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bioRxiv2018

Genetic diversity and distribution of indigenous soybean-nodulating bradyrhizobia in the Philippines

The diversity of indigenous bradyrhizobia from soils collected at 11 locations in the Philippines was investigated using PSB-SY2 local soybean cultivar as the host plant. Polymerase Chain Reaction-Restriction Fragment Length Polymorphism (PCR-RFLP) treatment for 16S rRNA, 16S-23S rRNA internal transcribed spacer (ITS) region and rpoB housekeeping gene was performed primarily to detect the genetic variation among the 424 isolates collected. Then, sequence analysis of 16S rRNA, ITS region and rpoB gene was performed for the representative isolates. Majority of the isolates were classified under Bradyrhizobium elkanii, B. diazoefficiens, B. japonicum, Bradyrhizobium sp., and few isolates were related to B. yuanmingense. Genetic variations observed through PCR-RFLP and sequence analyses of the ITS region and rpoB gene generally occurred in B. elkanii, suggesting an occurrence of gene transfer. Shannons diversity index showed varied results with a lowest score of 0.00 and highest at 0.98 indicating a very diverse population of bradyrhizobia across the country. Among all the factors considered in this work, soil management such as period of flooding and some soil properties provided major influence on the distribution and diversity of soybean bradyrhizobia in the country. Thus, it is proposed that the major micro-symbiont of soybean in the Philippines are B. elkanii for non-flooded soils, then B. diazoefficiens and B. japonicum for flooded soils.\n\nImportanceAgriculture production in the Philippines has been and is currently heavily dependent on chemical inputs with mainly rice or corn mono-cropping that it rendered the soil acidic and unproductive. Legume research in the country are mainly focused on plant varietal improvements and very few are aimed at understanding the ecological niche of rhizobia present in the soil. Since soybean has mutual relationship with rhizobia, this legume is a good fallow crop or a rotation crop after rice and corn to help build up the nitrogen stock in the soil. The significance of this research is the better understanding of the ecological niche of indigenous soybean bradyrhizobia, particularly in a tropical archipelago like the Philippines. This work was conceptualized with the utmost goal to increase soybean yield by harnessing and evaluating the indigenous rhizobia in the soil to make production more sustainable and human-friendly.

microbiology↗
bioRxiv2018

Soil viruses are underexplored players in ecosystem carbon processing

Rapidly thawing permafrost harbors ~30-50% of global soil carbon, and the fate of this carbon remains unknown. Microorganisms will play a central role in its fate, and their viruses could modulate that impact via induced mortality and metabolic controls. Because of the challenges of recovering viruses from soils, little is known about soil viruses or their role(s) in microbial biogeochemical cycling. Here, we describe 53 viral populations (vOTUs) recovered from seven quantitatively-derived (i.e. not multiple-displacement-amplified) viral-particle metagenomes (viromes) along a permafrost thaw gradient. Only 15% of these vOTUs had genetic similarity to publicly available viruses in the RefSeq database, and ~30% of the genes could be annotated, supporting the concept of soils as reservoirs of substantial undescribed viral genetic diversity. The vOTUs exhibited distinct ecology, with dramatically different distributions along the thaw gradient habitats, and a shift from soil-virus-like assemblages in the dry palsas to aquatic-virus-like in the inundated fen. Seventeen vOTUs were linked to microbial hosts (in silico), implicating viruses in infecting abundant microbial lineages from Acidobacteria, Verrucomicrobia, and Deltaproteoacteria, including those encoding key biogeochemical functions such as organic matter degradation. Thirty-one auxiliary metabolic genes (AMGs) were identified, and suggested viral-mediated modulation of central carbon metabolism, soil organic matter degradation, polysaccharide-binding, and regulation of sporulation. Together these findings suggest that these soil viruses have distinct ecology, impact host-mediated biogeochemistry, and likely impact ecosystem function in the rapidly changing Arctic.

microbiology↗
bioRxiv2018

Arabidopsis species deploy distinct strategies to cope with drought stress

O_LIBackground and Aims Water limitation is an important determinant of the distribution, abundance and diversity of plant species. Yet, little is known about how the response to limiting water supply changes among closely related plant species with distinct ecological preferences. Comparison of the model annual species A. thaliana to its close perennial relatives A. lyrata and A. halleri, can help disentangle the molecular and physiological changes contributing to tolerance and avoidance mechanisms, because these species must maintain tolerance and avoidance mechanisms to increase long-term survival, but they are exposed to different levels of water stress and competition in their natural habitat.\nC_LIO_LIMethods We conducted a dry-down experiment that mimics a period of missing precipitation. We quantified the covariation of progressive decrease in soil water content (SWC) with various physiological and morphological plant traits across a set of representative genotypes in Arabidopsis thaliana, A. lyrata and A. halleri. To quantify the degree of plant stress, transcriptome changes were also monitored.\nC_LIO_LIKey Results The analysis of trait co-variation demonstrates that the three species differ in the strategies they deploy to respond to drought stress. A. thaliana showed drought avoidance reaction but failed to survive wilting. A. lyrata efficiently combined avoidance and tolerance mechanisms. By contrast, A. halleri showed some degree of tolerance to wilting but it did not seem to protect itself from the stress imposed by drought. Transcriptome data collected just before plant wilting and after recovery corroborated the phenotypic analysis, with A. lyrata and A. halleri showing a stronger activation of recovery- and stress-related genes, respectively.\nC_LIO_LIConclusions We conclude that these three Arabidopsis species have evolved distinct strategies to face drought stress, and discuss the extent to which these strategic differences reflect their respective ecological priorities.\nC_LI

plant biology↗
bioRxiv2018

Species’ range dynamics affect the evolution of spatial variation in plasticity under environmental change

While clines in environmental tolerance and phenotypic plasticity along a single species range are widespread and of special interest in the context of adaptation to environmental changes, we know little about their evolution. Recent empirical findings in ectotherms suggest that processes underlying dynamic species ranges can give rise to spatial differences in environmental tolerance and phenotypic plasticity within species. We used individual-based simulations to investigate how plasticity and tolerance evolve in the course of three scenarios of species range shifts and range expansions on environmental gradients. We found that regions of a species range which experienced a longer history or larger extent of environmental change generally exhibited increased plasticity or tolerance. Such regions may be at the trailing edge when a species is tracking its ecological niche in space (e.g., in a climate change scenario) or at the front edge when a species expands into a new habitat (e.g., in an expansion/invasion scenario). Elevated tolerance and plasticity in the distribution center was detected when asymmetric environmental change (e.g., polar amplification) led to a range expansion. Greater gene flow across the range had a dual effect on plasticity and tolerance clines, with an amplifying effect in niche expansion scenarios (allowing for faster colonization into novel environments), but with a dampening effect in range shift scenarios (favoring spatial translocation of adapted genotypes). However, tolerance and plasticity clines were transient and slowly flattened out after range dynamics because of genetic assimilation. In general, our approach allowed us to investigate the evolution of environmental tolerance and phenotypic plasticity under transient evolutionary dynamics in non-equilibrium situations, which contributes to a better understanding of observed patterns and of how species may respond to future environmental changes.\n\nImpact SummaryIn a variable and changing environment, the ability of a species to cope with a range of selection pressures and a multitude of environmental conditions is critical, both for its spatial distribution and its long-term persistence. Striking examples of spatial differences in environmental tolerance have been found within species, when single populations differed from each other in their environmental optimum and tolerance breadth, a characteristic that might strongly modify a species response to future environmental change. However, we still know little about the evolutionary processes causing these tolerance differences between populations, especially when the differences result from transient evolutionary dynamics in non-equilibrium situations. We demonstrate with individual-based simulations, how spatial differences in environmental tolerance and phenotypic plasticity evolved across a species range during three scenarios of range shifts and range expansion. Range dynamics were either driven by environmental change or by the expansion of the ecological niche. The outcome strongly differed between scenarios as tolerance and plasticity were maximized either at the leading edge, at the trailing edge, or in the middle of the species range. Spatial tolerance variation resulted from colonization chronologies and histories of environmental change that varied along the range. Subsequent to the range dynamics, the tolerance and plasticity clines slowly leveled out again as result of genetic assimilation such that the described responses are long-lasting, but in the end temporary. These findings help us better understand species evolutionary responses during range shifts and range expansion, especially when facing environmental change.

evolutionary biology↗
bioRxiv2018

Long-read metagenomics reveals cryptic and abundant marine viruses

Marine viruses impact global biogeochemical cycles via their influence on host community structure and function, yet our understanding of viral ecology is constrained by limitations in culturing of important hosts and the lack of a universal gene to facilitate community surveys. Short-read viral metagenomic studies have provided clues to viral function and first estimates of global viral gene abundance and distribution. However, short-read assemblies are confounded by populations with high levels of strain evenness and nucleotide diversity (microdiversity), limiting assembly of some of the most abundant viruses on Earth. Assembly across genomic islands which likely contain niche-defining genes that drive ecological speciation is also challenging. While such populations and features are successfully captured by single-virus genomics and fosmid-based approaches, both techniques require considerable cost and technical expertise. Here we established a low-cost, low-input, high throughput alternative method for improving assembly of viral metagenomics using long read technology. Named VirION (Viral, long-read metagenomics via MinION sequencing), our sequencing approach and complementary bioinformatics pipeline (i) increased number and completeness of assembled viral genomes compared to short-read sequencing methods; (ii) captured populations of abundant viruses with high microdiversity missed by short-read methods and (iii) captured more and longer genomic islands than short-read methods. Thus, VirION provides a high throughput and cost-effective alternative to fosmid and single-virus genomic approaches to more comprehensively explore viral communities in nature.

genomics↗
bioRxiv2018

The immune checkpoint kick start: Optimization of neoadjuvant combination therapy using game theory

An upcoming clinical trial at the Moffitt Cancer Center for women with stage 2/3 ER+breast cancer combines an aromatase inhibitor and a PD-L1 checkpoint inhibitor, and aims to lower a preoperative endocrine prognostic index (PEPI) that correlates with relapse-free survival. PEPI is fundamentally a static index, measured at the end of neoadjuvant therapy before surgery. We develop a mathematical model of the essential components of the PEPI score in order to identify successful combination therapy regimens that minimize both tumor burden and metastatic potential, based on time-dependent trade-offs in the system. We consider two molecular traits, CCR7 and PD-L1 which correlate with treatment response and increased metastatic risk. We use a matrix game model with the four phenotypic strategies to examine the frequency-dependent interactions of cancer cells. This game was embedded into an ecological model of tumor population growth dynamics. The resulting model predicts both evolutionary and ecological dynamics that track with changes in the PEPI score. We consider various treatment regimens based on combinations of the two therapies with drug holidays. By considering the trade off between tumor burden and metastatic potential, the optimal therapy plan was found to be a 1 month kick start of the immune checkpoint inhibitor followed by five months of continuous combination therapy. Relative to a protocol with both therapeutics given together from the start, this delayed regimen results in transient sub-optimal tumor regression while maintaining a phenotypic constitution that is more amenable to fast tumor regression for the final five months of therapy. The mathematical model provides a useful abstraction of clinical intuition, enabling hypothesis generation and testing of clinical assumptions.

cancer biology↗
bioRxiv2018

Whole genome scan reveals the multigenic basis of recent tidal marsh adaptation in a sparrow

Natural selection acts on functional molecular variation to create local adaptation, the \"good fit\" we observe between an organisms phenotype and its environment. Genomic comparisons of lineages in the earliest stages of adaptive divergence have high power to reveal genes under natural selection because molecular signatures of selection on functional loci are maximally detectable when overall genomic divergence is low. We conducted a scan for local adaptation genes in the North American swamp sparrow (Melospiza georgiana), a species that includes geographically connected populations that are differentially adapted to freshwater vs. brackish tidal marshes. The brackish tidal marsh form has rapidly evolved tolerance for salinity, a deeper bill, and darker plumage since colonizing coastal habitats within the last 15,000 years. Despite their phenotypic differences, background genomic divergence between these populations is very low, rendering signatures of natural selection associated with this recent coastal adaptation highly detectable. We recovered a multigenic snapshot of ecological selection via a whole genome scan that revealed robust signatures of selection at 31 genes with functional connections to bill shape, plumage melanism and salt tolerance. As in Darwins finches, BMP signaling appears responsible for changes in bill depth, a putative magic trait for ecological speciation. A signal of selection at BNC2, a melanocyte transcription factor responsible for human skin color saturation, implicates a shared genetic mechanism for sparrow plumage color and human skin tone. Genes for salinity tolerance constituted the majority of adaptive candidates identified in this genome scan (23/31) and included vasoconstriction hormones that can flexibly modify osmotic balance in tune with the tidal cycle by influencing both drinking behavior and kidney physiology. Other salt tolerance genes had potential pleiotropic effects on bill depth and melanism (6/31), offering a mechanistic explanation for why these traits have evolved together in coastal swamp sparrows, and in other organisms that have converged on the same \"salt marsh syndrome\". As a set, these candidates capture the suite of physiological changes that coastal swamp sparrows have evolved in response to selection pressures exerted by a novel and challenging habitat.

evolutionary biology↗
bioRxiv2018

A migration-associated supergene reveals loss of biocomplexity in Atlantic cod

Intraspecific phenotypic diversity is integral to ecological resilience and the provision of ecosystem services1. Chromosome structural variation may underpin intraspecific diversity and complex phenotypes2 by reducing recombination within supergenes containing linked, co-adapted alleles. Connecting ecologically-relevant phenotypes to genomic variation can enable more precise conservation of exploited marine species by protecting important genetic diversity3,4. Here, using genome-wide association analysis of a 12K single nucleotide polymorphism (SNP) array we confirm that an ancient, derived chromosomal rearrangement consisting of two adjacent inversions is strongly associated with migratory phenotype and individual-level genetic structure in Atlantic cod (Gadus morhua) across the Northwest Atlantic. The presence of all identified migration-associated loci within this rearrangement indicates that pervasive variation in migration phenotype is in part controlled by a recombination-resistant supergene, facilitating fine-scale individual phenotypic variation within Northern cod. Furthermore, we reconstruct trends in effective population size over the last century, and find genomic signatures of population collapse, and different patterns of population expansion and decline among individuals based on supergene alleles. We demonstrate declines in effective population size consistent with the onset of industrialized harvest (post 1950) and substantially reduced effective size of individuals homozygous for the derived chromosomal rearrangement relative to heterozygous individuals or those homozygous for the ancestral version of this chromosomal region. These results illustrate how chromosomal structural diversity can mediate fine-scale genetic and phenotypic variation in a highly connected marine species, and suggest a loss of biocomplexity from a migration-associated supergene within Northern cod by overfishing.

genomics↗
bioRxiv2018

Dynamics of genomic change during evolutionary rescue in the seed beetle Callosobruchus maculatus

Rapid adaptation can be necessary to prevent extinction when populations are exposed to extremely marginal or stressful environments. Factors that affect the likelihood of evolutionary rescue from extinction have been identified, but much less is known about the evolutionary dynamics and genomic basis of successful evolutionary rescue, particularly in multicellular organisms. We conducted an evolve and resequence experiment to investigate the dynamics and repeatability of evolutionary rescue at the genetic level in the cowpea seed beetle, Callosobruchus maculatus, when it is experimentally shifted to a stressful host plant, lentil (Lens culinaris). Low survival (~ 1%) at the onset of the experiment caused population decline. But adaptive evolution quickly rescued the population with survival rates climbing to 69% by the F5 generation and 90% by the F10 generation. Population genomic data showed that rescue likely was caused by rapid evolutionary change at multiple loci, with many alleles fixing or nearly fixing within five generations of selection on lentil. By comparing estimates of selection across five lentil-adapted C. maculatus populations (two new sublines and three long-established lines), we found that adaptation to lentil involves a mixture of parallel and idiosyncratic evolutionary changes. Parallelism was particularly pronounced in sublines that were formed after the parent line had passed through an initial bottleneck. Overall, our results suggest that evolutionary rescue in this system is driven by very strong selection on a modest number of loci, and these results provide empirical evidence that ecological dynamics during evolutionary rescue cause distinct evolutionary trajectories and genomic signatures relative to adaptation in less stressful environments.\n\nImpact StatementEvolutionary adaptation is an ongoing process in most populations, but when populations occupy particularly stressful or marginal environments, adaptation can be necessary to prevent extinction. Adaptation that reverses demographic decline and allows for population persistence is termed evolutionary rescue. Evolutionary rescue can prevent species loss from climate change or other environmental stresses, but it can also thwart attempts to control or eradicate agricultural pests and pathogens. Many factors affect the likelihood of evolutionary rescue, but little is known about the underlying evolutionary dynamics, particularly molecular evolutionary changes in multicellular organisms. Here we use a powerful combination of experimental evolution and genomics to track the evolutionary dynamics and genomic outcomes of evolutionary rescue. We focus on the seed beetle Callosobruchus maculatus, which is both an agricultural pest and a convenient model system. We specifically examine how this species is able to persist on a novel and very poor crop host, lentil.\n\nWe show that evolution in an experimental seed beetle populations increases survival on lentil from ~1% to >80% in fewer than a dozen generations. This rapid adaptive evolutionary change at the trait (i.e., phenotypic) level was associated with equally rapid evolution at the molecular level, with some gene variants (i.e., alleles) showing frequency shifts of around 30% in a single generation. In contrast to most other experimental evolution studies in multicellular organisms (particularly Drosophila fruit flies), we find that gene variants at multiple loci rapidly fix, that is, reach a frequency of 100%, during adaptation to lentil. Our results suggest that the dynamics and genetics of adaptation to severe conditions could be distinct from adaptation under more benign conditions. By comparing outcomes of adaptation across multiple lines and sublines, we show that repeated rapid adaptation at the trait level does not necessarily involve the same evolutionary changes at the molecular level. This limited parallelism was likely driven by extreme population bottlenecks caused by low survival in the early generations on lentil. Indeed, evolutionary changes in sublines formed after recovery from a common bottleneck were highly parallel. This coupling of demographic (i.e., ecological) and evolutionary changes during evolutionary rescue may therefore limit the predictability of evolution. Because colonization of novel environments may often occur after a bottleneck, our results could be of general significance for understanding patterns of parallel (and non-parallel) evolutionary change in nature.

evolutionary biology↗
bioRxiv2018

An integrative systems biology and experimental approach identifies convergence of epithelial plasticity, metabolism, and autophagy to promote chemoresistance

The evolution of therapeutic resistance is a major cause of death for patients with solid tumors. The development of therapy resistance is shaped by the ecological dynamics within the tumor microenvironment and the selective pressure induced by the host immune system. These ecological and selective forces often lead to evolutionary convergence on one or more pathways or hallmarks that drive progression. These hallmarks are, in turn, intimately linked to each other through gene expression networks. Thus, a deeper understanding of the evolutionary convergences that occur at the gene expression level could reveal vulnerabilities that could be targeted to treat therapy-resistant cancer. To this end, we used a combination of phylogenetic clustering, systems biology analyses, and wet-bench molecular experimentation to identify convergences in gene expression data onto common signaling pathways. We applied these methods to derive new insights about the networks at play during TGF-{beta}-mediated epithelial-mesenchymal transition in a lung cancer model system. Phylogenetics analyses of gene expression data from TGF-{beta} treated cells revealed evolutionary convergence of cells toward amine-metabolic pathways and autophagy during TGF-{beta} treatment. Using high-throughput drug screens, we found that knockdown of the autophagy regulatory, ATG16L1, re-sensitized lung cancer cells to cancer therapies following TGF-{beta}-induced resistance, implicating autophagy as a TGF-{beta}-mediated chemoresistance mechanism. Analysis of publicly-available clinical data sets validated the adverse prognostic importance of ATG16L expression in multiple cancer types including kidney, lung, and colon cancer patients. These analyses reveal the usefulness of combining evolutionary and systems biology methods with experimental validation to illuminate new therapeutic vulnerabilities.

cancer biology↗
bioRxiv2018

Adaptive Phenotypic Plasticity for Life History and Less Fitness-Related Traits

Organisms are faced with variable environments and one of the most common solutions to cope with such variability is phenotypic plasticity, a modification of the phenotype to the environment. These modifications influence ecological and evolutionary processes and are assumed to be adaptive. The assumption of adaptive plasticity allows to derive the prediction that the closer to fitness a trait is, the less plastic it would be. To test this hypothesis, we conducted a meta-analysis of 213 studies and measured the plasticity of each reported trait as coefficient of variation (CV). Traits were categorised according to their relationship to fitness into life-history traits (LHt) including reproduction and survival related-traits, and non-life-history traits (N-LHt) including traits related to development, metabolism and physiology, morphology and behaviour. Our results showed, unexpectedly, that although traits differed in their amounts of plasticity, trait plasticity did not correlate with its proximity to fitness. These findings were independent of taxonomic groups or environmental types assessed and raise questions about the ubiquity of adaptive plasticity. We caution about generalising the assumption that all plasticity is adaptive with respect to evolutionary and ecological population processes. More studies are needed that test the adaptive nature of plasticity, and additional theoretical explorations on adaptive and non-adaptive plasticity are encouraged.

evolutionary biology↗
bioRxiv2018

Evolutionary dynamics of specialization in herbivorous stick insects

Understanding the evolutionary dynamics underlying herbivorous insect mega-diversity requires investigating the ability of insects to shift and adapt to different host plants. Feeding experiments with nine related stick insect species revealed that insects retain the ability to use ancestral host plants after shifting to novel hosts, with host plant shifts generating fundamental feeding niche expansions. These expansions were not accompanied by expansions of the realized feeding niches however, as species on novel hosts are generally ecologically specialized. For shifts from angiosperm to chemically challenging conifer hosts, generalist fundamental feeding niches even evolved jointly with strong host plant specialization, indicating that host plant specialization is more likely driven by species interactions than by constraints imposed by plant chemistry. By coupling analyses of plant chemical compounds, fundamental and ecological feeding niches in multiple insect species, we provide novel insights into the evolutionary dynamics of host range expansion and contraction in herbivorous insects.

evolutionary biology↗
bioRxiv2018

Macroecological relationships in the dynamics of gut microbiota

The gut microbiome is now widely recognized as a dynamic ecosystem that plays an important role in health and disease1. While current sequencing technologies make it possible to estimate relative abundances of host-associated bacteria over time2, 3, the biological processes governing their dynamics remain poorly understood. Therefore, as in other ecological systems4, 5, it is important to identify quantitative relationships describing global aspects of gut microbiota dynamics. Here we use multiple high-resolution time series data obtained from humans and mice6-8 to demonstrate that despite their inherent complexity, gut microbiota dynamics can be characterized by several robust scaling relationships. Interestingly, these patterns are highly similar to those previously observed across diverse ecological communities and economic systems, including the temporal fluctuations of animal and plant populations9-12 and the performance of publicly traded companies13. Specifically, we find power law relationships describing short- and long-term changes in gut microbiota abundances, species residence and return times, and the connection between the mean and variance of species abundances. The observed scaling relationships are altered in mice receiving different diets and affected by context-specific perturbations in humans. We use these macroecological relationships to reveal specific bacterial taxa whose dynamics are significantly affected by dietary and environmental changes. Overall, our results suggest that a quantitative macroecological framework will be important for characterizing and understanding complex dynamics of microbial communities.

microbiology↗
bioRxiv2018

Convergent evolution of psilocybin biosynthesis by psychedelic mushrooms

Psilocybin is a psychoactive compound with clinical applications produced by dozens of mushroom species1. There has been a longstanding interest in psilocybin research with regard to treatment for addiction2, depression3, and end-of-life suffering4. However, until recently very little was known about psilocybin biosynthesis and its ecological role. Here we confirm and refine recent findings5 about the genes underpinning psilocybin biosynthesis, discover that there is more than one psilocybin biosynthesis cluster in mushrooms, and we provide the first data directly addressing psilocybins ecological role. By analysing independent genome assemblies for the hallucinogenic mushrooms Psilocybe cyanescens and Pluteus salicinus we recapture the recently discovered psilocybin biosynthesis cluster5,6 and show that a transcription factor previously implicated in its regulation is actually not part of the cluster. Further, we show that the mushroom Inocybe corydalina produces psilocybin but does not contain the established biosynthetic cluster, and we present an alternative cluster. Finally, a meta-transcriptome analysis of wild-collected mushrooms provides evidence for intra-mushroom insect gene expression of flies whose larvae grow inside Psilocybe cyanescens. These larvae were successfully reared into adults. Our results show that psilocybin does not confer complete protection against insect mycophagy, and the hypothesis that it is produced as an adaptive defense compound may need to be reconsidered.

evolutionary biology↗
bioRxiv2018

Climate Resilience Index as a tool to explore households’ resilience to climate change-induced shocks in Dinki watershed, central highlands of Ethiopia Households’ resilience to climate change impacts

This study assessed households resilience to climate change-induced shocks in Dinki watershed, northcentral highlands of Ethiopia. The data were collected through cross-sectional survey conducted on 288 households, six focus group discussions and 15 key informant interviews. The Climate Resilience Index (CRI) and the Livelihood Resilience Index (LRI) based on the three-resilience capacities (3Ds) frame, using absorptive, adaptive and transformative, were used to measure households resilience to climate change-induced shocks on agro-ecological unit of analysis. Findings indicate that the CRI and the resilience capacities based on the indexed scores of major components clearly differentiated the study communities in terms of their agro-ecological zones. Specifically, the LRI score showed that absorptive capacity (0.495) was the leading contributing factor to resilience followed by adaptive (0.449) and transformative (0.387) capacities. Likewise, the midland was relatively more resilient with a mean index value of 0.461. The study showed that access to and use of livelihood resources, such as farmlands and livestock holdings, diversity of income sources, infrastructure and social capital were determinants of households resilience. In general, it might be due to their exposure to recurrent shocks coupled with limited adaptive capacities including underdeveloped public services, poor livelihood diversification practices, among others, the study communities showed minimal resilience capacity with a mean score of 0.44. Thus, in addition to short-term buffering strategies, intervention priority focusing on both adaptive and transformative capacities, particularly focusing on most vulnerable localities and constrained livelihood strategies, would contribute to ensure long-term resilience in the study communities.

scientific communication and education↗
bioRxiv2018

A New Phylogenetic Framework for the Animal-adapted Mycobacterium tuberculosis Complex

Tuberculosis (TB) affects humans and other animals and is caused by bacteria from the Mycobacterium tuberculosis complex (MTBC). Previous studies have shown that there are at least nine members of the MTBC infecting animals other than humans; these have also been referred to as ecotypes. However, the ecology and the evolution of these animal-adapted MTBC ecotypes are poorly understood. Here we screened 12,886 publicly available MTBC genomes and newly sequenced 17 animal-adapted MTBC strains, gathering a total of 529 genomes of animal-adapted MTBC strains. Phylogenomic and comparative analyses confirm that the animal-adapted MTBC members are paraphyletic with some members more closely related to the human-adapted Mycobacterium africanum Lineage 6 than to other animal-adapted strains. Furthermore, we identified four main animal-adapted MTBC clades that might correspond to four main host shifts; two of these clades are proposed to reflect independent cattle domestication events. Contrary to what would be expected from an obligate pathogen, MTBC nucleotide diversity was not positively correlated with host phylogenetic distances, suggesting that host tropism in the animal-adapted MTBC seems to be driven more by contact rates and demographic aspects of the host population rather than host relatedness. By combining phylogenomics with ecological data, we propose an evolutionary scenario in which the ancestor of Lineage 6 and all animal-adapted MTBC ecotypes was a generalist pathogen that subsequently adapted to different host species. This study provides a new phylogenetic framework to better understand the evolution of the different ecotypes of the MTBC and guide future work aimed at elucidating the molecular mechanisms underlying host specificity.

evolutionary biology↗
bioRxiv2018

DAIRYdb: A manually curated gold standard reference database for improved taxonomy annotation of 16S rRNA gene sequences from dairy products

Reads assignment to taxonomic units is a key step in microbiome analysis pipelines. To date, accurate taxonomy annotation, particularly at species rank, is still challenging due to the short size of read sequences and differently curated classification databases. However, the close phylogenetic relationship between species encountered in dairy products requires accurate species annotation to achieve sufficient phylogenetic resolution for further downstream ecological studies or for food diagnostics. Taxonomy annotation in universal 16S databases with environmental sequences like Silva, RDP or Greengenes is based on predictions rather than on studies of type strains or isolates. We provide a manually curated database composed of 10290 full-length 16S rRNA gene sequences from prokaryotes tailored for dairy products analysis (https://github.com/marcomeola/DAIRYdb). The performance of the DAIRYdb was compared with the universal databases Silva, LTP, RDP and Greengenes. The DAIRYdb significantly outperformed all other databases independently of the classification algorithm by enabling higher accurate taxonomy annotation down to the species rank. The DAIRYdb accurately annotates over 90% of the sequences of either single or paired hypervariable regions automatically.\n\nThe manually curated DAIRYdb strongly improves taxonomic classification accuracy for microbiome studies in dairy environments. The DAIRYdb is a practical solution that enables automatization of this key step, thus facilitating the routine application of NGS microbiome analyses for microbial ecology studies and diagnostics in dairy products.

genomics↗
bioRxiv2018

Modern botanical analogue of endangered Yak (Bos mutus) dung from India: Plausible linkage with living and extinct megaherbivores

The study present to document the micro and macrobotanical remain on wild Yak dung to understand the diet, habitat, and ecology in relation to determining possible ecological relationships with extant and extinct megaherbivores. Grasses are the primary diet of the yak as indicated by the abundance of grass pollen and phytoliths, though it is obvious. The other associates non-arboreal and arboreal taxa namely, Cyperacaeae, Rosaceae, Chenopodiaceae, Artemisia, Prunus, and Rhododendron are also important dietary plants for their survival. The observation of plant macrobotanical remains especially the vegetative part and seed of the grasses and Cyperaceae also indicates good agreement with the palynodata. The documented micro and macrobotanical data is indicative of both Alpine meadow and steppe vegetation under cold and dry climate which exactly reflected the current vegetation composition and climate in the region. The recovery of Botryococcus, Arcella, and diatom was marked though in trace values and suggestive of the perennial water system in the region which incorporated through the ingestion of water. Energy dispersive spectroscopy analysis marked that the element contained in dung samples has variation in relation to the summer and winter which might be the availability of the food plants and vegetation. This generated multiproxy data serves as a strong supplementary data for modern pollen and vegetation relationship based on surface soil samples in the region. The recorded multiproxy data could be useful to interpret the coprolites of herbivorous fauna in relation to the palaeodietary and paleoecology in the region and to correlate with other mega herbivores in a global context.

paleontology↗