A Draft Sequence of the Neanderthal Genome: Review – 2nd Part

Chromosome 2

Continuing with a rather superficial analysis of some of the alleles that the research team suggested had been positively selected for in the human lineage since divergence from the Neanderthal 400,000 years ago. These alleles may give insights into important aspects of human evolution over the last 400,000 years. Excerpts are from Entrez Gene.

ZFP36L2: ‘This putative nuclear transcription factor most likely functions in regulating the response to growth factors’. Speculation: Difficult without more information.

THADA: Thyroid adenoma associated. NIDDM association. ‘Common Variants in the Trichohyalin Gene Are Associated with Straight Hair in Europeans’. ‘Genome-wide association study identifies two susceptibility loci for nonsyndromic cleft lip with or without cleft palate’. Speculation: Although there were a number of associations, I wasn’t clear on what the function of THADA is.

EVX2: Even skipped Homeobox 2.  ’causes synpolydactyly, a dominantly inherited disease resulting in limb malformation’. There looks to be an interesting paper on this clinical condition here. Speculation: As with other homeobox associated and homeobox genes this will relate to morphology.

MTX2: ‘it is thought that the encoded protein is peripherally associated with the cytosolic face of the outer mitochondrial membrane, and that it is involved in the import of proteins into the mitochondrion’. Speculation: Difficult without more information.

HOXD1: ‘This nuclear protein functions as a sequence-specific transcription factor that is involved in differentiation and limb development. Mutations in this gene have been associated with severe developmental defects on the anterior-posterior (a-p) limb axis’

HOXD3: ‘The homeobox genes encode a highly conserved family of transcription factors that play an important role in morphogenesis in all multicellular organisms’.

HOXD4: ‘The protein encoded by this gene may play a role in determining positional values in developing limb buds’.

HOXD8: ‘In addition to effects during embryogenesis, this particular gene may also play a role in adult urogenital tract function’.

HOXD9: ‘The exact role of this gene has not been determined’.

HOXD10: ‘Mutations in this gene have been associated with Wilm’s tumor and congenital vertical talus (also known as “rocker-bottom foot” deformity or congenital convex pes valgus and/or a foot deformity resembling that seen in Charcot-Marie-Tooth disease’. Speculation: May be associated with efficiency of locomotion – a noted difference between humans and neanderthals.

HOXD11: ‘The product of the mouse Hoxd11 gene plays a role in forelimb morphogenesis’.

HOXD12: ‘The exact role of this gene has not been determined’.

HOXD13: ‘Mutations in this particular gene cause synpolydactyly’

MIR10B: ‘The mature miRNA is incorporated into a RNA-induced silencing complex (RISC), which recognizes target mRNAs through imperfect base pairing with the miRNA and most commonly results in translational inhibition or destabilization of the target mRNA’.

Conclusions

It looks as though a number of Homeobox alleles have been conserved across humans over the past 400,000 years. Perhaps there are strong selection effects for morphology and this may relate to notions of body image. The mechanisms governing the appearance of hair as well as characteristics of locomotion may also be features that have been conserved across humans since divergence from Neanderthal.

References

A Draft Sequence of the Neandertal Genome.Richard E. Green, Johannes Krause, Adrian W. Briggs, Tomislav Maricic,  Udo Stenzel, Martin Kircher, Nick Patterson,  Heng Li, Weiwei Zhai,  Markus Hsi-Yang Fritz, Nancy F. Hansen, Eric Y. Durand, Anna-Sapfo Malaspinas, Jeffrey D. Jensen, Tomas Marques-Bonet, Can Alkan, Kay Prüfer, Matthias Meyer, Hernán A. Burbano, Jeffrey M. Good, Rigo Schultz, Ayinuer Aximu-Petri,  Anne Butthof, Barbara Höber, Barbara Höffner,  Madlen Siegemund, Antje Weihmann, Chad Nusbaum,  Eric S. Lander, Carsten Russ, Nathaniel Novod,  Jason Affourtit, Michael Egholm, Christine Verna, Pavao Rudan, Dejana Brajkovic,  Zeljko Kucan, Ivan Gusic,  Vladimir B. Doronichev, Liubov V. Golovanova,  Carles Lalueza-Fox, Marco de la Rasilla, Javier Fortea,  Antonio Rosas, Ralf W. Schmitz,  Philip L. F. Johnson, Evan E. Eichler, Daniel Falush, Ewan Birney, James C. Mullikin, Montgomery Slatkin, Rasmus Nielsen, Janet Kelso, Michael Lachmann, David Reich,Svante Pääbo. Science 7 May 2010:Vol. 328. no. 5979, pp. 710 – 722.

Acknowledgements

Picture of Chromosome 2 from Wikimedia Commons and originally from the National Institute of Health. It is in the Public Domain.

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7 thoughts on “A Draft Sequence of the Neanderthal Genome: Review – 2nd Part

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