Detecting invertebrate species in archived collections using next‐generation sequencing

Invertebrate biodiversity measured at mostly family level is widely used in biological monitoring programmes to assess anthropogenic impacts on ecosystems. However, next‐generation sequencing (NGS) could allow development of new more sensitive biomonitoring tools by allowing rapid species identification. This could be accelerated if archived invertebrate collections and environmental information from past programmes are used to understand species distributions and their environmental responses. In this study, we take archived macroinvertebrate samples from two sites collected on multiple occasions and test whether NGS can successfully detect species. Samples had been stored in 70% ethanol at room temperature for up to 12 years. Three amplicons ranging from 197 to 274 bps within the DNA barcode region were amplified from samples and compared to DNA barcoding libraries to identify species. We were able to amplify partial DNA barcodes from most samples, and species were often detected with multiple amplicons. However, some singletons and taxa poorly covered by DNA barcoding were missed. This suggests additional DNA barcodes will be required to fill ‘gaps’ in current DNA barcode libraries for aquatic macroinvertebrates and/or that it may not be possible to detect all taxa in a sample. Furthermore, older samples often detected fewer taxa and were less reliable for amplification, suggesting NGS is best used on samples within 8 years of collection. Nevertheless, many common taxa with existing DNA barcodes were reliably identified with NGS and were often present at sites across multiple years, showing the potential of NGS for detecting common and abundant species in archived material.     

Decoupled trophic responses to long‐term recovery from acidification and associated browning in lakes

Increases in the concentration of dissolved organic matter (DOM) have been documented in many inland waters in recent decades, a process known as “browning”. Previous studies have often used space‐for‐time substitution to examine the direct consequences of increased DOM on lake ecosystems. However, browning often occurs concomitant with other ecologically important water chemistry changes that may interact with or overwhelm any potential ecological response to browning itself. Here we examine a long‐term (~20 year) dataset of 28 lakes in the Adirondack Park, New York, USA, that have undergone strong browning in response to recovery from acidification. With these data, we explored how primary producer and zooplankton consumer populations changed during this time and what physical and chemical changes best predicted these long‐term ecosystem changes. Our results indicate that changes in primary producers are likely driven by reduced water clarity due to browning, independent of changes in nutrients, counter to previously hypothesized primary producer response to browning. In contrast, declines in calcium concomitant with browning play an important role in driving long‐term declines in zooplankton biomass. Our results indicate that responses to browning at different trophic levels are decoupled from one another. Concomitant chemical changes have important implications for our understanding of the response of aquatic ecosystems to browning.     

Impacts of introduced brown and rainbow trout on benthic invertebrate communities in shallow New Zealand lakes

1. Brown and rainbow trout have been introduced to many inland waters in New Zealand, but research on the impacts on native communities has focused mainly on streams. The purpose of this study was to compare the benthic communities of trout and troutless lakes. Based on previous studies in North America and Europe, we predicted that the benthic biomass, and especially the abundance of large invertebrates, would be lower in lakes with trout as compared to those without. We surveyed the invertebrate fauna of 43 shallow, high‐elevation lakes (26 with and 17 without trout) in four geographic clusters on the central South Island and then conducted a detailed quantitative study of invertebrate biomass and community structure in 12 of these lakes. 2. Benthic community composition and diversity of lakes with and without trout were nearly identical and biomass was as high or higher in the lakes with as without trout. There was no evidence that trout have caused local extinctions of benthic invertebrates. Although the proportional abundance of large‐bodied aquatic was slightly lower in lakes with than without trout, the abundance of several groups of large‐bodied benthic taxa (dragonflies, caddisflies and water bugs) did not differ. 3. Our findings are in contrast to those in North American and Europe where trout introductions into previously troutless lakes have led to declines in the abundance of benthic invertebrates, especially large‐bodied taxa. We propose that the modest effects of trout in New Zealand could be explained by (i) the high areal extent of submergent vegetation that acts as a benthic refuge, (ii) low intensity of trout predation on benthic communities and/or (iii) characteristics of the benthic invertebrates that make them relatively invulnerable to fish predation. 4. Regardless of the relative importance of these hypotheses, our results emphasise that the same invertebrates occurred in all of the lakes, regardless of size, elevation and presence of trout, suggesting habitat generalists dominate the benthic fauna in shallow New Zealand lakes.     

Persistence and stability of lotic invertebrate communities in New Zealand

1. Persistence and stability of lotic invertebrate communities were determined at an annual time scale over a 9‐year period (1990–98) at 26 river sites over the northern half of New Zealand. In addition, a number of water quality variables were measured monthly and flow information collected continuously over the same period at each site. 2. The aim of the study was to describe the levels of interannual variability in invertebrate communities, and relate community changes to variability in environmental conditions. The consequences of this temporal variability for the sensitivity of predictive models were also investigated. 3. Levels of change in environmental conditions varied significantly between years, but were relatively similar across sites. In contrast, community persistence (similarity between years in species assemblage composition), and stability (similarity between years with respect to relative abundance of species in the community) both varied significantly between sites, but changes between years were similar. Community stability was highest at sites with relatively harsh flow conditions (high coefficient of variation, high relative size of floods), and was also greater in communities dominated by Ephemeroptera. 4. Relationships between change in environmental conditions and changes in community composition and structure were relatively weak for most individual sites. However, when average levels of change for each of the 26 sites were used, communities showed greater persistence under conditions where flow conditions remained relatively constant. Water quality changes had no significant effect on community persistence when assessed for all 26 sites combined. 5. Results from this study suggest that lotic invertebrate communities fluctuate around a relatively stable state, at least over a 9‐year period. However, the extent of interannual variation in community composition and structure observed, along with the relatively low degree of cluster fidelity observed within a single region, suggests that predictive models based on reference site conditions extrapolated over several years should be applied with caution in New Zealand streams.     

Integration of lakes and streams in a landscape perspective: the importance of material processing on spatial patterns and temporal coherence

1. We studied the spatial and temporal patterns of change in a suite of twenty‐one chemical and biological variables in a lake district in arctic Alaska, U.S.A. The study included fourteen stream sites and ten lake sites, nine of which were in a direct series of surface drainage. All twenty‐four sites were sampled between one and five times a year from 1991 to 1997. 2. Stream sites tended to have higher values of major anions and cations than the lake sites, while the lake sites had higher values of particulate carbon, nitrogen, phosphorous and chlorophyll a. There were consistent and statistically significant differences in concentrations of variables measured at the inlet versus the outlet of lakes, and in variables measured at upstream versus downstream sites in the stream reaches which connect the lakes. In‐lake processing tended to consume alkalinity, conductivity, H⁺, DIC, Ca²⁺, Mg²⁺, CO₂, CH₄, and NO₃^–, and produce K⁺ and dissolved organic carbon (DOC). In‐stream processing resulted in the opposite trends (e.g. consumption of K⁺ and DOC), and the magnitudes of change were often similar to those measured in the lakes but with the opposite sign. 3. Observed spatial patterns in the study lakes included mean concentrations of variables which increased, decreased or were constant along the lake chain from high to low altitude in the catchment (stream sites showed no spatial patterns with any variables). The strongest spatial patterns were of increasing conductivity, Ca²⁺, Mg²⁺, alkalinity, dissolved inorganic carbon and pH with lake chain number (high to low altitude in the basin). These patterns were partly determined by the effect of increasing catchment area feeding into lakes further downslope, and partly by the systematic processing of materials in lakes and in the stream segments between lakes. 4. Synchrony (the temporal coherence or correlation of response) of variables across all lakes ranged from 0.18 for particulate phosphorus to 0.90 for Mg²⁺ the average synchrony for all twenty‐one variables was 0.50. The synchronous behaviour of lake pairs was primarily related to the spatial location or proximity of the lakes for all variables taken together and for many individual variables, and secondarily, to the catchment to lake area ratio and the water residence time. 5. These results illustrate that, over small geographic areas, and somewhat independent of lake or stream morphometry, the consistent and directional (downslope) processing of materials helps produce spatial patterns which are coherent over time for many limnological variables. We combine concepts from stream, lake and landscape ecology, and develop a conceptual view of landscape mass balance. This view highlights that the integration of material processing in both lakes and rivers is critical for understanding the structure and function of surface waters, especially from a landscape perspective.     

Low concordance of short‐term and long‐term selection responses in experimental Drosophila populations

Experimental evolution is becoming a popular approach to study the genomic selection response of evolving populations. Computer simulation studies suggest that the accuracy of the signature increases with the duration of the experiment. Since some assumptions of the computer simulations may be violated, it is important to scrutinize the influence of the experimental duration with real data. Here, we use a highly replicated Evolve and Resequence study in Drosophila simulans to compare the selection targets inferred at different time points. At each time point, approximately the same number of SNPs deviates from neutral expectations, but only 10% of the selected haplotype blocks identified from the full data set can be detected after 20 generations. Those haplotype blocks that emerge already after 20 generations differ from the others by being strongly selected at the beginning of the experiment and display a more parallel selection response. Consistent with previous computer simulations, our results demonstrate that only Evolve and Resequence experiments with a sufficient number of generations can characterize complex adaptive architectures.     

Large‐scale patterns in summer diffusive CH4 fluxes across boreal lakes,and contribution to diffusive C emissions

Lakes are a major component of boreal landscapes, and whereas lake CO₂ emissions are recognized as a major component of regional C budgets, there is still much uncertainty associated to lake CH₄ fluxes. Here, we present a large‐scale study of the magnitude and regulation of boreal lake summer diffusive CH₄ fluxes, and their contribution to total lake carbon (C) emissions, based on in situ measurements of concentration and fluxes of CH₄ and CO₂ in 224 lakes across a wide range of lake type and environmental gradients in Québec. The diffusive CH₄ flux was highly variable (mean 11.6 ± 26.4 SD mg m^?2 d^?1), and it was positively correlated with temperature and lake nutrient status, and negatively correlated with lake area and colored dissolved organic matter (CDOM). The relationship between CH₄ and CO₂ concentrations fluxes was weak, suggesting major differences in their respective sources and/or regulation. For example, increasing water temperature leads to higher CH₄ flux but does not significantly affect CO₂ flux, whereas increasing CDOM concentration leads to higher CO₂ flux but lower CH₄ flux. CH₄ contributed to 8 ± 23% to the total lake C emissions (CH₄ + CO₂), but 18 ± 25% to the total flux in terms of atmospheric warming potential, expressed as CO₂‐equivalents. The incorporation of ebullition and plant‐mediated CH₄ fluxes would further increase the importance of lake CH₄. The average Q₁₀ of CH₄ flux was 3.7, once other covarying factors were accounted for, but this apparent Q₁₀ varied with lake morphometry and was higher for shallow lakes. We conclude that global climate change and the resulting shifts in temperature will strongly influence lake CH₄ fluxes across the boreal biome, but these climate effects may be altered by regional patterns in lake morphometry, nutrient status, and browning.     

Flow intermittency alters longitudinal patterns of invertebrate diversity and assemblage composition in an arid‐land stream network

1. Temporary streams comprise a large proportion of the total length of most stream networks, and the great majority of arid‐land stream networks, so it is important to understand their contribution to biotic diversity at both local and landscape scales. 2. In late winter 2010, we sampled invertebrate assemblages in 12 reaches of a large arid‐land stream network (including perennial and intermittent headwaters, intermittent middle reaches and perennial rivers) in south‐east Arizona, U.S.A. Intermittent reaches had then been flowing for c. 60 days, following a dry period of more than 450 days. We sampled a subset of the perennial study reaches three more times between 2009 and 2011. Since intermittent reaches were dry during these additional sampling periods, we used assemblage data from two other intermittent streams in the study network (sampled in 2004–05 and 2010) to explore interannual variability in intermittent stream assemblage composition. 3. Invertebrate richness was lowest in intermittent reaches, despite their often being connected to species‐rich perennial reaches. The assemblages of these intermittent reaches were not simply a subset of the species in perennial streams, but rather were dominated by a suite of stoneflies, blackflies and midges with adaptations to intermittency (e.g. egg and/or larval diapause). On average, 86% of individuals in these samples were specialists or exclusive to intermittent streams. Predators were 7–14 times more abundant in perennial than in intermittent reaches. 4. Despite being separated by long distances (12–25 km) and having very different physical characteristics, the assemblages of perennial headwaters and rivers were more similar to one another than to intervening intermittent reaches, emphasising the prime importance of local hydrology in this system. 5. The duration and recurrence intervals of dry periods, and the relative importance of dispersal from perennial refuges, probably influence the magnitude of biological differences between neighbouring perennial and temporary streams. Although perennial headwaters supported the highest diversity of invertebrates, intermittent reaches supported a number of unique or locally rare species and as such contribute to regional species diversity and should be included in conservation planning.     

Predation,sediment stability and food availability as determinants of the benthic invertebrate fauna in two shallow lakes

The sedimentary benthos of a series of shallow, eutrophicated lakes, the Norfolk Broads is, in general, low not only in number of species but unexpectedly in number of individuals. In two of the lakes, Hudsons Bay and Hoveton Great Broad, chironomids and oligochaetes dominated the fauna. Hudsons Bay has an extensive stand of water lilies (Nuphar lutea); Hoveton Great Broad does not. There were significant relationships between number of chironomids and of Potamothrix hammoniensis with organic content of the sediments, but these were due not to food availability but to the structure imparted to the otherwise fluid sediment by the organic matter. Sediment stabilised in plastic bowls developed much larger populations of oligochaetes than found in the unrestricted sediment. Protection of the community from fish predation resulted in a further major increase in numbers. Sediment stability and predation rather than food supply were the major determinants of these benthic populations.     

Species colonisation,not competitive exclusion,drives community overdispersion over long‐term succession

Ecological communities often transition from phylogenetic and functional clustering to overdispersion over succession as judged by space‐for‐time substitution studies. Such a pattern has been generally attributed to the increase in competitive exclusion of closely related species with similar traits through time, although colonisation and extinction have rarely been examined. Using 44 years of uninterrupted old‐field succession in New Jersey, USA, we confirmed that phylogenetic and functional clustering decreased as succession unfolded, but the transition was largely driven by colonisation. Early colonists were closely related and functionally similar to residents, while later colonists became less similar to the species present. Extirpated species were generally more distantly related to residents than by chance, or exhibited random phylogenetic/functional patterns, and their relatedness to residents was not associated with time. These results provide direct evidence that the colonisation of distant relatives, rather than extinction of close relatives, drives phylogenetic and functional overdispersion over succession.     

Gradual changes in range size accompany long‐term trends in species richness

Species richness has long been used as an indicator of ecosystem functioning and health. Global richness is declining, but it is unclear whether sub‐global trends differ. Regional trends are especially understudied, with most focused on island regions where richness is strongly impacted by novel colonisations. We addressed this knowledge gap by testing for multi‐decade trends in species richness in nine open marine regions around North America (197 region‐years) while accounting for imperfect observations and grounding our findings in species‐level range dynamics. We found positive richness trends in eight of nine regions, four of which were statistically significant. Species' range sizes generally contracted pre‐extinction and expanded post‐colonisation, but the ranges of transient species expanded over the long‐term, slowly increasing their regional retention and driving increasing richness. These results provide more evidence that sub‐global richness trends are stable or increasing, and highlight the utility of range size for understanding richness dynamics.     

Inconsistencies of interannual variability and trends in long‐term satellite leaf area index products

Understanding the long‐term performance of global satellite leaf area index (LAI) products is important for global change research. However, few effort has been devoted to evaluating the long‐term time‐series consistencies of LAI products. This study compared four long‐term LAI products (GLASS, GLOBMAP, LAI3g, and TCDR) in terms of trends, interannual variabilities, and uncertainty variations from 1982 through 2011. This study also used four ancillary LAI products (GEOV1, MERIS, MODIS C5, and MODIS C6) from 2003 through 2011 to help clarify the performances of the four long‐term LAI products. In general, there were marked discrepancies between the four long‐term LAI products. During the pre‐MODIS period (1982–1999), both linear trends and interannual variabilities of global mean LAI followed the order GLASS>LAI3g>TCDR>GLOBMAP. The GLASS linear trend and interannual variability were almost 4.5 times those of GLOBMAP. During the overlap period (2003–2011), GLASS and GLOBMAP exhibited a decreasing trend, TCDR no trend, and LAI3g an increasing trend. GEOV1, MERIS, and MODIS C6 also exhibited an increasing trend, but to a much smaller extent than that from LAI3g. During both periods, the R² of detrended anomalies between the four long‐term LAI products was smaller than 0.4 for most regions. Interannual variabilities of the four long‐term LAI products were considerably different over the two periods, and the differences followed the order GLASS>LAI3g>TCDR>GLOBMAP. Uncertainty variations quantified by a collocation error model followed the same order. Our results indicate that the four long‐term LAI products were neither intraconsistent over time nor interconsistent with each other. These inconsistencies may be due to NOAA satellite orbit changes and MODIS sensor degradation. Caution should be used in the interpretation of global changes derived from the four long‐term LAI products.     

A long‐term record of Quercus decline,logging and fires in a southern Swedish Fagus‐Picea forest

Abstract. We reconstructed forest development and disturbance events (fire and logging) during the last 1000 yr with tree‐ring data, pollen and charcoal analysis from a semi‐natural Fagus sylvatica‐Picea abies forest (ca. 1 km²) in the hemiboreal zone. According to pollen analysis, Quercus robur together with Pinus sylvestris was abundant in the forest until the turn of the 18th/19th centuries when these species disappeared completely (Quercus) or nearly completely (Pinus) and were replaced by Fagus and Picea. The disappearance of Quercus was corroborated by the remarkable discovery of a single Quercus stump that had been cut in the 18th century and had become overgrown and preserved by a very old Picea. In total 11 fires were dated from 1555 to 1748 from fire scars in several Pinus stumps cut 100 ‐ 200 yr ago. Since the last fire in 1748, no Quercus or Pinus have regenerated in the core of the reserve apart from single pines in neighbouring managed forest (80 yr ago). During the period of documented fires Fagus was protected from fires in a refuge made up of large boulders. Picea colonized the region at the time when the fires ceased 250 yr ago. We hypothesize that most of the fires were probably of human origin because of their patchiness and high frequency compared to the natural background levels of lightning ignitions in the region. On a 300‐yr time scale, logging and fire suppression seem to strongly overshadow the effect of climate change on forest composition and dynamics.     

Pronounced chemical response of Subarctic lakes to climate‐driven losses in surface area

Losses in lake area have been observed for several Arctic and Subarctic regions in recent decades, with unknown consequences for lake ecosystems. These reductions are primarily attributed to two climate‐sensitive mechanisms, both of which may also cause changes in water chemistry: (i) increased imbalance of evaporation relative to inflow, whereby increased evaporation and decreased inflow act to concentrate solutes into smaller volumes; and (ii) accelerated permafrost degradation, which enhances sublacustrine drainage while simultaneously leaching previously frozen solutes into lakes. We documented changes in nutrients [total nitrogen (TN), total phosphorus (TP)] and ions (calcium, chloride, magnesium, sodium) over a 25 year interval in shrinking, stable, and expanding Subarctic lakes of the Yukon Flats, Alaska. Concentrations of all six solutes increased in shrinking lakes from 1985–1989 to 2010–2012, while simultaneously undergoing little change in stable or expanding lakes. This created a present‐day pattern, much weaker or absent in the 1980s, in which shrinking lakes had higher solute concentrations than their stable or expanding counterparts. An imbalanced evaporation‐to‐inflow ratio (E/I) was the most likely mechanism behind such changes; all four ions, which behave semiconservatively and are prone to evapoconcentration, increased in shrinking lakes and, along with TN and TP, were positively related to isotopically derived E/I estimates. Moreover, the most conservative ion, chloride, increased >500% in shrinking lakes. Conversely, only TP concentration was related to probability of permafrost presence, being highest at intermediate probabilities. Overall, the substantial increases of nutrients (TN >200%, TP >100%) and ions (>100%) may shift shrinking lakes towards overly eutrophic or saline states, with potentially severe consequences for ecosystems of northern lakes.     

A survey of long‐term terrestrial ecology studies in Australia

Long‐term ecological studies (LTES) are critical for understanding and managing landscapes. To identify important research gaps, facilitate collaborations and communicate results, several countries have established long‐term ecological research networks. A few initiatives to create such a network in Australia have been undertaken, but relatively few published data exist on the current state of LTES in Australia. In this paper, we present the results of an online survey of terrestrial LTES projects sent to academic, government and non‐governmental organization‐based researchers across Australia. We asked questions pertaining to the focus, scope, support and outcomes of LTES spanning 7 years or longer. Based on the information reported from 85 Australian LTES, we: (i) identify the biomes, processes and species that are under‐represented in the current body of research; (ii) discuss important contributing factors to the successful development and survival of these projects; and (iii) make recommendations to help increase the productivity and influence of LTES across research, management and policy sectors.     

An analysis of changes in the invertebrate community along a southern New Zealand montane stream

Changes in benthic community structure at four sites along a flood-prone montane stream continuum in the South Island of New Zealand were analysed using rank correlation (Kendall's Tau and Spearman's r_s) and a community similarity index (S_c) developed initially for stream pollution assessment. Species richness was highest in a forested headwater stream, which is attributed to its relatively greater physical stability and habitat heterogeneity. Community similarity decreased with distance apart, and pairs of open and forested sites showed the greatest similarity. Species composition and relative abundance along the continuum changed least in the numerically dominant Ephemeroptera and Plecoptera, groups in which several species had broad habitat requirements. In contrast, a number of dipteran and trichopteran species had more restricted distributions. The more specialised niche requirements of some species in these orders are attributed to their generally small size, their ability to spin silk, and their holometabolous development. Physical rather than biological factors appeared to limit the distributions of most invertebrates, and there was little evidence of ecological segregation by either food resource partitioning or differences in life history patterns amongst many closely related species. Theories that stream communities are well ordered entities maximising the efficiency of energy utilisation cannot realistically be applied to such unstable stream systems.