Mapping biodiversity value worldwide: combining higher-taxon richness from different groups

Maps of large-scale biodiversity are urgently needed to guide conservation, and yet complete enumeration of organisms is impractical at present. One indirect approach is to measure richness at higher taxonomic ranks, such as families. The difficulty is how to combine information from different groups on numbers of higher taxa, when these taxa may in effect have been defined in different ways, particularly for more distantly related major groups. In this paper, the regional family richness of terrestrial and freshwater seed plants, amphibians, reptiles and mammals is mapped worldwide by combining: (i) absolute family richness; (ii) proportional family richness; and (iii) proportional family richness weighted for the total species richness in each major group. The assumptions of the three methods and their effects on the results are discussed, although for these data the broad pattern is surprisingly robust with respect to the method of combination. Scores from each of the methods of combining families are used to rank the top five richness hotspots and complementary areas, and hotspots of endemism are mapped by unweighted combination of range-size rarity scores

Differential effects of oilseed supplements on methane production and milk fatty acid concentrations in dairy cows

It is known that supplementing dairy cow diets with full-fat oilseeds can be used as a strategy to mitigate methane emissions, through their action on rumen fermentation. However, direct comparisons of the effect of different oil sources are very few, as are studies implementing supplementation levels that reflect what is commonly fed on commercial farms. The objective was to investigate the effect of feeding different forms of supplemental plant oils on both methane emissions and milk fatty acid (FA) profile. Four multiparous, Holstein-Friesian cows in mid-lactation were randomly allocated to one of four treatment diets in a 4 x 4 Latin square design with 28-day periods. Diets were fed as a TMR with a 50:50 forage:concentrate ratio (dry matter, DM basis) with the forage consisting of 75:25 maize silage:grass silage (DM). Dietary treatments were a control diet containing no supplemental fat, and three treatment diets containing extruded linseed (EL), calcium salts of palm and linseed oil (CPLO) or milled rapeseed (MR) formulated to provide each cow with an estimated 500 g additional oil/d (22 g oil/kg diet DM). Dry matter intake (DMI), milk yield, milk composition and methane production were measured at the end of each experimental period when cows were housed in respiration chambers for 4 days. There was no effect of treatment diet on DMI or milk protein or lactose concentration, but oilseed-based supplements increased milk yield compared with the control diet and milk fat concentration relative to control was reduced by 4 g/kg by supplemental EL. Feeding CPLO reduced methane production, and both linseed-based supplements decreased methane yield (by 1.8 L/kg DMI) and intensity (by 2.7 L/kg milk yield) compared with the control diet, but feeding MR had no effect on methane emission. All the fat supplements decreased milk total saturated fatty acid (SFA) concentration compared with the control, and SFA were replaced with mainly cis-9 18:1 but also trans FA (and in the case of EL and CPLO there were increases in polyunsaturated FA concentration). Supplementing dairy cow diets with these oilseed-based preparations affected milk FA profile and increased milk yield. However, only the linseed-based supplements reduced methane production, yield, or intensity, whilst feeding MR had no effect

Global analysis reveals the complexity of the human glomerular extracellular matrix.

The glomerulus contains unique cellular and extracellular matrix (ECM) components, which are required for intact barrier function. Studies of the cellular components have helped to build understanding of glomerular disease; however, the full composition and regulation of glomerular ECM remains poorly understood. We used mass spectrometry-based proteomics of enriched ECM extracts for a global analysis of human glomerular ECM in vivo and identified a tissue-specific proteome of 144 structural and regulatory ECM proteins. This catalog includes all previously identified glomerular components plus many new and abundant components. Relative protein quantification showed a dominance of collagen IV, collagen I, and laminin isoforms in the glomerular ECM together with abundant collagen VI and TINAGL1. Protein network analysis enabled the creation of a glomerular ECM interactome, which revealed a core of highly connected structural components. More than one half of the glomerular ECM proteome was validated using colocalization studies and data from the Human Protein Atlas. This study yields the greatest number of ECM proteins relative to previous investigations of whole glomerular extracts, highlighting the importance of sample enrichment. It also shows that the composition of glomerular ECM is far more complex than previously appreciated and suggests that many more ECM components may contribute to glomerular development and disease processes. The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium with the dataset identifier PXD000456

Catch Composition and Selectivity of Fishing Gears in a Multi-Species Indonesian Coral Reef Fishery

There are millions of small-scale fishers worldwide that rely on coral reefs for their livelihood. Yields from many of these coral reef fisheries, however, have been declining. In Indonesia and other coral reefs worldwide, management approaches are dominated by marine protected areas but other options including gear-restrictions may be feasible and more adaptive to local ecological and social conditions. Yet, there is little data on the impacts and selectivity of fishing gears for coral reef fisheries. In this paper, we present results from a case study on the island of Lombok, where we examine the selectivity and overlap in catch composition of the two main fishing gear types: spearguns and handlines. The catch per unit effort (CPUE) was greater in handlines than spearguns, 10.8 and 9.97 kg trip-1, respectively. The two gears targeted different fish communities with little overlap in dominant species, suggesting a partitioning of resources; handlines targeted piscivores, whereas spearguns targeted mostly herbivores. Mean trophic level was 3.6 for the handline catch and 2.8 for spearguns, where it was inversely related to CPUE. Spearguns captured more species overall and the number of species increased as the CPUE increased. Length parameters of maturity indicated that neither gear showed signs of (growth) overfishing and fishing grounds dominated by speargun fishers had catches associated with younger ages at first maturity than handlines. Our findings provide local baseline data on the potential utility of gear restrictions as a management tool. Specifically, managers could monitor reefs and reduce handlines when piscivorous fishes are low and on spearguns when species diversity is low or algal abundance is high. Should it become more desirable to implement ecosystem approaches to management that are adaptive to changing ecological and social conditions, these indicators may be used as starting points along with local management preferences of fishers

Optimized fishing through periodically harvested closures

1. Periodically harvested closures (PHCs) are a traditional form of fisheries management that improve fishing efficiency during harvests, partly by reducing fish wariness to fishers during closed periods. However, whether PHCs also result in high yields and healthy marine ecosystems is unknown, even as PHCs are being promoted as a culturally appropriate management tool in the Indo-Pacific.2. We integrated field-derived estimates of change in fish wariness into a bioeconomic fisheries model to quantify to what degree PHCs can maximize harvest efficiency, fisheries yield and fish stock biomass.3. Our model indicated that PHCs that had a closure period of one to a few years between a single pulse harvest were able to generate equivalent fisheries yield and stock biomass levels, with greater harvest efficiency than was able to be achieved using permanent closures and other fisheries management tools.4. Fish life-history traits had little impact on the optimality of PHCs in maximizing the triple objective of harvest efficiency, fisheries yield and stock abundance, with overfishing similarly having little effect at anything under extreme levels. Under moderate overfishing, there was a trade-off between PHCs, which maximised harvest efficiency, and no-take permanent closures that maximised yield. However, the former outweighed the latter, and only at extreme levels of overfishing, where stock was reduced to < 18 % of unfished biomass, were permanent closures favoured over PHCs

Common variants of the TCF7L2 gene are associated with increased risk of type 2 diabetes mellitus in a UK-resident South Asian population

Background Recent studies have implicated variants of the transcription factor 7-like 2 (TCF7L2) gene in genetic susceptibility to type 2 diabetes mellitus in several different populations. The aim of this study was to determine whether variants of this gene are also risk factors for type 2 diabetes development in a UK-resident South Asian cohort of Punjabi ancestry. Methods We genotyped four single nucleotide polymorphisms (SNPs) of TCF7L2 (rs7901695, rs7903146, rs11196205 and rs12255372) in 831 subjects with diabetes and 437 control subjects. Results The minor allele of each variant was significantly associated with type 2 diabetes; the greatest risk of developing the disease was conferred by rs7903146, with an allelic odds ratio (OR) of 1.31 (95% CI: 1.11 – 1.56, p = 1.96 × 10-3). For each variant, disease risk associated with homozygosity for the minor allele was greater than that for heterozygotes, with the exception of rs12255372. To determine the effect on the observed associations of including young control subjects in our data set, we reanalysed the data using subsets of the control group defined by different minimum age thresholds. Increasing the minimum age of our control subjects resulted in a corresponding increase in OR for all variants of the gene (p ≤ 1.04 × 10-7). Conclusion Our results support recent findings that TCF7L2 is an important genetic risk factor for the development of type 2 diabetes in multiple ethnic groups

Analysis of parameters that affect human hematopoietic cell outputs in mutant c-kit-immunodeficient mice.

Xenograft models are transforming our understanding of the output capabilities of primitive human hematopoietic cells in vivo. However, many variables that affect posttransplantation reconstitution dynamics remain poorly understood. Here, we show that an equivalent level of human chimerism can be regenerated from human CD34(+) cord blood cells transplanted intravenously either with or without additional radiation-inactivated cells into 2- to 6-month-old NOD-Rag1(-/-)-IL2Rγc(-/-) (NRG) mice given a more radioprotective conditioning regimen than is possible in conventionally used, repair-deficient NOD-Prkdc(scid/scid)-IL2Rγc(-/-) (NSG) hosts. Comparison of sublethally irradiated and non-irradiated NRG mice and W(41)/W(41) derivatives showed superior chimerism in the W(41)-deficient recipients, with some differential effects on different lineage outputs. Consistently superior outputs were observed in female recipients regardless of their genotype, age, or pretransplantation conditioning, with greater differences apparent later after transplantation. These results define key parameters for optimizing the sensitivity and minimizing the intraexperimental variability of human hematopoietic xenografts generated in increasingly supportive immunodeficient host mice. Exp Hematol 2017 Apr; 48:41-49

The response of perennial and temporary headwater stream invertebrate communities to hydrological extremes

The headwaters of karst rivers experience considerable hydrological variability, including spates and streambed drying. Extreme summer flooding on the River Lathkill (Derbyshire, UK) provided the opportunity to examine the invertebrate community response to unseasonal spate flows, flow recession and, at temporary sites, streambed drying. Invertebrates were sampled at sites with differing flow permanence regimes during and after the spates. Following streambed drying at temporary sites, dewatered surface sediments were investigated as a refugium for aquatic invertebrates. Experimental rehydration of these dewatered sediments was conducted to promote development of desiccation-tolerant life stages. At perennial sites, spate flows reduced invertebrate abundance and diversity, whilst at temporary sites, flow reactivation facilitated rapid colonisation of the surface channel by a limited number of invertebrate taxa. Following streambed drying, 38 taxa were recorded from the dewatered and rehydrated sediments, with Oligochaeta being the most abundant taxon and Chironomidae (Diptera) the most diverse. Experimental rehydration of dewatered sediments revealed the presence of additional taxa, including Stenophylax sp. (Trichoptera: Limnephilidae) and Nemoura sp. (Plecoptera: Nemouridae). The influence of flow permanence on invertebrate community composition was apparent despite the aseasonal high-magnitude flood events

Characterizing Atmospheric Transport Pathways to Antarctica and the Remote Southern Ocean Using Radon-222

We discuss remote terrestrial influences on boundary layer air over the Southern Ocean and Antarctica, and the mechanisms by which they arise, using atmospheric radon observations as a proxy. Our primary motivation was to enhance the scientific community’s ability to understand and quantify the potential effects of pollution, nutrient or pollen transport from distant land masses to these remote, sparsely instrumented regions. Seasonal radon characteristics are discussed at 6 stations (Macquarie Island, King Sejong, Neumayer, Dumont d’Urville, Jang Bogo and Dome Concordia) using 1–4 years of continuous observations. Context is provided for differences observed between these sites by Southern Ocean radon transects between 45 and 67°S made by the Research Vessel Investigator. Synoptic transport of continental air within the marine boundary layer (MBL) dominated radon seasonal cycles in the mid-Southern Ocean site (Macquarie Island). MBL synoptic transport, tropospheric injection, and Antarctic outflow all contributed to the seasonal cycle at the sub-Antarctic site (King Sejong). Tropospheric subsidence and injection events delivered terrestrially influenced air to the Southern Ocean MBL in the vicinity of the circumpolar trough (or “Polar Front”). Katabatic outflow events from Antarctica were observed to modify trace gas and aerosol characteristics of the MBL 100–200 km off the coast. Radon seasonal cycles at coastal Antarctic sites were dominated by a combination of local radon sources in summer and subsidence of terrestrially influenced tropospheric air, whereas those on the Antarctic Plateau were primarily controlled by tropospheric subsidence. Separate characterization of long-term marine and katabatic flow air masses at Dumont d’Urville revealed monthly mean differences in summer of up to 5 ppbv in ozone and 0.3 ng m-3 in gaseous elemental mercury. These differences were largely attributed to chemical processes on the Antarctic Plateau. A comparison of our observations with some Antarctic radon simulations by global climate models over the past two decades indicated that: (i) some models overestimate synoptic transport to Antarctica in the MBL, (ii) the seasonality of the Antarctic ice sheet needs to be better represented in models, (iii) coastal Antarctic radon sources need to be taken into account, and (iv) the underestimation of radon in subsiding tropospheric air needs to be investigated