The relative contribution of top-down and bottom-up processes regulating primary decomposers can influence the strength of the link between the soil animal community and ecosystem functioning. ...Although soil bacterial communities are regulated by bottom-up and top-down processes, the latter are considered to be less important in structuring the diversity and functioning of fungal-dominated ecosystems. Despite the huge diversity of mycophagous (fungal-feeding) soil fauna, and their potential to reverse the outcomes of competitive fungal interactions, top-down grazing effects have never been found to translate to community-level changes. We constructed soil mesocosms to investigate the potential of isopods grazing on cord-forming basidiomycete fungi to influence the community composition and functioning of a complex woodland soil microbial community. Using metagenomic sequencing we provide conclusive evidence of direct top-down control at the community scale in fungal-dominated woodland soil. By suppressing the dominant cord-forming basidiomycete fungi, isopods prevented the competitive exclusion of surrounding litter fungi, increasing diversity in a community containing several hundred fungal species. This isopod-induced modification of community composition drove a shift in the soil enzyme profile, and led to a restructuring of the wider mycophagous invertebrate community. We highlight characteristics of different soil ecosystems that will give rise to such top-down control. Given the ubiquity of isopods and basidiomycete fungi in temperate and boreal woodland ecosystems, such top-down community control could be of widespread significance for global carbon and nutrient cycling.
Many wild species have suffered drastic population size declines over the past centuries, which have led to 'genomic erosion' processes characterized by reduced genetic diversity, increased ...inbreeding, and accumulation of harmful mutations. Yet, genomic erosion estimates of modern-day populations often lack concordance with dwindling population sizes and conservation status of threatened species. One way to directly quantify the genomic consequences of population declines is to compare genome-wide data from pre-decline museum samples and modern samples. However, doing so requires computational data processing and analysis tools specifically adapted to comparative analyses of degraded, ancient or historical, DNA data with modern DNA data as well as personnel trained to perform such analyses.
Here, we present a highly flexible, scalable, and modular pipeline to compare patterns of genomic erosion using samples from disparate time periods. The GenErode pipeline uses state-of-the-art bioinformatics tools to simultaneously process whole-genome re-sequencing data from ancient/historical and modern samples, and to produce comparable estimates of several genomic erosion indices. No programming knowledge is required to run the pipeline and all bioinformatic steps are well-documented, making the pipeline accessible to users with different backgrounds. GenErode is written in Snakemake and Python3 and uses Conda and Singularity containers to achieve reproducibility on high-performance compute clusters. The source code is freely available on GitHub ( https://github.com/NBISweden/GenErode ).
GenErode is a user-friendly and reproducible pipeline that enables the standardization of genomic erosion indices from temporally sampled whole genome re-sequencing data.
Species delimitation is one of the most contested areas in modern biology, with widespread disagreement about almost every aspect of the definition and implementation of the “species” label. While ...this debate is intellectually stimulating, it also has real implications for conservation, where its impacts on taxonomic inflation or inertia can mean that specific populations receive adequate conservation measures or are ignored. Recently, the rise of next generation sequencing and phylogenomics has revolutionised phylogenetic understanding of many organismal groups but has simultaneously highlighted the porosity of genomes in terms of admixture across previously delineated species barriers. The extraordinary power of genomic data is increasingly being used to delineate species, and several publications in this domain have recently attracted significant attention and criticism. Here we revisit the question of species delimitation, but from a genomic context. We ask how and whether the large amounts of data provided by genomic methods can resolve the longstanding discussion on the validity and application of phylogenetic and allied species concepts, and how some recent examples can inform this debate. We argue that conserving adaptive potential is a priority for conservation, and no single species concept currently does that adequately on its own. Genomic data holds the potential to add unprecedented detail, but frequently falls short of this potential.
The cave lion is an extinct felid that was widespread across the Holarctic throughout the Late Pleistocene. Its closest extant relative is the lion (Panthera leo), but the timing of the divergence ...between these two taxa, as well as their taxonomic ranking are contentious. In this study we analyse 31 mitochondrial genome sequences from cave lion individuals that, through a combination of
C and genetic tip dating, are estimated to be from dates extending well into the mid-Pleistocene. We identified two deeply diverged and well-supported reciprocally monophyletic mitogenome clades in the cave lion, and an additional third distinct lineage represented by a single individual. One of these clades was restricted to Beringia while the other was prevalent across western Eurasia. These observed clade distributions are in line with previous observations that Beringian and European cave lions were morphologically distinct. The divergence dates for these lineages are estimated to be far older than those between extant lions subspecies. By combining our radiocarbon tip-dates with a split time prior that takes into account the most up-to-date fossil stem calibrations, we estimated the mitochondrial DNA divergence between cave lions and lions to be 1.85 Million ya (95% 0.52- 2.91 Mya). Taken together, these results support previous hypotheses that cave lions existed as at least two subspecies during the Pleistocene, and that lions and cave lions were distinct species.
Ancient DNA has significantly improved our understanding of the evolution and population history of extinct megafauna. However, few studies have used complete ancient genomes to examine species ...responses to climate change prior to extinction. The woolly rhinoceros (Coelodonta antiquitatis) was a cold-adapted megaherbivore widely distributed across northern Eurasia during the Late Pleistocene and became extinct approximately 14 thousand years before present (ka BP). While humans and climate change have been proposed as potential causes of extinction 1–3, knowledge is limited on how the woolly rhinoceros was impacted by human arrival and climatic fluctuations 2. Here, we use one complete nuclear genome and 14 mitogenomes to investigate the demographic history of woolly rhinoceros leading up to its extinction. Unlike other northern megafauna, the effective population size of woolly rhinoceros likely increased at 29.7 ka BP and subsequently remained stable until close to the species’ extinction. Analysis of the nuclear genome from a ∼18.5-ka-old specimen did not indicate any increased inbreeding or reduced genetic diversity, suggesting that the population size remained steady for more than 13 ka following the arrival of humans 4. The population contraction leading to extinction of the woolly rhinoceros may have thus been sudden and mostly driven by rapid warming in the Bølling-Allerød interstadial. Furthermore, we identify woolly rhinoceros-specific adaptations to arctic climate, similar to those of the woolly mammoth. This study highlights how species respond differently to climatic fluctuations and further illustrates the potential of palaeogenomics to study the evolutionary history of extinct species.
•Complete genome and mitogenome analysis of the extinct woolly rhinoceros•Demographic analysis suggests stable population size until close to extinction•No increased inbreeding or reduced genomic diversity coinciding with human arrival•Woolly rhinoceros had genetic adaptations to arctic climate
Here, Lord et al. sequence a complete nuclear genome and 14 mitogenomes from the extinct woolly rhinoceros. Demographic analyses show that the woolly rhinoceros population size was large until close to extinction and not affected by modern human arrival in northeastern Siberia. The extinction may have been mostly driven by climate warming.
Carefully developed quantitative structure-activity and structure-property relationship models contain detailed information regarding how differences in the molecular structure of compounds correlate ...with differences in the observed biological or other physicochemical properties of those compounds. The ability to understand the behavior of existing molecules and to design new molecules is facilitated by using an objective method to extract and explain the details of the underlying structure-activity or structure-property relationship. Furthermore, a clear understanding of how and why compounds behave as they do can lead to new innovations through model-directed selection of compounds to be used in complex mixtures such as laundry detergents, fabric softeners, and shampoos. Such a method has been developed based on partial least-squares (PLS) regression analysis that allows for the identification of specific structural trends that relate to differences in observed properties. But the analysis of the completed model is only the last step of the process. The model development process itself affects the ability to extract a clear interpretation of the model. Everything from the selection of initial pool of molecular descriptors to evaluate to data set and model optimization impacts the ability to derive detailed molecular design information. This review describes the method details and examples of the use of PLS for model interpretation and also outlines suggestions regarding model development and model and data set optimization that enable the interpretation process.
Abstract Metorchis spp. are flukes (Platyhelminthes: Digenea) that infect vertebrates, including humans, dogs, cats, poultry and wild game, with cyprinid freshwater fish serving as typical second ...intermediate hosts. In their definitive hosts, the Metorchis spp. are difficult to identify to species. We provide and analyze sequences of two nuclear (18S rDNA and ITS2) and two mitochondrial (CO1 and ND1) DNA loci of four morphologically identified European species of the Metorchis , namely Metorchis albidus , Metorchis bilis , Metorchis crassiusculus and Metorchis xanthosomus , and of another opisthorchiid, Euamphimerus pancreaticus . DNA analysis suggests that the Metorchis specimens identified morphologically as M. albidus (from Lutra lutra ), M. bilis (from Phalacrocorax carbo ) and M. crassiusculus (from Aquila heliaca and Buteo rufinus ) represent a single species. Thus, M. albidus (Braun, 1893) Loos, 1899 and M. crassiusculus (Rudolphi, 1809) Looss, 1899 are recognized as junior subjective synonyms of M. bilis (Braun, 1790) Odening, 1962. We also provide comparative measurements of the Central European Metorchis spp., and address their tissue specificity and prevalence based on the examination of extensive bird cohort from 1962 to 2015. M. bilis and M. xanthosomus can be morphologically diagnosed by measuring the extent of genitalia relative to body length and by the size ratio of their suckers. They also differ in their core definitive hosts, with ducks ( Anas , Aythya ) and coots ( Fulica ) hosting M. xanthosomus , and cormorants ( Phalacrocorax ), the birds of prey ( Buteo , Aquila , etc.), piscivorous mammals ( Lutra , Vulpes , Ursus , etc.) and humans hosting M. bilis . Previous reports on the Metorchis spp. contain numerous suspected misidentifications.
The okapi is an endangered, evolutionarily distinctive even-toed ungulate classified within the giraffidae family that is endemic to the Democratic Republic of Congo. The okapi is currently under ...major anthropogenic threat, yet to date nothing is known about its genetic structure and evolutionary history, information important for conservation management given the species' current plight. The distribution of the okapi, being confined to the Congo Basin and yet spanning the Congo River, also makes it an important species for testing general biogeographic hypotheses for Congo Basin fauna, a currently understudied area of research. Here we describe the evolutionary history and genetic structure of okapi, in the context of other African ungulates including the giraffe, and use this information to shed light on the biogeographic history of Congo Basin fauna in general. Using nuclear and mitochondrial DNA sequence analysis of mainly non-invasively collected samples, we show that the okapi is both highly genetically distinct and highly genetically diverse, an unusual combination of genetic traits for an endangered species, and feature a complex evolutionary history. Genetic data are consistent with repeated climatic cycles leading to multiple Plio-Pleistocene refugia in isolated forests in the Congo catchment but also imply historic gene flow across the Congo River.
The peroxisome proliferator-activated receptors (PPARs) have been previously implicated in the pathophysiology of skeletal muscle dysfunction in women with breast cancer (BC) and animal models of BC. ...This study investigated alterations induced in skeletal muscle by BC-derived factors in an in vitro conditioned media (CM) system and tested the hypothesis that BC cells secrete a factor that represses PPAR-γ (PPARG) expression and its transcriptional activity, leading to downregulation of PPARG target genes involved in mitochondrial function and other metabolic pathways. We found that BC-derived factors repress PPAR-mediated transcriptional activity without altering protein expression of PPARG. Furthermore, we show that BC-derived factors induce significant alterations in skeletal muscle mitochondrial function and lipid accumulation, which are rescued with exogenous expression of PPARG. The PPARG agonist drug rosiglitazone was able to rescue BC-induced lipid accumulation but did not rescue effects of BC-derived factors on PPAR-mediated transcription or mitochondrial function. These data suggest that BC-derived factors alter lipid accumulation and mitochondrial function via different mechanisms that are both related to PPARG signaling, with mitochondrial dysfunction likely being altered via repression of PPAR-mediated transcription, and lipid accumulation being altered via transcription-independent functions of PPARG.
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