April 23, 2014

Neandertal populations were small (+ differences along the Neandertal/sapiens evolutionary lineages)

PNAS doi: 10.1073/pnas.1405138111

Patterns of coding variation in the complete exomes of three Neandertals

Sergi Castellano et al.

We present the DNA sequence of 17,367 protein-coding genes in two Neandertals from Spain and Croatia and analyze them together with the genome sequence recently determined from a Neandertal from southern Siberia. Comparisons with present-day humans from Africa, Europe, and Asia reveal that genetic diversity among Neandertals was remarkably low, and that they carried a higher proportion of amino acid-changing (nonsynonymous) alleles inferred to alter protein structure or function than present-day humans. Thus, Neandertals across Eurasia had a smaller long-term effective population than present-day humans. We also identify amino acid substitutions in Neandertals and present-day humans that may underlie phenotypic differences between the two groups. We find that genes involved in skeletal morphology have changed more in the lineage leading to Neandertals than in the ancestral lineage common to archaic and modern humans, whereas genes involved in behavior and pigmentation have changed more on the modern human lineage.

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8 comments:

terryt said...

"Thus, Neandertals across Eurasia had a smaller long-term effective population than present-day humans".

That was probably because conditions were difficult for humans at their stage of technological development. Biological selection would have been stringent.

"We find that genes involved in skeletal morphology have changed more in the lineage leading to Neandertals than in the ancestral lineage common to archaic and modern humans"

Probably related to the selection necessary for survival in the environmental extremes they were subject to.

Grognard said...

What is the ancient modern human they sequenced to decide this?

German Dziebel said...

"The average heterozygosity among the three Neandertals (0.128) is 25%, 33%, and 36% of the average heterozygosity in the three African (0.507), European (0.387), and Asian (0.358) individuals, respectively (Table S12), and thus significantly smaller than that in humans today (P = 4.5 × 10−3; Mann–Whitney U test). The three Neandertals also have longer runs of homozygosity (Fig. S9), suggesting that mating among related individuals may have been more common in Neandertals than in present-day humans, compatible with the observations in the Altai Neandertal (10). Also compatible with these observations is that the genetic differentiation among individuals, as measured by the pairwise fixation index (FST) (Fig. 1B), is greater among Neandertals than among the Africans, Europeans, and Asians (P = 1.3 × 10−2; Mann–Whitney U test), suggesting that mating in small and isolated populations may have caused Neandertal populations to be more differentiated from one another than what is typical for present-day humans."

Consistently with a number of earlier studies, Neandertal genetic structure (heterozygosity, Fst, IBD) is most similar to that of Amerindians, among modern human populations. No surprise, Amerindians were excluded from this study.

Marcel F. Williams said...

Not surprising, IMO, since the monopolization of caves seems to have been the primary means for survival for the Neanderthals in Europe. In fact, Neanderthals appear to have continued this cave monopolizing culture even in the Middle East.

The invention of centrally heated structures appears to have allowed non-Neanderthals to finally invade Europe on a permanent basis. And their massive numbers simply overwhelmed the stationary cave monopolizing Neanderthals.

Marcel

eurologist said...

Marcel,

There is no question that owning a largish cave had a survival benefit to any humans around the ice ages, but even heidelbergensis knew how to build tents and palisades or fences. And the tent-in-tent methods is a time-proven method to survive brutal night-time low temperatures. So, no - Neanderthals did not rely on caves, although I agree that Neanderthals show little if any advancement from heidelbergensis, but instead much genetic decline, although they apparently got a more modern human input ooA as apparent from mtDNA.

ron quiroriano said...

Eurologist,
I would have to strongly disagree with your assertion,"Neanderthals show little if any advancement from heidelbergensis, but instead much genetic decline".
The skeletal changes from hsh to hsn are likely adaptations to a northerly climate and to ambush hunting in the dense forests of north central Eurasia. Their robust physic is both an adaptation to the cold and to the "up close and personal" business of ambush hunting, where brute strength is paramount. The enlarged eyes and vision oriented parts of the brain indicate that they initially evolved in low light conditions, such as you would find in
a dense conifer forest.
The 400k year old spears found in Germany show that Hsh had the ability to throw overhand, as three of the spears are certainly throwing spears, while recent work shows that Hsn had lost the ability to throw overhand, through the construction of the shoulder.
Natural selection pressures drove Hsn into an evolutionarily cup-de-sac.
On the idea that Hsn didn't contribute to Hss development is way off base, neaderthals learned to make leather, not just use hides but make leather, the settled the arctic before Hss. In order to.settle the arctic you have to be able to make fitted clothing. They made use of personal adornment, and showed signs of some sort of religious beliefs, as they buried the dead with grave goods. They made rudimentary musical instruments, and their livings spaces were subdivided according to the type of task at hand. They made use of water craft to settle islands of the med and procure rescources.
After reading several papers of the wide array of injuries suffered by Hsn males , broken arms, ribs and facial injuries lead me to believe that there were cultural/societal practices that may have lead to consistently small populations, such as a matriarchal society. These injuries could be explained by males fighting for the right to mate with an available female.

terryt said...

@ ron quiroriano:

Some very interesting comments and speculation there. I agree completely with, 'the idea that Hsn didn't contribute to Hss development is way off base'.

Liutauras said...

http://www.youtube.com/watch?v=z9m_MvXJVLU
Ral neanderthals