Letter | Published:

A progressively wetter climate in southern East Africa over the past 1.3 million years

Nature volume 537, pages 220224 (08 September 2016) | Download Citation


African climate is generally considered to have evolved towards progressively drier conditions over the past few million years, with increased variability as glacial–interglacial change intensified worldwide1,2,3. Palaeoclimate records derived mainly from northern Africa exhibit a 100,000-year (eccentricity) cycle overprinted on a pronounced 20,000-year (precession) beat, driven by orbital forcing of summer insolation, global ice volume and long-lived atmospheric greenhouse gases4. Here we present a 1.3-million-year-long climate history from the Lake Malawi basin (10°–14° S in eastern Africa), which displays strong 100,000-year (eccentricity) cycles of temperature and rainfall following the Mid-Pleistocene Transition around 900,000 years ago. Interglacial periods were relatively warm and moist, while ice ages were cool and dry. The Malawi record shows limited evidence for precessional variability, which we attribute to the opposing effects of austral summer insolation and the temporal/spatial pattern of sea surface temperature in the Indian Ocean. The temperature history of the Malawi basin, at least for the past 500,000 years, strongly resembles past changes in atmospheric carbon dioxide and terrigenous dust flux in the tropical Pacific Ocean, but not in global ice volume. Climate in this sector of eastern Africa (unlike northern Africa) evolved from a predominantly arid environment with high-frequency variability to generally wetter conditions with more prolonged wet and dry intervals.

Access optionsAccess options

Rent or Buy article

Get time limited or full article access on ReadCube.


All prices are NET prices.


  1. 1.

    Development of grasslands, savannas in East Africa during the Neogene. Palaeogeogr. Palaeoclimatol. Palaeoecol. 97, 241–247 (1992)

  2. 2.

    African climate change and faunal evolution during the Pliocene-Pleistocene. Earth Planet. Sci. Lett. 220, 3–24 (2004)

  3. 3.

    Evolution and climate variability. Science 273, 922–923 (1996)

  4. 4.

    et al. Coherent changes of southeastern equatorial and northern African rainfall during the last deglaciation. Science 346, 1223–1227 (2014)

  5. 5.

    , , & Late Cenozoic moisture history of East Africa. Science 309, 2051–2053 (2005)

  6. 6.

    & A Pliocene-Pleistocene stack of 57 globally distributed benthic δ18O records. Paleoceanography 20, PA1003 (2004)

  7. 7.

    et al. High-resolution carbon dioxide concentration record 650,000–800,000 years before present. Nature 453, 379–382 (2008)

  8. 8.

    , , , & in The Limnology, Climatology, and Palaeoclimatology of the East African Lakes (eds & ) 495–508 (Gordon and Breach, 1996)

  9. 9.

    et al. East African megadroughts between 135–75 kyr ago and implications for early human history. Proc. Natl Acad. Sci. USA 104, 16416–16421 (2007)

  10. 10.

    & Assessing the use of archaeal lipids as marine environmental proxies. Annu. Rev. Earth Planet. Sci. 41, 359–384 (2013)

  11. 11.

    , & The organic geochemistry of glycerol dialkyl glycerol tetraether lipids: a review. Org. Geochem. 54, 19–61 (2013)

  12. 12.

    , , , & Covariant glacial–interglacial dust fluxes in the equatorial Pacific and Antarctica. Science 320, 93–96 (2008)

  13. 13.

    et al. Improved dust representation in the Community Atmosphere Model. J. Adv. Model. Earth Syst. 6, 541–570 (2014)

  14. 14.

    et al. A continuous 1.3 million year record of East African hydroclimate, and implications for patterns of evolution and biodiversity. Proc. Natl Acad. Sci. 112, 15568–15573 (2015)

  15. 15.

    , , & Late Quaternary stratigraphic analysis of the Lake Malawi Rift, East Africa: an integration of drill-core and seismic-reflection data. Palaeogeogr. Palaeoclimatol. Palaeoecol. 303, 20–37 (2011)

  16. 16.

    , & Ecosystem variability and early human habitats in eastern Africa. Proc. Natl Acad. Sci. USA 110, 1167–1174 (2013)

  17. 17.

    et al. Woody cover and hominin environments in the past 6 million years. Nature 476, 51–56 (2011)

  18. 18.

    et al. Ecological consequences of early Late Pleistocene megadroughts in tropical Africa. Proc. Natl Acad. Sci. 104, 16422–16427 (2007)

  19. 19.

    et al. Abrupt onset and termination of the African Humid Period: rapid climate responses to gradual insolation forcing. Quat. Sci. Rev. 19, 347–361 (2000)

  20. 20.

    & Sedimentation in Lake Malawi (East Africa) during the past 10,000 years: a continuous paleoclimate record from the southern tropics. Palaeogeogr. Palaeoclimatol. Palaeoecol. 85, 351–366 (1991)

  21. 21.

    , , & Stratigraphy and paleoenvironments of the early to middle Holocene Chipalamawamba Beds (Malawi, Africa). Biogeosciences 9, 4497–4512 (2012)

  22. 22.

    , & Mega-lake in the Kalahari: a Late Pleistocene record of the paleolake Makgadikgadi system. Quat. Sci. Rev. 28, 1392–1411 (2009)

  23. 23.

    , , , & Late Quaternary highstands at Lake Chilwa, Malawi: frequency, timing and possible forcing mechanisms in the last 44 ka. Quat. Sci. Rev. 28, 526–539 (2009)

  24. 24.

    & Importance of the Indian Ocean for simulating rainfall anomalies over eastern and southern Africa. J. Geophys. Res. 104, 19099–19116 (1999)

  25. 25.

    , , & Multidecadal variability in East African hydroclimate controlled by the Indian Ocean. Nature 493, 389–392 (2013)

  26. 26.

    & Closing of the Indonesian seaway as a precursor to east African arifidication around 3–4 million years ago. Nature 411, 157–162 (2001)

  27. 27.

    , , & African vegetation controlled by tropical sea surface temperatures in the mid-Pleistocene period. Nature 422, 418–421 (2003)

  28. 28.

    et al. High- and low-latitude forcing of Plio-Pleistocene East African climate and human evolution. J. Hum. Evol. 53, 475–486 (2007)

  29. 29.

    et al. IGBP PAGES, https://www.ncdc.noaa.gov/cdo/f?p=519:1:0::::P1_STUDY_ID:19139 (NOAA World Data Center for Paleoclimatology, 2011)

  30. 30.

    , & Interhemispheric synchrony of the last deglaciation inferred from alkenone palaeothermometry. Nature 385, 707–710 (1997)

  31. 31.

    et al. Applicability and calibration of the TEX86 paleothermometer in lakes. Org. Geochem. 41, 404–413 (2010)

  32. 32.

    & A review of molecular organic proxies for examining modern and ancient lacustrine environments. Quat. Sci. Rev. 30, 2851–2891 (2011)

  33. 33.

    et al. Vertical and temporal variability in concentration and distribution of thaumarchaeotal tetraether lipids in Lake Superior and the implications for the application of the TEX86 temperature proxy. Geochim. Cosmochim. Acta 87, 136–153 (2012)

  34. 34.

    Thaumarchaeota Distribution in the Water Column of Lake Superior and Malawi: Implications for the TEX86 Temperature Proxy. , PhD thesis, Univ. Minnesota (2011)

  35. 35.

    , , , & A TEX86 lake record suggests simultaneous shifts in temperature in central Europe and Greenland during the last deglaciation. Geophys. Res. Lett. 40, 948–953 (2013)

  36. 36.

    et al. Seasonal changes in glycerol dialkyl glycerol tetraether concentrations and fluxes in a perialpine lake: implications for the use of the TEX86 and BIT proxies. Geochim. Cosmochim. Acta 75, 6416–6428 (2011)

  37. 37.

    et al. Extremely high sea-surface temperatures at low latitutudes during the middle Cretaceous as revealed by archaeal membrane lipids. Geology 31, 1069–1072 (2003)

  38. 38.

    , & Wet and arid phases in the southeast African tropics since the Last Glacial Maximum. Geology 35, 823–826 (2007)

  39. 39.

    , , , & Analytical methodology for TEX86 paleothermometry by high-performance liquid chromatography/atmospheric pressure chemical ionization-mass spectrometry. Anal. Chem. 79, 2940–2944 (2007)

  40. 40.

    , , & Distributional variations in marine crenarchaeotal membrane lipids: a new tool for reconstructing ancient sea water temperatures? Earth Planet. Sci. Lett. 204, 265–274 (2002)

  41. 41.

    & Corrigendum to “A review of molecular organic proxies for examining modern and ancient lacustrine environments”. Quat. Sci. Rev. 125, 174–176 (2015)

  42. 42.

    , , , & Global sediment core-top calibration of the TEX86 paleothermometer in the ocean. Geochim. Cosmochim. Acta 72, 1154–1173 (2008)

  43. 43.

    , , & Distribution of tetraether lipids in the 25-ka sedimentary record of Lake Challa: extracting reliable TEX86 and MBT/CBT palaeotemperatures from an equatorial African lake. Quat. Sci. Rev. 50, 43–54 (2012)

  44. 44.

    Lake Malawi’s response to “megadrought” terminations: sedimentary records of flooding, weathering and erosion. Palaeogeogr. Palaeoclimatol. Palaeoecol. 303, 120–125 (2011)

  45. 45.

    & in The Limnology, Climatology and Paleoclimatology of the East African lakes (eds & ) 475–493 (Gordon and Breach, 1996)

  46. 46.

    , & Ash from the Toba supereruption in Lake Malawi shows no volcanic winter in East Africa at 75 ka. Proc. Natl Acad. Sci. USA 110, 8025–8029 (2013)

  47. 47.

    Environment and climate of early human evolution. Annu. Rev. Earth Planet. Sci. 43, 405–429 (2015)

  48. 48.

    Plio-Pleistocene African climate. Science 270, 53–59 (1995)

Download references


We thank the engineering and design team of the Lake Malawi Scientific Drilling Project for overcoming substantial technical challenges associated with drilling on Lake Malawi, especially the efforts of D. Schnurrenberger, M. Pardy and Lengeek Vessel Engineering. B. Otto-Bliesner and S. Albani provided advice on climate model results relevant to this study. J. King provided the palaeomagnetic reversal data that contributed substantially to the age model of the Malawi sediment record. We thank the scientists and technicians of LacCore, University of Minnesota, for their assistance in the splitting, initial analyses, sampling and archiving of the sediment cores obtained by the Lake Malawi Drilling Project. Financial support was provided by the US National Science Foundation EAR and P2C2 programmes and by the International Continental Scientific Drilling Program. S.S. and J.S.S.D. were supported by the Netherlands Earth System Science Centre (NESSC), which is financially supported by the Dutch Ministry of Education, Culture and Science (OCW).

Author information

Author notes

    • R. P. Lyons

    Present address: Chevron Corporation, 1400 Smith Street, Houston, Texas 77002, USA.


  1. Large Lakes Observatory and Department of Earth and Environmental Sciences, University of Minnesota Duluth, Duluth, Minnesota 55812, USA

    • T. C. Johnson
    • , E. T. Brown
    • , B. A. Steinman
    • , J. Halbur
    •  & S. Grosshuesch
  2. Department of Geosciences, University of Massachusetts Amherst, Amherst, Massachusetts 01003, USA

    • T. C. Johnson
  3. Department of Geology and Planetary Science, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, USA

    • J. P. Werne
  4. Department of Earth and Planetary Sciences, Faculty of Science and Engineering, Macquarie University, Sydney, New South Wales 2109, Australia

    • A. Abbott
  5. Department of Civil & Environmental Engineering & Earth Sciences, University of Notre Dame, 257 Fitzpatrick Hall, Notre Dame, Indiana 46556, USA

    • M. Berke
  6. Departamento de Química Ambiental and Centro de Investigación en Biodiversidad y Ambientes Sustentables (CIBAS), Universidad Católica de la Santísima Concepción, Casilla 297, Concepción, Chile

    • S. Contreras
  7. Berkeley Geochronology Center, 2455 Ridge Road, Berkeley, California 94709, USA

    • A. Deino
  8. Earth Sciences Department, Syracuse University, 011a Heroy Geology Laboratory, Syracuse, New York 13244, USA

    • C. A. Scholz
    •  & R. P. Lyons
  9. NIOZ Netherlands Institute for Sea Research, Department of Marine Microbiology and Biogeochemistry, and Utrecht University, PO Box 59, 1790 AB Den Burg, The Netherlands

    • S. Schouten
    •  & J. S. Sinninghe Damsté
  10. Faculty of Geosciences, Department of Earth Sciences, Utrecht University, PO Box 80.021, 3508 TA Utrecht, The Netherlands

    • S. Schouten
    •  & J. S. Sinninghe Damsté


  1. Search for T. C. Johnson in:

  2. Search for J. P. Werne in:

  3. Search for E. T. Brown in:

  4. Search for A. Abbott in:

  5. Search for M. Berke in:

  6. Search for B. A. Steinman in:

  7. Search for J. Halbur in:

  8. Search for S. Contreras in:

  9. Search for S. Grosshuesch in:

  10. Search for A. Deino in:

  11. Search for C. A. Scholz in:

  12. Search for R. P. Lyons in:

  13. Search for S. Schouten in:

  14. Search for J. S. Sinninghe Damsté in:


T.C.J., J.P.W. and E.T.B. conceptualized the project. C.A.S. and T.C.J. were two of the Principal Investigators on the Lake Malawi Drilling Project. J.P.W., J.S.S.D. and S.S. supervised and interpreted the biomarker analyses conducted by A.A., M.B., J.H., S.C. and S.G. E.T.B. supervised the X-ray fluorescence analyses for calcium. A.D. provided Ar–Ar dates on tephra. R.P.L. provided the lake level history. B.A.S. conducted the statistical analyses. T.C.J. and E.T.B. wrote the manuscript with substantial contributions from J.P.W., A.A., M.B., B.A.S., S.C., S.S. and J.S.S.D. All authors reviewed the paper prior to submission.

Competing interests

The authors declare no competing financial interests.

Corresponding author

Correspondence to T. C. Johnson.

The data used in this study are available as Supplementary Data.

Reviewer Information

Nature thanks K. Freeman, P. Polissar and the other anonymous reviewer(s) for their contribution to the peer review of this work.

Extended data

Supplementary information

Excel files

  1. 1.

    Supplementary Data

    This file contains Supplementary Data.

About this article

Publication history






Further reading


By submitting a comment you agree to abide by our Terms and Community Guidelines. If you find something abusive or that does not comply with our terms or guidelines please flag it as inappropriate.