that the issue is being addressed so soon after it first appeared. If any of the people who had written to me/commented on the topic get their new updated results and want to comment, feel free to do so in this post.

I am not sure how 23andMe plans to handle their Ancestry Composition feature in the future, but I would suggest that they periodically re-update it as they get more samples. According to a recent estimate, there are over 180,000 people in their database at the moment, a fraction of which meets the twin requirements of: (i) having 4 grandparents from the same country, and (ii) not being an outlier. As this number increases over time, it might be a good idea to occasionally re-partition the sample and re-calculate participants' ancestry composition results.

The fact that they are ready to roll out their updated results so soon after the initial ones tells me that they do have the computing power to do so, and it might be a good idea to update Ancestry Composition periodically, say on a quarterly basis or when a certain increase in the training set (say, 10%) is achieved. Eventually the admixture estimates may stabilize, in which case the way forward may involve rethinking the choice of ancestral populations currently in use.

Indonesian mega-study (Tumonggor et al. 2013)

Indonesian mega-study (Tumonggor et al. 2013)

A new comprehensive survey of Y chromosome/mtDNA variation in Indonesia has just appeared online. From the paper:

The first stage of Indonesian prehistory represents the archipelago’s initial settlement as part of the African dispersal ~50 kya. The geography of the region was then markedly different from today. Sea levels were much lower, most modern islands had merged into larger landmasses, and the westernmost parts of Indonesia were physically contiguous with mainland Asia. This first stage is recorded by deep mtDNA lineages (M17a, M73, M47, N21, N22, R21, R22 and R23), which trace back to the main branching of macrohaplogroups M and N, and have a spotty distribution across both mainland and island southeast Asia today.

and:

The second stage reflects recurrent colonization events from mainland Asia throughout the later Paleolithic. Many haplogroups (B4a, B4b, B4c, B4c1b3, B5a, B5b, B5b1, D and E) show origin dates of 10-40 kya (Supplementary Table 6) 25, 63 and are distributed across a wide range of mainland and island southeast Asian populations. 

and:

The third stage represents Neolithic movements into and around island southeast Asia. Some of these may involve population dispersals from (and perhaps to) Taiwan, while others reflect movements between Indonesian island groups. Representative haplogroups include M7b3, E1a1a, M7c3c and Y2. Autosomal data strongly supports large demic movements of Asian populations into eastern Indonesia from around 4 kya 67.

and, finally:

The fourth stage reflects historic movements into Indonesia, largely involving trade and the associated spread of major religions from India, Arabia and China 71. Although found at relatively low frequency today, Y chromosome lineages representing these movements occur across Indonesia 20, notably in the west, such as the Hindu dominated island of Bali

It would be useful to study Indonesian haplogroups as a means of testing the hypothesis of Indian settlement in Australia, since it is difficult to see any such settlement that would not have passed through the Indonesian archipelago.

Of the lineages found in Indonesia, the deepest ancestry appears to be associated with mtDNA haplogroups P (54+/-16ky) and Q (38+/-9ky), both of which appear to have clear "Australo-Melanesian" associations. Of the B subclades that are lately of interest due to the publication of Tianyuan ancient DNA, the oldest one appears to be B4a (33+/-13ky).

One of the major puzzles in prehistory is the co-occurrence of mtDNA macro-haplogroups M and N in the eastern portion of Eurasia vs. the dominance of N in the western part thereof. The peninsulas of Arabia and India probably hold a key to this riddle, although in both cases the situation is obscured by subsequent events: in Arabia, there has probably been substantial population turnover during its "desert" phases, while in India there has been recent admixture between the aboriginal population and West Eurasian-derived inhabitants.

Journal of Human Genetics , (24 January 2013) | doi:10.1038/jhg.2012.154

The Indonesian archipelago: an ancient genetic highway linking Asia and the Pacific 

Meryanne K Tumonggor et al.

Indonesia, an island nation linking mainland Asia with the Pacific world, hosts a wide range of linguistic, ethnic and genetic diversity. Despite the complexity of this cultural environment, genetic studies in Indonesia remain surprisingly sparse. Here, we report mitochondrial DNA (mtDNA) and associated Y-chromosome diversity for the largest cohort of Indonesians examined to date—2740 individuals from 70 communities spanning 12 islands across the breadth of the Indonesian archipelago. We reconstruct 50 000 years of population movements, from mitochondrial lineages reflecting the very earliest settlers in island southeast Asia, to Neolithic population dispersals. Historic contacts from Chinese, Indians, Arabs and Europeans comprise a noticeable fraction of Y-chromosome variation, but are not reflected in the maternally inherited mtDNA. While this historic immigration favored men, patterns of genetic diversity show that women moved more widely in earlier times. However, measures of population differentiation signal that Indonesian communities are trending away from the matri- or ambilocality of early Austronesian societies toward the more common practice of patrilocal residence today. Such sex-specific dispersal patterns remain even after correcting for the different mutation rates of mtDNA and the Y chromosome. This detailed palimpsest of Indonesian genetic diversity is a direct outcome of the region’s complex history of immigration, transitory migrants and populations that have endured in situ since the region’s first settlement.

Link

Beware of who you kiss

Beware of who you kiss

Forensic Sci Int Genet. 2013 Jan;7(1):124-8. doi: 10.1016/j.fsigen.2012.07.007. Epub 2012 Aug 20.

Prevalence and persistence of male DNA identified in mixed saliva samples after intense kissing.

Kamodyová N, Durdiaková J, Celec P, Sedláčková T, Repiská G, Sviežená B, Minárik G.

Abstract

Identification of foreign biological material by genetic profiling is widely used in forensic DNA testing in different cases of sexual violence, sexual abuse or sexual harassment. In all these kinds of sexual assaults, the perpetrator could constrain the victim to kissing. The value of the victim's saliva taken after such an assault has not been investigated in the past with currently widely used molecular methods of extremely high sensitivity (e.g. qPCR) and specificity (e.g. multiplex Y-STR PCR). In our study, 12 voluntary pairs were tested at various intervals after intense kissing and saliva samples were taken from the women to assess the presence of male DNA. Sensitivity-focused assays based on the SRY (single-copy gene) and DYS (multi-copy gene) sequence motifs confirmed the presence of male DNA in female saliva after 10 and even 60min after kissing, respectively. For specificity, standard multiplex Y-STR PCR profiling was performed and male DNA was found in female saliva samples, as the entire Y-STR profile, even after 30min in one sample. Our study confirms that foreign DNA tends to persist for a restricted period of time in the victim's mouth, can be isolated from saliva after prompt collection and can be used as a valuable source of evidence.

Link