Soil nutrients and beta diversity in the Bornean Dipterocarpaceae: evidence for niche partitioning by tropical rain forest trees

1   The relative importance of niche- and dispersal-mediated processes in structuring diverse tropical plant communities remains poorly understood. Here, we link mesoscale beta diversity to soil variation throughout a lowland Bornean watershed underlain by alluvium, sedimentary and granite parent materials ( c . 340 ha, 8–200 m a.s.l.). We test the hypothesis that species turnover across the habitat gradient reflects interspecific partitioning of soil resources. 2   Floristic inventories (≥ 1 cm d.b.h.) of the Dipterocarpaceae, the dominant Bornean canopy tree family, were combined with extensive soil analyses in 30 (0.16 ha) plots. Six samples per plot were analysed for total C, N, P, K, Ca and Mg, exchangeable K, Ca and Mg, extractable P, texture, and pH. 3   Extractable P, exchangeable K, and total C, N and P varied significantly among substrates and were highest on alluvium. Thirty-one dipterocarp species ( n  = 2634 individuals, five genera) were recorded. Dipterocarp density was similar across substrates, but richness and diversity were highest on nutrient-poor granite and lowest on nutrient-rich alluvium. 4   Eighteen of 22 species were positively or negatively associated with parent material. In 8 of 16 abundant species, tree distribution (≥ 10 cm d.b.h.) was more strongly non-random than juveniles (1–10 cm d.b.h.), suggesting higher juvenile mortality in unsuitable habitats. The dominant species Dipterocarpus sublamellatus (> 50% of stems) was indifferent to substrate, but nine of 11 ‘subdominant’ species (> 8 individuals ha −1 ) were substrate specialists. 5   Eighteen of 22 species were significantly associated with soil nutrients, especially P, Mg and Ca. Floristic variation was significantly correlated with edaphic and geographical distance for all stems ≥ 1 cm d.b.h. in Mantel analyses. However, juvenile variation (1–10 cm d.b.h.) was more strongly related to geographical distance than edaphic factors, while the converse held for established trees (≥ 10 cm d.b.h.), suggesting increased importance of niche processes with size class. 6   Pervasive dipterocarp associations with soil factors suggest that niche partitioning structures dipterocarp tree communities. Yet, much floristic variation unrelated to soil was correlated with geographical distance between plots, suggesting that dispersal and niche processes jointly determine mesoscale beta diversity in the Bornean Dipterocarpaceae. Journal of Ecology (2005) doi: 10.1111/j.1365-2745.2005.01077.xPeer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/72822/1/j.1365-2745.2005.01077.x.pd

El Niño Southern Oscillation signal in a new East Antarctic ice core, Mount Brown South

Abstract. Paleoclimate archives, such as high-resolution ice core records, provide a means to investigate long-term (multi-centennial) climate variability. Until recently, the Law Dome (Dome Summit South) ice core record remained one of few long-term high-resolution records in East Antarctica. A new ice core drilled in 2017/2018 at Mount Brown South, approximately 1000 km west of Law Dome, provides an additional high-resolution record that will likely span the last millennium in the Indian Ocean sector of East Antarctica. Here, we compare snowfall accumulation rates and sea salt concentrations in the upper portion (~21 m) of the Mount Brown South record, and an updated Law Dome record over the period 1975–2016. Annual sea salt concentrations from the Mount Brown South record preserves a stronger signal for the El Niño-Southern Oscillation (ENSO; in austral winter and spring, r = 0.521, p r = −0.387, p = 0.018, Niño 3.4). The Mount Brown South and Law Dome ice cores record inverse signals for the ENSO, suggesting the occurrence of distinct moisture and aerosol intrusions. We suggest that ENSO-related sea surface temperature anomalies in the equatorial Pacific drive atmospheric teleconnections in the southern mid-latitudes. These anomalies are associated with a weakening (strengthening) of regional westerly winds to the north of Mount Brown South that corresponds to years of low (high) sea salt deposition at Mount Brown South during La Niña (El Niño) events. The Mount Brown South annual sea salt record when complete will offer a new proxy record for reconstructions of the ENSO over the recent millennium, along with improved understanding of regional atmospheric variability in the southern Indian Ocean in addition to that derived from Law Dome

Global extent and drivers of mammal population declines in protected areas under illegal hunting pressure

Illegal hunting is a persistent problem in many protected areas, but an overview of the extent of this problem and its impact on wildlife is lacking. We reviewed 40 years (1980–2020) of global research to examine the spatial distribution of research and socio-ecological factors influencing population decline within protected areas under illegal hunting pressure. From 81 papers reporting 988 species/site combinations, 294 mammal species were reported to have been illegally hunted from 155 protected areas across 48 countries. Research in illegal hunting has increased substantially during the review period and showed biases towards strictly protected areas and the African continent. Population declines were most frequent in countries with a low human development index, particularly in strict protected areas and for species with a body mass over 100 kg. Our results provide evidence that illegal hunting is most likely to cause declines of large-bodied species in protected areas of resource-poor countries regardless of protected area conservation status. Given the growing pressures of illegal hunting, increased investments in people’s development and additional conservation efforts such as improving anti-poaching strategies and conservation resources in terms of improving funding and personnel directed at this problem are a growing priority

Novel genetic loci associated with hippocampal volume

The hippocampal formation is a brain structure integrally involved in episodic memory, spatial navigation, cognition and stress responsiveness. Structural abnormalities in hippocampal volume and shape are found in several common neuropsychiatric disorders. To identify the genetic underpinnings of hippocampal structure here we perform a genome-wide association study (GWAS) of 33,536 individuals and discover six independent loci significantly associated with hippocampal volume, four of them novel. Of the novel loci, three lie within genes (ASTN2, DPP4 and MAST4) and one is found 200 kb upstream of SHH. A hippocampal subfield analysis shows that a locus within the MSRB3 gene shows evidence of a localized effect along the dentate gyrus, subiculum, CA1 and fissure. Further, we show that genetic variants associated with decreased hippocampal volume are also associated with increased risk for Alzheimer's disease (rg =-0.155). Our findings suggest novel biological pathways through which human genetic variation influences hippocampal volume and risk for neuropsychiatric illness

Whole-genome sequencing in diverse subjects identifies genetic correlates of leukocyte traits: The NHLBI TOPMed program

Many common and rare variants associated with hematologic traits have been discovered through imputation on large-scale reference panels. However, the majority of genome-wide association studies (GWASs) have been conducted in Europeans, and determining causal variants has proved challenging. We performed a GWAS of total leukocyte, neutrophil, lymphocyte, monocyte, eosinophil, and basophil counts generated from 109,563,748 variants in the autosomes and the X chromosome in the Trans-Omics for Precision Medicine (TOPMed) program, which included data from 61,802 individuals of diverse ancestry. We discovered and replicated 7 leukocyte trait associations, including (1) the association between a chromosome X, pseudo-autosomal region (PAR), noncoding variant located between cytokine receptor genes (CSF2RA and CLRF2) and lower eosinophil count; and (2) associations between single variants found predominantly among African Americans at the S1PR3 (9q22.1) and HBB (11p15.4) loci and monocyte and lymphocyte counts, respectively. We further provide evidence indicating that the newly discovered eosinophil-lowering chromosome X PAR variant might be associated with reduced susceptibility to common allergic diseases such as atopic dermatitis and asthma. Additionally, we found a burden of very rare FLT3 (13q12.2) variants associated with monocyte counts. Together, these results emphasize the utility of whole-genome sequencing in diverse samples in identifying associations missed by European-ancestry-driven GWASs

Whole genome sequence analysis of platelet traits in the NHLBI Trans-Omics for Precision Medicine (TOPMed) initiative

Platelets play a key role in thrombosis and hemostasis. Platelet count (PLT) and mean platelet volume (MPV) are highly heritable quantitative traits, with hundreds of genetic signals previously identified, mostly in European ancestry populations. We here utilize whole genome sequencing (WGS) from NHLBI's Trans-Omics for Precision Medicine initiative (TOPMed) in a large multi-ethnic sample to further explore common and rare variation contributing to PLT (n = 61 200) and MPV (n = 23 485). We identified and replicated secondary signals at MPL (rs532784633) and PECAM1 (rs73345162), both more common in African ancestry populations. We also observed rare variation in Mendelian platelet-related disorder genes influencing variation in platelet traits in TOPMed cohorts (not enriched for blood disorders). For example, association of GP9 with lower PLT and higher MPV was partly driven by a pathogenic Bernard-Soulier syndrome variant (rs5030764, p.Asn61Ser), and the signals at TUBB1 and CD36 were partly driven by loss of function variants not annotated as pathogenic in ClinVar (rs199948010 and rs571975065). However, residual signal remained for these gene-based signals after adjusting for lead variants, suggesting that additional variants in Mendelian genes with impacts in general population cohorts remain to be identified. Gene-based signals were also identified at several genome-wide association study identified loci for genes not annotated for Mendelian platelet disorders (PTPRH, TET2, CHEK2), with somatic variation driving the result at TET2. These results highlight the value of WGS in populations of diverse genetic ancestry to identify novel regulatory and coding signals, even for well-studied traits like platelet traits