Holocene climatic change and the development of the lake-effect snowbelt in Michigan, USA

Lake-effect snow is an important constraint on ecological and socio-economic systems near the North American Great Lakes. Little is known about the Holocene history of lake-effect snowbelts, and it is difficult to decipher how lake-effect snowfall abundance affected ecosystem development. We conducted oxygen-isotope analysis of calcite in lake-sediment cores from northern Lower Michigan to infer Holocene climatic variation and assess snowbelt development. The two lakes experience the same synoptic-scale climatic systems, but only one of them (Huffman Lake) receives a significant amount of lake-effect snow. A 177-cm difference in annual snowfall causes groundwater inflow at Huffman Lake to be 18O-depleted by 2.3‰ relative to O'Brien Lake. To assess when the lake-effect snowbelt became established, we compared calcite-δ18O profiles of the last 11,500 years from these two sites. The chronologies are based on accelerator-mass-spectrometry 14C ages of 11 and 17 terrestrial-plant samples from Huffman and O'Brien lakes, respectively. The values of δ18O are low at both sites from 11,500 to 9500 cal yr BP when the Laurentide Ice Sheet (LIS) exerted a dominant control over the regional climate and provided periodic pulses of meltwater to the Great Lakes basin. Carbonate δ18O increases by 2.6‰ at O'Brien Lake and by 1.4‰ at Huffman Lake between 9500 and 7000 cal yr BP, suggesting a regional decline in the proportion of runoff derived from winter precipitation. The Great Lakes snowbelt probably developed between 9500 and 5500 cal yr BP as inferred from the progressive 18O-depletion at Huffman Lake relative to O'Brien Lake, with the largest increase of lake-effect snow around 7000 cal yr BP. Lake-effect snow became possible at this time because of increasing contact between the Great Lakes and frigid arctic air. These changes resulted from enhanced westerly flow over the Great Lakes as the LIS collapsed, and from rapidly rising Great Lakes levels during the Nipissing Transgression. The δ18O difference between Huffman and O'Brien lakes declines after 5500 cal yr BP, probably because of a northward shift of the polar vortex that brought increasing winter precipitation to the entire region. However, δ18O remains depleted at Huffman Lake relative to O'Brien Lake because of the continued production of lake-effect snow.

Beyond the tree of texts: Building an empirical model of scribal variation through graph analysis of texts and stemmata

Stemmatology, or the reconstruction of the transmission history of texts, is a field that stands particularly to gain from digital methods. Many scholars already take stemmatic approaches that rely heavily on computational analysis of the collated text (e.g. Robinson and O’Hara 1996; Salemans 2000; Heikkilä 2005; Windram et al. 2008 among many others). Although there is great value in computationally assisted stemmatology, providing as it does a reproducible result and allowing access to the relevant methodological process in related fields such as evolutionary biology, computational stemmatics is not without its critics. The current state-of-the-art effectively forces scholars to choose between a preconceived judgment of the significance of textual differences (the Lachmannian or neo-Lachmannian approach, and the weighted phylogenetic approach) or to make no judgment at all (the unweighted phylogenetic approach). Some basis for judgment of the significance of variation is sorely needed for medieval text criticism in particular. By this, we mean that there is a need for a statistical empirical profile of the text-genealogical significance of the different sorts of variation in different sorts of medieval texts. The rules that apply to copies of Greek and Latin classics may not apply to copies of medieval Dutch story collections; the practices of copying authoritative texts such as the Bible will most likely have been different from the practices of copying the Lives of local saints and other commonly adapted texts. It is nevertheless imperative that we have a consistent, flexible, and analytically tractable model for capturing these phenomena of transmission. In this article, we present a computational model that captures most of the phenomena of text variation, and a method for analysis of one or more stemma hypotheses against the variation model. We apply this method to three ‘artificial traditions’ (i.e. texts copied under laboratory conditions by scholars to study the properties of text variation) and four genuine medieval traditions whose transmission history is known or deduced in varying degrees. Although our findings are necessarily limited by the small number of texts at our disposal, we demonstrate here some of the wide variety of calculations that can be made using our model. Certain of our results call sharply into question the utility of excluding ‘trivial’ variation such as orthographic and spelling changes from stemmatic analysis.

High variability and non-neutral evolution of the mammalian avpr1a gene

BACKGROUND: The arginine-vasopressin 1a receptor has been identified as a key determinant for social behaviour in Microtus voles, humans and other mammals. Nevertheless, the genetic bases of complex phenotypic traits like differences in social and mating behaviour among species and individuals remain largely unknown. Contrary to previous studies focusing on differences in the promotor region of the gene, we investigate here the level of functional variation in the coding region (exon 1) of this locus. RESULTS: We detected high sequence diversity between higher mammalian taxa as well as between species of the genus Microtus. This includes length variation and radical amino acid changes, as well as the presence of distinct protein variants within individuals. Additionally, negative selection prevails on most parts of the first exon of the arginine-vasopressin receptor 1a (avpr1a) gene but it contains regions with higher rates of change that harbour positively selected sites. Synonymous and non-synonymous substitution rates in the avpr1a gene are not exceptional compared to other genes, but they exceed those found in related hormone receptors with similar functions. DISCUSSION: These results stress the importance of considering variation in the coding sequence of avpr1a in regards to associations with life history traits (e.g. social behaviour, mating system, habitat requirements) of voles, other mammals and humans in particular.

Diversification in the South American Pampas: the genetic and morphological variation of the widespread Petunia axillaris complex (Solanaceae)

Understanding the spatiotemporal distribution of genetic variation and the ways in which this distribution is connected to the ecological context of natural populations is fundamental for understanding the nature and mode of intraspecific and, ultimately, interspecific differentiation. The Petunia axillaris complex is endemic to the grasslands of southern South America and includes three subspecies: P.a.axillaris, P.a.parodii and P.a.subandina. These subspecies are traditionally delimited based on both geography and floral morphology, although the latter is highly variable. Here, we determined the patterns of genetic (nuclear and cpDNA), morphological and ecological (bioclimatic) variation of a large number of P.axillaris populations and found that they are mostly coincident with subspecies delimitation. The nuclear data suggest that the subspecies are likely independent evolutionary units, and their morphological differences may be associated with local adaptations to diverse climatic and/or edaphic conditions and population isolation. The demographic dynamics over time estimated by skyline plot analyses showed different patterns for each subspecies in the last 100000years, which is compatible with a divergence time between 35000 and 107000years ago between P.a.axillaris and P.a.parodii, as estimated with the IMa program. Coalescent simulation tests using Approximate Bayesian Computation do not support previous suggestions of extensive gene flow between P.a.axillaris and P.a.parodii in their contact zone.

A genome-to-genome analysis of associations between human genetic variation, HIV-1 sequence diversity, and viral control

HIV-1 sequence diversity is affected by selection pressures arising from host genomic factors. Using paired human and viral data from 1071 individuals, we ran >3000 genome-wide scans, testing for associations between host DNA polymorphisms, HIV-1 sequence variation and plasma viral load (VL), while considering human and viral population structure. We observed significant human SNP associations to a total of 48 HIV-1 amino acid variants (p<2.4 × 10−12). All associated SNPs mapped to the HLA class I region. Clinical relevance of host and pathogen variation was assessed using VL results. We identified two critical advantages to the use of viral variation for identifying host factors: (1) association signals are much stronger for HIV-1 sequence variants than VL, reflecting the ‘intermediate phenotype’ nature of viral variation; (2) association testing can be run without any clinical data. The proposed genome-to-genome approach highlights sites of genomic conflict and is a strategy generally applicable to studies of host–pathogen interaction.

Does Sex Speed Up Evolutionary Rate and Increase Biodiversity?

Most empirical and theoretical studies have shown that sex increases the rate of evolution, although evidence of sex constraining genomic and epigenetic variation and slowing down evolution also exists. Faster rates with sex have been attributed to new gene combinations, removal of deleterious mutations, and adaptation to heterogeneous environments. Slower rates with sex have been attributed to removal of major genetic rearrangements, the cost of finding a mate, vulnerability to predation, and exposure to sexually transmitted diseases. Whether sex speeds or slows evolution, the connection between reproductive mode, the evolutionary rate, and species diversity remains largely unexplored. Here we present a spatially explicit model of ecological and evolutionary dynamics based on DNA sequence change to study the connection between mutation, speciation, and the resulting biodiversity in sexual and asexual populations. We show that faster speciation can decrease the abundance of newly formed species and thus decrease long-term biodiversity. In this way, sex can reduce diversity relative to asexual populations, because it leads to a higher rate of production of new species, but with lower abundances. Our results show that reproductive mode and the mechanisms underlying it can alter the link between mutation, evolutionary rate, speciation and biodiversity and we suggest that a high rate of evolution may not be required to yield high biodiversity.

Biological variation of established and novel biomarkers for atherosclerosis: Results from a prospective, parallel-group cohort study.

BACKGROUND Biomarkers are a promising tool for the management of patients with atherosclerosis, but their variation is largely unknown. We assessed within-subject and between-subject biological variation of biomarkers in peripheral artery disease (PAD) patients and healthy controls, and defined which biomarkers have a favorable variation profile for future studies. METHODS Prospective, parallel-group cohort study, including 62 patients with stable PAD (79% men, 65±7years) and 18 healthy control subjects (44% men, 57±7years). Blood samples were taken at baseline, and after 3-, 6-, and 12-months. We calculated within-subject (CVI) and between-subject (CVG) coefficients of variation and intra-class correlation coefficient (ICC). RESULTS Mean levels of D-dimer, hs-CRP, IL-6, IL-8, MMP-9, MMP-3, S100A8/A9, PAI-1, sICAM-1, and sP-selectin levels were higher in PAD patients than in healthy controls (P≤.05 for all). CVI and CVG of the different biomarkers varied considerably in both groups. An ICC≥0.5 (indicating moderate-to-good reliability) was found for hs-CRP, D-Dimer, E-selectin, IL-10, MCP-1, MMP-3, oxLDL, sICAM-1 and sP-selectin in both groups, for sVCAM in healthy controls and for MMP-9, PAI-1 and sCD40L in PAD patients. CONCLUSIONS Single biomarker measurements are of limited utility due to large within-subject variation, both in PAD patients and healthy subjects. D-dimer, hs-CRP, MMP-9, MMP-3, PAI-1, sP-selectin and sICAM-1 are biomarkers with both higher mean levels in PAD patients and a favorable variation profile making them most suitable for future studies.

Drought coping and adaptation strategies: Understanding adaptations to climate change in agro-pastoral livestock production in Makueni district, Kenya

Using drought as a lens, this article analyses how agro-pastoralists in Makueni district, Kenya adapt their livestock production to climate variability and change. Data were collected from a longitudinal survey of 127 agro-pastoral households. Approximately one-third of the households have inadequate feeds, and livestock diseases are major challenges during non-drought and drought periods. Agro-pastoralists’ responses to drought are reactive and mainly involve intensifying exploitation of resources and the commons. Proactive responses such as improving production resources are few. Poverty, limited responses to market dynamics and inadequate skills constrain adaptations. Many agro-pastoralists’ attachment to livestock deters livestock divestment, favouring disadvantageous sales that result in declining incomes. To improve adaptive capacity, interventions should expose agro-pastoralists to other forms of savings, incorporate agro-pastoralists as agents of change by building their capacity to provide extension services, and maintain infrastructure. Securing livestock mobility, pasture production and access is crucial under the variable social-ecological conditions.

A variationist approach to the examination of insertion and deletion of /h/ in Kosraean English

I report on language variation in the unresearched variety of English emerging on Kosrae, Federated States of Micronesia. English is spoken as the inter-island lingua franca throughout Micronesia and has been the official language of FSM since gaining its independence in 1986, though still retaining close ties with the US through and economic “compact” agreement. I present here an analysis of a corpus of over 90 Kosraean English speakers, compiled during a three month fieldwork trip to the island in the Western Pacific. The 45 minute sociolinguistically sensitive recordings are drawn from a corpus of old and young, with varying levels of education and occupations, and off-island experiences. In the paper I analyse two variables. The first variable is the realisation of /h/, often subject to deletion in both L1 and L2 varieties of English. Such occurrences are commonly associated with Cockney English, but also found in Caribbean English and the postcolonial English of Australia. For example:  Male, 31: yeah I build their house their local huts and they pay me /h/ deletion is frequent in Kosraean English, but, perhaps expectedly, occurs slightly less among people with higher contact with American English, through having spent longer periods off island. The second feature under scrutiny is the variable epenthesis of [h] to provide a consonantal onset to vowel-initial syllables.  Male, 31: that guy is really hold now This practice is also found beyond Kosraean English. Previous studies find h-epenthesis arising in L1 varieties including Newfoundland and Tristan de Cunha English, while similar manifestations are identified in Francophone L2 learners of English. My variationist statistical analysis has shown [h] insertion:  to disproportionately occur intervocalically;  to be constrained by both speaker gender and age: older males are much more likely to epenthesis [h] in their speech;  to be more likely in the onset of stressed as opposed to unstressed syllables. In light of the findings of my analysis, I consider the relationship between h-deletion and h-epenthesis, the plausibility of hypercorrection as a motivation for the variation, and the potential influence of the substrate language, alongside sociolinguistic factors such as attitudes towards the US based on mobility. The analysis sheds light on the extent to which different varieties share this characteristic and the comparability of them in terms of linguistic constraints and attributes. Clarke, S. (2010). Newfoundland and Labrador English. Edinburgh: Edinburgh University Press Hackert, S. (2004). Urban Bahamian Creole: System and Variation. Varieties of English Around the World G32. Amsterdam: Benjamins Milroy, J. (1983). On the Sociolinguistic History of H-dropping in English in Current topics in English historical linguistics: Odense UP

Is hatchery stocking a help or harm? Evidence, limitations and future directions in ecological and genetic surveys

Hatchery fish stocking for stock enhancement has been operated at a massive and global scale. However, the use of hatchery fish as a means of stock enhancement is highly controversial, and little is known about its effects on wild stock and consequences for stock enhancement. Here we review the scientific literature on this subject in order to address a fundamental - question is hatchery stocking a help or harm for wild stock and stock enhancement? We summarized 266 peer-reviewed papers that were published in the last 50 years, which describe empirical case studies on ecology and genetics of hatchery stocks and their effects on stock enhancement. Specifically, we asked whether hatchery stock and wild stock differed in fitness and the level of genetic variation, and whether stocking affected population abundance. Seventy studies contained comparisons between hatchery and wild stocks, out of which 23 studies showed significantly negative effects of hatchery rearing on the fitness of stocked fish, and 28 studies showed reduced genetic variation in hatchery populations. None of these studies suggested a positive genetic effect on the fitness of hatchery-reared individuals after release. These results suggest that negative effects of hatchery rearing are not just a concern but undeniably present in many aquaculture species. In a few cases, however, no obvious effect of hatchery rearing was observed, and a positive contribution of hatchery stock to the abundance of fish populations was indicated. These examples suggest that there is a chance to improve hatchery practices and mitigate the negative effects on wild stocks, although scientific data supporting the positive effect on stock enhancement are largely missing at this moment. Technically, microsatellite-based parentage assignments have been proven as a useful tool for the evaluation of reproductive fitness in natural settings, which is a key for stock enhancement by hatchery-based stocking. We discuss implications of these results, as well as their limitations and future directions. (C) 2010 Elsevier B.V. All rights reserved.

Lunar tractive forces and renal stone incidence

Background. Several factors are implicated in renal stone formation and peak incidence of renal colic admissions to emergency departments (ED). Little is known about the influence of potential environmental triggers such as lunar gravitational forces. We conducted a retrospective study to test the hypothesis that the incidence of symptomatic renal colics increases at the time of the full and new moon because of increased lunar gravitational forces. Methods. We analysed 1500 patients who attended our ED between 2000 and 2010 because of nephrolithiasis-induced renal colic. The lunar phases were defined as full moon ± 1 day, new moon ± 1 day, and the days in-between as "normal" days. Results. During this 11-year period, 156 cases of acute nephrolithiasis were diagnosed at the time of a full moon and 146 at the time of a new moon (mean of 0.4 per day for both). 1198 cases were diagnosed on "normal" days (mean 0.4 per day). The incidence of nephrolithiasis in peak and other lunar gravitational phases, the circannual variation and the gender-specific analysis showed no statistically significant differences. Conclusion. In this adequate powered longitudinal study, changes in tractive force during the different lunar phases did not influence the incidence of renal colic admissions in emergency department.

Plant volatiles: production, function and pharmacology

Plant volatiles typically occur as a complex mixture of low-molecular weight lipophilic compounds derived from different biosynthetic pathways, and are seemingly produced as part of a defense strategy against biotic and abiotic stress, as well as contributing to various physiological functions of the producer organism. The biochemistry and molecular biology of plant volatiles is complex, and involves the interplay of several biochemical pathways and hundreds of genes. All plants are able to store and emit volatile organic compounds (VOCs), but the process shows remarkable genotypic variation and phenotypic plasticity. From a physiological standpoint, plant volatiles are involved in three critical processes, namely plant–plant interaction, the signaling between symbiotic organisms, and the attraction of pollinating insects. Their role in these ‘‘housekeeping’’ activities underlies agricultural applications that range from the search for sustainable methods for pest control to the production of flavors and fragrances. On the other hand, there is also growing evidence that VOCs are endowed with a range of biological activities in mammals, and that they represent a substantially under-exploited and still largely untapped source of novel drugs and drug leads. This review summarizes recent major developments in the study of biosynthesis, ecological functions and medicinal applications of plant VOCs.

Structural and procedural properties important in promoting bio-enterprises as alternative livelihoods to pastoral and agro-pastoral livelihoods

Alternative livelihoods to pastoral and agro-pastoral livelihoods are increasingly gaining attention in rural development but few empirical evidence exist on how to go about supporting such initiatives. As pastoral and agro-pastoral production conditions change due to various factors including market conditions, climate variability and change, pastoralists and agro-pastoralists are increasingly faced with the challenge of finding alternative livelihoods. Bio-enterprises offer such alternatives or complementary activities for rural actors to adapt to changing socio-ecological conditions. This study examines the roles of bio-enterprise initiatives from a livelihood perspective and identifies the features important for such initiatives to reduce poverty and improve the adaptive capacities of pastoralists and agro-pastoralists. It draws on four different bio-enterprise initiatives on agro-pastoral and pastoral livelihoods and on improved natural resources management (NRM) in the drylands of Kenya. Data were collected through interviews, focus group discussions, informal discussions and the study of reports. Results shows among other factors that diversification into enterprises requires cooperation among the stakeholders with their varying experiences in development, NRM and business development. Other factors such as sustained financial support, capacity development to survive the market introduction phase, as well as quantity and quality of the product, are critical. Mentoring proved to be a driver of success in some initiatives.

Caenorhabditis elegans Heterochromatin protein 1 (HPL-2) links developmental plasticity, longevity and lipid metabolism

Background Heterochromatin protein 1 (HP1) family proteins have a well-characterized role in heterochromatin packaging and gene regulation. Their function in organismal development, however, is less well understood. Here we used genome-wide expression profiling to assess novel functions of the Caenorhabditis elegans HP1 homolog HPL-2 at specific developmental stages. Results We show that HPL-2 regulates the expression of germline genes, extracellular matrix components and genes involved in lipid metabolism. Comparison of our expression data with HPL-2 ChIP-on-chip profiles reveals that a significant number of genes up- and down-regulated in the absence of HPL-2 are bound by HPL-2. Germline genes are specifically up-regulated in hpl-2 mutants, consistent with the function of HPL-2 as a repressor of ectopic germ cell fate. In addition, microarray results and phenotypic analysis suggest that HPL-2 regulates the dauer developmental decision, a striking example of phenotypic plasticity in which environmental conditions determine developmental fate. HPL-2 acts in dauer at least partly through modulation of daf-2/IIS and TGF-β signaling pathways, major determinants of the dauer program. hpl-2 mutants also show increased longevity and altered lipid metabolism, hallmarks of the long-lived, stress resistant dauers. Conclusions Our results suggest that the worm HP1 homologue HPL-2 may coordinately regulate dauer diapause, longevity and lipid metabolism, three processes dependent on developmental input and environmental conditions. Our findings are of general interest as a paradigm of how chromatin factors can both stabilize development by buffering environmental variation, and guide the organism through remodeling events that require plasticity of cell fate regulation.