there’s a new hbd-er in the world!

CONGRATULATIONS to jayman and mrs. jayman and their extended familiy members! (^_^)

what a cutie!: Meet JayMan Jr. (^_^)

save the tibetans!

’cause (according to reddit) they make stuff like this:

i was already really impressed by the tibetans and their sky burials, but now they’ve truly surpassed themselves! (^_^)

runs of homozygosity again

**update below**

here’s an exciting new paper!: Genomic Patterns of Homozygosity in Worldwide Human Populations. i don’t have access to the paper itself, but there are lots o’ neat figures and tables in the supplemental data [opens pdf] that relate to runs of homozygosity (roh). roh are identical stretches of dna within an individual’s genome (i.e. identical on each of the dna strands, paternally and maternally inherited). (roh shouldn’t be confused with blocks of identity by descent [ibd], which i did once! ibd blocks are identical stretches of dna as compared between different individuals, iiuc.)

recall that possessing lots of long roh indicates that one’s parents are/were quite similiar genetically speaking. that can be as a result of a couple of different genetic scenarios like (as greying wanderer has brought up a lot recently) simply being from a small sized population (i.e. having a small effective population size) and/or from regular inbreeding (consanguineous/endogamous mating). so, a population having a lot of long roh is either small and/or inbreeds a lot. populations having LOTS of short roh have probably been through some sort of bottleneck (see previous post).

in the paper i looked at in that previous post, the researchers had looked at the different roh lengths for large, regional populations like “europeans” or “east asians.” amongst other things, they had found that some of my regular inbreeders — the fbd marriage folks — had some of the highest numbers of medium and long roh, a state of genetic affairs which likely reflects their long-term close mating patterns. interestingly, the researchers had found that east asians had roh lengths similar to those of europeans across the board, something which surprised me since, at least according to what i’ve been reading, east asians (i.e. the chinese) have been inbreeding for a much longer time than europeans. one drawback of that previous study, though, was that, apart from the french, most of the european populations they looked at were peripheral groups who have had a tendency to inbreed more than my “core” europeans (see mating patterns in europe series below ↓ in left-hand column).

the new paper suffers from some of the same problems since the data come from the same sources (hgdp-ceph and hapmap phase 3 populations), so northern europeans — apart from the french — aren’t included in this paper either. (what can you do? it’s early days yet. i look forward to when there’s lots more genetic data available out there for teh scientists to work with! (^_^) )

what the researchers in this paper have done, though, is to look at both the different mean lengths of roh in each of the different populations sampled AND they looked at total numbers of roh within individuals for each population. this has, i think, drawn out some interesting differences between the populations.

first, here are two graphics from the supplmental data (linked to above). click on each for LARGER views (they should open in new tabs/windows — you might have to click on them again there to super-size them).

i’ve highlighted a handful of populations i want to focus on ’cause i know a little something about their historic mating patterns: the bedouin (as a proxy for the arabs — note that the bedouin have probably inbred more than more settled arabs); italians (not sure if they’re northern or southern italians or a mix of both — however, there are tuscans in the samples with which these “italians” can be compared); pathan or pastuns (more fbd marriage folks, like the bedouins/arabs); and han chinese (there are some northern han chinese with whom this groups can be compared). ok. here are the charts:

as you can see, the researchers have split up the roh into three classes (note that the short and medium classes here are a lot shorter than those in the paper looked at previously):

– A: 0.25-0.40 Mb (short)
– B: 0.6-1.2 Mb (medium)
– C: 0-35 Mb (long)

the interesting thing in the first chart above (Fig. S3 – Mean ROH Length for Each of the Three Size Classes in Each Population), is that the han chinese have lower means of roh length in all of the size classes compared to the other populations i’ve highlighted. in the previous study, the researchers found that east asians had similar means to europeans for all roh lengths. i found this surprising since, from what i’ve read, the han chinese have been inbreeding for a longer period of time than europeans. what might be confounding the results though, once again, is the fact that nw europeans (the outbreeders extraordinaire) are not really included in either of these studies apart from a handful of french samples.

in this latest study, both the bedouin and the pashtun, for instance, have higher means — and wider spreads — of long (class C) roh than the italians, which is what i would’ve expected since those two groups (the bedouins and the pashtuns) are, being fbd marriage folks, serious inbreeders. perhaps the reason the han chinese long roh mean is comparatively low is partly due to the fact that they historically practiced mother’s brother’s daughter (mbd) marriage which doesn’t push towards such close inbreeding as fbd marriage. still, i would’ve expected to see greater means of roh for the chinese than the italians — or, at least, around the same. not so much lower. (unless the italians practiced fbd marriage, too — or fzd marriage — but i don’t think so.)

if you look at the second chart (Fig. S4 – Total Number of ROH in Individual Genomes), however, you’ll see that, overall, the han chinese have more short, medium and long roh totally in individual genomes than any of the other three populations i’ve highlighted. both the bedouins and the pashtuns have greater numbers/wider total spread of long roh than the italians, but the han chinese have a much greater total number of long roh than any of the other three groups — three or four times as many.

but they’re, on average, shorter long roh don’t forget. (confusing, eh?!)

perhaps this is what you get when you have — as the chinese have had — a pretty good-sized effective population size for such a long time. there have been a LOT of han chinese for — wow — millennia.

so, it looks like this (in this order of inbrededness — i think):

– bedouins: highest mean, and very wide spread, of long roh; high total numbers, and widest spread, of long roh.
– pashtun: low mean, but widest spread, of long roh; low total number, but very wide spread, of long roh.
– han chinese: very low mean, and very narrow spread, of long roh; highest total numbers, and wide spread, of long roh.
– italians: low mean, and rather wide spread, of long roh; very low total number, and very small spread, of long roh.

other interesting points are that:

– the tuscans/tsi (toscani) appear to have lower short, medium and long mean roh than the generic “italian” category. however, the tuscans have lower total numbers of long roh than the “italians” while the toscani (tsi), on the other hand, appear to have a greater total number of long roh than the “italians.” while the tuscan samples and the toscani/tsi samples are from different studies (hgdp vs. hapmap), they are all supposed to be from tuscany, so it’s surprising that they’re so different. perhaps the individuals in the toscani/tsi sample were more closely related somehow?

– the northern han samples have lower short, medium and long mean roh than the generic “han” category. this would fit my general impression that historically inbreeding has been greater in southern china than in the north. however, the total number of long roh are greater in the northern han sample than in the “han” sample. not sure what that means.

don’t forget that there can be all sorts of reasons for differences in roh: inbreeding vs. outbreeding, yes, but also effective population size, population movement (migration in or out), bottlenecks, etc. i just happen to be interested in trying to pick out the effects of inbreeding/outbreeding — if possible.
_____

**update – here are a couple of excerpts from the article (thnx, b.b.!) [pgs. 277, 279-281]:

“Size Classification of ROH

“Separately in each population, we modeled the distribution of ROH lengths as a mixture of three Gaussian distributions that we interpreted as representing three ROH classes: (A) short ROH measuring tens of kb that probably reflect homozygosity for ancient haplotypes that contribute to local LD [linkage disequilibrium] patterns, (B) intermediate ROH measuring hundreds of kb to several Mb that probably result from background relatedness owing to limited population size, and (c) long ROH measuring multiple Mb that probably result from recent parental relatedness….

“In each population, the size distribution of ROH appears to contain multiple components (Figure 2A). Using a three-component Gaussian mixture model, we classified ROH in each population into three size classes (Figure 2B): short (class A), intermediate (class B), and long (class C). Size boundaries between different classes vary across populations (Table S1); however, considering all populations, all A-B boundaries are strictly smaller than all B-C boundaries (Figure 2C). The mean sizes of class A and B ROH are similar among populations from the same geographic region (Figure S3), with the exception that Africa and East Asia have greater variability. The class C mean is generally largest in the Middle East, Central/South Asia, and the Americas and smallest in East Asia (Figure S3), with the exception that the Tujia population has the largest values. In the admixed Mexican population (MXL), mean ROH sizes are similar to those in European populations. In the admixted African American population (ASW), however, mean ROH sizes are among the smallest in our data set, notably smaller than in most Africans and Europeans.

“Geographic Pattern of ROH

“Several patterns emerge from a comparison of the per-individual total lengths of ROH across populations (Figure 3). First, the total lengths of class A (Figure 3A) and class B (Figure 3B) ROH generally increase with distance from Africa, rising in a stepwise fashion in successive continental groups. This trend is similar to the observed reduction in haplotype diversity with increasing distance from Africa. Second, total lengths of class C ROH (Figure 3C) do not show the stepwise increase. Instead, they are higher and more variable in most populations from the Middle East, Central/South Asia, Oceania, and the Americas than in most populations from Africa, Europe, and East Asia. This pattern suggests that a larger fraction of individuals from the Middle East, Central/South Asia, Oceanis, and the Americas tend to have higher levels of parental relatedness, in accordance with demographic estimates of high levels of consanguineous marriage particularly in populations from the Middle East and central/South Asia, and it is similar to that observed for inbreeding-coefficient and identity-by-descent estimates. Third, in the admixed ASW and MXL individuals, total lengths of ROH in each size class are similar to those observed in populations from Africa and Europe, respectively (Figure 3).

“The total numbers of ROH per individual (Figure S4) show similar patterns to those observed for total lengths (Figure 3). However, in East Asian populations, total numbers of class B and class C ROH per individual are notably more variable across populations than are ROH total lengths.”

previously: runs of homozygosity and inbreeding (and outbreeding) and ibd and historic mating patterns in europe

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red deer cave people

Mysterious Chinese Fossils May Be New Human Species

“Mysterious fossils of what may be a previously unknown type of human have been uncovered in caves in China, ones that possess a highly unusual mix of bygone and modern human features, scientists reveal.

“Surprisingly, the fossils are only between 11,500 and 14,500 years old. That means they would have shared the landscape with modern humans when China’s earliest farmers were first appearing.

“‘These new fossils might be of a previously unknown species, one that survived until the very end of the ice age around 11,000 years ago,’ said researcher Darren Curnoe, a palaeoanthropologist at the University of New South Wales in Australia.

“‘Alternatively, they might represent a very early and previously unknown migration of modern humans out of Africa, a population who may not have contributed genetically to living people,’ Curnoe added….”
_____

more from dienekes.

see also: Human Remains from the Pleistocene-Holocene Transition of Southwest China Suggest a Complex Evolutionary History for East Asians

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even confused beetles do it!

back in the 70s, michael wade ran an altruism experiment with some confused flour beetles.

confused flour beetle larvae have a tendency to cannibalize nearby eggs (’cause they’re confused? (~_^) ). wade wanted to find out if there were any differences in the cannibalization rates between more closely related versus not so closely related hatches. so, he outbred some groups of beetles and inbred other groups to see what would happen.

i don’t have access to the paper related to this research, but here’s a summary of what he found from another one of his papers [pgs. 844-45]:

“In experimental studies of kin selection, using laboratory populations of the flour beetle, Tribolium confusum, Wade (1980a) investigated the effects of discontinuities in population breeding structure on the predictions of kin selection theory. The experiment consisted of synthesizing a strain of T. confusum with genetic variability for the tendency of larvae to cannibalize eggs. Beetles randomly chosen from this strain were then placed in six different treatments, each representing a different population structure, and the evolution of the cannibalism behavior was followed for several generations….

“The population structure was varied by varying both the degree of genetic relatedness between the larval cannibals and their egg victims and the degree of random mating. Depending on the treatment, the genetic relationship between the larvae and eggs was .50 (full-sibs), .25 (half-sibs), or .00 (no relationship). These ‘interaction treatments’ were factorially combined with two different breeding structures, representing the extremes of (1) random mating and (2) within-group mating. Wade (1980a) observed that the egg cannibalism rates, which were initially equal, diverged significantly from one another only in the within-group mating treatments. Specifically, in that treatment where the larvae and eggs were full-sibs, cannibalism rates declined relative to the treatment where the larvae and eggs were unrelated. Cannibalism rates in the half-sib treatment were intermediate. In those treatments with random mating, however, no differences in cannibalism rates were observed regardless of the larval-egg relationship….

“On the basis of this comparison of two extreme mating systems, Wade (1980a) concluded that inbreeding should accelerate the rate of evolution of social behaviors.”

so, inbreeding makes the evolution of altruism (and other social behaviors) easier.
_____

digression. this research with bugs reminded of an amusing story from bill hamilton about doing research at the univ. of michigan and some other bugs [pg. 51]:

“I mathematized them [some models] as far as I could and then used simulation on the Michigan main computer, accessing it either from a huge cave-like room called NUBS in the basement of the herbarium (our nearest-neighbour building) or, later, from a smaller terminal room in my own floor of the Museum of Zoology. NUBS had firebrats plus a spectrum of dazed, earnest, and sometimes frighteningly expert freshmen. Freshmen are first-year university students; firebrats, not arsonists but primitive insects. Smartly striped like football players, the latter dashed swiftly about on the floor under the piles of unwanted output paper, especially favouring that mounded against walls. I think their name’s origin lies in their being commonly found near bakery ovens. The nature of their food there is obvious; but what it was under the paper in NUBS is hard to imagine unless perhaps there were mummified students, dead of their sorrow at their unco-operating programs.”

(^_^)

previously: technical stuff and even plants do it! and more plants playing favorites and even ROBOTS do it! and even monkeys do it and even slime molds do it!

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curioser and curioser

just when you think you’ve got inbreeding and genetics sorted out in your head (almost — well, no, not really), they throw something new at ya.

here’s an article that linton @nobabies.net pointed out to me (thanks, linton!):

“Epigenetics Linked to Inbreeding Depression”
16 September 2011

“Inbreeding depression is the bane of conservation biology. When closely related individuals mate, which can happen when there aren’t too many members of a species left, their offspring are often less fit and less fertile, making the species all the more vulnerable. Both plants and animals can suffer from inbreeding depression, and textbooks typically attribute this phenonmenon to genetics: Recessive genes with harmful effects, whose negative influences are normally masked by a dominant copy of a gene, are more likely to pair up in offspring of more genetically similar parents.

“Or so the theory goes.

“But Philippine Vergeer, an evolutionary ecologist at Radboud University Nijmegen in the Netherlands, suspects that epigenetics — chemical modifications to the DNA that alter gene activity — may also be to blame, at least in plants….

“Vergeer and her Radboud colleagues Niels Wagemaker and Joop Ouborg compared DNA methylation between outbred and inbred S. columbaria — also known as small scabious — derived from the same mother plant. Methylation was 10% higher in inbred plants…. Also, inbred and outbred plants have different parts of their genomes methylated.

“The scientists then decided to look at what happened to plant offspring if they reconfigured the flora’s methylation. Every day for a week, they exposed germinating seeds of inbred and outbred plants to a demethylating agent. The result: ‘Phenotypic differences between outbred and inbred plants are nullified,’ Vergeer reported….”

so, at least in the case of these little plants, inbreeding depression seems to be connected to epigenetics and not genetics. when they reversed the epigenetics in these plants, the inbred plants photosynthesized (which is what the researchers were measuring) just as well as the outbred plants.

neato!

there has been some research done showing that epigenetic states are probably regulated (if that’s the right way to put it) by the underlying genetics, so perhaps the inbreeding depression in these plants was still a result of too many “bad genes.” but it’s cool that they could reverse the inbreeding depression by getting rid of the methylation!

there have also been studies, of course, showing that some epigentic states can be inherited across a few or several generations.

see also: Inbreeding and epigenetics: beneficial as well as deleterious effects

previously: the genetics of epigenetics

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runs of homozygosity and inbreeding (and outbreeding)

here’s a really neat chart! (click on image for LARGER view. should open in new tab/window.):

what does it mean? well…

some very clever researchers/geneticists took a look for “runs of homozygosity” (roh) in the genomes of the individuals in the human genome diversity project (hgdp) — that’s 1043 individuals from 51 different populations. “runs of homozygosity” are stretches in the genome where identical dna was inherited from each parent. if you inbreed, you’re gonna have a greater number of longer runs of homozygosity in your genome than if you don’t.

apart from being just plain fun, sex shuffles up genomes from one generation to the next (presumably for some good reason or another). if you were to clone yourself, your descendants would have (pretty much) the same exact genome as you. if you were to mate with your mother or your sister (i know — ewwww!), your descendants would have different genomes from you, but they’d have lots of roh in their genomes ’cause their dna came from you and someone with whom you share a lot dna in common. the farther out you mate, the less homozygosity there’s likely to be.

you might also have lots of roh in your genome if you come from a population that has little genetic diversity — ’cause maybe your ancestors went through some sort of bottleneck or something.

inbreeding with close relatives — like marrying your first- or second-cousins (consanguineous matings) — leads to long roh since you share so much of your dna with your closest family members. endogamous mating — just mating within your population but not your close cousins — also leads to roh, but not ones as long as mating with your close relatives. you share dna with others in your population (say your clan or your ethnic group), but not so much of exactly the same dna or genes in certain stretches as with your closer relatives. a population will little genetic diversity, but that does not inbreed, will have lots of short roh — they share a lot of stretches of dna in common, but all of the outbreeding shuffles up the genomes within the population.

so that’s:

– long roh = inbreeding, probably consanguineous (first-/second-cousin matings)
– medium roh = endogmaous mating within a population
– short roh = little genetic diversity in the population probably from an event like a population bottleneck

i’m oversimplifying, but that’s the gist of it.

so what did the researchers find when they looked at the 51 populations in the hgdp (see chart)?

– LOTS of short roh (1-2 Mb) within populations from oceania and central/south america, probably because those populations went through bottlenecks. the people from oceania have low amounts of long roh (>16 Mb), which means that they don’t inbreed closely much. however, the people from central/south america have the highest amount of long roh of all the groups, so that’s means they must inbreed closely a LOT.

– central/south asians, west asians, east asians, europeans and africans don’t have huge amounts of short roh — at least not compared to the folks in oceania and the americas. no big bottlenecks there. and africans, in fact, have the fewest short roh.

– central/south asians and west asians have pretty high amounts of roh in all of the middle ranges and the highest long roh after the native american populations. this indicates significant amounts of endogamy and close relative marriages (but we already knew that).

– the groups with the lowest amounts of long roh are the europeans, africans and east asians — in that order. in other words, it appears as though, of these three groups, africans and europeans inbreed more closely (first- or second-cousin marriage, say) than east asians.

if you’ve been following along, you know that’s not what hbd chick expected. i thought that east asians would’ve had more short roh than europeans ’cause they have a fairly recent history of close marriages. hmmmm….

i checked to see which populations of europeans are included in the hdgp (you can find a list in the article’s supplemental material here [opens pdf]) and they are: adygeis, basques, french folks, italians, orcadians, russians, sardinians and tuscans. apart from the french and the tuscans, all of these groups have recent (or current) histories of consanguineous or endogamous mating practices (see Inbreeding in Europe series below in left-hand column for more details), so they are not a fully representative sample of europeans. unfortunately, “core” europe, which contains the most outbred populations in europe, is not included in the hgdp and, therefore, not in this study.

*sigh*

still — this is interesting stuff! genetics. cool! i’m going to post more about this ’cause, for one thing, it should be possible to drill down further into these populations to compare them more specifically (there are some data available in the supplemental materials). so, more anon…!

thanks to prof. harpending for pointing out this article! (^_^)

*update 08/20: see also runs of homozygosity again

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micro-chimerism

biology is so cool:

“Our Selves, Other Cells”

“[F]or any woman that has ever been pregnant, some of her baby’s cells may circulate in her bloodstream for as long as she lives. Those cells often take residence in her lungs, spinal cord, skin, thyroid gland, liver, intestine, cervix, gallbladder, spleen, lymph nodes, and blood vessels. And, yes, the baby’s cells can also live a lifetime in her heart and mind.

“Here’s what happens.

“During pregnancy, cells sneak across the placenta in both directions. The fetus’s cells enter his mother, and the mother’s cells enter the fetus. A baby’s cells are detectable in his mother’s bloodstream as early as four weeks after conception, and a mother’s cells are detectable in her fetus by week 13. In the first trimester, one out of every fifty thousand cells in her body are from her baby-to-be (this is how some noninvasive prenatal tests check for genetic disorders). In the second and third trimesters, the count is up to one out of every thousand maternal cells. At the end of the pregnancy, up to 6 percent of the DNA in a pregnant woman’s blood plasma comes from the fetus. After birth, the mother’s fetal cell count plummets, but some stick around for the long haul. Those lingerers create their own lineages. Imagine colonies in the motherland….

“How many people have left their DNA in us? Any baby we’ve ever conceived, even ones we’ve miscarried unknowingly. Sons leave their Y chromosome genes in their mothers. The fetal cells from each pregnancy, flowing in a mother’s bloodstream, can be passed on to her successive kids. If we have an older sibling, that older sibling’s cells may be in us. The baby in a large family may harbor the genes of many brothers and sisters. My mother’s cells are in my body, and so are my daughter’s cells, and half my daughter’s DNA comes from her dad. Some of those cells may be in my brain….”

whoa.

wikipedia says (so it must be true): “After giving birth, about 50-75 % of women carry fetal immune cell lines. Maternal immune cells are also found in the offspring yielding in maternal→fetal microchimerism, though this phenomenon is about half as frequent as the former”

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