Hominin Evolution TheoryCHRISTOPHER GOMES · A RESEARCH FRAMEWORKRead the manuscript
Chapters & navigation

SOURCE MATERIAL

References & source notes

The manuscript’s references, kept distinct from the website’s explanatory prose.

The list below reproduces the corrected version 2 bibliography. Unauthenticated citations were removed and bibliographic details corrected during the manuscript revision. A verified publication identity should not be confused with independent confirmation of every evolutionary inference made from it.

Verified bibliographic clarifications

The pregnancy-hair study is Nissimov and Elchalal (2003), Clinical and Experimental Dermatology 28, 525–530: publisher record. The corrected version 2 bibliography uses this publication information.

The Mussi et al. (2023) high-altitude Homo erectus paper appears in Science 382, 713–718: publisher record.

The Hubbard et al. (2016) paper is titled “Divergent Ah Receptor Ligand Selectivity during Hominin Evolution,” Molecular Biology and Evolution 33, 2648–2658: publisher record. These corrections are incorporated in the version 2 download; the existing Zenodo record is linked separately.

Coffee lineage and species timing

Salojärvi et al. (2024) report the founding polyploid event of modern Coffea arabica at approximately 350,000–610,000 years ago. This is different from the age of the wider Coffea lineage. Earlier exposure scenarios require additional botanical evidence. Primary study; author-institution record.

Bibliography from the manuscript

Aiello, L. C., & Wheeler, P. (1995). The expensive-tissue hypothesis: The brain and the digestive system in human and primate evolution. Current Anthropology, 36(2), 199-221.

Antón, S. C., Potts, R., & Aiello, L. C. (2014). Evolution of early Homo: An integrated biological perspective. Science, 345(6192), 1236828.

Anthony, F., Combes, M. C., Astorga, C., Bertrand, B., Graziosi, G., & Lashermes, P. (2002). The origin of cultivated Coffea arabica L. varieties revealed by AFLP and SSR markers. Theoretical and Applied Genetics, 104, 894–900. https://doi.org/10.1007/s00122-001-0798-8

Armstrong, L. E., Pumerantz, A. C., Roti, M. W., Judelson, D. A., Watson, G., Dias, J. C., Sökmen, B., Casa, D. J., Maresh, C. M., Lieberman, H., & Kellogg, M. (2005). Fluid, electrolyte, and renal indices of hydration during 11 days of controlled caffeine consumption. International Journal of Sport Nutrition and Exercise Metabolism, 15(3), 252–265. https://doi.org/10.1123/ijsnem.15.3.252

Attwell, D., & Laughlin, S. B. (2001). An energy budget for signaling in the grey matter of the brain. Journal of Cerebral Blood Flow & Metabolism, 21(10), 1133-1145.

Bonnefille, R. (2010). Cenozoic vegetation, climate changes and hominid evolution in tropical Africa. Global and Planetary Change, 72(4), 390–411. https://doi.org/10.1016/j.gloplacha.2010.01.015

Bramble, D. M., & Lieberman, D. E. (2004). Endurance running and the evolution of Homo. Nature, 432(7015), 345-352.

Bullmore, E., & Sporns, O. (2012). The economy of brain network organization. Nature Reviews Neuroscience, 13(5), 336-349.

Aarts, J. M. M. J. G., Alink, G. M., Scherjon, F., MacDonald, K., Smith, A. C., Nijveen, H., & Roebroeks, W. (2016). Fire usage and ancient hominin detoxification genes: Protective ancestral variants dominate while additional derived risk variants appear in modern humans. PLOS ONE, 11(9), e0161102. https://doi.org/10.1371/journal.pone.0161102

Cerling, T. E., Harris, J. M., MacFadden, B. J., Leakey, M. G., Quade, J., Eisenmann, V., & Ehleringer, J. R. (1997). Global vegetation change through the Miocene/Pliocene boundary. Nature, 389(6647), 153-158.

Davidson, R. J. L. (1964). Exertional haemoglobinuria: A report on three cases with studies on the haemolytic mechanism. Journal of Clinical Pathology, 17(5), 536–540. https://doi.org/10.1136/jcp.17.5.536

Davis, A. P., Govaerts, R., Bridson, D. M., & Stoffelen, P. (2006). An annotated taxonomic conspectus of the genus Coffea (Rubiaceae). Botanical Journal of the Linnean Society, 152(4), 465–512. https://doi.org/10.1111/j.1095-8339.2006.00584.x

deMenocal, P. B. (1995). Plio-Pleistocene African climate. Science, 270(5233), 53-59.

Eugster, H. P., & Jones, B. F. (1979). Behavior of major solutes during closed-basin brine evolution. American Journal of Science, 279(6), 609–631. https://doi.org/10.2475/ajs.279.6.609

Falsetti, H. L., Burke, E. R., Feld, R. D., Frederick, E. C., & Ratering, C. (1983). Hematological variations after endurance running with hard- and soft-soled running shoes. The Physician and Sportsmedicine, 11(8), 118–127. https://doi.org/10.1080/00913847.1983.11708609

Farag, N. H., Vincent, A. S., Sung, B. H., Whitsett, T. L., Wilson, M. F., & Lovallo, W. R. (2005). Caffeine tolerance is incomplete: Persistent blood pressure responses in the ambulatory setting. American Journal of Hypertension, 18(5), 714–719. https://doi.org/10.1016/j.amjhyper.2005.03.738

Folk, G. E., & Semken, H. A. (1991). The evolution of sweat glands. International Journal of Biometeorology, 35(3), 180-186.

Fredholm, B. B., Bättig, K., Holmén, J., Nehlig, A., & Zvartau, E. E. (1999). Actions of caffeine in the brain with special reference to factors that contribute to its widespread use. Pharmacological Reviews, 51(1), 83–133.

Friis, I. (1992). Forests and forest trees of northeast tropical Africa: Their natural habitats and distribution patterns in Ethiopia, Djibouti and Somalia. Kew Bulletin Additional Series, 15. HMSO.

Goodall, J. (1967). My friends the wild chimpanzees. National Geographic Society.

Hamon, P., et al. (2017). Genotyping-by-sequencing provides the first well-resolved phylogeny for coffee (Coffea) and insights into the evolution of caffeine content in its species: GBS coffee phylogeny and the evolution of caffeine content. Molecular Phylogenetics and Evolution, 109, 351–361. https://doi.org/10.1016/j.ympev.2017.02.009

Harrison, S., & Bergfeld, W. (2009). Diffuse hair loss: Its triggers and management. Cleveland Clinic Journal of Medicine, 76(6), 361–367. https://doi.org/10.3949/ccjm.76a.08080

Herculano-Houzel, S. (2012). The remarkable, yet not extraordinary, human brain as a scaled-up primate brain and its associated cost. Proceedings of the National Academy of Sciences, 109(Supplement 1), 10661-10668.

Herculano-Houzel, S., & Lent, R. (2005). Isotropic fractionator: A simple, rapid method for the quantification of total cell and neuron numbers in the brain. The Journal of Neuroscience, 25(10), 2518–2521. https://doi.org/10.1523/JNEUROSCI.4526-04.2005

Hockings, K. J., & McLennan, M. R. (2012). From forest to farm: Systematic review of cultivar feeding by chimpanzees—Management implications for wildlife in anthropogenic landscapes. PLOS ONE, 7(4), e33391. https://doi.org/10.1371/journal.pone.0033391

Holloway, R. L., Broadfield, D. C., & Yuan, M. S. (2004). The Human Fossil Record, Volume 3: Brain Endocasts—The Paleoneurological Evidence. New York, NY: Wiley-Liss.

Hubbard, T. D., Murray, I. A., Bisson, W. H., Sullivan, A. P., Sebastian, A., Perry, G. H., Jablonski, N. G., & Perdew, G. H. (2016). Divergent Ah receptor ligand selectivity during hominin evolution. Molecular Biology and Evolution, 33(10), 2648–2658. https://doi.org/10.1093/molbev/msw143

Jacobson, K. A., von Lubitz, D. K. J. E., Daly, J. W., & Fredholm, B. B. (1996). Adenosine receptor ligands: Differences with acute versus chronic treatment. Trends in Pharmacological Sciences, 17(3), 108–113. https://doi.org/10.1016/0165-6147(96)10002-X

Jolly, A. (1972). The evolution of primate behavior. Macmillan.

King, G., & Bailey, G. N. (2006). Tectonics and human evolution. Antiquity, 80(308), 265-286.

Krijgsman, W., Hilgen, F. J., Raffi, I., Sierro, F. J., & Wilson, D. S. (1999). Chronology, causes and progression of the Messinian salinity crisis. Nature, 400(6745), 652-655.

Lippi, G., & Sanchis-Gomar, F. (2019). Epidemiological, biological and clinical update on exercise-induced hemolysis. Annals of Translational Medicine, 7(12), 270. https://doi.org/10.21037/atm.2019.05.41

Maslin, M. A., Brierley, C. M., Milner, A. M., Shultz, S., Trauth, M. H., & Wilson, K. E. (2014). East African climate pulses and early human evolution. Quaternary Science Reviews, 101, 1–17. https://doi.org/10.1016/j.quascirev.2014.06.012

McClintock, B. (1984). The significance of responses of the genome to challenge. Science, 226(4676), 792-801.

Moat, J., et al. (2017). Resilience potential of the Ethiopian coffee sector under climate change. Nature Plants, 3, 17081. https://doi.org/10.1038/nplants.2017.81

Mussi, M., et al. (2023). Early Homo erectus lived at high altitudes and produced both Oldowan and Acheulean tools. Science, 382(6671), 713–718. https://doi.org/10.1126/science.add9115

Navarrete, A., van Schaik, C. P., & Isler, K. (2011). Energetics and the evolution of human brain size. Nature, 480(7375), 91–93. https://doi.org/10.1038/nature10629

Nehlig, A., Daval, J. L., & Debry, G. (1992). Caffeine and the central nervous system: Mechanisms of action, biochemical, metabolic and psychostimulant effects. Brain Research Reviews, 17(2), 139-170.

Nissimov, J., & Elchalal, U. (2003). Scalp hair diameter increases during pregnancy. Clinical and Experimental Dermatology, 28(5), 525–530. https://doi.org/10.1046/j.1365-2230.2003.01331.x

Organ, C., Nunn, C. L., Machanda, Z., & Wrangham, R. W. (2011). Phylogenetic rate shifts in feeding time during the evolution of Homo. Proceedings of the National Academy of Sciences, 108(35), 14555-14559.

Passingham, R. E., & Wise, S. P. (2012). The neurobiology of the prefrontal cortex: Anatomy, evolution, and the origin of insight. Oxford University Press. https://doi.org/10.1093/acprof:osobl/9780199552917.001.0001

Pawlak, R., Berger, J., & Hines, I. (2018). Iron status of vegetarian adults: A review of literature. American Journal of Lifestyle Medicine, 12(6), 486–498.

Pontzer, H., Brown, M. H., Wood, B. M., Raichlen, D. A., Mabulla, A. Z., Harris, J. A., ... & Ross, S. R. (2021). Evolution of water conservation in humans. Current Biology, 31(8), 1804–1810.

Potts, R. (1998). Environmental hypotheses of hominin evolution. American Journal of Physical Anthropology, 107(S27), 93-136.

Potts, R. (2012). Evolution and environmental change in early human prehistory. Annual Review of Anthropology, 41, 151–167. https://doi.org/10.1146/annurev-anthro-092611-145754

Robertson, D., Wade, D., Workman, R., Woosley, R. L., & Oates, J. A. (1981). Tolerance to the humoral and hemodynamic effects of caffeine in man. Journal of Clinical Investigation, 67(4), 1111–1117. https://doi.org/10.1172/JCI110124

Salojärvi, J., et al. (2024). The genome and population genomics of allopolyploid Coffea arabica reveal the diversification history of modern coffee cultivars. Nature Genetics, 56, 721–731. https://doi.org/10.1038/s41588-024-01695-w

Sepulchre, P., Ramstein, G., Fluteau, F., Schuster, M., Tiercelin, J. J., & Brunet, M. (2006). Tectonic uplift and Eastern Africa aridification. Science, 313(5792), 1419-1423.

Shapiro, J. A. (2013). How life changes itself: The Read-Write (RW) genome. Physics of Life Reviews, 10(3), 287-323.

Stabler, S. P. (2013). Vitamin B12 deficiency. New England Journal of Medicine, 368(2), 149–160.

Chamarthi, V. S., Gunasekaran, V., & Daley, S. F. (2026). Primitive reflexes: Comprehensive neurological assessment across the lifespan. In StatPearls. StatPearls Publishing. Updated June 17, 2026. https://www.ncbi.nlm.nih.gov/books/NBK554606/

Telford, R. D., Sly, G. J., Hahn, A. G., Cunningham, R. B., Bryant, C., & Smith, J. A. (2003). Footstrike is the major cause of hemolysis during running. Journal of Applied Physiology, 94(1), 38-42.

Aarts, J. M. M. J. G., Alink, G. M., Franssen, H. J., & Roebroeks, W. (2021). Evolution of hominin detoxification: Neanderthal and modern human Ah receptor respond similarly to TCDD. Molecular Biology and Evolution, 38(4), 1292–1305. https://doi.org/10.1093/molbev/msaa287

Wood, B., & Richmond, B. G. (2000). Human evolution: Taxonomy and paleobiology. Journal of Anatomy, 197(1), 19–60. https://doi.org/10.1046/j.1469-7580.2000.19710019.x

Zhang, Z., Ramstein, G., Schuster, M., Li, C., Contoux, C., & Yan, Q. (2014). Aridification of the Sahara desert caused by Tethys Sea shrinkage during the Late Miocene. Nature, 513(7518), 401–404. https://doi.org/10.1038/nature13705

Amaral, L. Q. (2008). Mechanical analysis of infant carrying in hominoids. Naturwissenschaften, 95(4), 281–292. https://doi.org/10.1007/s00114-007-0325-0

Anthony, F., Diniz, L. E. C., Combes, M.-C., & Lashermes, P. (2010). Adaptive radiation in Coffea subgenus Coffea L. (Rubiaceae) in Africa and Madagascar. Plant Systematics and Evolution, 285, 51–64. https://doi.org/10.1007/s00606-009-0255-8

Helmbrecht, N., Lackner, M., Maricic, T., & Pääbo, S. (2024). The modern human aryl hydrocarbon receptor is more active when ancestralized by genome editing. Proceedings of the National Academy of Sciences, 121(22), e2402159121. https://doi.org/10.1073/pnas.2402159121

View the corrected reference pages ↗