race/history/evolution notes: July 2015

"Mormons are largely Puritans" (JayMan's latest embarrassing averral)

On twitter, someone responds to a story about Glenn Beck's banning coverage of Donald Trump from his show with "Mormons r becoming some the worst #cuckservatives-missions to Haiti & China & letting their daughters marry Samoans". JayMan seizes the opportunity to inform us: "Mormons are largely Puritans (augmented with Scandinavians)."

This is of course simply false. While Puritan ancestry is found at higher levels among Mormons than in the US population in general, it's not true that Mormons today are of predominantly Puritan descent. (Nor is any other major population in America today of predominantly Puritan descent.)

In addition to Scandinavians, converts from missionary efforts in Britain form a major component in the ancestry of those with early Mormon roots. Moreover, most of the British converts came from areas outside of East Anglia and should tend to be "clannish" relative to New England Puritans in the JayMan understanding of things.

Hail, looking at Mitt Romney's ancestry, found:

Most of his ancestral stock consists of early converts to Mormonism from Britain (most from Northwest-England and Scotland) who were impelled to the USA from the 1830s to the 1850s, settling directly in Mormon communities.
Colonial-Yankees account for 27% of Romney’s ancestral stock.
12.5% (one-eighth) of his ancestral stock comes from Northern-Germany.

The current president of the Mormon church, Thomas S. Monson, has no colonial American ancestry whatsoever. He's half Scottish, 1/4 northern English, and 1/4 Swedish.

What makes this all even more amusing is that Glenn Beck was not even born a Mormon. He's a convert, and per wikipedia:

He is descended from German immigrants who came to the United States in the 19th century.[24] Beck was raised as a Roman Catholic and attended Immaculate Conception Catholic School in Mount Vernon.
Glenn and his older sister moved with their mother to Sumner, Washington, attending a Jesuit school[25] in Puyallup.

Iron Age and Anglo-Saxon genomes from East England reveal British migration history

A preprint on some ancient DNA work in England is up. Researchers sequenced samples from seven early and middle Anglo-Saxon period and three late Iron Age (presumably Celtic) skeletons.

We generated a principal component plot of the ten ancient samples together with relevant European populations selected from published data 10,11 (Extended data Figure 3). The ancient samples fall within the range of modern English and Scottish samples, with the Iron Age samples from Hinxton and Linton falling closer to modern English and French samples, while most Anglo-Saxon era samples are closer to modern Scottish and Norwegian samples. Overall, though, population genetic differences between these samples at common alleles are very slight.
While principal component analysis can reveal relatively old population structure, such as generated from long-‐term isolation-‐by-‐distance models 12 , whole genome sequences let us study rare variants to gain insight into more recent population structure. [. . .]
There are striking differences in the sharing patterns of the samples, illustrated by the ratio of the number of rare alleles shared with Dutch individuals to the number shared with Spanish individuals (Figure 2a). The middle Anglo-‐Saxon samples from Hinxton (HS1, HS2, HS3) share relatively more rare variants with modern Dutch than the Iron Age samples from Hinxton (HI1, HI2) and Linton (L). The early Anglo-‐Saxon samples from Oakington are more diverse, with O1 and O2 being closer to the middle Anglo-‐Saxon samples, O4 exhibiting the same pattern as the Iron Age samples, and O3 showing an intermediate level of allele sharing, suggesting mixed ancestry. The differences between the samples are highest in low frequency alleles and decrease with increasing allele frequency. This is consistent with mutations of lower frequency on average being younger, reflecting more recent distinct ancestry, compared with higher frequency mutations reflecting older shared ancestry.

Comparing the relative number of rare alleles shared with the Dutch and Spanish samples, the researchers estimate 30% Anglo-Saxon admixture in the present-day East English and 20% in the Scottish and Welsh.

We also examined using the same method 30 modern samples from the UK10K project 16 , 10 each with birthplaces in East England, Wales and Scotland. Overall, these samples are closer to the Iron Age samples than to the Anglo-‐Saxon era samples (Figure 2a). There is a small but significant difference between the three modern British sample groups, with East English samples sharing slightly more alleles with the Dutch, and Scottish samples looking more like the Iron Age samples. To quantify the ancestry fractions, we fit the modern British samples with a mixture model of ancient components, by placing all the samples on a linear axis of relative Dutch allele sharing that integrates data from allele counts one to five (Figure 2b). By this measure the East England samples are consistent with 30% Anglo-‐Saxon ancestry on average, with a spread from 20% to 40%, and the Welsh and Scottish samples are consistent with 20% Anglo-‐Saxon ancestry on average, again with a large spread (Supplementary Table 2). An alternative and potentially more direct approach to estimate these fractions is to measure rare allele sharing directly between the modern British and the ancient samples. While being much noisier than the analysis using Dutch and Spanish outgroups, this yields consistent results (Extended Data Figure 4 and Supplementary Table 2). In summary, this analysis suggests that only 20-‐30% of the ancestry of modern Britons was contributed by Anglo-‐Saxon immigrants, with the higher number in East England closer to the immigrant source. The difference between the three modern groups is surprisingly small compared to the large differences seen in the ancient samples, although we note that the UK10K sample locations may not fully reflect historical geographical population structure because of recent population mixing.

I have not thought about it deeply, but the rare variant comparison method used by the authors seems like it should produce reasonable results, at least for the relatively straightforward admixture estimates (with the understanding that Anglo-Saxons and Iron Age Britons are not the only two possible source populations for the modern British). I will say I was surprised to see Britain sharing a branch with Finland in this plot (even though it's a short one) to the exclusion of Denmark and Netherlands:

I've seen a few people interpret this study's estimates as a vindication of the ridiculous admixture estimates featured in the People of the British Isles project paper. For me, the ancient DNA results confirm my initial impression: the methods the POBI authors used to generate their estimates of ancient admixture were useless for divining what they thought they could divine.

That this 30% estimate informed by ancient DNA falls within the range of estimates suggested by the POBI authors is primarily a testament to the extremely broad range of possible admixture estimates they offered up (spanning 10% to 50%, depending on what one subjectively deemed "likely"). The POBI authors themselves were pushing for ~10% Anglo-Saxon admixture in the 19th-century Central and South English population (and if I recall correctly ~0% in the Welsh). POBI volunteers were primarily middle-aged or older people who could document four grandparents all born in particular locations. The UK10K modern British samples appearing in the ancient DNA paper are not screened in a similar manner, but are simply classified based on the sample donor's birth place. This means at least a couple generations (and probably disproportionately important generations, at that, as concerns mobility) of additional homogenization will have taken place.

So I have little doubt POBI samples from East Anglia (proxies for 19th-century East Anglians) would produce higher estimates of Anglo-Saxon admixture than "East England" UK10K samples (though apparently at present only microarray data, and not the whole genome sequencing data that would be necessary for the rare variant comparisons, is available for POBI samples). Levels up to 40% or higher Anglo-Saxon admixture in 19th-century East Anglians would not surprise me. And whatever the 19th-century number turns out to be, Anglo-Saxon admixture in England likely would have been progressively higher going back in time toward before the Norman conquest.

Gene flow into England over the past millennium (from Wales, Scotland, Ireland, and France) will have tended to make the English look less Anglo-Saxon and more "Iron Age". The Scandinavian component in the Normans and particularly their followers was probably outweighed by the French; and subsequently France probably remained one of the main sources of continental immigrants into England at least down to the Huguenots. It's said around 50,000 Huguenots came to England (against a 17th-century English population of around 5 million). 1% does not sound like an especially large wave (and it's certainly not by the standards of modern mass immigration), but these immigrants were concentrated in south and east England:

Huguenot settlement was concentrated in London and the south, East Anglia and the Fens

Even a relative trickle of continental immigrants over the past 1000 years might have had a noticeable cumulative effect on the English gene pool, and Scottish, Welsh, and Irish gene flow into England over the past millennium is likely even more significant. 24% of British claim Irish ancestry recent enough to be aware of, including 77% of those in London. Around 10% of the UK population is estimated to have an Irish grandparent.

Filtering recent Irish immigration into Scotland might also lead to higher estimates of Anglo-Saxon admixture there, as well (though recent English immigration too would need to be excluded). Recent English immigration into Wales may mean the 20% Anglo-Saxon admixture estimate is significantly inflated (though going off the 20% estimate for modern Welsh I would guess 19th-century Welsh speakers had at least ~10% Anglo-Saxon-like admixture).

According to the authors:

The genetic analyses described above add significantly to our picture of Anglo-Saxon migration into Britain. In the cemetery at Oakington we see evidence even in the early Anglo-Saxon period for a genetically mixed but culturally Anglo-Saxon community ^21,22 , in contrast to claims for strong segregation between newcomers and indigenous peoples ⁷ . The genomes of two sequenced individuals are consistent with them being of recent immigrant origin, from different continental source populations, one was genetically similar to native Iron Age samples, and the fourth was an admixed individual, indicating intermarriage. Despite this, their graves were conspicuously similar, with all four individuals buried in flexed position, and with similar grave furnishing. Interestingly the wealthiest grave, with a large cruciform brooch, belonged to the individual of native British ancestry (O4), and the individual without grave goods was one of the two genetically “foreign” ones (O2), an observation consistent with isotope analysis at West Heslerton which suggests that new immigrants were frequently poorer ^23,24 . Given this mixing apparent around 500CE, and that the modern population is no more than 30% of Anglo-Saxon ancestry, it is perhaps surprising that the middle Anglo-Saxon individuals from the more dispersed field cemetery in Hinxton all look genetically consistent with unmixed immigrant ancestry. One possibility is that this reflects continued immigration until at least the Middle Saxon period.

In fact, there's nothing really inconsistent with the "Anglo-Saxon apartheid" paper in the mixed earlier samples and unmixed later samples. The Anglo-Saxon period samples tested here are all female. It's easy to imagine intermarriage rates may have been higher among the earliest Anglo-Saxon settlers, when their fraction of the total British population would have been smallest -- especially if females were to any degree underrepresented among the incoming Anglo-Saxons.

From the "Anglo-Saxon apartheid" paper (Evidence for an apartheid-like social structure in early Anglo-Saxon England):

We have only considered the effects of differences in ethnic reproductive advantage and inter-ethnic marriage rate on patterns of genetic variation. If there were no sex bias in the intermarriage rate, then we would expect these effects to be equal for the different genetic systems (mitochondrial DNA, Y-chromosome, X-chromosome, autosomes). However, part of the motivation for this study was to seek an explanation for the discrepancy between archaeological estimates of the size of the Anglo-Saxon migration (Härke 1998, 2002; Hills 2003) and estimates based on Y-chromosome data (Weale et al. 2002; Capelli et al. 2003). There are three further factors that could exacerbate replacement of indigenous Y-chromosomes. The first is that when intermarriage does occur the offspring may be more likely to assume the identity of the father, thus reducing the effective intermarriage rate, as it would affect patterns of Y-chromosome diversity. The second is that forced extra-marital matings are more likely to occur between Anglo-Saxon men and native British women than the reverse since, as the law codes of Ine indicate, the degree of punishment was determined by the social status of the victim. The third is based on the theory that relatively ‘good condition’ males tend to out-reproduce females of a similar condition, whereas relatively ‘poor condition’ females tend to out-reproduce their male counterparts (Trivers & Willard 1973). From this, a strategy of sex-biased parental investment, whereby relatively wealthy parents favour wealth transfer to their sons, should emerge (Hartung 1976). Such a phenomenon is supported by genealogical data (Boone 1986) and should lead to an asymmetric increase in the population frequency of Y-chromosomes carried by wealthy men, when compared to the other genetic systems.
The motivation for this study was to reconcile the discrepancy between, on the one hand, archaeological and historical ideas about the scale of the Anglo-Saxon immigration (Hills 2003), and on the other, estimates of the genetic contribution of the Anglo-Saxon immigrants to the modern English gene pool (Weale et al. 2002; Capelli et al. 2003). We have shown that this discrepancy can be resolved by the assumption of an apartheid-like social structure within a range of plausible values for interethnic marriage and socially driven reproductive advantage following immigration (Woolf 2004). Perhaps most strikingly, our model indicates that, by using plausible parameter values, the genetic contribution of an immigrant population can rise from less than 10% to more than 50% in as little as five generations, and certainly less than fifteen generations. Similar processes are likely to have shaped patterns of genetic variation in other ‘conquest societies’ of the period, and perhaps more recently (Carvajal-Carmona et al. 2000).

Reply to RCB on the evolution and adaptiveness of ethnocentric altruism

Continued from this discussion.

"you are unable to explain to a competent person why you believe what you believe."

I'm trying to be patient here, but I don't know how much better I can explain this. You either get it, or you don't. If you don't, you're not as competent as you believe; you either don't really understand the basic concepts we're talking about or have mental blocks when it comes to applying them to humans, and this is something you need to deal with yourself.

No matter how many times I explain this, you don't want to get it. Your starting point is that Salter can't be right; so when I explain to you how your reasoning is flawed, regardless of how many times we go through this or how many times I address a particular objection, your response is just to throw out additional confused reasoning, often forgetting things you previously agreed I was correct on and switching back to objections that have already been addressed.

The benefit of the ethnocentric altruism alleles comes from between-group selection, not within-group selection. Even in the first generation, an allele for ethnocentric altruism can potentially boost its odds of representation in future generations by, for example, reducing the chance of extinction of the group it's found in (whether by contributing to avoiding defeat and extermination by rival groups in an ancestral environment, or resisting replacement-level immigration in the modern world).

It makes no difference whether there is enough between-group relative to within-group competition at modern scales to maintain or grow this sort of variation in the long run (and certainly Hamilton speculated that self-sacrificing altruism would be found at higher levels in tribal people than in the long-civilized). In a particular instance of intergroup competition of the sort we're discussing, ethnocentric altruism alleles attuned to Hamilton's rule would by definition be adaptive.

This will always be true, regardless of scale, and regardless of how often the group is actually faced with the threat of intergroup competition. In the face of such a threat, the alleles (ones that enhance group competitiveness in a generalized fashion and are sensitive to cost, benefit, and relatedness) will be adaptive.

Your argument is somewhat analogous to claiming sickle-cell alleles can't be adaptive (or even exist in the first place!) in a malarial environment because their frequency would not increase in the long run in the absence of malaria. Even if malaria is nearly wiped out and the frequency of sickle-cell alleles begins to decline, this does not prove that if a mosquito with malaria does land on you you'd be better off not having a sickle-cell allele.

"Yes, the behaviors are polygenic. But all genes have to start at low frequency, and you have not explained how they get to high frequency"

Again: positive selection will come from intergroup competition. If your argument is that all relevant variants would be snuffed out immediately, leaving no variation on which group-level selection could act, this is of course absurd. Yet again: we're talking about very large numbers of weakly-selected variants, and a large surface on which new mutations can arise.

Crow and Aoki modeled group selection for polygenic behavioral traits. Again, it boils down to Hamilton's rule.

Group selection for a polygenic behavioral trait: a differential proliferation model [pdf]
Group selection for a polygenic behavioral trait: estimating the degree of population subdivision [pdf]
Our general approach is to use molecular markers, which are selected very weakly at most, as neutral indicators of population structure. G_ST gives us an appropriate description of the relevant aspect of the structure. By using Eq. 3 we can state the maximum value of cost/benefit of a quantitative trait if that trait is to increase in average value or frequency in the population. G_ST describes the present structure of the population; it does not tell us how it got that way. If this value has been roughly stable in the past, we could expect that traits with c/b up to this value would have increased in the population, assuming of course that such traits exist and have heritability greater than zero.

Empirically, ethnocentrism exists, and no doubt has since before we were humans. Empirically, ethnocentrism has heritability greater than zero.

Nature, nurture, and ethnocentrism in the Minnesota Twin Study [pdf]
Common Heritable Effects Underpin Concerns Over Norm Maintenance and In-Group Favoritism: Evidence From Genetic Analyses of Right-Wing Authoritarianism and Traditionalism [pdf]
Genetic evidence for multiple biological mechanisms underlying in-group favoritism [pdf]

Your issue is with reality, not with Salter or me.

"Of course, ethnic altruist genes could be maladaptive relics of the past, when groups were small. But Salter says they are adaptive now."

Again, see above.

And Salter never claims we are well-adapted to ethnic competition in the modern world. If he'd believed that to be the case, he would have had little reason to write the book. From the introduction:

On Genetic Interests is an attempt to answer the empirical question: How would an individual behave in order to be adaptive in the modern world? I adopt the neo-Darwinian meaning of adaptive, which is to maximize the survival chances of one’s genes. I begin by describing humans as an evolved species and thus as creatures for whom genetic continuity consists of personal reproduction or reproduction of kin. [. . .]
Humans can no longer rely on their instincts
There is nothing immutable or necessarily perfect about adaptations or the understanding, appetites and preferences they organize. Natural selection is constrained by evolutionary history and environment. It shapes bodies and behaviours in small increments by modifying existing species. Much in nature is badly designed, if one examines it from an engineer’s viewpoint. [. . .]
Like adaptations that advance them, proximate interests can be imperfect in promoting genetic interests. The main problem is the slowness of natural selection compared to the rapidity of technological and social change since the Neolithic. The inertia of adaptations can cause them to continue to promote proximate interests that no longer serve fitness. For most of humans’ evolutionary history, adaptations tracked slow-moving environmental change, including technological advances. In the species’ distant hominid and pre-hominid past, proximate interests that reduced an actor’s fitness were valued less and less as the genes that coded for such valuation failed to reproduce. For this reason, at most moments in time proximate interests have correlated with ultimate interests because the environment has changed so slowly that physiology and behaviour could keep track with it. Proximate and ultimate interests have been in equilibrium except where rapid changes in environment occurred. The equilibrium applying to humans has been upset in recent generations, so that we can no longer rely on subjectively designated proximate interests to serve our ultimate interest. We must rely more on science to perceive the causal links between the things we value and formulate synthetic goals based on that rational appraisal.
Proximate interests, often reflected in consciously held values, have become increasingly fallible guides to ultimate interests because modern humans live in a rapidly changing world. Humans evolved in small bands consisting of a few families, sometimes grouped into tribes numbering in the hundreds. For most of their evolutionary history humans made a living by hunting and gathering in largely natural environments. They lacked formal organization and hierarchy. Adults coordinated activities by negotiating simple demographic role specializations — by age and sex — on an egalitarian basis with familiar band members. Most information was common. Humans now live in societies numbering in the millions where the great majority of interactants are strangers or acquaintances. They make their living through a great diversity of occupations resulting in radical asymmetries in information. They live and work in largely man-made urban environments. They are formally organized into states administered by extended hierarchies of rank and resources actuated by authoritative commands, impersonal contracts enforced by the state authority, and powerful forms of indoctrination performed by universal education, centralized media and entertainment.

However, to the extent we are able to correctly reason about what would be adaptive in the context of intergroup competition, and act in accordance with this, we have the equivalent of our generalized ethnocentric altruism alleles.

Related:

NW-SE cline of brain volume in Europe

The authors of Modeling the 3D Geometry of the Cortical Surface with Genetic Ancestry mention:

In our group’s previous study, we found that area measures of cortical surface and total brain volumes of individuals of European descent in the United States correlate significantly with their ancestral geographic locations in Europe [ 9 ].

This 2011 study ("A Geographic Cline of Skull and Brain Morphology among Individuals of European Ancestry") is freely accessible:

Background: Human skull and brain morphology are strongly influenced by genetic factors, and skull size and shape vary worldwide. However, the relationship between specific brain morphology and genetically-determined ancestry is largely unknown. Methods: We used two independent data sets to characterize variation in skull and brain morphology among individuals of European ancestry. The first data set is a historical sample of 1,170 male skulls with 37 shape measurements drawn from 27 European populations. The second data set includes 626 North American individuals of European ancestry participating in the Alzheimer’s Disease Neuroimaging Initiative (ADNI) with magnetic resonance imaging, height and weight, neurological diagnosis, and genome-wide single nucleotide polymorphism (SNP) data. Results: We found that both skull and brain morphological variation exhibit a population-genetic fingerprint among individuals of European ancestry. This fingerprint shows a Northwest to Southeast gradient, is independent of body size, and involves frontotemporal cortical regions. Conclusion: Our findings are consistent with prior evidence for gene flow in Europe due to historical population movements and indicate that genetic background should be considered in studies seeking to identify genes involved in human cortical development and neuropsychiatric disease. [. . .]

Apparently the two main groups being compared in the neuroimaging sample are Americans of Northwestern European ancestry and Ashkenazi Jews ("ADNI subjects are spread out primarily along a NW-SE axis and form two distinct clusters corresponding to NW European and Ashkenazi Jewish ancestry"):

To determine if brain morphometry exhibits similar geospatial population trends to the skull morphometry data, we estimated the ancestry of each individual in the ADNI sample using available genome-wide genotype data and confined attention to 626 individuals with a high probability of having European ancestry. In order to assign the European region of origin most likely to reflect the genetic background of each individual, genotypes from ADNI subjects were merged with publically available genotypes from 34 reference populations geographically distributed across Europe, and PCA was pursued. [. . .]
A plot of the first two principal components separates ADNI subjects into two main clusters: one overlaps NW populations and one lies SE of Europe ( fig. 3 a) and overlaps individuals with self-reported Ashkenazi Jewish ancestry (online suppl. fig. S5). [. . .]
We found that ADNI individuals with a NW ancestry are on average 4 cm taller than ADNI individuals with a SE or Ashkenazi Jewish ancestry (p = 7.3 ! 10–6 ), consistent with previously observed differences in height across Europe [30] . [. . .]

Intracranial and brain volumes and cortical surface area progressively increase with the amount of inferred NW European ancestry (fig. (fig.3b),3b), and these measures are approximately 5% larger in the 10% of individuals with the most NW European ancestry compared to the 10% with the most SE European ancestry. This percentage increase matches the percentage increase in cranial length and breadth observed along the same NW-SE geographic axis in the skull data set (fig. (fig.2b)2b) and cannot be attributed to a correlation with body size since we controlled for height and weight. This correlation involves specific – not global – brain morphology because hippocampal, basal ganglia, ventricular, and cerebellar volumes and average cortical thickness are not associated with NW-SE ancestry.
Next, we performed both a region of interest analysis and vertex-based tests across the cortex to test whether the surface area of specific cortical regions showed more significant association with the degree of NW-SE ancestry. We found that cortical surface area predominantly in the frontal and temporal lobes from both hemispheres is significantly associated (online suppl. table S4) and is 4–9% larger among 10% of individuals with the most NW European ancestry compared to 10% with the most SE European ancestry. We found a similar frontotemporal pattern of association with the degree of NW-SE ancestry with a vertex-based analysis (fig. (fig.4;4; online suppl. fig. S6).
[. . .] the existence of genetic and craniometric clines in modern European populations suggests at least two theories: (1) pre-historic population movements made such a dominant contribution to the structure of genetic variation in Europe that more recent gene flow has not masked it, and (2) local environmental factors and selection generated clinal variation or acted to restore clinal variation after gene flow occurred. One intriguing possibility for such an environmental factor is the cultural conditions associated with possessing agricultural technologies, e.g. sedentarism, altered diet including milk consumption [40] , and new disease exposures [41] . As these technologies spread progressively from SE to NW Europe over several 1,000 years [33] , natural selection may have acted either directly or indirectly to alter brain morphology, thus creating the clinal variation found in this study.

Plots of cranial measures from this study (left) and map of head size from Coon's 1939 book The Races of Europe (right):

The trend observed here is also consistent with that reported by Maurice Fishberg over a century ago in The Jews: A Study of Race and Environment:

One of the methods of determining the volume of the brain case, and approximately the weight of the brain, is the determination of the cranial capacity. Very few direct measurements of this kind have been taken, because only few Jewish skulls have found their way into anthropological museums, where they could be studied carefully. But from the few studies of this character that have been made, it appears that the Jews are somewhat at a disadvantage. Lombroso's studies of the Jews in Turin, Italy, which were made in an indirect fashion, showed that the Jews have a smaller cranial capacity than the Catholics of that city.2 Weinberg collected measurements of seventeen Jewish skulls in various museums of Europe, which were made properly, and are not approximations. The average cranial capacity was 1421 c.cm., which is about thirty to forty c.cm. below the average cranial capacity of the population of Europe. Of course the small number of skulls thus measured is not sufficient to draw positive conclusions.
As to the weight of the brain, there are also very few observations on record. The author knows only of twentythree Jewish brains reported by Giltchenko,3 four by Weisbach,4 and three by Weinberg.5 The average weight of these brains, as calculated by Weinberg, was 1320.4 gm. Since the average weight of the brain of the European is 1350 gms., the brain of Jews is rather lighter by 30 gms. , or nearly one ounce. Considering that the Jews are shorter of stature than the average Europeans, it would be expected that their brain should also be smaller. But, as Weinberg points out, the average for Germans was found to be 8.22 gm. of brain tissue for each centimetre of stature, while for the Jews it is only 8.05 gms. This shows the Jewish brain lighter not only absolutely, but also relatively.

Evolutionary significance of Denisovan admixture in Oceanians

Investigating the Evolutionary Importance of Denisovan Introgressions in Papua New Guineans and Australians

Previous research reported that Papua New Guineans (PNG) and Australians contain introgressions from Denisovans. Here we present a genome-wide analysis of Denisovan introgressions in PNG and Australians. We firstly developed a two-phase method to detect Denisovan introgressions from whole-genome sequencing data. This method has relatively high detection power (79.74%) and low false positive rate (2.44%) based on simulations. Using this method, we identified 1.34 Gb of Denisovan introgressions from sixteen PNG and four Australian genomes, in which we identified 38,877 Denisovan introgressive alleles (DIAs). We found that 78 Denisovan introgressions were under positive selection. Genes located in the 78 introgressions are related to evolutionarily important functions, such as spermatogenesis, fertilization, cold acclimation, circadian rhythm, development of brain, neural tube, face, and olfactory pit, immunity, etc. We also found that 121 DIAs are missense. Genes harboring the 121 missense DIAs are also related to evolutionarily important functions, such as female pregnancy, development of face, lung, heart, skin, nervous system, and male gonad, visual and smell perception, response to heat, pain, hypoxia, and UV, lipid transport, metabolism, blood coagulation, wound healing, aging, etc. Taken together, this study suggests that Denisovan introgressions in PNG and Australians are evolutionarily important, and may help PNG and Australians in local adaptation. In this study, we also proposed a method that could efficiently identify archaic hominin introgressions in modern non-African genomes.

Racial differences in brain shape

A press release:

Researchers at the University of California, San Diego and the School of Medicine have found that the three-dimensional shape of the cerebral cortex -- the wrinkled outer layer of the brain controlling many functions of thinking and sensation -- strongly correlates with ancestral background.

Modeling the 3D Geometry of the Cortical Surface with Genetic Ancestry

Knowing how the human brain is shaped by migration and admixture is a critical step in studying human evolution [ 1, 2 ], as well as in preventing the bias of hidden population structure in brain research [ 3, 4 ]. [. . .] The geometry of the cortical surface contains richer information about ancestry than the areal variability of the cortical surface, independent of total brain volumes. Besides explaining more ancestry variance than other brain imaging measurements, the 3D geometry of the cortical surface further characterizes distinct regional patterns in the folding and gyrification of the human brain associated with each ancestral lineage.

Chris Stringer on the possibility of a Eurasian origin for Homo heidelbergensis

Who is Homo heidelbergensis?

H. heidelbergensis is a critical human species in the Middle Pleistocene (∼130–780 thousand years ago (ka)). We know from several beautifully preserved crania that this species had a large brain, within the lower range of modern human variation, and a less robust face than early fossil humans. We know from their long bones that they were tall, strong people. From their associated archaeology we know they were capable of producing beautiful tools such as the large handaxes found in huge numbers at Boxgrove in Sussex. But there are many unanswered questions: who exactly belongs to the species Homo heidelbergensis, where did they live, how do they fit into the human family tree, and are they a separate species at all? [. . .]
Are they our ancestors? African H. heidelbergensis material, such as Broken Hill, shares numerous features with European fossils such as Petralona, leading many to group them together. As long as Mauer is also included, this taxon can be named H. heidelbergensis. Proponents of this wide concept of H. heidelbergensis assert that the mosaic of primitive and derived features shared by this group of fossils is unique, with few traits linking them exclusively to either modern humans or Neanderthals ( Figure 1B). H. heidelbergensis is thus hypothesised to be the last common ancestor of both Neanderthals in Eurasia and H. sapiens in Africa. This scenario is probably the most popular and well supported at present. [. . .]
The geographic origin of H. heidelbergensis is still unknown, but the early fossils from Asia suggest that continent is as likely a place of origin as Europe or Africa at the moment. An Asian origin for a species directly ancestral to our own would certainly shake up the current rather Afro-centric view of our evolution.

Related:

Inbreeding and inclusive fitness

Inbreeding avoidance, tolerance, or preference in animals?

The widespread presumption that inbreeding depression will inevitably cause net selection for inbreeding avoidance ignores the inclusive fitness benefit of inbreeding that exists because parents are more closely related to inbred offspring than to outbred offspring. This increased relatedness arises because inbred offspring, by definition, inherit alleles from one parent that are identical by descent to those carried by, and potentially inherited from, the other parent. Inbreeding thereby increases the expected proportion of alleles that any one parent shares with its offspring, including alleles favouring inbreeding [10,24,25]. This inclusive fitness benefit underpins extensive theory predicting the evolution of self-fertilisation in plants [10,25–27]. That this same benefit could also cause the evolution of biparental inbreeding was suggested three decades ago (Box 1) [28,29], but remained widely ignored by animal ecologists. The assumption that inbreeding depression inevitably causes selection for inbreeding avoidance continued to pervade hypotheses explaining dispersal, mate choice, and polyandry [3,5,6,11,30–32]. Recent theory has re-emphasised that biparental inbreeding could be adaptive, even given inbreeding depression, with the inclusive fitness benefit phrased as ‘helping relatives to breed’ and hence kin selection [12,13,33].

What Happens after Inbreeding Avoidance? Inbreeding by Rejected Relatives and the Inclusive Fitness Benefit of Inbreeding Avoidance

The fitness costs associated with inbreeding, primarily inbreeding depression in resulting offspring, have caused a widespread assumption among animal ecologists that inbreeding avoidance must be adaptive [10, 21, 22]. Meanwhile, empirical studies have reported a lack of inbreeding avoidance [34, 42–47], or even an apparent preference for inbreeding [48–52], causing a mismatch between expectations and data [27]. This mismatch is partially resolved by basic conceptual models of biparental inbreeding that imply that the inclusive fitness benefit of inbreeding might cause inbreeding tolerance or preference to be adaptive even given inbreeding depression in offspring fitness, and that predict sexual conflict over inbreeding [24–28]. [. . .]
Our models imply that the inclusive fitness costs and benefits of inbreeding versus avoiding inbreeding will vary among individuals depending on their interactions with multiple different relatives of both sexes, and on the degree to which focal individuals are themselves inbred. Understanding these costs and benefits and their combined consequences for the evolution of inbreeding strategies therefore requires consideration of not only the relatedness of an individual to its potential mate(s), but also the relatedness between the individual and the subsequent mates of rejected relatives. Knowledge of the distribution of relatedness within a population is therefore likely to be critical for understanding the evolution of inbreeding strategies. This distribution will in turn depend on the distribution of relatedness in previous generations and on previously realised inbreeding strategies and inbreeding loads, thereby generating complex feedbacks between inbreeding strategy, load, and relatedness. [. . .]
Sexual conflict and interactions among multiple non-self relatives are particular to biparental reproduction rather than self-fertilisation, but both types of inbreeding increase the expression of inbreeding load causing inbreeding depression in offspring [1, 2, 7, 12]. Inbreeding depression may decrease inbreeding load by exposing deleterious homozygous recessive alleles to selection [9, 71]. Resulting purging of deleterious recessive alleles may in turn affect the inclusive fitness benefit of inbreeding versus avoiding inbreeding causing inbreeding strategy and inbreeding load to coevolve [12, 72, 73]. The consequences of this coevolution have been modelled extensively with respect to outcrossing versus selfing [12, 18, 72, 74–76], but have not yet been modelled for the evolution of biparental inbreeding strategies [10]. Future theoretical developments will therefore need to explicitly consider coevolution between biparental inbreeding strategy and inbreeding load.
Predictive models of biparental inbreeding evolution cannot be simple, but their complexity need not preclude generality [77]. Tractable approaches for developing inbreeding theory might include game-theoretic models, or individual-based models that explicitly track ancestry and inbreeding load, and thereby incorporate feedbacks among relatedness, load, and inbreeding strategy.

Related:

David Agus: inbred retard?

Discussing a recent study (Directional dominance on stature and cognition in diverse human populations) that found an effect for runs of homozygosity on height and IQ within populations, Greg Cochran notes:

Some retards (British papers) have been spinning this as saying that there are big benefits to mixed-race marriage. Untrue: to avoid lots of ROH (runs of homozygosity), just marry someone who isn’t from the same isolated population as you. We’re talking outside the valley or across the river : intercontinental travel is not necessary. Now there might be a degree of hybrid vigor in some distant crosses (currently unclear) – but likely not enough to compensate for someone coming from a group that has low trait values. Marry a Pygmy and your kids are going to be short. Marry someone from a population whose average IQ is below 90 (much of the world) and your kids will on average be less smart.

CBS medical contributor David Agus (who, wikipedia informs us, "graduated cum laude in molecular biology from Princeton University and received his medical degree from the University of Pennsylvania School of Medicine in 1991") promotes this misinterpretation of the study in a segment on CBS This Morning:

Do kids from mixed genetic backgrounds have an advantage?

Additionally, although one would hope someone who majored in molecular biology at Princeton and co-founded a personal genomics company would know that any benefits from outcrossing will fully accrue in the first generation, Agus gleefully urges the viewer to imagine how much "taller and smarter" children will be if "people of different backgrounds" continue interbreeding generation after generation.

It's a pretty interesting study that tells us a lot because this is really the first couple generations where people of different backgrounds are having children and if this happens in one, one generation children are 1.2 cm shorter, think of if this continues to happen, so, taller and smarter.

Curiously, Agus, the grandson of a rabbi, married a pre-Connie Chung daughter of Maury Povich. That is, Agus chose to mate with a member of the same rather inbred narrow ethnic group as himself. But I'm sure now that he's aware of this study (confused though he may be about it) and excited about the eugenic prospects of racial mixing, he's urged his own children to marry Africans, with that same gleeful look in his eyes.

It’s Sunday night, and Agus is at Jerusalem’s Mamilla Hotel. He just arrived for the Global Forum, a gathering of 70 of the world’s thinkers hosted by Israel’s National Library, to discuss how the People of the Book can use their ancient lore for contemporary needs.
It was Shimon Peres, the honorary chairman of the event, who convinced Agus to attend. Agus and Peres are friends – though he’s not the nonagenarian’s doctor – and the two meet every six months or so. This time, Agus will be discussing Maimonides at the National Library, from the perspective of what he, Agus, believes.
But first he had to go back and read some of the good doctor’s words. It’s been a long time since Agus studied Maimonides at Philadelphia’s Akiba Hebrew Academy. What he found resonated. [. . .]
Now Agus combines teaching, research and patient work, along with spending a lot of time at places like the World Economic Forum, the Aspen Ideas Festival and TEDMED – TED for the health field. He’s also at the CBS studio at 4 a.m., several mornings per week.
“You get a passion to change things, and I decided I don’t care if I’m uncomfortable on camera,” said Agus, who calls himself an introvert by nature. “I need to be a role model and it’s awkward, but you have to do it, over and over again. I get to talk to four million people every morning on CBS. I can just talk, I can call a spade a spade. I look at my patients losing their lives on a daily basis, so I’ve got nothing to lose.”
[Steve Jobs’ ex-doctor is in, and he’s quoting Maimonides. http://www.timesofisrael.com/steve-jobs-ex-doctor-is-in-and-hes-quoting-maimonides/]