Thursday, March 22, 2018

The Impossible Early Galaxy Problem

This paper and its proposed solution is less notable than its discussion of the problem with the standard model of cosmology, which is known as the "impossible early galaxy problem". In general, modified gravity theories lead to earlier structure development in cosmology, so this problem favors such theories relative to dark matter, although modified gravity isn't necessarily the only possible solution.
To understand the formation and evolution of galaxies at redshifts z < 10, one must invariably introduce specific models (e.g., for the star formation) in order to fully interpret the data. Unfortunately, this tends to render the analysis compliant to the theory and its assumptions, so consensus is still somewhat elusive. 
Nonetheless, the surprisingly early appearance of massive galaxies challenges the standard model, and the halo mass function estimated from galaxy surveys at z > 4 appears to be inconsistent with the predictions of LCDM, giving rise to what has been termed "The Impossibly Early Galaxy Problem" by some workers in the field. A simple resolution to this question may not be forthcoming. 
The situation with the halos themselves, however, is more straightforward and, in this paper, we use linear perturbation theory to derive the halo mass function over the redshift range z < 10 for the R_h=ct universe. We use this predicted halo distribution to demonstrate that both its dependence on mass and its very weak dependence on redshift are compatible with the data. 
The difficulties with LCDM may eventually be overcome with refinements to the underlying theory of star formation and galaxy evolution within the halos. For now, however, we demonstrate that the unexpected early formation of structure may also simply be due to an incorrect choice of the cosmology, rather than to yet unknown astrophysical issues associated with the condensation of mass fluctuations and subsequent galaxy formation.
Manoj K. Yennapureddy, Fulvio Melia, "A Cosmological Solution to the Impossibly Early Galaxy Problem" (March 19, 2018).

A related issue is that we don't know how black holes got so big so fast under existing cosmology models.

Metal enrichment in the intergalactic medium in the very early universe also challenges our models.

Wednesday, March 21, 2018

More Archaic Admixture Data

More Ancient Neanderthal Genomes

An article in Nature provides great understanding of Neanderthal admixture by adding five new autosomal Neanderthal genomes to our pool of knowledge:
Although it has previously been shown that Neanderthals contributed DNA to modern humans, not much is known about the genetic diversity of Neanderthals or the relationship between late Neanderthal populations at the time at which their last interactions with early modern humans occurred and before they eventually disappeared. 
Our ability to retrieve DNA from a larger number of Neanderthal individuals has been limited by poor preservation of endogenous DNA and contamination of Neanderthal skeletal remains by large amounts of microbial and present-day human DNA. Here we use hypochlorite treatment6 of as little as 9 mg of bone or tooth powder to generate between 1- and 2.7-fold genomic coverage of five Neanderthals who lived around 39,000 to 47,000 years ago (that is, late Neanderthals), thereby doubling the number of Neanderthals for which genome sequences are available. 
Genetic similarity among late Neanderthals is well predicted by their geographical location, and comparison to the genome of an older Neanderthal from the Caucasus indicates that a population turnover is likely to have occurred, either in the Caucasus or throughout Europe, towards the end of Neanderthal history. We find that the bulk of Neanderthal gene flow into early modern humans originated from one or more source populations that diverged from the Neanderthals that were studied here at least 70,000 years ago, but after they split from a previously sequenced Neanderthal from Siberia around 150,000 years ago. Although four of the Neanderthals studied here post-date the putative arrival of early modern humans into Europe, we do not detect any recent gene flow from early modern humans in their ancestry.
The bottom line is that most Neanderthal admixture in modern humans can be traced to the Out of Africa era in a population that would have been basal to almost all non-African modern humans, even Papuans who together with Australian Aborigines who diverge from other non-African modern humans at the most basal point, probably around 65,000-70,000 years ago. If modern humans made it into Asia and Europe before then, and Altai Neanderthal admixture dated to ca. 100,000 years ago suggests that this did happen somewhere, they have not left much of a genetic trace in modern humans.

This makes sense. First wave modern humans in Europe and Siberia mostly went extinct in an ice age about 20,000 years ago, so any subsequent admixture in the Neanderthals European homeland would have been lost. By the time that modern humans recolonized Europe, Neanderthals were extinct.

Inferred Archaic Admixture In Africans

There is essentially no Neanderthal admixture or Denisovan admixture in sub-Saharan Africans that can't be traced to Eurasian back migration to Africa. But, that doesn't mean that the ancestors of today's sub-Saharan Africans didn't also experience admixture with archaic hominins. It just means that they admixed with different hominins from whom we have no ancient DNA, in part due to poor conditions for preserving it, and in part due to insufficient resources devote to looking for potential samples.

But, it is possible to reliably estimate ancient admixture from "ghost populations" of hominins by statistically analyzing patterns in the genomes of people who are alive today and these methods have been validated by comparing their results to those obtained from direct comparisons to ancient homin genomes.

What have scientists found?

According to a new preprint at bioarXiv that largely confirms a couple of prior studies along the same lines:
Analyses of Neanderthal and Denisovan genomes have characterized multiple interbreeding events between archaic and modern human populations. 
While several studies have suggested the presence of deeply diverged lineages in present-day African populations, we lack methods to precisely characterize these introgression events without access to reference archaic genomes. We present a novel reference-free method that combines diverse population genetic summary statistics to identify segments of archaic ancestry in present-day individuals.  
Using this method, we find that ~7.97±0.6% of the genetic ancestry from the West African Yoruba population traces its origin to an unidentified, archaic population (FDR [false discovery rate] ≤20%). We find several loci that harbor archaic ancestry at elevated frequencies and that the archaic ancestry in the Yoruba is reduced near selectively constrained regions of the genome suggesting that archaic admixture has had a systematic impact on the fitness of modern human populations both within and outside of Africa.
This admixture percentage rivals that of Papuans and aboriginal Australians. It is equivalent to a situation at the time shortly after archaic introgression had ceased, in which the average person had 1.5 great-grandparents who were archaic hominins. This is roughly four times the archaic admixture proportion found in Europeans, and a somewhat lower multiple of Asians who have no Papuan ancestry. It is similar to the total amount of archaic admixture in Papuans. 

But, in this case, it involves West Africans who, unlike early of of Africa modern human populations and proto-Papuan populations, did not experience a really severe population bottleneck in their demographic history that the other populations did.

The study controlled for admixture with highly diverged African populations like Biaka Pygmies.

It is kind of nuts that we can see this huge amount of archaic admixture, and yet have no meaningful idea what kind of hominin was those source of this admixture, just as it is pretty crazy that we can document Denisovan admixture so well while having no real idea what a Denisovan looked like.

As in other cases of archaic admixture, with Neanderthals and Denisovans, it also appears that natural selection has weeded out archaic ancestry from our genomes in areas where modern human genes provide a fitness advantage relative to archaic hominins, who were, on average, less fit than modern humans. But, as in other cases of archaic admixture, there are a few loci where archaic admixture is elevated, suggesting that the introgressed genes provided their descendants with selective advantages involving those loci.

Other studies have found a distinct source of archaic admixture in a different sub-Saharan African Paleo-African population.

While this method was superior in identifying particular loci where archaic introgression did or did not take place, unlike prior studies of this type, the paper does not expressly identify how deeply diverged the archaic population is from the modern humans who admixed (other than that they are much more diverged than the most divergent modern human populations), nor does it identity how long ago this admixture event probably took place, something that prior studies have put shortly before the Holocene era (i.e. more than 10,000 years ago, but not that much earlier than that; certainly in the Upper Paleolithic era).

A finding for the West African Yoruba has wide relevance to sub-Saharan Africa because almost all populations except for a handful of relicts, gained substantial Bantu admixture in the mid-Holocene era, and the Bantu have origins geographically close to that of the Yoruba.

Linguistic Analysis Argues For Expansion Of Proto-Dravidian With South Indian Neolithic

Languages attested in writing more than 950 years ago shown in bold.

A new linguistic analysis argues that the Dravidian languages arose ca. 2500 BCE, the same time as the South Indian Neolithic Revolution. This is one very plausible date, although other studies have argued for a more recent origin on linguistic grounds (and one study argued, implausibly, for a 13000 years BP date). If this is the date of origin it pre-dates the arrival of Indo-Europeans in India by 500-1000 years, and precedes the arrival of Indo-Europeans in the Dravidian linguistic area by a bit longer than that.

The study is an honest effort, but not necessarily terribly reliable as any study is only as good as its assumptions and methods, which aren't terribly convincing, and no serious effort is made in  the paper to validate the assumptions they use or even to clearly describe those assumptions. The methods used are fairly reliable for creating a branching phylogeny of the language family (something that has never been in serious doubt), but is less reliable for purposes of estimating time depth.

For example, the analysis puts all Dravidian languages on an equal footing based upon a Swaedesh vocabulary list, but really, to do it right, they should be limiting themselves to what can be determined from the historic content of the four Dravidian languages that are attested earliest. And, they should be pretty much ignoring North Dravidian languages for which there is a strong case to be made that they didn't arise until about 1000 CE, entirely.

Their own error bars are 1000 BCE to 4500 BCE, with the archaeology of the South Indian Neolithic used to support a mid-range value. The most reliable youngest possible date comes from Dravidian loan words in the Rig Veda:
There is clear evidence of Dravidian loanwords into Old-Indo-Aryan (1750–250 BCE) dating to the middle Rigvedic period (ca 1200 BCE) in a source area that might have been Sindh, contemporary Southwest Pakistan [6], [8, pp. 69ff, 88]. Southworth [8, p. 64] proposes Sindh, Gujarat and eastern Maharashtra as areas where Dravidian would have been spoken at earlier stages.
Thus a range of perhaps 1500 BCE to 2500 BCE is quite plausible.

But, many linguists have doubted that the amount of linguistic diversity really supports a 4500 years time depth, which could be consistent with a bottleneck effect of diversification from surviving dialects after the language family temporarily went extinct in a large part of its range. Indeed, it is very likely that the particular dialect of Dravidian that was the source of the Rig Vedic substrate is extinct.

The study is: Kolipakam et al. A Bayesian phylogenetic study of the Dravidian language family. Royal Society Open Science (2018).