A continuous fish fossil record reveals key insights into adaptive radiation.

Adaptive radiations have been instrumental in generating a considerable amount of life's diversity. Ecological opportunity is thought to be a prerequisite for adaptive radiation1, but little is known about the relative importance of species' ecological versatility versus effects of arrival order in determining which lineage radiates2. Palaeontological records that could help answer this are scarce. In Lake Victoria, a large adaptive radiation of cichlid fishes evolved in an exceptionally short and recent time interval3. We present a rich continuous fossil record extracted from a series of long sediment cores along an onshore-offshore gradient. We reconstruct the temporal sequence of events in the assembly of the fish community from thousands of tooth fossils. We reveal arrival order, relative abundance and habitat occupation of all major fish lineages in the system. We show that all major taxa arrived simultaneously as soon as the modern lake began to form. There is no evidence of the radiating haplochromine cichlid lineage arriving before others, nor of their numerical dominance upon colonization; therefore, there is no support for ecological priority effects. However, although many taxa colonized the lake early and several became abundant, only cichlids persisted in the new deep and open-water habitats once these emerged. Because these habitat gradients are also known to have played a major role in speciation, our findings are consistent with the hypothesis that ecological versatility was key to adaptive radiation, not priority by arrival order nor initial numerical dominance.

Testing alternative hypotheses for the decline of cichlid fish in Lake Victoria using fish tooth time series from sediment cores.

Lake Victoria is well known for its high diversity of endemic fish species and provides livelihoods for millions of people. The lake garnered widespread attention during the twentieth century as major environmental and ecological changes modified the fish community with the extinction of approximately 40% of endemic cichlid species by the 1980s. Suggested causal factors include anthropogenic eutrophication, fishing, and introduced non-native species but their relative importance remains unresolved, partly because monitoring data started in the 1970s when changes were already underway. Here, for the first time, we reconstruct two time series, covering the last approximately 200 years, of fish assemblage using fish teeth preserved in lake sediments. Two sediment cores from the Mwanza Gulf of Lake Victoria, were subsampled continuously at an intra-decadal resolution, and teeth were identified to major taxa: Cyprinoidea, Haplochromini, Mochokidae and Oreochromini. None of the fossils could be confidently assigned to non-native Nile perch. Our data show significant decreases in haplochromine and oreochromine cichlid fish abundances that began long before the arrival of Nile perch. Cyprinoids, on the other hand, have generally been increasing. Our study is the first to reconstruct a time series of any fish assemblage in Lake Victoria extending deeper back in time than the past 50 years, helping shed light on the processes underlying Lake Victoria's biodiversity loss.

Temperature change as a driver of spatial patterns and long-term trends in chironomid (Insecta: Diptera) diversity.

Anthropogenic activities have led to a global decline in biodiversity, and monitoring studies indicate that both insect communities and wetland ecosystems are particularly affected. However, there is a need for long-term data (over centennial or millennial timescales) to better understand natural community dynamics and the processes that govern the observed trends. Chironomids (Insecta: Diptera: Chironomidae) are often the most abundant insects in lake ecosystems, sensitive to environmental change, and, because their larval exoskeleton head capsules preserve well in lake sediments, they provide a unique record of insect community dynamics through time. Here, we provide the results of a metadata analysis of chironomid diversity across a range of spatial and temporal scales. First, we analyse spatial trends in chironomid diversity using Northern Hemispheric data sets overall consisting of 837 lakes. Our results indicate that in most of our data sets, summer temperature (Tjul ) is strongly associated with spatial trends in modern-day chironomid diversity. We observe a strong increase in chironomid alpha diversity with increasing Tjul in regions with present-day Tjul between 2.5 and 14°C. In some areas with Tjul  > 14°C, chironomid diversity stabilizes or declines. Second, we demonstrate that the direction and amplitude of change in alpha diversity in a compilation of subfossil chironomid records spanning the last glacial-interglacial transition (~15,000-11,000 years ago) are similar to those observed in our modern data. A compilation of Holocene records shows that during phases when the amplitude of temperature change was small, site-specific factors had a greater influence on the chironomid fauna obscuring the chironomid diversity-temperature relationship. Our results imply expected overall chironomid diversity increases in colder regions such as the Arctic under sustained global warming, but with complex and not necessarily predictable responses for individual sites.

Trophic state changes can affect the importance of methane-derived carbon in aquatic food webs.

Methane-derived carbon, incorporated by methane-oxidizing bacteria, has been identified as a significant source of carbon in food webs of many lakes. By measuring the stable carbon isotopic composition (δ13C values) of particulate organic matter, Chironomidae and Daphnia spp. and their resting eggs (ephippia), we show that methane-derived carbon presently plays a relevant role in the food web of hypertrophic Lake De Waay, The Netherlands. Sediment geochemistry, diatom analyses and δ13C measurements of chironomid and Daphnia remains in the lake sediments indicate that oligotrophication and re-eutrophication of the lake during the twentieth century had a strong impact on in-lake oxygen availability. This, in turn, influenced the relevance of methane-derived carbon in the diet of aquatic invertebrates. Our results show that, contrary to expectations, methane-derived relative to photosynthetically produced organic carbon became more relevant for at least some invertebrates during periods with higher nutrient availability for algal growth, indicating a proportionally higher use of methane-derived carbon in the lake's food web during peak eutrophication phases. Contributions of methane-derived carbon to the diet of the investigated invertebrates are estimated to have ranged from 0-11% during the phase with the lowest nutrient availability to 13-20% during the peak eutrophication phase.

Anthropogenic Eutrophication Drives Major Food Web Changes in Mwanza Gulf, Lake Victoria.

Discerning ecosystem change and food web dynamics underlying anthropogenic eutrophication and the introduction of non-native species is necessary for ensuring the long-term sustainability of fisheries and lake biodiversity. Previous studies of eutrophication in Lake Victoria, eastern Africa, have focused on the loss of endemic fish biodiversity over the past several decades, but changes in the plankton communities over this same time remain unclear. To fill this gap, we examined sediment cores from a eutrophic embayment, Mwanza Gulf, to determine the timing and magnitude of changes in the phytoplankton and zooplankton assemblages over the past century. Biogeochemical proxies indicate nutrient enrichment began around ~ 1920 CE and led to rapid increases in primary production, and our analysis of photosynthetic pigments revealed three zones: pre-eutrophication (prior to 1920 CE), onset of eutrophication with increases in all pigments (1920-1990 CE), and sustained eutrophication with cyanobacterial dominance (1990 CE-present). Cladoceran remains indicate an abrupt decline in biomass in ~ 1960 CE, in response to the cumulative effects of eutrophication and lake-level rise, preceding the collapse of haplochromine cichlids in the 1980s. Alona and Chydorus, typically benthic littoral taxa, have remained at relatively low abundances since the 1960s, whereas the abundance of Bosmina, typically a planktonic taxon, increased in the 1990s concurrently with the biomass recovery of haplochromine cichlid fishes. Overall, our results demonstrate substantial changes over the past century in the biomass structure and taxonomic composition of Mwanza Gulf phytoplankton and zooplankton communities, providing a historical food web perspective that can help understand the recent changes and inform future resource management decisions in the Lake Victoria ecosystem. Supplementary Information: The online version contains supplementary material available at 10.1007/s10021-024-00908-x.

Chironomid dataset from Mutterbergersee: A late-Holocene paleotemperature proxy record for the Central Eastern Alps, Austria.

We present a dataset of subfossil chironomid assemblages in the MUT-10 sediment core obtained from the high alpine lake Mutterbergersee in the Austrian Alps in 2010. The data were presented in the research article by Ilyashuk et al. (2019) "The Little Ice Age signature in a 700-year high-resolution chironomid record of summer temperatures in the Central Eastern Alps". In addition to the results of the chironomid analysis of 100 sediment samples presented in this article, we also include chironomid assemblage data from an additional 48 sediment samples that complement this dataset. The data includes raw chironomid counts, percent abundance of chironomid taxa, as well as mean July air temperature estimates derived from the chironomid record based on a chironomid-temperature transfer function. We also provide information on age-dating of the sedimentary sequence. Given the high temporal resolution and the robust age-depth model of the record, the chironomid-based reconstruction of temperature since AD 1300 provides a detailed documentation of climate change in the Eastern Alps from the Little Ice Age onwards and can be used for comparison with other independent proxy-based climate reconstructions. In addition to the data, we detail the sample processing for subfossil chironomid analysis and provide a detailed description of the reconstruction technique used for producing chironomid-based quantitative temperature inferences.

An integrative paleolimnological approach for studying evolutionary processes.

The field of paleolimnology has made tremendous progress in reconstructing past biotic and abiotic environmental conditions of aquatic ecosystems based on sediment records. This, together with the rapid development of molecular technologies, provides new opportunities for studying evolutionary processes affecting lacustrine communities over multicentennial to millennial timescales. From an evolutionary perspective, such analyses provide important insights into the chronology of past environmental conditions, the dynamics of phenotypic evolution, and species diversification. Here, we review recent advances in paleolimnological, paleogenetic, and molecular approaches and highlight how their integrative use can help us better understand the ecological and evolutionary responses of species and communities to environmental change.

High resolution ancient sedimentary DNA shows that alpine plant diversity is associated with human land use and climate change.

The European Alps are highly rich in species, but their future may be threatened by ongoing changes in human land use and climate. Here, we reconstructed vegetation, temperature, human impact and livestock over the past ~12,000 years from Lake Sulsseewli, based on sedimentary ancient plant and mammal DNA, pollen, spores, chironomids, and microcharcoal. We assembled a highly-complete local DNA reference library (PhyloAlps, 3923 plant taxa), and used this to obtain an exceptionally rich sedaDNA record of 366 plant taxa. Vegetation mainly responded to climate during the early Holocene, while human activity had an additional influence on vegetation from 6 ka onwards. Land-use shifted from episodic grazing during the Neolithic and Bronze Age to agropastoralism in the Middle Ages. Associated human deforestation allowed the coexistence of plant species typically found at different elevational belts, leading to levels of plant richness that characterise the current high diversity of this region. Our findings indicate a positive association between low intensity agropastoral activities and precipitation with the maintenance of the unique subalpine and alpine plant diversity of the European Alps.

Holocene temperature variations at a high-altitude site in the Eastern Alps: a chironomid record from Schwarzsee ob Sölden, Austria.

Few well-dated, quantitative Holocene temperature reconstructions exist from high-altitude sites in the Central Eastern Alps. Here, we present a chironomid-based quantitative reconstruction of mean July air temperatures (T(July)) throughout the Holocene for a remote high-mountain lake, Schwarzsee ob Sölden, situated above the treeline at 2796 m a.s.l. in the Austrian Alps. Applying a chironomid-temperature inference model developed from lakes of the Alpine region to a high-resolution chironomid record from the lake provides evidence for early Holocene (ca 10000-8600 cal yr BP) T(July) of up to 8.5 °C, i.e. >4 °C above the modern (1977-2006) mean July temperature. The reconstruction reveals the so-called '8.2-ka cold event' centered at ca 8250-8000 cal yr BP with temperatures ca 3 °C below the early-Holocene thermal maximum. Rather warm (ca 6 °C) and productive conditions prevailed during ca 7900-4500 cal yr BP. The chironomid record suggests a climate transition between ca 5200 and 4500 cal yr BP to cooler T(July). A distinct cooling trend is evident from ca 4500 until ca 2500 cal yr BP. Thereafter, the study site experienced its coldest conditions (around 4 °C or less) throughout the rest of the Holocene, with the exception of the warming trend during the late 20th century. Beside other factors, the Northern Hemisphere summer insolation seems to be the major driving force for the long-term trends in T(July) at high altitudes in the Eastern Alps. Due to the extreme location of the lake and the limited temperature range represented by the applied calibration data set, the chironomid-based temperature reconstruction fails to track phases of the late-Holocene climatic history with T(July) cooler than 4 °C. Further chironomid-based palaeoclimate model and down-core studies are required to address this problem, provide more realistic T(July) estimates from undisturbed high-altitude lakes in the Alps, and extract a reliable regional temperature signal.

Holocene global mean surface temperature, a multi-method reconstruction approach.

An extensive new multi-proxy database of paleo-temperature time series (Temperature 12k) enables a more robust analysis of global mean surface temperature (GMST) and associated uncertainties than was previously available. We applied five different statistical methods to reconstruct the GMST of the past 12,000 years (Holocene). Each method used different approaches to averaging the globally distributed time series and to characterizing various sources of uncertainty, including proxy temperature, chronology and methodological choices. The results were aggregated to generate a multi-method ensemble of plausible GMST and latitudinal-zone temperature reconstructions with a realistic range of uncertainties. The warmest 200-year-long interval took place around 6500 years ago when GMST was 0.7 °C (0.3, 1.8) warmer than the 19th Century (median, 5th, 95th percentiles). Following the Holocene global thermal maximum, GMST cooled at an average rate -0.08 °C per 1000 years (-0.24, -0.05). The multi-method ensembles and the code used to generate them highlight the utility of the Temperature 12k database, and they are now available for future use by studies aimed at understanding Holocene evolution of the Earth system.

Publisher Correction: A global database of Holocene paleotemperature records.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

Author Correction: A global database of Holocene paleotemperature records.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

A global database of Holocene paleotemperature records.

A comprehensive database of paleoclimate records is needed to place recent warming into the longer-term context of natural climate variability. We present a global compilation of quality-controlled, published, temperature-sensitive proxy records extending back 12,000 years through the Holocene. Data were compiled from 679 sites where time series cover at least 4000 years, are resolved at sub-millennial scale (median spacing of 400 years or finer) and have at least one age control point every 3000 years, with cut-off values slackened in data-sparse regions. The data derive from lake sediment (51%), marine sediment (31%), peat (11%), glacier ice (3%), and other natural archives. The database contains 1319 records, including 157 from the Southern Hemisphere. The multi-proxy database comprises paleotemperature time series based on ecological assemblages, as well as biophysical and geochemical indicators that reflect mean annual or seasonal temperatures, as encoded in the database. This database can be used to reconstruct the spatiotemporal evolution of Holocene temperature at global to regional scales, and is publicly available in Linked Paleo Data (LiPD) format.

Publisher Correction: A global database of Holocene paleotemperature records.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

The Little Ice Age signature in a 700-year high-resolution chironomid record of summer temperatures in the Central Eastern Alps.

Despite the fact that the Little Ice Age (LIA) is well documented for the European Alps, substantial uncertainties concerning the regional spatio-temporal patterns of temperature changes associated with the LIA still exist, especially for their eastern sector. Here we present a high-resolution (4-10 years) 700-year long mean July air temperature reconstruction based on subfossil chironomid assemblages from a remote lake in the Austrian Eastern Alps to gain further insights into the LIA climatic deterioration in the region. The record provides evidence for a prolonged period of predominantly cooler conditions during AD 1530-1920, broadly equivalent to the climatically defined LIA in Europe. The main LIA phase appears to have consisted of two cold time intervals divided by slightly warmer episodes in the second half of the 1600s. The most severe cooling occurred during the eighteenth century. The LIA temperature minimum about 1.5 °C below the long-term mean recorded in the mid-1780 s coincides with the strongest volcanic signal found in the Greenland ice cores over the past 700 years and may be, at least in part, a manifestation of cooling that followed the long-lasting AD 1783-1784 Laki eruption. A continuous warming trend is evident since ca AD 1890 (1.1 °C in 120 years). The chironomid-inferred temperatures show a clear correlation with the instrumental data and reveal a close agreement with paleotemperature evidence from regional high-elevation tree-ring chronologies. A considerable amount of the variability in the temperature record may be linked to changes in the North Atlantic Oscillation.

Interpretation and application of carbon isotope ratios in freshwater diatom silica.

Carbon incorporated into diatom frustule walls is protected from degradation enabling analysis for carbon isotope composition (δ13Cdiatom). This presents potential for tracing carbon cycles via a single photosynthetic host with well-constrained ecophysiology. Improved understanding of environmental processes controlling carbon delivery and assimilation is essential to interpret changes in freshwater δ13Cdiatom. Here relationships between water chemistry and δ13Cdiatom from contemporary regional data sets are investigated. Modern diatom and water samples were collected from river catchments within England and lake sediments from across Europe. The data suggest dissolved, biogenically produced carbon supplied proportionately to catchment productivity was critical in the rivers and soft water lakes. However, dissolved carbon from calcareous geology overwhelmed the carbon signature in hard water catchments. Both results demonstrate carbon source characteristics were the most important control on δ13Cdiatom, with a greater impact than productivity. Application of these principles was made to a sediment record from Lake Tanganyika. δ13Cdiatom co-varied with δ13Cbulk through the last glacial and Holocene. This suggests carbon supply was again dominant and exceeded authigenic demand. This first systematic evaluation of contemporary δ13Cdiatom controls demonstrates that diatoms have the potential to supply a record of carbon cycling through lake catchments from sediment records over millennial timescales.

Land Use Affects Carbon Sources to the Pelagic Food Web in a Small Boreal Lake.

Small humic forest lakes often have high contributions of methane-derived carbon in their food webs but little is known about the temporal stability of this carbon pathway and how it responds to environmental changes on longer time scales. We reconstructed past variations in the contribution of methanogenic carbon in the pelagic food web of a small boreal lake in Finland by analyzing the stable carbon isotopic composition (δ13C values) of chitinous fossils of planktivorous invertebrates in sediments from the lake. The δ13C values of zooplankton remains show several marked shifts (approx. 10 ‰), consistent with changes in the proportional contribution of carbon from methane-oxidizing bacteria in zooplankton diets. The results indicate that the lake only recently (1950s) obtained its present state with a high contribution of methanogenic carbon to the pelagic food web. A comparison with historical and palaeobotanical evidence indicates that this most recent shift coincided with agricultural land-use changes and forestation of the lake catchment and implies that earlier shifts may also have been related to changes in forest and land use. Our study demonstrates the sensitivity of the carbon cycle in small forest lakes to external forcing and that the effects of past changes in local land use on lacustrine carbon cycling have to be taken into account when defining environmental and ecological reference conditions in boreal headwater lakes.

Validation of climate model-inferred regional temperature change for late-glacial Europe.

Comparisons of climate model hindcasts with independent proxy data are essential for assessing model performance in non-analogue situations. However, standardized palaeoclimate data sets for assessing the spatial pattern of past climatic change across continents are lacking for some of the most dynamic episodes of Earth's recent past. Here we present a new chironomid-based palaeotemperature dataset designed to assess climate model hindcasts of regional summer temperature change in Europe during the late-glacial and early Holocene. Latitudinal and longitudinal patterns of inferred temperature change are in excellent agreement with simulations by the ECHAM-4 model, implying that atmospheric general circulation models like ECHAM-4 can successfully predict regionally diverging temperature trends in Europe, even when conditions differ significantly from present. However, ECHAM-4 infers larger amplitudes of change and higher temperatures during warm phases than our palaeotemperature estimates, suggesting that this and similar models may overestimate past and potentially also future summer temperature changes in Europe.

The chironomid-temperature relationship: expression in nature and palaeoenvironmental implications.

Fossils of chironomid larvae (non-biting midges) preserved in lake sediments are well-established palaeotemperature indicators which, with the aid of numerical chironomid-based inference models (transfer functions), can provide quantitative estimates of past temperature change. This approach to temperature reconstruction relies on the strong relationship between air and lake surface water temperature and the distribution of individual chironomid taxa (species, species groups, genera) that has been observed in different climate regions (arctic, subarctic, temperate and tropical) in both the Northern and Southern hemisphere. A major complicating factor for the use of chironomids for palaeoclimate reconstruction which increases the uncertainty associated with chironomid-based temperature estimates is that the exact nature of the mechanism responsible for the strong relationship between temperature and chironomid assemblages in lakes remains uncertain. While a number of authors have provided state of the art overviews of fossil chironomid palaeoecology and the use of chironomids for temperature reconstruction, few have focused on examining the ecological basis for this approach. Here, we review the nature of the relationship between chironomids and temperature based on the available ecological evidence. After discussing many of the surveys describing the distribution of chironomid taxa in lake surface sediments in relation to temperature, we also examine evidence from laboratory and field studies exploring the effects of temperature on chironomid physiology, life cycles and behaviour. We show that, even though a direct influence of water temperature on chironomid development, growth and survival is well described, chironomid palaeoclimatology is presently faced with the paradoxical situation that the relationship between chironomid distribution and temperature seems strongest in relatively deep, thermally stratified lakes in temperate and subarctic regions in which the benthic chironomid fauna lives largely decoupled from the direct influence of air and surface water temperature. This finding suggests that indirect effects of temperature on physical and chemical characteristics of lakes play an important role in determining the distribution of lake-living chironomid larvae. However, we also demonstrate that no single indirect mechanism has been identified that can explain the strong relationship between chironomid distribution and temperature in all regions and datasets presently available. This observation contrasts with the previously published hypothesis that climatic effects on lake nutrient status and productivity may be largely responsible for the apparent correlation between chironomid assemblage distribution and temperature. We conclude our review by summarizing the implications of our findings for chironomid-based palaeoclimatology and by pointing towards further avenues of research necessary to improve our mechanistic understanding of the chironomid-temperature relationship.