Phylogenetic analysis and a time tree for a large drosophilid data set (Diptera: Drosophilidae)

Drosophila is the genus responsible for the birth of experimental genetics, but the taxonomy of drosophilids is difficult because of the overwhelming diversity of the group. In this study, we assembled sequences for 358 species (14 genera, eight subgenera, 57 species groups, and 65 subgroups) to generate a maximum‐likelihood topology and a Bayesian timescale. In addition to sampling an unprecedented diversity of Drosophila lineages, our analyses incorporated a geographical perspective because of the high levels of endemism. In our topology, Drosophila funebris (Fabricius, 1787) (the type species of Drosophila) is tightly clustered with the pinicola subgroup in a North American clade within subgenus Drosophila. The type species of other drosophilid genera fall within the Drosophila radiation, presenting interesting prospects for the phylogenetic taxonomy of the group. Our timescale suggests that a few drosophilid lineages survived the Cretaceous–Palaeogene (K‐Pg) extinction. The drosophilid diversification began during the Palaeocene in Eurasia, but peaked during the Miocene, an epoch of drastic climatic changes. The most recent common ancestor of the clades corresponding to subgenera Sophophora and Drosophila lived approximately 56 Mya. Additionally, Hawaiian drosophilids diverged from an East Asian lineage approximately 26 Mya, which is similar to the age of the oldest emerging atoll in the Hawaiian–Emperor Chain. Interestingly, the time estimates for major geographical splits (New World versus Asia and Africa versus Asia) were highly similar for independent lineages. These results suggest that vicariance played a significant role in the radiation of fruit flies. © 2013 The Linnean Society of London     

Ant assemblage composition explains high predation pressure on artificial caterpillars during early night

1. Predator–prey interactions, especially those involving herbivorous insects, are of great importance in maintaining biodiversity. Predation pressure varies temporally in response to prey availability and activity. However, little is known about the patterns and drivers of fluctuations in predation pressure at fine temporal scales. 2. Artificial caterpillars (placed on plant leaves at breast height) were used to assess changes in predation pressure across four time intervals of the day in a monsoonal tropical rainforest in south-west China. The study examined how assemblage composition of arboreal ants, the dominant predators, changed across the same time intervals. The potential linkages between biotic (arboreal ants) and abiotic (temperature and light intensity) factors with predation rate were evaluated. 3. Predation rate on caterpillars during the early part of the night (19.00–01.00 hours) was significantly higher than in the morning, afternoon, or late night. Ant assemblage composition, rather than species richness or total abundance, best explained the variations in predation rate on artificial caterpillars. 4. The results help to strengthen understanding of trophic interactions by demonstrating that predation pressure fluctuates at finer timescales than previously tested, and that a particular set of ant species may play major roles in predation on caterpillars and possibly other organisms.     

Comparing the effects of even‐ and uneven‐aged silviculture on ecological diversity and processes: A review

With an increasing pressure on forested landscapes, conservation areas may fail to maintain biodiversity if they are not supported by the surrounding managed forest matrix. Worldwide, forests are managed by one of two broad approaches—even‐ and uneven‐aged silviculture. In recent decades, there has been rising public pressure against the systematic use of even‐aged silviculture (especially clear‐cutting) because of its perceived negative esthetic and ecological impacts. This led to an increased interest for uneven‐aged silviculture. However, to date, there has been no worldwide ecological comparison of the two approaches, based on multiple indicators. Overall, for the 99 combinations of properties or processes verified (one study may have evaluated more than one property or process), we found nineteen (23) combinations that clearly showed uneven‐aged silviculture improved the evaluated metrics compared to even‐aged silviculture, eleven (16) combinations that showed the opposite, and 60 combinations that were equivocal. Furthermore, many studies were based on a limited study design without either a timescale (44 of the 76) or spatial (54 of the 76) scale consideration. Current views that uneven‐aged silviculture is better suited than even‐aged silviculture for maintaining ecological diversity and processes are not substantiated by our analyses. Our review, by studying a large range of indicators and many different taxonomic groups, also clearly demonstrates that no single approach can be relied on and that both approaches are needed to ensure a greater number of positive impacts. Moreover, the review clearly highlights the importance of maintaining protected areas as some taxonomic groups were found to be negatively affected no matter the management approach used. Finally, our review points to a lack of knowledge for determining the use of even‐ or uneven‐aged silviculture in terms of both their respective proportion in the landscape and their spatial agency.     

Integrated stratigraphy and astronomical calibration of the Serravallian/Tortonian boundary section at Monte Gibliscemi (Sicily, Italy)

Results are presented of an integrated stratigraphic (calcareous plankton biostratigraphy, cyclostratigraphy and magnetostratigraphy) study of the Serravallian/Tortonian (S/T) boundary section of Monte Gibliscemi (Sicily, Italy). Astronomical calibration of the sedimentary cycles provides absolute ages for calcareous plankton bio-events in the interval between 9.8 and 12.1 Ma. The first occurrence (FO) of Neogloboquadrina acostaensis, usually taken to delimit the S/T boundary, is dated astronomically at 11.781 Ma, pre-dating the migratory arrival of the species at low latitudes in the Atlantic by almost 2 million years. In contrast to delayed low-latitude arrival of N. acostaensis, Paragloborotalia mayeri shows a delayed low-latitude extinction of slightly more than 0.7 million years with respect to the Mediterranean (last occurrence (LO) at 10.49 Ma at Ceara Rise; LO at 11.205 Ma in the Mediterranean). The Discoaster hamatus FO, dated at 10.150 Ma, is clearly delayed with respect to the open ocean. The ages of D. kugleri first and last common occurrence (FCO and LCO), Catinaster coalitus FO, Coccolithus miopelagicus last (regular) occurrence (L(R)O) and the D. hamatus/neohamatus cross-over, however, are in good to excellent agreement with astronomically tuned ages for the same events at Ceara Rise (tropical Atlantic), suggesting that both independently established timescales are consistent with one another. The lack of a reliable magnetostratigraphy hampers a direct comparison with the geomagnetic polarity timescale of Cande and Kent (1995; CK95), but ages of calcareous nannofossil events suggests that CK95 is significantly younger over the studied time interval. Approximate astronomical ages for the polarity reversals were obtained by exporting astronomical ages of selected nannofossil events from Ceara Rise (and the Mediterranean) to eastern equatorial Pacific ODP Leg 138 Site 845, which has a reliable magnetostratigraphy.Our data from the Rio Mazzapiedi–Castellania section reveal that the base of the Tortonian stratotype corresponds almost exactly with the first regular occurrence (FRO) of N. acostaensis s.s. as defined in the present study, dated at 10.554 Ma. An extrapolated age of 11.8 Ma calculated for the top of the Serravallian stratotype indicates that there is a gap between the top of the Serravallian and the base of the Tortonian stratotype, potentially rendering all bio-events in the interval between 11.8 and 10.554 Ma suitable for delimiting the S/T boundary. Despite the tectonic deformation and the lack of a magnetostratigraphy, Gibliscemi remains a candidate to define the S/T boundary by means of the Tortonian global boundary stratotype section and point (GSSP).     

BioDeepTime: A database of biodiversity time series for modern and fossil assemblages

Motivation

We have little understanding of how communities respond to varying magnitudes and rates of environmental perturbations across temporal scales. BioDeepTime harmonizes assemblage time series of presence and abundance data to help facilitate investigations of community dynamics across timescales and the response of communities to natural and anthropogenic stressors. BioDeepTime includes time series of terrestrial and aquatic assemblages of varying spatial and temporal grain and extent from the present-day to millions of years ago.

Main Types of Variables Included

BioDeepTime currently contains 7,437,847 taxon records from 10,062 assemblage time series, each with a minimum of 10 time steps. Age constraints, sampling method, environment and taxonomic scope are provided for each time series.

Spatial Location and Grain

The database includes 8752 unique sampling locations from freshwater, marine and terrestrial ecosystems. Spatial grain represented by individual samples varies from quadrats on the order of several cm² to grid cells of ~100 km².

Time Period and Grain

BioDeepTime in aggregate currently spans the last 451 million years, with the 10,062 modern and fossil assemblage time series ranging in extent from years to millions of years. The median extent of modern time series is 18.7 years and for fossil series is 54,872 years. Temporal grain, the time encompassed by individual samples, ranges from days to tens of thousands of years.

Major Taxa and Level of Measurement

The database contains information on 28,777 unique taxa with 4,769,789 records at the species level and another 271,218 records known to the genus level, including time series of benthic and planktonic foraminifera, coccolithophores, diatoms, ostracods, plants (pollen), radiolarians and other invertebrates and vertebrates. There are to date 7012 modern and 3050 fossil time series in BioDeepTime.

Software Format

SQLite, Comma-separated values.     

Population responses to observed climate variability across multiple organismal groups

A major challenge in ecology is to understand how populations are affected by increased climate variability. Here, we assessed the effects of observed climate variability on different organismal groups (amphibians, insects, mammals, herbaceous plants and reptiles) by estimating the extent to which interannual variation in the annual population growth rates (CV_λ) and the absolute value of the long-term population growth rate (|log λ|) were associated with short-term climate variability. We used empirical data (≥ 20 consecutive years of annual abundances) from 59 wild populations in the Northern Hemisphere, and quantified variabilities in population growth rates and climatic conditions (temperature and precipitation in active and inactive seasons) calculated over four- and eight-year sliding time windows. We observed a positive relationship between the variability of growth rate (CV_λ) and the variability of temperature in the active season at the shorter timescale only. Moreover, |log λ| was positively associated with the variability of precipitation in the inactive season at both timescales. Otherwise, the direction of the relationships between population dynamics and climate variability (if any) depended largely on the season and organismal group in question. Both CV_λ and |log λ| correlated negatively with species' lifespan, indicating general differences in population dynamics between short-lived and long-lived species that were not related to climate variability. Our results suggest that although temporal variation in population growth rates and the magnitude of long-term population growth rates are partially associated with short-term interannual climate variability, demographic responses to climate fluctuations might still be population-specific rather than specific to given organismal groups, and driven by other factors than the observed climate variability.     

Large-Scale Phylogenomic Analyses Reveal the Monophyly of Bryophytes and Neoproterozoic Origin of Land Plants

The relationships among the four major embryophyte lineages (mosses, liverworts, hornworts, vascular plants) and the timing of the origin of land plants are enigmatic problems in plant evolution. Here, we resolve the monophyly of bryophytes by improving taxon sampling of hornworts and eliminating the effect of synonymous substitutions. We then estimate the divergence time of crown embryophytes based on three fossil calibration strategies, and reveal that maximum calibration constraints have a major effect on estimating the time of origin of land plants. Moreover, comparison of priors and posteriors provides a guide for evaluating the optimal calibration strategy. By considering the reliability of fossil calibrations and the influences of molecular data, we estimate that land plants originated in the Precambrian (980–682 Ma), much older than widely recognized. Our study highlights the important contribution of molecular data when faced with contentious fossil evidence, and that fossil calibrations used in estimating the timescale of plant evolution require critical scrutiny.     

Constraining estimates of global soil respiration by quantifying sources of variability

Quantifying global soil respiration (R_SG) and its response to temperature change are critical for predicting the turnover of terrestrial carbon stocks and their feedbacks to climate change. Currently, estimates of R_SG range from 68 to 98 Pg C year^?1, causing considerable uncertainty in the global carbon budget. We argue the source of this variability lies in the upscaling assumptions regarding the model format, data timescales, and precipitation component. To quantify the variability and constrain R_SG, we developed R_SG models using Random Forest and exponential models, and used different timescales (daily, monthly, and annual) of soil respiration (R_S) and climate data to predict R_SG. From the resulting R_SG estimates (range = 66.62–100.72 Pg), we calculated variability associated with each assumption. Among model formats, using monthly R_S data rather than annual data decreased R_SG by 7.43–9.46 Pg; however, R_SG calculated from daily R_S data was only 1.83 Pg lower than the R_SG from monthly data. Using mean annual precipitation and temperature data instead of monthly data caused +4.84 and ?4.36 Pg C differences, respectively. If the timescale of R_S data is constant, R_SG estimated by the first‐order exponential (93.2 Pg) was greater than the Random Forest (78.76 Pg) or second‐order exponential (76.18 Pg) estimates. These results highlight the importance of variation at subannual timescales for upscaling to R_SG. The results indicated R_SG is lower than in recent papers and the current benchmark for land models (98 Pg C year^?1), and thus may change the predicted rates of terrestrial carbon turnover and the carbon to climate feedback as global temperatures rise.