## Description

This track displays Neandertal alleles for human-chimp protein-coding differences on the human lineage using orangutan as the outgroup to determine which allele is more likely to be ancestral.

## Display Conventions and Configuration

Neandertal ancestral alleles are colored blue; derived (human) alleles are colored green.

The item names show the number of Neandertal reads for the ancestral and derived alleles, followed by the ancestral and derived codons enclosed in parentheses. For example, if no Neandertal reads matched the ancestral base G and three Neandertal reads matched the derived base A, and the ancestral and derived codons were GTA and ATA respectively, then the item name would be "0G>3A(GTA>ATA)". If N Neandertal reads match neither ancestral nor derived base, then a "+N?" is added before the codons (i.e. "0G>3A+N?(GTA>ATA)").

## Methods

Neandertal DNA was extracted from a ~49,000-year-old bone (Sidrón 1253), which was excavated in El Sidrón cave, Asturias, Spain. Non-synonymous changes that occurred on the human lineage since the ancestral split with chimpanzee were identified by aligning human, chimpanzee and orangutan protein sequences for all orthologous proteins in HomoloGene (Build 58) . Comparison of these three species allowed the assignment of human/chimpanzee differences to their respective evolutionary lineages. An Agilent custom oligonucleotide array covering the 13,841 non-synonymous changes inferred to have occurred in the human lineage was designed and used to capture Neandertal sequences.

## Reference

Burbano HA, Hodges E, Green RE, Briggs AW, Krause J, Meyer M, Good JM, Maricic T, Johnson PLF, Xuan Z et al. Targeted Investigation of the Neandertal Genome by Array-Based Sequence Capture. Science. 2010 7 May;328(5979):723-5.