Multi-locus sequence data illuminate demographic drivers of Pleistocene speciation in semi-arid southern Australian birds (Cinclosoma spp.)

Background: During the Pleistocene, shifts of species distributions and their isolation in disjunct refugia led to varied outcomes in how taxa diversified. Some species diverged, others did not. Here, we begin to address another facet of the role of the Pleistocene in generating today's diversity. We ask which processes contributed to divergence in semi-arid southern Australian birds. We isolated 11 autosomal nuclear loci and one mitochondrial locus from a total of 29 specimens of the sister species pair, Chestnut Quail-thrush Cinclosoma castanotum and Copperback Quail-thrush C. clarum. results: A population clustering analysis confirmed the location of the current species boundary as a well-known biogeographical barrier in southern Australia, the Eyrean Barrier. Coalescent-based analyses placed the time of species divergence to the Middle Pleistocene. Gene flow between the species since divergence has been low. The analyses suggest the effective population size of the ancestor was 54 to 178 times smaller than populations since divergence. This contrasts with recent multi-locus studies in some other Australian birds (butcherbirds, ducks) where a lack of phenotypic divergence was accompanied by larger historical population sizes. Post-divergence population size histories of C. clarum and C. castanotum were inferred using the extended Bayesian skyline model. The population size of C. clarum increased substantially during the late Pleistocene and continued to increase through the Last Glacial Maximum and Holocene. The timing of this expansion across its vast range is broadly concordant with that documented in several other Australian birds. In contrast, effective population size of C. castanotum was much more constrained and may reflect its smaller range and more restricted habitat east of the Eyrean Barrier compared with that available to C. clarum to the west. Conclusions: Our results contribute to awareness of increased population sizes, following significant contractions, as having been important in shaping diversity in Australian arid and semi-arid zones. Further, we improve knowledge of the role of Pleistocene climatic shifts in areas of the planet that were not glaciated at that time but which still experienced that period's cyclical climatic fluctuations.Gaynor Dolman and Leo Josep

A summer climate regime over Europe modulated by the North Atlantic Oscillation

Recent summer heat waves in Europe were found to be preceded by precipitation deficits in winter. Numerical studies suggest that these phenomena are dynamically linked by land-atmosphere interactions. However, there exists as yet no complete observational evidence that connects summer climate variability to winter precipitation and the relevant circulation patterns. In this paper, we investigate the functional responses of summer mean and maximum temperature (June–August, <i>T</i><sub>mean</sub> and <i>T</i><sub>max</sub>) as well as soil moisture proxied by the self-calibrating Palmer drought severity index (<i>scPDSI</i>) to preceding winter precipitation (January–March, <i>P</i><sub>JFM</sub>) for the period 1901–2005. All the analyzed summer fields show distinctive responses to <i>P</i><sub>JFM</sub> over the Mediterranean. We estimate that 10 ~ 15% of the interannual variability of <i>T</i><sub>max</sub> and <i>T</i><sub>mean</sub> over the Mediterranean is statistically forced by <i>P</i><sub>JFM</sub>. For the <i>scPDSI</i> this amounts to 10 ~ 25%. Further analysis shows that these responses are highly correlated to the North Atlantic Oscillation (NAO) regime over the Mediterranean. We suggest that NAO modulates European summer temperature by controlling winter precipitation that initializes the moisture states that subsequently interact with temperature. This picture of relations between European summer climate and NAO as well as winter precipitation suggests potential for improved seasonal prediction of summer climate for particular extreme events

Lesions mimicking lacrimal gland pleomorphic adenoma

Aim: To report a series of patients with lacrimal gland lesions simulating the clinicoradiological features of lacrimal gland pleomorphic adenoma (LGPA). Methods: Multicentre retrospective, interventional case series. Clinical records of all patients with lesions mimicking LGPA seen in five orbital units were reviewed. Results: The study included 14 patients (seven men and seven women) with a mean age of 50.9 years. The diagnosis of LGPA was made in all cases by experienced orbital surgeons, based on clinicoradiological features, and lacrimal gland excision was performed. Postoperative histology revealed lymphoma (four patients), chronic dacryoadenitis (three patients), adenoid cystic carcinoma (two patients), Sjogren's syndrome (two patients), cavernous haemangioma (one patient), benign lymphoid hyperplasia (one patient) and granulomatous dacryoadenitis (one patient). Comparison with the total number of histologically confirmed LGPA cases seen during the study period revealed that 22.6% of cases of suspected LGPA were misdiagnosed based on clinicoradiological criteria. Conclusions: Many different lesions may mimic the clinicoradiological features of LGPA. The accepted clinicoradiological criteria used for the diagnosis of LGPA have a high false-positive rate, even in experienced hands. Based on this study, the authors believe that fine-needle aspiration biopsy or intraoperative biopsy and frozen section diagnosis may help reduce unnecessary lacrimal gland excision.Venkatesh C Prabhakaran, Paul S Cannon, Alan McNab, Garry Davis, Brett O’Donnell, Peter J Dolman, Raf Ghabrial, Dinesh Selv

Fluctuation regimes of soil moisture in ERA-40 re-analysis data

Soil moisture variability is analysed in the re-analysis data ERA-40 of the European Centre for Medium-Range Weather Forecasts (ECMWF) which includes four layers within 189 cm depth. Short-term correlations are characterised by an e-folding time scale assuming an exponential decay, whilst long-term memory is described by power law decays with exponents determined by detrended fluctuation analysis. On a global scale, the short-term variability varies congruently with long-term memory in the surface layer. Key climatic regions (Europe, Amazon and Sahara) reveal that soil moisture time series are non-stationary in arid regions and in deep layers within the time horizon of ERA-40. The physical processes leading to soil moisture variability are linear according to an analysis of volatility (the absolute differences), which is substantiated by surrogate data analysis preserving the long-term memory

Contribution of water-limited ecoregions to their own supply of rainfall

The occurrence of wet and dry growing seasons in water-limited regions remains poorly understood, partly due to the complex role that these regions play in the genesis of their own rainfall. This limits the predictability of global carbon and water budgets, and hinders the regional management of naturalresources. Using novel satellite observations and atmospheric trajectory modelling, we unravel the origin and immediate drivers of growing-season precipitation, and the extent to which ecoregions themselves contribute to their own supply of rainfall. Results show that persistent anomalies in growing-season precipitation—and subsequent biomass anomalies—are caused by a complex interplay of land and ocean evaporation, air circulation and local atmospheric stability changes. For regions such as the Kalahari and Australia, the volumes of moisture recycling decline in dry years, providing a positive feedback that intensifies dry conditions. However, recycling ratios increase up to40%, pointing to the crucial role of these regions in generating their own supply of rainfall; transpiration in periods of water stress allows vegetation to partly offset the decrease in regional precipitation. Findings highlight the need to adequately represent vegetation–atmosphere feedbacks in models to predict biomass changes and to simulate the fate of water-limited regions in our warming climate

Modelling representation errors of atmospheric CO2 mixing ratios at a regional scale

Inverse modelling of carbon sources and sinks requires an accurate quality estimate of the modelling framework to obtain a realistic estimate of the inferred fluxes and their uncertainties. So-called "representation errors" result from our inability to correctly represent point observations with simulated average values of model grid cells. They may add substantial uncertainty to the interpretation of atmospheric CO2 mixing ratio data. We simulated detailed variations in the CO2 mixing ratios with a high resolution (2 km) mesoscale model (RAMS) to estimate the representation errors introduced at larger model grid sizes of 10 100 km. We found that meteorology is the main driver of representation errors in our study causing spatial and temporal variations in the error estimate. Within the nocturnal boundary layer, the representation errors are relatively large and mainly caused by unresolved topography at lower model resolutions. During the day, convective structures, mesoscale circulations, and surface CO2 flux variability were found to be the main sources of representation errors. Interpreting observations near a mesoscale circulation as representative for air with the correct footprint relative to the front can reduce the representation error substantially. The remaining representation error is 0.5 1.5 ppm at 20 100 km resolution

Response of methane emissions from wetlands to the Last Glacial Maximum and an idealized Dansgaard-Oeschger climate event: insights from two models of different complexity

The role of different sources and sinks of CH₄ in changes in atmospheric methane ([CH₄]) concentration during the last 100 000 yr is still not fully understood. In particular, the magnitude of the change in wetland CH₄ emissions at the Last Glacial Maximum (LGM) relative to the pre-industrial period (PI), as well as during abrupt climatic warming or Dansgaard–Oeschger (D–O) events of the last glacial period, is largely unconstrained. In the present study, we aim to understand the uncertainties related to the parameterization of the wetland CH₄ emission models relevant to these time periods by using two wetland models of different complexity (SDGVM and ORCHIDEE). These models have been forced by identical climate fields from low-resolution coupled atmosphere–ocean general circulation model (FAMOUS) simulations of these time periods. Both emission models simulate a large decrease in emissions during LGM in comparison to PI consistent with ice core observations and previous modelling studies. The global reduction is much larger in ORCHIDEE than in SDGVM (respectively −67 and −46%), and whilst the differences can be partially explained by different model sensitivities to temperature, the major reason for spatial differences between the models is the inclusion of freezing of soil water in ORCHIDEE and the resultant impact on methanogenesis substrate availability in boreal regions. Besides, a sensitivity test performed with ORCHIDEE in which the methanogenesis substrate sensitivity to the precipitations is modified to be more realistic gives a LGM reduction of −36%. The range of the global LGM decrease is still prone to uncertainty, and here we underline its sensitivity to different process parameterizations. Over the course of an idealized D–O warming, the magnitude of the change in wetland CH₄ emissions simulated by the two models at global scale is very similar at around 15 Tg yr⁻¹, but this is only around 25% of the ice-core measured changes in [CH₄]. The two models do show regional differences in emission sensitivity to climate with much larger magnitudes of northern and southern tropical anomalies in ORCHIDEE. However, the simulated northern and southern tropical anomalies partially compensate each other in both models limiting the net flux change. Future work may need to consider the inclusion of more detailed wetland processes (e.g. linked to permafrost or tropical floodplains), other non-wetland CH₄ sources or different patterns of D–O climate change in order to be able to reconcile emission estimates with the ice-core data for rapid CH₄ events

Effects of habitat and livestock on nest productivity of the Asian houbara Chlamydotis macqueenii in Bukhara Province, Uzbekistan

To inform population support measures for the unsustainably hunted Asian houbara Chlamydotis macqueenii (IUCN Vulnerable) we examined potential habitat and land-use effects on nest productivity in the Kyzylkum Desert, Uzbekistan. We monitored 177 nests across different semi-arid shrub assemblages (clay-sand and salinity gradients) and a range of livestock densities (0–80 km-2). Nest success (mean 51.4%, 95% CI 42.4–60.4%) was similar across four years; predation caused 85% of those failures for which the cause was known, and only three nests were trampled by livestock. Nesting begins within a few weeks of arrival when food appears scarce, but later nests were more likely to fail owing to the emergence of a key predator, suggesting foraging conditions on wintering and passage sites may be important for nest productivity. Nest success was similar across three shrub assemblages and was unrelated to landscape rugosity, shrub frequency or livestock density, but was greater with taller mean shrub height (range 13–67 cm) within 50 m. Clutch size (mean = 3.2 eggs) and per-egg hatchability in successful nests (87.5%) did not differ with laying date, shrub assemblage or livestock density. We therefore found no evidence that livestock density reduced nest productivity across the range examined, while differing shrub assemblages appeared to offer similar habitat quality. Asian houbara appear well-adapted to a range of semi-desert habitats and tolerate moderate disturbance by pastoralism. No obvious in situ mitigation measures arise from these findings, leaving regulation and control as the key requirement to render hunting sustainable

Deer reduce habitat quality for a woodland songbird: evidence from settlement patterns, demographic parameters, and body condition.

Understanding avian responses to ungulate-induced habitat modification is important because deer populations are increasing across much of temperate Europe and North America. Our experimental study examined whether habitat quality for Blackcaps (Sylvia atricapilla) in young woodland in eastern England was affected by deer, by comparing Blackcap behavior, abundance, and condition between paired plots (half of each pair protected from deer). The vegetation in each pair of plots was the same age. The Blackcap is an ideal model species for testing effects of deer on avian habitat quality because it is dependent on dense understory vegetation and is abundant throughout much of Europe. We compared timing of settlement, abundance, age structure (second-year vs. after-second-year), and phenotypic quality (measured as a body condition index, body mass divided by tarsus length) between experimental and control plots. We used point counts to examine Blackcap distribution, and standardized mist netting to collect demographic and biometric data. Incidence of singing Blackcaps was higher in nonbrowsed than in browsed plots, and singing males were recorded in nonbrowsed plots earlier in the season, indicating earlier and preferential territory establishment. Most Blackcaps, both males and females, were captured in vegetation prior to canopy closure (2–4 years of regrowth). Body condition was superior for male Blackcaps captured in nonbrowsed plots; for second-year males this was most marked in vegetation prior to canopy closure. We conclude that deer browsing in young woodland can alter habitat quality for understory-dependent species, with potential consequences for individual fitness and population productivity beyond the more obvious effects on population density