Horses in middle earth

Orwell wrote:

Amarië wrote:Skuggfaks is a lovely name, why do you assume a Norwegian word should have a English pronunciation? It's not "Skagg".

Skuggfaks. Skagg. Shagrat. Noweigan. Norc. Norcish. Orcish. My gawwwwwd!

Norc wrote:lool .. well, i think it's the reason that we know what "skugg" means and can pronounce it right. and the x looks ridiculous in norwegian words  i wonder what he's called in the nynorsk-one

Eldorion wrote:Yeah, phonetically skuggfaks sounds pretty dumb to English speakers.  No sense of majesty or power or ancientness or anything else that would be associated with the "lord of horses".  Not that the word Shadowfax would automatically bring those things to mind, but it doesn't have any opposite connotations.

David H wrote:

halfwise wrote:
That would only work if you have a monotonic population growth, whereas the abstract says the population size fluctuated several times.  Yeah, worth digging up that paper if only to figure out how they got that.

The title of the article, Recalibrating Equus evolution using the genome sequence of an early Middle Pleistocene horse, seems to imply that there's  an existing evolutionary model that's being recalibrated, as opposed to creating a new model from the 9 individuals listed,  so presumably there's a pile of genetic and paleontological data we're not aware of.  I wish we could download that Nature article without paying and see what's really going on..... 

Nature wrote: we reconstructed horse population demography over the last 2 Myr. The pairwise sequential Markovian coalescent (PSMC) approach (21) shows that horses experienced a population minimum approximately 125 kyr bp, corresponding to the last interglacial when environmental conditions were similar to now throughout their range. The population expanded during the cold stages of marine isotope stage (MIS) 4 and 3 as grasslands expanded. A peak was reached 25–50 kyr bp and was followed by an approximately 100-fold collapse, probably resulting from major climatic changes and related grassland contraction after the Last Glacial Maximum(22) (Fig. 4 and Supplementary Figs 9.4–9.5). A similar demographic history was inferred from Bayesian skyline reconstructions using 23 newly characterized ancient mitochondrial genomes (Supplementary Fig. 9.6). These results support suggestions (22) that climatic changes are major demographic drivers for horse populations. PSMC analyses also revealed two earlier demographic phases (Fig. 4b and Supplementary Figs 9.4–9.5), with population sizes peaking 190–260 kyr bp and 1.2–1.6 Myr bp, respectively, followed by 1.7-fold and 8.1-fold collapses. Extremely low population sizes were inferred approximately 500–800 kyr bp, a time period that covers the divergence time of the Thistle Creek and contemporary horse populations. This result may relate to population fragmentation when horses colonized Eurasia from America, in agreement with the earliest presence of horses in Eurasia 750 kyr bp4.

chris63 wrote:

halfwise wrote:

Nature wrote: we reconstructed horse population demography over the last 2 Myr. The pairwise sequential Markovian coalescent (PSMC) approach (21) shows that horses experienced a population minimum approximately 125 kyr bp, corresponding to the last interglacial when environmental conditions were similar to now throughout their range. The population expanded during the cold stages of marine isotope stage (MIS) 4 and 3 as grasslands expanded. A peak was reached 25–50 kyr bp and was followed by an approximately 100-fold collapse, probably resulting from major climatic changes and related grassland contraction after the Last Glacial Maximum(22) (Fig. 4 and Supplementary Figs 9.4–9.5). A similar demographic history was inferred from Bayesian skyline reconstructions using 23 newly characterized ancient mitochondrial genomes (Supplementary Fig. 9.6). These results support suggestions (22) that climatic changes are major demographic drivers for horse populations. PSMC analyses also revealed two earlier demographic phases (Fig. 4b and Supplementary Figs 9.4–9.5), with population sizes peaking 190–260 kyr bp and 1.2–1.6 Myr bp, respectively, followed by 1.7-fold and 8.1-fold collapses. Extremely low population sizes were inferred approximately 500–800 kyr bp, a time period that covers the divergence time of the Thistle Creek and contemporary horse populations. This result may relate to population fragmentation when horses colonized Eurasia from America, in agreement with the earliest presence of horses in Eurasia 750 kyr bp4.

So we need to go at least to reference 21.  But since I had already come home I couldn't look up reference 21.    In case you make it to the library before I do (dubious, I live 2 blocks away) here's the reference:

Li, H. & Durbin, R. Inference of human population history from individual whole-genome sequences. Nature 475, 493–496 (2011)

No doubt it will reference yet another article and we'll end up earning an extra degree before we figure this out.

Unless you just happen to know off the top of your head what the Pairwise Sequential Markovian Coalescent technique might be?  Maybe you are familiar with Bayesian skyline reconstructions?

In this paper we have introduced a novel method to infer the history of effective population size from genome wide diploid sequence data. It is relatively straightforward to apply, with less potential ascertainment bias in comparison to existing methods that use selective genotyping data or the resequencing data from a few loci. Furthermore, our method is computationally tractable and typically uses much more primary sequence data than the existing methods, which allows us to estimate population size at each time going back in history, rather than assume a parametric structure of times, divergences and size changes. The results described above concerning the timing and depth of the out-of-Africa bottleneck are broadly consistent with previous studies though our results are more detailed

Ringdrotten wrote: So Shadowfax is white/silver during daytime and grey when it's dark?