Nature Ecology & Evolution

Published by Springer Nature

Online ISSN: 2397-334X


When two are better than one
  • Article
  • Full-text available

July 2021


69 Reads


A clever experimental design in bacteria with engineered obligate mutualisms shows that interdependency can allow pairs of bacteria to survive in environments that are uninhabitable by the individual strains.

Surface scans of DNH 155
Specimen positioned in a, posterior, b, basal, and c, right lateral views. Scale bar = 10mm.
Position of the zygomatic root
Right lateral views of P. robustus specimens a, DNH 7, c, SK 48, e, SK 52, f, SKW11, and g, SK 12. Left lateral views of b, DNH 155, and d, TM 1517. Vertical red lines pass through P⁴/M¹ on each specimen. The anterior aspect of the root is positioned at this line in a and b but anterior to the line in c–g. Scale bar = 10mm.
Thickness of the zygomatic root
Paranthropus robustus specimens shown slightly offset from palatal view in order to visualize the lateral wall of the maxilla. a, DNH 7. b, DNH 155. c, SK 12. d, TM 1517. e, SK 48. All specimens are scaled to the same P⁴ – M² length. Red and yellow lines represent the anterior- and posterior-most aspects of the zygomatic root on the maxilla. The root is proportionally thinnest in DNH 7 and DNH 155.
Zygomaticomaxillary step
Oblique views of P. robustus specimens a, DNH 155, b, DNH 7, c, SK 46, d, SK 12, e, SK 52, f, TM 1517, and g, SK 48. Arrows indicate change of contour between the surfaces of the zygomatic bone and maxillary trigon. Shading indicates that the change in contour is abrupt and coincident with the zygomaticomaxillary suture in c–g, In a and b the change in contour is gentle (brackets) and positioned above the suture such that the suture lies within the trigon as opposed to being its superolateral margin. Scale bar = 10mm.
Supraorbital corner
Frontal views of P. robustus specimens a, DNH 152, b, DNH 7, c, DNH 155, d, SK 46, and e, SK 48. Arrows indicate a squared supraorbital corner associated with a roughly horizontal supraorbital torus in d and e. In a and b the homologous region of the orbital margin is rounded, and in c the corner is not squared and the supraorbital torus is inclined. Note that specimen SK 46 is badly distorted, but the torus and corner are locally undistorted. Images not to the same scale.


Drimolen cranium DNH 155 documents microevolution in an early hominin species

January 2021


1,262 Reads






Paranthropus robustus is a small-brained extinct hominin from South Africa characterized by derived, robust craniodental morphology. The most complete known skull of this species is DNH 7 from Drimolen Main Quarry, which differs from P. robustus specimens recovered elsewhere in ways attributed to sexual dimorphism. Here, we describe a new fossil specimen from Drimolen Main Quarry, dated from approximately 2.04–1.95 million years ago, that challenges this view. DNH 155 is a well-preserved adult male cranium that shares with DNH 7 a suite of primitive and derived features unlike those seen in adult P. robustus specimens from other chronologically younger deposits. This refutes existing hypotheses linking sexual dimorphism, ontogeny and social behaviour within this taxon, and clarifies hypotheses concerning hominin phylogeny. We document small-scale morphological changes in P. robustus associated with ecological change within a short time frame and restricted geography. This represents the most highly resolved evidence yet of microevolutionary change within an early hominin species.

Species distribution models are inappropriate for COVID-19

May 2020


274 Reads

Species distribution models are a powerful tool for ecological inference, but not every use is biologically justified. Applying these tools to the COVID-19 pandemic is unlikely to yield new insights, and could mislead policymakers at a critical moment.

Field-based sciences must transform in response to COVID-19

September 2020


251 Reads

The pandemic will allow us to fundamentally remodel the way field-based sciences are taught, conducted and funded — but only if we stop waiting for a ‘return to normal’.

Fig. 1 | Illustrating the research potential of the recently launched covID-19 Bio-logging Initiative. Top: locations of a subsample of active animal tracking ('bio-logging') studies superimposed on human population density. Data sources: 801 publicly visible animal tracking studies from the Movebank research platform ( that are likely to contain data overlapping with the COVID-19 period (data extracted 18 May 2020). 'Marine' includes seabirds and other marine species, 'avian' refers to all other bird species, and 'terrestrial' are non-avian species living mostly on land. Population density data sourced from ref. 15 (data accessed 15 May 2020). Bottom: median percentage of change based on daily values (with reference to the data provider's default baseline from the five-week period between 3 January and 6 February 2020) in visits to places like local parks, national parks, public beaches, marinas, dog parks, plazas and public gardens for the month of April 2020. Data are plotted for 900 subregions within 131 countries (note that for 1.6% of the subregions fewer than 5 daily values were available for April 2020). This information should be interpreted cautiously, and is shown here merely to provide a preliminary, coarse-scale illustration of some recent changes in human mobility; scientific analyses will require higher-resolution, calibrated data. Data sourced from ref. 16 (data accessed 7 May 2020). Both maps were drawn with the QGIS Geographic Information System (, using freely available data (2018) for country borders from GADM ( (data accessed 6 May 2020).
COVID-19 lockdown allows researchers to quantify the effects of human activity on wildlife

June 2020


1,658 Reads

Reduced human mobility during the pandemic will reveal critical aspects of our impact on animals, providing important guidance on how best to share space on this crowded planet.

Amotz Zahavi (1928–2017)

July 2017


81 Reads

Evolutionary biologist who proposed the handicap principle.

Edward O. Wilson (1929–2021)

February 2022


54 Reads

Naturalist, synthesizer and conservation champion.

Norman Myers (1934–2019)

February 2020


873 Reads

Conservationist who changed how we think about threats to biodiversity.

J. Philip Grime (1935–2021)

May 2021


212 Reads

The founder of plant functional ecology.

Michael E. Soulé (1936–2020)

August 2020


74 Reads

Founder of conservation biology, expansive thinker and inspiring mentor.

Thomas H. Kunz (1938–2020)

June 2020


35 Reads

Bat biologist and inspirational mentor who developed the concept of aeroecology.

Paul Mellars (1939–2022)

June 2022


11 Reads

Archaeologist who emphasized the importance of chronology in understanding Palaeolithic Europe, and laid the framework for the archaeology of modern human origins.

William G. Hill (1940–2021)

February 2022


11 Reads

Quantitative geneticist who made fundamental contributions to understanding the nature of genetic variation.

Thomas E. Lovejoy (1941–2021)

February 2022


62 Reads

Biodiversity advocate and Amazon expert

Colin Groves (1942–2017)

April 2018


42 Reads

Evolutionary biologist who brought taxonomy to life.

John Alcock (1943–2023)
  • New
  • Article

May 2023


3 Reads

Dorothy L. Cheney (1950–2018)

January 2019


38 Reads

Primatologist who gave voice to animal communication and cognition.

Harold L. Dibble (1951–2018)

September 2018


237 Reads

Archaeologist who transformed our understanding of Neanderthals.

Brian Maurer (1954–2018)

October 2018


31 Reads

Ecologist who co-founded the discipline of macroecology.

Isaiah Odhiambo Nengo (1961–2022)

April 2022


131 Reads

Primate palaeontologist and passionate advocate for diversity in human origins research.

Ruth D. Gates (1962–2018)

December 2018


39 Reads

Coral biologist and tireless reef advocate.

Matthew J. G. Gage (1967–2022)

April 2022


5 Reads

Researcher who studied fundamental questions about sexual selection, and an inspiring and kind colleague and friend.

Ben Collen (1978–2018)

July 2018


238 Reads

Inspirational conservation scientist.

2,100 years of human adaptation to climate change in the High Andes

January 2020


933 Reads

Humid montane forests are challenging environments for human habitation. We used high-resolution fossil pollen, charcoal, diatom and sediment chemistry data from the iconic archaeological setting of Laguna de los Condores, Peru to reconstruct changing land uses and climates in a forested Andean valley. Forest clearance and maize cultivation were initiated during periods of drought, with periods of forest recovery occurring during wetter conditions. Between ad 800 and 1000 forest regrowth was evident, but this trend was reversed between ad 1000 and 1200 as drier conditions coincided with renewed land clearance, the establishment of a permanent village and the use of cliffs overlooking the lake as a burial site. By ad 1230 forests had regrown in the valley and maize cultivation was greatly reduced. An elevational transect investigating regional patterns showed a parallel, but earlier, history of reduced maize cultivation and forest regeneration at mid-elevation. However, a lowland site showed continuous maize agriculture until European conquest but very little subsequent change in forest cover. Divergent, climate-sensitive landscape histories do not support categorical assessments that forest regrowth and peak carbon sequestration coincided with European arrival. Multi-proxy palaeoecological methods reconstruct phases of land clearance, maize cultivation and forest regrowth in the High Andes centuries before European incursion, and do not support the idea that forest regrowth and peak carbon sequestration were coincident with European arrival.

Figure 1 | Geological map and stratigraphic section of the Griqualand West sub-basin, showing the location of Agouron drill hole GTF01 (28° 49′ 39.7′′ S, 23° 07′ 24.1′′ E). The fossiliferous sample is from the lower part of the Ongeluk Formation (drill depth 21.79 m). Fm., formation; subgrp, subgroup. Modified from ref. 53 , Geological Society of America.
Figure 2 | Ongeluk vesicular basalt with filamentous fossils, petrographic thin sections. a, Basalt with vesicles frequently connected by veins; Swedish Museum of Natural History X6129. b,c, Anastomosing network; X6130. d,e, Vesicle with broom structure; note distinction between calcite (light) and chlorite (dark) cement; X6131. f, Anastomosis; X6132. g, Broom structure in fracture (same specimen as in Fig. 4); X6133. h, Broom; X6134. i, Vesicle connected to vein filled with calcite (light) and chlorite (dark) cement; X6135. j-l, Basal film and marginal network; X6136. Panels a-i show transmitted light images; panels j-l show ESEM images produced in backscatter mode. Lettered frames indicate position of enlargements in other panels. an, anastomosis; bf, basal film; Ca, calcite; Chl1, chlorite 1; hy, hypha; ve, vein; Yj, Y-junction.
Figure 3 | Ongeluk vesicle with filamentous fossils, SRXTM surface/ volume renderings; Swedish Museum of Natural History X6137. a, Section through complete vesicle; frame indicates region depicted in e. b,c, Anastomoses and false branching. d,e, Brooms. f,g, Y-junctions, T-junctions and touching filaments. h,i, Loops and touching filaments. j, Bulbous protrusions. an, anastomosis; bf, basal film; bp, bulbous protrusion; br, broom; fb, false branching; lo, loop; tf, touching filaments; Tj, T-junction; Yj, Y-junction. 
Figure 4 | Calcite-and chlorite-filled fracture with filamentous fossils in Ongeluk vesicular basalt, petrographic thin section; Swedish Museum of Natural History X6133. a, Overview of fracture, which is truncated along centre by edge of section. b-e, Fracture filling divided into central zone and peripheral filamentous zone, parted by a band of chlorite 2; note truncation of filaments by chlorite 2 band. Different intensity of calcite interference colours in filamentous zone (e) indicates blocky distribution of calcite crystals, not related to filament morphology; chloritic filaments are too thin to reveal interference colours of chlorite 1 (black arrow). Panels a-d show plane-polarized transmitted light images; the image in panel e was produced using crossed nicols. Lettered frames indicate position of enlargements in other panels. Ca, calcite; Chl1, chlorite 1; Chl2, chlorite 2. 
Fungus-like mycelial fossils in 2.4-billion-year-old vesicular basalt

April 2017


1,827 Reads

Fungi have recently been found to comprise a significant part of the deep biosphere in oceanic sediments and crustal rocks. Fossils occupying fractures and pores in Phanerozoic volcanics indicate that this habitat is at least 400 million years old, but its origin may be considerably older. A 2.4-billion-year-old basalt from the Palaeoproterozoic Ongeluk Formation in South Africa contains filamentous fossils in vesicles and fractures. The filaments form mycelium-like structures growing from a basal film attached to the internal rock surfaces. Filaments branch and anastomose, touch and entangle each other. They are indistinguishable from mycelial fossils found in similar deep-biosphere habitats in the Phanerozoic, where they are attributed to fungi on the basis of chemical and morphological similarities to living fungi. The Ongeluk fossils, however, are two to three times older than current age estimates of the fungal clade. Unless they represent an unknown branch of fungus-like organisms, the fossils imply that the fungal clade is considerably older than previously thought, and that fungal origin and early evolution may lie in the oceanic deep biosphere rather than on land. The Ongeluk discovery suggests that life has inhabited submarine volcanics for more than 2.4 billion years.

Scientific foundations for an ecosystem goal, milestones and indicators for the post-2020 global biodiversity framework

August 2021


445 Reads

Despite substantial conservation efforts, the loss of ecosystems continues globally, along with related declines in species and nature’s contributions to people. An effective ecosystem goal, supported by clear milestones, targets and indicators, is urgently needed for the post-2020 global biodiversity framework and beyond to support biodiversity conservation, the UN Sustainable Development Goals and efforts to abate climate change. Here, we describe the scientific foundations for an ecosystem goal and milestones, founded on a theory of change, and review available indicators to measure progress. An ecosystem goal should include three core components: area, integrity and risk of collapse. Targets—the actions that are necessary for the goals to be met—should address the pathways to ecosystem loss and recovery, including safeguarding remnants of threatened ecosystems, restoring their area and integrity to reduce risk of collapse and retaining intact areas. Multiple indicators are needed to capture the different dimensions of ecosystem area, integrity and risk of collapse across all ecosystem types, and should be selected for their fitness for purpose and relevance to goal components. Science-based goals, supported by well-formulated action targets and fit-for-purpose indicators, will provide the best foundation for reversing biodiversity loss and sustaining human well-being.

Fig. 2 | Chemical structures of stelliferasterol, isostelliferasterol and strongylosterol. These are the three known natural sterol precursors of the 26-mes sterane biomarker 20,21,23,39,40. They are found only in certain demosponges, but not detected in other groups of eukaryotes. Note: (1) the methyl-substituent at the terminal position of the sterol side chain, which remains preserved at C-26 in 26-mes; and (2) the unusual double bond positions in the side chains of stelliferasterol and strongylosterol. The biological configuration is 20R for all three sterols, 24R for strongylosterol and stelliferasterol, and 25S for isostelliferasterol. Three stereogenic carbon atoms exist in the side chain of 26-mes (chirality at C-20, C-24 and C-25), but only C-20 stereoisomers give separate compound peaks, producing up to four regular stereoisomers of 26-mes (α α α S, α β β R, α β β S and α α α R) in ancient rocks and oils, as has also been found for other sterane compounds.
Fig. 3 | A revised Neoproterozoic-Cambrian timeline showing cooccurrences of 26-mes and 24-ipc sterane biomarkers. The South Oman record commences in the Cryogenian period (> 635 Ma) after the Sturtian glaciation (terminating at around 660 Ma 6 ) and continues throughout the Ediacaran period into the Early Cambrian for Huqf Supergroup rocks (Supplementary Tables 1-2). Other Ediacaran oils also contain the C 30 steranes series (Supplementary Table 3), but some Ediacaran rocks are devoid of the C 30 sterane series, although they contain predominantly algal steranes with a C 29 dominance 40. The distribution and abundance patterns of the C 30 sterane 26-mes have yet to be fully established for the Phanerozoic rock record; however, it can be detected in some Phanerozoic rocks and oils (see Supplementary Table 3). Cryostane is a potentially older biomarker for sponges or unicellular protists, and it has been detected in pre-Sturtian rocks in the 800-717 Myr age range 29 but not in older samples. Cryostane is a C 28 sterane analogue of 26-mes, but corresponding sterol precursors for cryostane have never been reported from any extant taxa despite the identification of 26-mes demosponge sterols many decades ago 20,21,23,38,39. 'M' signifies the Marinoan glaciation; cryostane temporal range is represented by red shading although possible ocurrences in younger rocks and oils require further investigation; 26-mes and 24-ipc range is represented by the black bar.
Fig. 4 | Chemical structures for a selection of conventional, unconventional and unsaturated sterols found in modern eukaryotic taxa. Chemical structures numbered 1-15 (top) represent possible variations of the part of the structure labelled 'R' in structures A-C (bottom). Conventional sterols show side chain alkylation of the C 27 cholestane core skeleton restricted to the C-24 position, while all examples of unconventional sterols shown here have extended side chains arising from terminal methylation at C-26 and/or C-27. Note that the tetracyclic core and/or side chain of sterols may or may not contain an alkene bond, and when alkene bonds are present these sterols are known as unsaturated compounds. In this scheme, cholesterol is compound B1, stelliferasterol is B13, isostelliferasterol is B14 and strongylosterol is B15. The dominant ancient fossil form is sterane (A), with alcohol and alkene bonds removed by chemical reduction.
MRM-GC-MS ion chromatograms of C30 sterane distributions (414 → 217 Da ion transitions)
a, Results from Neoproterozoic–Cambrian rock bitumens and oils. b, HyPy products from the cells of three modern demosponges (see Supplementary Table 4 for taxonomic assignments). Ancient samples, having undergone protracted burial and alteration, exhibit a more complex distribution of diastereoisomers compared with modern sponge biomass. Four regular sterane diastereoisomers can be found in ancient samples of oil window-maturity (αααS, αββR, αββS and αααR), while two diastereoisomers (βααR and αααR) result from laboratory hydrogenation of individual Δ5-sterols in modern sponge biomass. The signal peak for the αααS geoisomer of 26-mes often co-elutes with other C30 steranes, so this isomer peak is usually obscured in chromatograms. Direct correlation with modern sponges uses the αααR isomer, as shown by the dashed lines. The αββ isomers show expected enhancement of the signal in 414 → 218 Da ion chromatograms relative to ααα stereoisomers (not shown here). Examples from the Proterozoic rock record show three distinct resolvable sterane series co-occurring (24-npc, 24-ipc and 26-mes). The rock from Ghadir Manquil Formation, South Oman, was deposited during the Cryogenian period (probably around 660–635 Ma) and is the oldest example in the rock record known with 24-ipc and 26-mes co-occurring. The 26-mes sterane biomarker was detected in significant amounts in the South Oman rock extracts and kerogen pyrolysates reported previously² (Supplementary Tables 1 and 2). The oil from the Usol’ye Formation, Eastern Siberia, is probably Ediacaran to Early Cambrian in source age⁹, as is the Baghewala-1 oil from India⁷. An ‘o’ symbol represents 24-npc, a plus 24-ipc and an asterisk 26-mes. Thymo, thymosiosterane (24,26,26’-trimethylcholestane).
Demosponge steroid biomarker 26-methylstigmastane provides evidence for Neoproterozoic animals

November 2018


1,110 Reads

Sterane biomarkers preserved in ancient sedimentary rocks hold promise for tracking the diversification and ecological expansion of eukaryotes. The earliest proposed animal biomarkers from demosponges (Demospongiae) are recorded in a sequence around 100 Myr long of Neoproterozoic–Cambrian marine sedimentary strata from the Huqf Supergroup, South Oman Salt Basin. This C30 sterane biomarker, informally known as 24-isopropylcholestane (24-ipc), possesses the same carbon skeleton as sterols found in some modern-day demosponges. However, this evidence is controversial because 24-ipc is not exclusive to demosponges since 24-ipc sterols are found in trace amounts in some pelagophyte algae. Here, we report a new fossil sterane biomarker that co-occurs with 24-ipc in a suite of late Neoproterozoic–Cambrian sedimentary rocks and oils, which possesses a rare hydrocarbon skeleton that is uniquely found within extant demosponge taxa. This sterane is informally designated as 26-methylstigmastane (26-mes), reflecting the very unusual methylation at the terminus of the steroid side chain. It is the first animal-specific sterane marker detected in the geological record that can be unambiguously linked to precursor sterols only reported from extant demosponges. These new findings strongly suggest that demosponges, and hence multicellular animals, were prominent in some late Neoproterozoic marine environments at least extending back to the Cryogenian period.

Predicting 3D protein structures in light of evolution

July 2021


274 Reads

Recent advances in AI-based 3D protein structure prediction could help address health-related questions, but may also have far-reaching implications for evolution. Here we discuss the advantages and limitations of high-quality 3D structural predictions by AlphaFold2 in unravelling the relationship between protein properties and their impact on fitness, and emphasize the need to integrate in silico structural predictions with functional genomic studies.

A genome sequence from a modern human skull over 45,000 years old from Zlatý kůň in Czechia

June 2021


1,768 Reads

Modern humans expanded into Eurasia more than 40,000 years ago following their dispersal out of Africa. These Eurasians carried ~2–3% Neanderthal ancestry in their genomes, originating from admixture with Neanderthals that took place sometime between 50,000 and 60,000 years ago, probably in the Middle East. In Europe, the modern human expansion preceded the disappearance of Neanderthals from the fossil record by 3,000–5,000 years. The genetic makeup of the first Europeans who colonized the continent more than 40,000 years ago remains poorly understood since few specimens have been studied. Here, we analyse a genome generated from the skull of a female individual from Zlatý kůň, Czechia. We found that she belonged to a population that appears to have contributed genetically neither to later Europeans nor to Asians. Her genome carries ~3% Neanderthal ancestry, similar to those of other Upper Palaeolithic hunter-gatherers. However, the lengths of the Neanderthal segments are longer than those observed in the currently oldest modern human genome of the ~45,000-year-old Ust’-Ishim individual from Siberia, suggesting that this individual from Zlatý kůň is one of the earliest Eurasian inhabitants following the expansion out of Africa. The authors present the genome sequence of a >45,000-year-old female Homo sapiens individual from the site of Zlatý kůň, Czechia. Although radiometric dating of the human remains was inconclusive, the authors were able to use molecular methods to demonstrate that she was probably among the earliest Eurasian inhabitants following expansion out of Africa.

Milk and bulk deamidation and peptide counts.
Ruminant and equine dairying in prehistoric Eurasia and contemporary Mongolia
a, Map of Eurasia showing major geographical features referred to in the text and sites where evidence of dairying has been previously found using proteomic approaches: (1) Khövsgöl¹, (2) Xiaohe¹¹, (3) Gumugou¹⁰, (4) Subeixi⁶⁸, (5) Bulanovo²⁹, (6) Hatsarat²⁹, (7) Çatalhöyük West⁶⁹, (8) Tomb of Ptahmes⁷⁰, (9) Szöreg-C (Sziv Utca)²⁹ and (10) Olmo di Nogara²⁹. Locations for the earliest evidence of ruminant dairying based on the presence of milk fats in ceramics are shown in blue⁷ and the earliest evidence of horse dairying⁹ are shown in pink. Details for each site included in this figure are referenced in Supplementary Table 3. b–f, Mongolian dairy products from Khövsgöl aimag: yoghurt starter culture, Khöröngö (Хөрөнгө) (b); curd from reindeer milk, ‘kurd’ (c); dried curd from mixed yak and cow milk, aaruul (ааруул) (d); clotted cream from mixed yak and cow milk, öröm (өрөм) (e); and fermented horse milk, airag (айраг) (f). g, Dairying ritual from Dundgobi aimag, Mongolia blessing the first horse airag production of the season. Credit: Photograph c provided by Matthäus Rest; photograph d provided by Jessica Hendy; and all others provided by Björn Reichhardt.
Mongolian dairy consumption by period
a–d, Maps showing changes in dairy consumption for Neolithic to Early Bronze Age (a), Middle–Late Bronze Age (b), Iron Age and Early Medieval (c) and Late Medieval (d). Archaeological site cultural affiliation is indicated by colours and symbols. Solid filled symbols indicate individuals with positive evidence of milk proteins, while symbols bisected with a diagonal line indicate individuals where no milk proteins were identified. Individuals of the same site are contained within brackets. Individual AT-923, associated with Ulaanzuukh, is not directly radiocarbon dated and is not included in this figure. Taxonomic icons only indicate the most specific taxa identified in a phylogenetic branch. The full list of dairy species identified for each individual is given in Table 1 and Supplementary Dataset 2. Data used in the creation of this figure are included in Supplementary Table 4.
Alignment of observed BLG peptides for two individuals analysed in this study, showing the number of Equus and ruminant BLG peptides detected
For Equus, peptides from both LGB1 and LGB2 paralogues are shown (see Supplementary Table 5 for data associated with figure). Where peptides from these two taxa overlap, this has been indicated by a blue/orange cross-hatch pattern. The arrow in Individual AT-775 indicates two contiguous but independent peptides. Beneath each individual is a consensus sequence of B. taurus BLG (UniProt: P02754) and E. caballus BLG1 (UniProt: P02758) with dark grey indicating sequence identity and pale grey indicating sites with sequence differences.
Timeline of evidence for the consumption of different livestock milk in prehistoric and historic Mongolia
Radiocarbon dates for each individual were calibrated using OxCal (OxCal v.4.3.2 Bronk Ramsey⁶⁶; r:5 IntCal13 atmospheric curve⁶⁷) and resulting radiocarbon probabilities were grouped by the taxa of dairy proteins identified in that individual (indicated by AT-numbers), with ruminant taxa (Ovis, Capra and Bovinae) indicated in purple, Equus indicated by orange and Camelus indicated by green. Dairy peptides identified in individual AT-26 (indicated with an asterisk) are specific to Bovinae/Ovis. Individuals without direct radiocarbon dates are indicated by unfilled boxes and are placed on the timeline based on the estimated time spans for the Xiongnu and Mongol Empires. For data used in this figure, refer to Supplementary Table 6.
Dairy pastoralism sustained Eastern Eurasian steppe populations for 5000 years

March 2020


1,434 Reads

Dairy pastoralism is integral to contemporary and past lifeways on the eastern Eurasian steppe, facilitating survival in agriculturally challenging environments. While previous research has indicated that ruminant dairy pastoralism was practiced in the region by circa 1300 bc, the origin, extent and diversity of this custom remain poorly understood. Here, we analyse ancient proteins from human dental calculus recovered from geographically diverse locations across Mongolia and spanning 5,000 years. We present the earliest evidence for dairy consumption on the eastern Eurasian steppe by circa 3000 bc and the later emergence of horse milking at circa 1200 bc, concurrent with the first evidence for horse riding. We argue that ruminant dairying contributed to the demographic success of Bronze Age Mongolian populations and that the origins of traditional horse dairy products in eastern Eurasia are closely tied to the regional emergence of mounted herding societies during the late second millennium bc.

Radiocarbon dating from Yuzhniy Oleniy Ostrov cemetery reveals complex human responses to socio-ecological stress during the 8.2 ka cooling event

February 2022


535 Reads

Yuzhniy Oleniy Ostrov in Karelia, northwest Russia, is one of the largest Early Holocene cemeteries in northern Eurasia, with 177 burials recovered in excavations in the 1930s; originally, more than 400 graves may have been present. A new radiocarbon dating programme, taking into account a correction for freshwater reservoir effects, suggests that the main use of the cemetery spanned only some 100–300 years, centring on ca. 8250 to 8000 cal bp. This coincides remarkably closely with the 8.2 ka cooling event, the most dramatic climatic downturn in the Holocene in the northern hemisphere, inviting an interpretation in terms of human response to a climate-driven environmental change. Rather than suggesting a simple deterministic relationship, we draw on a body of anthropological and archaeological theory to argue that the burial of the dead at this location served to demarcate and negotiate rights of access to a favoured locality with particularly rich and resilient fish and game stocks during a period of regional resource depression. This resulted in increased social stress in human communities that exceeded and subverted the ‘normal’ commitment of many hunter-gatherers to egalitarianism and widespread resource sharing, and gave rise to greater mortuary complexity. However, this seems to have lasted only for the duration of the climate downturn. Our results have implications for understanding the context of the emergence—and dissolution—of socio-economic inequality and territoriality under conditions of socio-ecological stress.

Location and biogeographic context of Varsche Rivier 003
a, Aridity map of southern Africa, with the Varsche Rivier 003 (VR003, white dot) and relevant MSA sites referred to in the text (yellow dots) indicated. Aridity index data from ref. ⁷², with definitions according to ref. ⁷³. Red box shows location of inset map (b). b, VR003 in relation to modern biome–bioregion boundaries from ref. ⁷⁴ and Fynbos Biome sites immediately south: DRS, Diepkloof; EBC, Elands Bay Cave; HRS, Hollow Rock Shelter; KFR, Klipfonteinrand 1; MRS, Mertenhof; PL8, Putslaagte 8. c, Site photo of VR003 and the Varsche Rivier 003 valley, looking west. d, Excavation plan at conclusion of most recent season in 2016. The original deep sounding is highlighted in red.
East section of deep sounding with key artefact type and location of geochronology samples
Per convention, luminescence ages are presented here at 1 σ uncertainty, U–Th ages at 2 σ. For artefacts, aggregate contexts refer to silcrete cores recovered during the initial seasons (2009, 2011), during which individual artefacts were typically not plotted. These cores were recovered from bucket aggregates and include up to two cores in some cases. Inset a, Microphotographs showing the typical components and structure of I-08. Bone (B) fragments range in size from gravel to sand. Another typical anthropogenic component at the site is ostrich eggshell (OES). Note also the coarse crystalline limestone (Li) and calcite crystals (C), and fine coating of these coarse grains. Inset b, Microscopic silcrete (Si) knapping debris and rounded soil aggregates (Agg) from the plateau above the site in a calcareous matrix.
Comparison of primary factors determining long-term regional climate dynamics with VR003 phytolith data
Top: 25° S December–February (DJF) insolation and eccentricity. Middle: C4:C3 grass ratios. Bottom: the percentage of Restionaceae and woody taxa, a classification reflecting the abundance of fynbos vegetation75,76. Data for orbital parameters are from ref. ⁷⁷ and the SE Atlantic wind strength composite is as calculated in ref. ⁷⁸, using the data of refs. 79–82. The phytolith data are depicted as uncertainty spaces defined by the multiplication of probability density functions derived from (1) stratigraphic unit ages and errors for the Lower Deposits and Howiesons Poort layers, and (2) aggregated phytolith data and the associated standard deviation of sample values from these units (see Supplementary Information for more detail).
Flaked OES fragments from the Lower Deposits
Artefacts 9220 and 7693 have simple perforations similar to those made by hyenas⁸³, but 9340, 7974 and 9300 show apparent elaborations of similar perforations through more extensive flaking. The artefacts in the central column may thus represent production stages leading to more finely ‘finished’ pieces in the left two columns. The ‘hypothetical fit’ in the top right is an indicative photo montage of VR003 samples 6147, 7833, 8415, 8348 and 6307. These pieces do not actually refit. Artefact SAM AA 8438 (bottom right) is from the Ethnographic Collection at Iziko: South African Museum (SAM), and was recovered from Ysterfontein Village by G. E. Loedalf in June 1968 and donated to the museum in December 1968.
A selection of silcrete cores from the Lower Deposits
White arrows indicate location of HINC surfaces; yellow arrows indicate location of flaking initiations. All artefacts shown, except 2815, were made on heat shatter. a, 1421: minimal core on heat shatter. Inset a shows the contact between the smooth post-heat removal and the scalar features on the older shatter surface. 1462: simple prepared platform core on heat shatter. 1520: minimal core on heat shatter. 3450: single platform core with small laminar removals on heat shatter. 5391: prepared core on heat shatter with one laminar removal. 7379: multiplatform core on heat shatter. 2815: unheated single platform core with small laminar removals. (Also see Supplementary Fig. 24.)
Environmental influences on human innovation and behavioural diversity in southern Africa 92–80 thousand years ago
Africa’s Middle Stone Age preserves sporadic evidence for novel behaviours among early modern humans, prompting a range of questions about the influence of social and environmental factors on patterns of human behavioural evolution. Here we document a suite of novel adaptations dating approximately 92–80 thousand years before the present at the archaeological site Varsche Rivier 003 (VR003), located in southern Africa’s arid Succulent Karoo biome. Distinctive innovations include the production of ostrich eggshell artefacts, long-distance transportation of marine molluscs and systematic use of heat shatter in stone tool production, none of which occur in coeval assemblages at sites in more humid, well-studied regions immediately to the south. The appearance of these novelties at VR003 corresponds with a period of reduced regional wind strength and enhanced summer rainfall, and all of them disappear with increasing winter rainfall dominance after 80 thousand years before the present, following which a pattern of technological similarity emerges at sites throughout the broader region. The results indicate complex and environmentally contingent processes of innovation and cultural transmission in southern Africa during the Middle Stone Age.

The deepening of Darwin's abominable mystery

May 2017


432 Reads

To the Editor — In 1879 in a private letter to Joseph Hooker, Charles Darwin grumbled 1 : “The rapid development as far as we can judge of all the higher plants within recent geological times is an abominable mystery.”Although this abominable mystery is often cited today, and sometimes declared solved, few realize that the mystery is deeper today than it was for Darwin.

Fig. 1 | Relative stabilities of amino acid pairs. The stability values of two amino acid residues (Res, labelled with standard three-letter abbreviations) are shown on the two axes (ϕ(Res)). a-l, The relative local contributions to stability are shown for glutamic acid and lysine in different site classes (a-d), for different population sizes for site class 1 and 3 (e-h) or various amino acid pairs in site class 3 (i-l). Points were sampled when the amino acid on the x axis was resident (green), when the amino acid on the y axis was resident (pink) or during transitions between the two (yellow). m-p, The distributions of local contributions to stability in the reference state are shown when the non-interacting null amino acid was present (ρ(ϕ α , ϕ β |Ø), pink), when the amino acid on the x axis was present as predicted using equation (7) ( ( , )
Fig. 2 | comparison of predicted and observed substitution rates. Predicted and observed rates are shown for all pairs of amino acids separated by a single base change for all sites in the different site classes (class 1, blue circles; class 2, pink squares; class 3, black triangles; class 4, orange diamonds). a-c, The predicted substitution rates calculated by integrating over ρ(ϕ α , ϕ β |α) for three different population sizes. d-f, Predicted substitution rates calculated using transition state theory (equation (6)), which assumes only near-neutral substitutions occur. g-i, Predicted substitution rates calculated using transition state theory with parameters estimated using equation (7). 
Fig. 3 | example of a trajectory before and after a substitution from glutamic acid to lysine. Stabilities on the x axis and y axis are shown as in Fig. 1. Local contribution to stability when either is resident is shown before (green) and after the substitution (pink). Values during the substitution are shown in yellow; beginning and end points are shown as black circles. The observed distributions over the simulations when glutamic acid or lysine is resident shown as the shaded region. Grey diagonal lines mark regions of near-neutral substitutions. 
Relative stabilities of amino acid pairs
The stability values of two amino acid residues (Res, labelled with standard three-letter abbreviations) are shown on the two axes (φ(Res)). a–l, The relative local contributions to stability are shown for glutamic acid and lysine in different site classes (a–d), for different population sizes for site class 1 and 3 (e–h) or various amino acid pairs in site class 3 (i–l). Points were sampled when the amino acid on the x axis was resident (green), when the amino acid on the y axis was resident (pink) or during transitions between the two (yellow). m–p, The distributions of local contributions to stability in the reference state are shown when the non-interacting null amino acid was present (ρ(φα, φβ|Ø), pink), when the amino acid on the x axis was present as predicted using equation (7) (ρ̃(φα,φβ|α)\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$\widetilde{\rho }({\varphi }_{\alpha },{\varphi }_{\beta }|\alpha )$$\end{document}, cyan), or as observed (ρ(φα, φβ|α), green). Grey diagonal lines mark the boundaries of regions of near-neutral substitutions. These and all other stability values are in kcal mol⁻¹.
Accuracy of site-specific stability and evolutionary Stokes shift predictions
a–c, Observed versus estimated values of the evolutionary Stokes shift (ζα|α) are shown for all four site rate classes (class 1, blue circles; class 2, pink squares; class 3, black triangles; class 4, orange diamonds), for three different population sizes. d–f, The linear relationship between the observed evolutionary Stokes shift and the variance in amino-acid-specific stability contributions in the absence of selection on the site (σα∣∅2\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$${\sigma }_{\alpha | \varnothing }^{2}$$\end{document}) are shown. The lines shown are theoretical predictions with γ = 1.26.
Sequence entropy of folding and the absolute rate of amino acid substitutions

December 2017


265 Reads

Adequate representations of protein evolution should consider how the acceptance of mutations depends on the sequence context in which they arise. However, epistatic interactions among sites in a protein result in hererogeneities in the substitution rate, both temporal and spatial, that are beyond the capabilities of current models. Here we use parallels between amino acid substitutions and chemical reaction kinetics to develop an improved theory of protein evolution. We constructed a mechanistic framework for modelling amino acid substitution rates that uses the formalisms of statistical mechanics, with principles of population genetics underlying the analysis. Theoretical analyses and computer simulations of proteins under purifying selection for thermodynamic stability show that substitution rates and the stabilization of resident amino acids (the 'evolutionary Stokes shift') can be predicted from biophysics and the effect of sequence entropy alone. Furthermore, we demonstrate that substitutions predominantly occur when epistatic interactions result in near neutrality; substitution rates are determined by how often epistasis results in such nearly neutral conditions. This theory provides a general framework for modelling protein sequence change under purifying selection, potentially explains patterns of convergence and mutation rates in real proteins that are incompatible with previous models, and provides a better null model for the detection of adaptive changes.

Figure 2 | Climate change impacts on local communities. a, The geographic location of each dataset (symbols explained in Supplementary Fig. 3) within central Europe; the colours behind the symbols represent the strength to which each community shifted towards warm (pink) or cold-dwelling species (blue) (that is, the correlation coefficient of the relationship between temperature preference and population trend). Significant effects are circled with a dark grey outline. b, The modelled average effect size (correlation coefficient ± 95% CI) of temperature preference on population trends in each realm, predicted at average start year, log number of sampling sites and log number of species across all datasets.  
Cross-realm assessment of climate change impacts on species’ abundance trends

February 2017


1,587 Reads

Climate change, land-use change, pollution and exploitation are among the main drivers of species’ population trends; however, their relative importance is much debated. We used a unique collection of over 1,000 local population time series in 22 communities across terrestrial, freshwater and marine realms within central Europe to compare the impacts of long-term temperature change and other environmental drivers from 1980 onwards. To disentangle different drivers, we related species’ population trends to species- and driver-specific attributes, such as temperature and habitat preference or pollution tolerance. We found a consistent impact of temperature change on the local abundances of terrestrial species. Populations of warm-dwelling species increased more than those of cold-dwelling species. In contrast, impacts of temperature change on aquatic species’ abundances were variable. Effects of temperature preference were more consistent in terrestrial communities than effects of habitat preference, suggesting that the impacts of temperature change have become widespread for recent changes in abundance within many terrestrial communities of central Europe.

Diversity in nature and academia

March 2021


34 Reads

We talk to Dr Swanne Gordon, a Jamaican-Canadian Assistant Professor of Biology at Washington University in St. Louis, United States, about her research on natural diversity and experience as a Black person in academia.

Academic ecosystems must evolve to support a sustainable postdoc workforce
The postdoctoral workforce comprises a growing proportion of the science, technology, engineering and mathematics (STEM) community, and plays a vital role in advancing science. Postdoc professional development, however, remains rooted in outdated realities. We propose enhancements to postdoc-centred policies and practices to better align this career stage with contemporary job markets and work life. By facilitating productivity, wellness and career advancement, the proposed changes will benefit all stakeholders in postdoc success—including research teams, institutions, professional societies and the scientific community as a whole. To catalyse reform, we outline recommendations for (1) skills-based training tailored to the current career landscape, and (2) supportive policies and tools outlined in postdoc handbooks. We also invite the ecology and evolution community to lead further progressive reform. The postdoctoral experience is in need of reform. Here the authors outline concrete steps that institutions, postdocs and mentors can take to improve the landscape.

Renegotiating identities in international academic careers

October 2022


134 Reads

Many academics move countries in pursuit of career opportunities. With every move, personal identities are renegotiated as people shift between belonging to majority and minority groups in different contexts. Institutes should consider people’s dynamic and intersectional identities in their diversity, equity and inclusion practices.

Fig. 2 | Architectures of three alternative networks in which research groups (nodes) interact in collecting and organizing trait data. Black nodes are individuals, groups or institutions conducting projects. Light-green nodes are those harmonizing data and developing protocols, where node size is proportional to available resources. Dark-green nodes are synthesis nodes that collect standardized trait data and knowledge. a, Groups are disconnected and decentralized, risking duplication of effort (often the status quo). b, Groups are linked to a centralized repository, potentially limiting innovation. c, The Open Traits Network, represented by orange lines. Nodes are linked within biological domains (for example, plants or marine) and include expertise from diverse disciplines (for example, systematics, palaeobiology, ecology and biomechanics) allowing for more efficient and specialized decisions about trait collection. Data synthesis across domains or disciplines is facilitated by joining nodes based on common workflows, theoretical frameworks and datasharing protocols that adhere to the principles of the Open Traits Network.
Open Science principles for accelerating trait-based science across the Tree of Life

February 2020


1,409 Reads

Synthesizing trait observations and knowledge across the Tree of Life remains a grand challenge for biodiversity science. Species traits are widely used in ecological and evolutionary science, and new data and methods have proliferated rapidly. Yet accessing and integrating disparate data sources remains a considerable challenge, slowing progress toward a global synthesis to integrate trait data across organisms. Trait science needs a vision for achieving global integration across all organisms. Here, we outline how the adoption of key Open Science principles—open data, open source and open methods—is transforming trait science, increasing transparency, democratizing access and accelerating global synthesis. To enhance widespread adoption of these principles, we introduce the Open Traits Network (OTN), a global, decentralized community welcoming all researchers and institutions pursuing the collaborative goal of standardizing and integrating trait data across organisms. We demonstrate how adherence to Open Science principles is key to the OTN community and outline five activities that can accelerate the synthesis of trait data across the Tree of Life, thereby facilitating rapid advances to address scientific inquiries and environmental issues. Lessons learned along the path to a global synthesis of trait data will provide a framework for addressing similarly complex data science and informatics challenges. A decentralized community is introduced that aims to standardize and integrate species trait data across organismal groups, based on principles of Open Science.

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