Reconstructing long‐term human impacts on plant communities: an ecological approach based on lake sediment DNA

Paleoenvironmental studies are essential to understand biodiversity changes over long timescales and to assess the relative importance of anthropogenic and environmental factors. Sedimentary ancient DNA (sedaDNA) is an emerging tool in the field of paleoecology and has proven to be a complementary approach to the use of pollen and macroremains for investigating past community changes. SedaDNA‐based reconstructions of ancient environments often rely on indicator taxa or expert knowledge, but quantitative ecological analyses might provide more objective information. Here, we analysed sedaDNA to investigate plant community trajectories in the catchment of a high‐elevation lake in the Alps over the last 6400 years. We combined data on past and present plant species assemblages along with sedimentological and geochemical records to assess the relative impact of human activities through pastoralism, and abiotic factors (temperature and soil evolution). Over the last 6400 years, we identified significant variation in plant communities, mostly related to soil evolution and pastoral activities. An abrupt vegetational change corresponding to the establishment of an agropastoral landscape was detected during the Late Holocene, approximately 4500 years ago, with the replacement of mountain forests and tall‐herb communities by heathlands and grazed lands. Our results highlight the importance of anthropogenic activities in mountain areas for the long‐term evolution of local plant assemblages. SedaDNA data, associated with other paleoenvironmental proxies and present plant assemblages, appear to be a relevant tool for reconstruction of plant cover history. Their integration, in conjunction with classical tools, offers interesting perspectives for a better understanding of long‐term ecosystem dynamics under the influence of human‐induced and environmental drivers.     

Arctic shrub colonization lagged peak postglacial warmth: Molecular evidence in lake sediment from Arctic Canada

Arctic shrubification is an observable consequence of climate change, already resulting in ecological shifts and global‐scale climate feedbacks including changes in land surface albedo and enhanced evapotranspiration. However, the rate at which shrubs can colonize previously glaciated terrain in a warming world is largely unknown. Reconstructions of past vegetation dynamics in conjunction with climate records can provide critical insights into shrubification rates and controls on plant migration, but paleoenvironmental reconstructions based on pollen may be biased by the influx of exotic pollen to tundra settings. Here, we reconstruct past plant communities using sedimentary ancient DNA (sedaDNA), which has a more local source area than pollen. We additionally reconstruct past temperature variability using bacterial cell membrane lipids (branched glycerol dialkyl glycerol tetraethers) and an aquatic productivity indicator (biogenic silica) to evaluate the relative timing of postglacial ecological and climate changes at a lake on southern Baffin Island, Arctic Canada. The sedaDNA record tightly constrains the colonization of dwarf birch (Betula, a thermophilous shrub) to 5.9 ± 0.1 ka, ~3 ka after local deglaciation as determined by cosmogenic ¹⁰Be moraine dating and >2 ka later than Betula pollen is recorded in nearby lake sediment. We then assess the paleovegetation history within the context of summer temperature and find that paleotemperatures were highest prior to 6.3 ka, followed by cooling in the centuries preceding Betula establishment. Together, these molecular proxies reveal that Betula colonization lagged peak summer temperatures, suggesting that inefficient dispersal, rather than climate, may have limited Arctic shrub migration in this region. In addition, these data suggest that pollen‐based climate reconstructions from high latitudes, which rely heavily on the presence and abundance of pollen from thermophilous taxa like Betula, can be compromised by both exotic pollen fluxes and vegetation migration lags.     

A comparison of sedimentary DNA and pollen from lake sediments in recording vegetation composition at the Siberian treeline

Reliable information on past and present vegetation is important to project future changes, especially for rapidly transitioning areas such as the boreal treeline. To study past vegetation, pollen analysis is common, while current vegetation is usually assessed by field surveys. Application of detailed sedimentary DNA (sedDNA) records has the potential to enhance our understanding of vegetation changes, but studies systematically investigating the power of this proxy are rare to date. This study compares sedDNA metabarcoding and pollen records from surface sediments of 31 lakes along a north–south gradient of increasing forest cover in northern Siberia (Taymyr peninsula) with data from field surveys in the surroundings of the lakes. sedDNA metabarcoding recorded 114 plant taxa, about half of them to species level, while pollen analyses identified 43 taxa, both exceeding the 31 taxa found by vegetation field surveys. Increasing Larix percentages from north to south were consistently recorded by all three methods and principal component analyses based on percentage data of vegetation surveys and DNA sequences separated tundra from forested sites. Comparisons of the ordinations using procrustes and protest analyses show a significant fit among all compared pairs of records. Despite similarities of sedDNA and pollen records, certain idiosyncrasies, such as high percentages of Alnus and Betula in all pollen and high percentages of Salix in all sedDNA spectra, are observable. Our results from the tundra to single‐tree tundra transition zone show that sedDNA analyses perform better than pollen in recording site‐specific richness (i.e., presence/absence of taxa in the vicinity of the lake) and perform as well as pollen in tracing vegetation composition.     

Molecular‐ and pollen‐based vegetation analysis in lake sediments from central Scandinavia

Plant and animal biodiversity can be studied by obtaining DNA directly from the environment. This new approach in combination with the use of generic barcoding primers (metabarcoding) has been suggested as complementary or alternative to traditional biodiversity monitoring in ancient soil sediments. However, the extent to which metabarcoding truly reflects plant composition remains unclear, as does its power to identify species with no pollen or macrofossil evidence. Here, we compared pollen‐based and metabarcoding approaches to explore the Holocene plant composition around two lakes in central Scandinavia. At one site, we also compared barcoding results with those obtained in earlier studies with species‐specific primers. The pollen analyses revealed a larger number of taxa (46), of which the majority (78%) was not identified by metabarcoding. The metabarcoding identified 14 taxa (MTUs), but allowed identification to a lower taxonomical level. The combined analyses identified 52 taxa. The barcoding primers may favour amplification of certain taxa, as they did not detect taxa previously identified with species‐specific primers. Taphonomy and selectiveness of the primers are likely the major factors influencing these results. We conclude that metabarcoding from lake sediments provides a complementary, but not an alternative, tool to pollen analysis for investigating past flora. In the absence of other fossil evidence, metabarcoding gives a local and important signal from the vegetation, but the resulting assemblages show limited capacity to detect all taxa, regardless of their abundance around the lake. We suggest that metabarcoding is followed by pollen analysis and the use of species‐specific primers to provide the most comprehensive signal from the environment.     

Pollen–vegetation relationships along steep climatic gradients in western Amazonia

Question: How accurately do Amazonian montane forest pollen spectra reflect the vegetation? Can compositional changes observed in the vegetation along environmental gradients be identified in the pollen spectra? How well do herbarium collection data and bioclimatic envelopes represent abundance changes along elevation gradients? Location: Amazonian montane forests, Peru. Methods: Moss polsters collected along five altitudinal transects spanning over 3000 m a.s.l. were used to characterize pollen spectra. Vegetation plot data from a network of 15 1‐ha permanent plots were used to correlate pollen spectra with present‐day vegetation. Probability density functions (PDFs) fitted to pollen and plot data allowed comparisons using Spearman correlation coefficients. Ordination analyses were used to summarize changes in pollen spectra. Correlations between pollen‐based PDFs and previously‐published herbarium collection PDFs were also evaluated. Results: Pollen spectra closely reflected changes in species composition along elevation gradients. A mid‐elevation shift in pollen spectra was identified using ordination analyses. Pollen spectra from the driest forest in our data set were statistically different from those of wet forests. Pollen abundance PDFs along the altitudinal gradient were significantly correlated (P<0.01) with PDFs fitted to plot abundance, basal area and herbarium collection data for ten out of 11 taxa analysed. Conclusions: Pollen spectra closely reflected the vegetation composition of Amazonian montane forests. The differentiation of pollen spectra from dry localities showed the potential of genus‐level pollen data to reflect precipitation gradients. Pollen spectra also reflected mid‐elevation compositional changes well along the lower elevation limit of ground cloud formation. Despite collection biases, herbarium‐based bioclimatic envelope PDFs also represented well forest compositional changes along elevation gradients.     

Next‐generation QTL mapping: crowdsourcing SNPs,without pedigrees

For many molecular ecologists, the mantra and mission of the field of ecological genomics could be encapsulated by the phrase ‘to find the genes that matter’ (Mitchell‐Olds 2001 ; Rockman 2012 ). This phrase of course refers to the early hope and current increasing success in the search for genes whose variation underlies phenotypic variation and fitness in natural populations. In the years since the modern incarnation of the field of ecological genomics, many would agree that the low‐hanging fruit has, at least in principle, been plucked: we now have several elegant examples of genes whose variation influences key adaptive traits in natural populations, and these examples have revealed important insights into the architecture of adaptive variation (Hoekstra et al. 2006 ; Shapiro et al. 2009 ; Chan et al. 2010 ). But how well will these early examples, often involving single genes of large effect on discrete or near‐discrete phenotypes, represent the dynamics of adaptive change for the totality of phenotypes in nature? Will traits exhibiting continuous rather than discrete variation in natural populations have as simple a genetic basis as these early examples suggest (Prasad et al. 2012 ; Rockman 2012 )? Two papers in this issue (Robinson et al. 2013 ; Santure et al. 2013 ) not only suggest answers to these questions but also provide useful extensions of statistical approaches for ecological geneticists to study the genetics of continuous variation in nature. Together these papers, by the same research groups studying evolution in a natural population of Great Tits (Parus major), provide a glimpse of what we should expect as the field begins to dissect the genetic basis of what is arguably the most common type of variation in nature, and how genome‐wide surveys of variation can be applied to natural populations without pedigrees.     

Modern pollen–vegetation relationships along transects on the Whangapoua Estuary, Great Barrier Island, northern New Zealand

Aims To quantify pollen–vegetation relationships from saline to freshwater in an estuarine gradient from surface samples of the modern pollen rain, to allow more accurate interpretations of the stratigraphic palynological record. Location Whangapoua Estuary, Great Barrier Island, northern New Zealand. Methods Six transects were laid out along a vegetation sequence running from estuarine mud to freshwater swamp. Along these transect lines, 108 plots were sampled for vegetation and surface sediments from wet sand, mud, plant litter or moss (sand and mud sites are inundated by most tides, other sites less frequently). All sediment samples were analysed for pollen. The relationships between plant species frequency and pollen representation were examined at a community scale using twinspan and ordination analyses, and for individual species using fidelity and dispersibility indices, regression and box‐plot analyses. Results The quantitative relationships between source taxon vegetation frequency and its pollen representation varied between species due to differential pollen production and dispersal. twinspan of the surface pollen samples suggests five vegetation types: (A) mangrove (Avicennia marina); (C) Leptocarpus similis salt meadow; (D) Baumea sedges; (E) Leptospermum shrubland; and (F) Typha/Cordyline swamp forest. The (B) Juncus kraussii community is not represented palynologically owing to the destruction of its delicate pollen grains during acetolysis of samples. Detrended correspondence analysis places these communities on an estuarine‐to‐freshwater gradient. However, pollen assemblages at the seaward end of the salinity gradient are less clearly representative of the associated vegetation than those at the landward end, probably because the open vegetation at the former allows the influx of wind‐ and water‐dispersed pollen from surrounding vegetation. Main conclusions The vegetation pattern (zonation) at Whangapoua is reflected in the pollen rain. When the long‐distance and over‐represented pollen types are excluded, five out of six of the broad vegetation communities can be identified by their pollen spectra. Species with high fidelity and low‐to‐moderate dispersibility indices can be used to identify the vegetation types in the sedimentary sequences. The more open vegetation types at the ‘marine end’ of the sequence tend to be ‘overwhelmed’ by regional pollen, but the nature of the sediments and the presence of discriminatory species (e.g. A. marina, Plagianthus divaricatus, Cordyline australis), even in small amounts, will allow correct identification of the local vegetation represented in sedimentary palynological sequences. A box‐plot analysis indicates that the pollen and spore types A. marina (mangroves), Sarcocornia quinqueflora (salt meadow), P. divaricatus (sedges), Gleichenia (shrubland) and C. australis (swamp forest) are highly discriminatory in relation to vegetation type. These discriminatory palynomorphs help with the interpretation of stratigraphic pollen studies. However, salt marsh vegetation communities in the sediments must be interpreted with caution as the marine sediments are easily affected by erosion, bioturbation and tidal inundation effects.     

Paleo‐metagenomics of North American fossil packrat middens: Past biodiversity revealed by ancient DNA

Fossil rodent middens are powerful tools in paleoecology. In arid parts of western North America, packrat (Neotoma spp.) middens preserve plant and animal remains for tens of thousands of years. Midden contents are so well preserved that fragments of endogenous ancient DNA (aDNA) can be extracted and analyzed across millennia. Here, we explore the use of shotgun metagenomics to study the aDNA obtained from packrat middens up to 32,000 C¹⁴ years old. Eleven Illumina HiSeq 2500 libraries were successfully sequenced, and between 0.11% and 6.7% of reads were classified using Centrifuge against the NCBI “nt” database. Eukaryotic taxa identified belonged primarily to vascular plants with smaller proportions mapping to ascomycete fungi, arthropods, chordates, and nematodes. Plant taxonomic diversity in the middens is shown to change through time and tracks changes in assemblages determined by morphological examination of the plant remains. Amplicon sequencing of ITS2 and rbcL provided minimal data for some middens, but failed at amplifying the highly fragmented DNA present in others. With repeated sampling and deep sequencing, analysis of packrat midden aDNA from well‐preserved midden material can provide highly detailed characterizations of past communities of plants, animals, bacteria, and fungi present as trace DNA fossils. The prospects for gaining more paleoecological insights from aDNA for rodent middens will continue to improve with optimization of laboratory methods, decreasing sequencing costs, and increasing computational power.     

Pathogen pollution and the emergence of a deadly amphibian pathogen

Imagine a single pathogen that is responsible for mass mortality of over a third of an entire vertebrate class. For example, if a single pathogen were causing the death, decline and extinction of 30% of mammal species (including humans), the entire world would be paying attention. This is what has been happening to the world's amphibians – the frogs, toads and salamanders that are affected by the chytrid fungal pathogen, Batrachochytrium dendrobatidis (referred to as Bd), which are consequently declining at an alarming rate. It has aptly been described as the worst pathogen in history in terms of its effects on biodiversity (Kilpatrick et al. 2010). The pathogen was only formally described about 13 years ago (Longcore et al. 1999), and scientists are still in the process of determining where it came from and investigating the question: why now? Healthy debate has ensued as to whether Bd is a globally endemic organism that only recently started causing high mortality due to shifting host responses and/or environmental change (e.g. Pounds et al. 2006) or whether a virulent strain of the pathogen has rapidly disseminated around the world in recent decades, affecting new regions with a vengeance (e.g. Morehouse et al. 2003; Weldon et al. 2004; Lips et al. 2008). We are finally beginning to shed more light on this question, due to significant discoveries that have emerged as a result of intensive DNA‐sequencing methods comparing Bd isolates from different amphibian species across the globe. Evidence is mounting that there is indeed a global panzootic lineage of Bd (BdGPL) in addition to what appear to be more localized endemic strains (Fisher et al. 2009; James et al. 2009; Farrer et al. 2011). Additionally, BdGPL appears to be a hypervirulent strain that has resulted from the hybridization of different Bd strains that came into contact in recent decades, and is now potentially replacing the less‐virulent endemic strains of the pathogen (Farrer et al. 2011). In a new study published in this issue of Molecular Ecology, Schloegel et al. (2012) identify an additional unique Bd lineage that is endemic to the Atlantic Brazilian rainforests (Bd‐Brazil) and provide striking evidence that the Bd‐Brazil lineage has sexually recombined with the BdGPL lineage in an area where the two lineages likely came into contact as a result of classic anthropogenically mediated ‘pathogen pollution’(see below). Fungal pathogens, including Bd, have the propensity to form recombinant lineages when allopatric populations that have not yet formed genetic reproductive barriers are provided with opportunities to intermingle, and virulent strains may be selected for because they tend to be highly transmissible (Fisher et al. 2012). As Schloegel et al. (2012) point out, the demonstrated ability for Bd to undergo meiosis may also mean that it has the capacity to form a resistant spore stage (as yet undiscovered), based on extrapolation from other sexually reproducing chytrids that all have spore stages.     

Pollen‐based biomes for Beringia 18,000, 6000 and 0 14C yr bp†

The objective biomization method developed by Prentice et al. (1996) for Europe was extended using modern pollen samples from Beringia and then applied to fossil pollen data to reconstruct palaeovegetation patterns at 6000 and 18,000 ¹⁴C yr bp . The predicted modern distribution of tundra, taiga and cool conifer forests in Alaska and north‐western Canada generally corresponds well to actual vegetation patterns, although sites in regions characterized today by a mosaic of forest and tundra vegetation tend to be preferentially assigned to tundra. Siberian larch forests are delimited less well, probably due to the extreme under‐representation of Larix in pollen spectra. The biome distribution across Beringia at 6000 ¹⁴C yr bp was broadly similar to today, with little change in the northern forest limit, except for a possible northward advance in the Mackenzie delta region. The western forest limit in Alaska was probably east of its modern position. At 18,000 ¹⁴C yr bp the whole of Beringia was covered by tundra. However, the importance of the various plant functional types varied from site to site, supporting the idea that the vegetation cover was a mosaic of different tundra types.     

Origins of endemic island tortoises in the western Indian Ocean: a critique of the human‐translocation hypothesis

How do organisms arrive on isolated islands, and how do insular evolutionary radiations arise? In a recent paper, Wilmé et al. ( 2016a ) argue that early Austronesians that colonized Madagascar from Southeast Asia translocated giant tortoises to islands in the western Indian Ocean. In the Mascarene Islands, moreover, the human‐translocated tortoises then evolved and radiated in an endemic genus (Cylindraspis). Their proposal ignores the broad, established understanding of the processes leading to the formation of native island biotas, including endemic radiations. We find Wilmé et al.'s suggestion poorly conceived, using a flawed methodology and missing two critical pieces of information: the timing and the specifics of proposed translocations. In response, we here summarize the arguments that could be used to defend the natural origin not only of Indian Ocean giant tortoises but also of scores of insular endemic radiations world‐wide. Reinforcing a generalist's objection, the phylogenetic and ecological data on giant tortoises, and current knowledge of environmental and palaeogeographical history of the Indian Ocean, make Wilmé et al.'s argument even more unlikely.     

Multiscale climate change impacts on plant diversity in the Atacama Desert

Comprehending ecological dynamics requires not only knowledge of modern communities but also detailed reconstructions of ecosystem history. Ancient DNA (aDNA) metabarcoding allows biodiversity responses to major climatic change to be explored at different spatial and temporal scales. We extracted aDNA preserved in fossil rodent middens to reconstruct late Quaternary vegetation dynamics in the hyperarid Atacama Desert. By comparing our paleo‐informed millennial record with contemporary observations of interannual variations in diversity, we show local plant communities behave differentially at different timescales. In the interannual (years to decades) time frame, only annual herbaceous expand and contract their distributional ranges (emerging from persistent seed banks) in response to precipitation, whereas perennials distribution appears to be extraordinarily resilient. In contrast, at longer timescales (thousands of years) many perennial species were displaced up to 1,000 m downslope during pluvial events. Given ongoing and future natural and anthropogenically induced climate change, our results not only provide baselines for vegetation in the Atacama Desert, but also help to inform how these and other high mountain plant communities may respond to fluctuations of climate in the future.     

Anthropogenic and climatic impacts on surface pollen assemblages along a precipitation gradient in north‐eastern China

Aim To understand the scenarios of ‘anthropogenic biomes’ that integrate human and ecological systems, we need to explore the impacts of climate and human disturbance on vegetation in the past and present. Interactions among surface pollen, modern vegetation and human activities along climate and land‐use gradients are tested to evaluate the natural and anthropogenic forces shaping the modern vegetation, and hence to aid the reconstruction of vegetation and climate in the past. This in turn will help with future predictions. Location The North‐east China Transect (NECT) in north‐eastern China. Methods We analysed 33 surface pollen samples and 213 quadrats across four vegetation zones along the moisture/land‐use gradients of the NECT. Detrended correspondence analysis (DCA) and redundancy analysis (RDA) of 52 pollen taxa and three environmental variables were used to distinguish anthropogenic and climatic factors that affect surface pollen assemblages along the NECT. Results The 33 surface samples are divided into four pollen zones (forest, meadow steppe, typical steppe and desert steppe) corresponding to major vegetation types in the NECT. Variations in pollen ratios of fern/herb (F/H), Artemisia/Chenopodiaceae (A/C) and arboreal pollen/non‐arboreal pollen (AP/NAP) represent the vegetation and precipitation gradient along the NECT. DCA and RDA analyses suggest that surface pollen assemblages are significantly influenced by the precipitation gradient. Changes in the abundance of Chenopodiaceae pollen are related to both human activities and precipitation. Main conclusions Surface pollen assemblages, fossil pollen records, archaeological evidence and historical documents in northern China show that a large increase of Chenopodiaceae pollen indicates human‐caused vegetation degradation in sandy habitats. The A/C ratio is a good indicator of climatic aridity, but should be used in conjunction with multiple proxies of human activities and climate change in the pollen‐based reconstruction of anthropogenic biomes.     

Holocene coastal vegetation changes at the mouth of the Amazon River

Wetland dynamics in the eastern Amazon region during the past 7000 years were studied using pollen, textural and structural analyses of sediment cores, as well as AMS radiocarbon dating. Four sediment cores were sampled from Marajó Island, which is located at the mouth of the Amazon River. Marajó Island is covered mainly by Amazon coastal forest, as well as herbaceous and varzea vegetation. Three cores were sampled from Lake Arari, which is surrounded by herbaceous vegetation flooded by freshwater. One core was sampled from a herbaceous plain located 15 km southeast of Lake Arari. Pollen preservation in the sedimentary deposits from this lake and from its drainage basin suggests significant vegetation changes on Marajó Island during the mid- and late-Holocene. Between 7328–7168 and 2306–2234 cal. yr BP, mangrove vegetation was more widely distributed on the island than it is today. During the past 2306–2234 cal. yr BP herbaceous vegetation expanded. Sedimentary structures and pollen data suggest a lagoon system until ~ 2300 cal. yr BP. The current distribution of mangroves along the Pará littoral, together with the presence of mangrove pollen and the sedimentary structures of the cores, indicates greater marine influence during the mid-Holocene. This may be attributed to the association between the eustatic sea-level change and the dry period recorded in Amazonia during the early- and mid-Holocene, followed by a wet phase over the past 2000 years.     

The relative lengths of individual telomeres are defined in the zygote and strictly maintained during life

Previous studies have indicated that average telomere length is partly inherited ( Slagboom et al., 1994 ; Rufer et al., 1999 ) and that there is an inherited telomere pattern in each cell ( Graakjaer et al., 2003 ); ( Londoño‐Vallejo et al., 2001 ). In this study, we quantify the importance of the initially inherited telomere lengths within cells, in relation to other factors that influence telomere length during life. We have estimated the inheritance by measuring telomere length in monozygotic (MZ) twins using Q‐FISH with a telomere specific peptide nucleic acid (PNA)‐probe. Homologous chromosomes were identified using subtelomeric polymorphic markers. We found that identical homologous telomeres from two aged MZ twins show significantly less differences in relative telomere length than when comparing the two homologues within one individual. This result means that towards the end of life, individual telomeres retain the characteristic relative length they had at the outset of life and that any length alteration during the lifespan impacts equally on genetically identical homologues. As the result applies across independent individuals, we conclude that, at least in lymphocytes, epigenetic/environmental effects on relative telomere length are relatively minor during life.     

Natural and anthropogenic forcing of aquatic macrophyte development in a shallow Danish lake during the last 7000 years

Aim To investigate the long‐term changes in aquatic vegetation in a lowland, shallow lake, and to assess the relationship between aquatic vegetation and natural and anthropogenic catchment changes. Location Gundsømagle Sø, Zealand, Denmark: a shallow (mean depth 1.2 m), hypereutrophic lake (mean annual total phosphorus (TP) c. 700 μg TP L^?1) located in a predominantly agricultural catchment (88% cultivated land). The lake is presently devoid of macrophytes. Methods One hundred and forty‐seven contiguous samples from a sediment core (taken in 2000) were analysed for macrofossil remains together with loss‐on‐ignition and dry weight. From an earlier sediment core (taken in 1992), 67 samples were analysed for pollen and the two cores were correlated using the ignition residue profiles. Core chronology was determined by ²¹⁰Pb and ¹³⁷Cs dating of the recent lake sediments, while older sediments were dated by pollen‐stratigraphical correlation, as ¹⁴C dating proved problematical. Aquatic macrofossil abundance was used to reconstruct past changes in the lake's plant community and water‐level. The contemporary catchment land‐use change was inferred from sedimentary pollen data, and soil erosion to the lake was deduced from the minerogenic content of the lake sediments. Results The macrofossil record covers the last 7000 years, but aquatic plant remains were scarce prior to c. 1300 bc . After this date the abundance of submerged and emergent macrophyte remains increased dramatically, paralleled by an increase in sediment minerogenic matter and non‐arboreal pollen (NAP). Aquatic plant remains were abundant for more than 3000 years until the mid 1900s. Macrofossils of Linum usitatissimum (L.) (flax) and high pollen percentages of ‘Cannabis type’ (hemp) were recorded in periods between c. 1150 bc and 1800 ad . Main conclusions Our study suggests that, between c. 5000 bc and 1300 bc , the submerged plant community was confined to the littoral zone. From 1300 bc onwards, the submerged macrophyte vegetation expanded rapidly across the lake bed, presumably as a response to lake shallowing caused by a combination of climatic‐induced water‐level lowering and enhanced erosional infilling of the lake basin due to intensified anthropogenic activities in the catchment. The lake was meso‐eutrophic and had an extensive and diverse aquatic flora for more than 3000 years, until the middle of the twentieth century. In periods between c. 1150 bc and 1800 ad , the lake experienced direct anthropogenic impact from retting of fibre plants (Linum and Cannabis). Over the last 200 years, erosional infilling of the lake basin increased drastically, probably as a result of agricultural intensification. In the twentieth century, the lake was strongly affected by nutrient enrichment from both point sources (sewage from built‐up areas) and diffuse agricultural run‐off which led to hypertrophic conditions and the collapse of the submerged vegetation c. 1950–60. The concept of ‘naturalness’ and the implications for lake conservation are discussed.     

A 250 year comparison of historical, macrofossil and pollen records of aquatic plants in a shallow lake

1. Sedimentary remains of aquatic plants, both vegetative (turions, leaves, spines) and reproductive (fruits, seeds, pollen), may provide a record of temporal changes in the submerged vegetation of lakes. An independent assessment of the degree to which these remains reflect past floristic change is, however, rarely possible. 2. By exploiting an extensive series of historical plant records for a small shallow lake we compare plant macrofossil (three cores) and pollen (one core) profiles with the documented sequence of submerged vegetation change since c. 1750 AD. The data set is based on 146 site visits with 658 observations including 42 taxa classified as aquatic, spanning 250 years. 3. Approximately 40% of the historically recorded aquatic taxa were represented by macro‐remains. In general macrofossils underestimated past species diversity, with pondweeds (three of eight historically recorded Potamogeton species were found) particularly poorly represented. Nonetheless, several taxa not reported from historical surveys (e.g. Myriophyllum alterniflorum and Characeae) were present in the sediment record. 4. The pollen record revealed taxa which left no macro‐remains (e.g. Littorella uniflora), and the macrofossil record provided improved taxonomic resolution for some taxa (e.g. Potamogeton) and a more reliable record of persistence, appearance and loss of others (e.g. Myriophyllum spp. and Nymphaeaceae). 5. Detrended correspondence analysis indicated that changes in the community composition evidenced by the palaeolimnological and historical records were synchronous and of a similar magnitude. Both records pointed to a major change at around 1800, with the historical record suggesting a more abrupt change than the sedimentary data. There was good agreement on a subsequent change c. 1930. 6. The palaeolimnological data did not provide a complete inventory of historically recorded species. Nevertheless, these results suggest that combined macrofossil and pollen records provide a reliable indication of temporal change in the dominant components of the submerged and floating‐leaved aquatic vegetation of shallow lakes. As such palaeolimnology may provide a useful tool for establishing community dynamics and successions of plants over decadal to centennial timescales.     

Palaeo‐ecology of the Gap and Coturaundee Ranges,western New South Wales,using stick‐nest rat (Leporillus spp.) (Muridae) middens

Pollen, plant and animal macrofossils recovered from nine Leporillus spp. (Muridae) middens found in the Gap and Coturaundee Ranges, western New South Wales were examined. By comparing current vegetation, pollen from modern surface samples and pollen from midden samples, general vegetation characteristics over the last 6500 years BP were reconstructed. Evidence shows that a greater shrub cover was apparent between 6500 and 5200 BP , while other aspects of the vegetation cover were similar to present. An increase in tree pollen, possibly indicating greater tree cover, occurred around 3400–2600 BP , while vegetation in the last 1300 years was similar to present. These interpretations, particularly from the older samples, are tentative due to spatial and temporal limitations. Animal macrofossils from the middens indicate that several mammal species now extinct or uncommon in western New South Wales have occurred in the area in the past 3000 years. This study also confirms that reconstruction of vegetation from Leporillus spp. midden evidence should be seen as separate ‘snapshots’, rather than continuous records over a stratigraphically defined timescale.     

Host plant richness explains diversity of ectomycorrhizal fungi: Response to the comment of Tedersoo et al. (2014)

Exploring the relationships between the biodiversity of groups of interacting organisms yields insight into ecosystem stability and function (Hooper et al. 2000 ; Wardle 2006 ). We demonstrated positive relationships between host plant richness and ectomycorrhizal (EM) fungal diversity both in a field study in subtropical China (Gutianshan) and in a meta‐analysis of temperate and tropical studies (Gao et al. 2013 ). However, based on re‐evaluation of our data sets, Tedersoo et al. ( 2014 ) argue that the observed positive correlation between EM fungal richness and EM plant richness at Gutianshan and also in our metastudies was based mainly from (i) a sampling design with inconsistent species pool and (ii) poor data compilation for the meta‐analysis. Accordingly, we checked our data sets and repeated the analysis performed by Tedersoo et al. ( 2014 ). In contrast to Tedersoo et al. ( 2014 ), our re‐analysis still confirms a positive effect of plant richness on EM fungal diversity in Gutianshan, temperate and tropical ecosystems, respectively.