The document details the sequencing of a neanderthal genome from the Altai Mountains, revealing it to be a distinct type of neanderthal with notable inbreeding patterns. Through comparative analysis, it was found that both neanderthals and denisovians share a closer relation to a common ancestor than humans do, with evidence of gene flow between these groups and early humans. Major findings suggest interbreeding events occurred among these populations, contributing to genetic similarities observed in modern humans.

1. The Complete Genome
Sequence of a Neanderthal from
the Altai Mountains
Prüfer et al., 2013
Presentation by Sveta Jagannathan

2.  Ancient toe phalanx found in Altai Mountains in
Denisova Cave
 Genome sequenced and compared to
Neanderthal, Denisovian and Human DNA
 Homozygosity compared to determine amount of
inbreeding
 Gene flow and evolutionary patterns predicted
Experiment Overview

3.  Gene flow- Different populations or species
interbreed and exchange DNA
 mtDNA is mitochondrial DNA- a type of DNA that
gets passed on from maternal lineage
 Not affected by sexual reproduction
 Stays roughly the same (except for mutations)
Background

4.  MtDNA used to sequence toe phalanx genome
 Toe phalanx genome compared to 6 neanderthal
genomes, 25 human genomes and 1 denisovian
genome
 Common ancestor was found between neanderthal and
toe genome while humans and Denisovians were
farther away
 Toe phalanx was determined to have been part of a
newly found type of Neanderthal- the Altai Neanderthal
Genome sequencing

5.  Researchers predicted a phylogenetic tree
 Denisovians and Neanderthals were closer to the
common ancestor
 Used two methods (one using mutation rates and
one using the frequency at which a certain allele is
derived) to estimate when each group diverged
 Altai Neanderthal predicted to diverge from other
known Neanderthals between 77,000-114,000 years
ago
Relationship between Altai
Neanderthal and other genomes

6. Phylogenetic Relationships of the Altai
Neanderthal (Figure 2 of Article)

7.  Altai Neanderthal genome examined for homozygosity
(related regions of DNA more than 10 cM long)
 20 regions of homozygosity found that indicated that the
Neanderthals parents were probably half-siblings
 These homozygous runs were removed and the remaining
DNA was examined for homozygous runs of smaller length
 Many found, which indicated that inbreeding was popular
among Altai Neanderthals
 Remaining Heterozygous regions were compared to
Denisovians’ heterozygosity to find that the amount of
inbreeding among Altai Neanderthals was similar to that of
Denisovians
 Heterozygosity of Denisovians and Neanderthals was among
the lowest of any organism!
Inbreeding and Homozygosity

8.  Similar or identical DNA was found in Neanderthals,
Denisovians and Humans
 Researchers compared that DNA to find patterns to show the
gene flow of that time period
 Similarity of Human DNA to Denisovian and Neanderthal
depended on region (the least similarity was in Africa, with
mainland Asians close)
 Americans and some Asians had higher amounts of
Denisovian DNA than Europeans!
 This suggested gene flow between Neanderthals and
Denisovians, between Neanderthals and humans and
between Denisovians and humans which was further
investigated
Gene Flow

9.  New Neanderthal in Altai Mountains near
Denisovians
 Neanderthals and Denisovians are more closely
related to their common ancestor than humans are
 Denisovians and Neanderthals had more
inbreeding than most other organisms
 Altai Neanderthals and other Neanderthals split
between 77,000 and 114,000 years ago
Major Findings Part 1

10.  Humans retain some Neanderthal and Denisovian
DNA, likely due to some sort of interbreeding event
 Gene flow occurred from Neanderthals into
Denisovians, most likely through some other
hominin (possibly Homo erectus)
 Genes provided by Neanderthals performed
necessary functions
 Gene flow from Neanderthals/Denisovians to
humans is most likely due to direct interbreeding
Major Findings Part 2- Gene Flow

11.  Humans and Neanderthals likely coexisted for
enough time to interbreed and exchange DNA
 Denisovians probably also interbred with humans
 Some other hominin existed that was able to
interbreed between Denisovians and Neanderthals
and pass on the DNA
 Neanderthal DNA found in humans may have
functional significance!
Implications

12. A possible model of gene flow events in
the Late Pleistocene (Figure 8 of
Article)