Shotgun Sequencing Decades-Old Lichen Specimens to Resolve Phylogenomic Placement of Type Material

Natural history collections, including name-bearing type specimens, are an important source of genetic information. These data can be critical for appropriate taxonomic revisions in cases where the phylogenetic position of name-bearing type specimens needs to be identified, including morphologically cryptic lichen-forming fungal species. Here, we use high-throughput metagenomic shotgun sequencing to generate genome-scale data from decades-old (i.e., more than 30 years old) isotype specimens representing three vagrant taxa in the lichen-forming fungal genus Rhizoplaca, including one species and two subspecies. We also use data from high-throughput metagenomic shotgun sequencing to infer the phylogenetic position of an enigmatic collection, originally identified as R. haydenii, that failed to yield genetic data via Sanger sequencing. We were able to construct a 1.64 Mb alignment from over 1200 single-copy nuclear gene regions for the Rhizoplaca specimens. Phylogenomic reconstructions recovered an isotype representing Rhizoplaca haydenii subsp. arbuscula within a clade comprising other specimens identified as Rhizoplaca haydenii subsp. arbuscula, while an isotype of R. idahoensis was recovered within a clade with substantial phylogenetic substructure comprising Rhizoplaca haydenii subsp. haydenii and other specimens. Based on these data and morphological differences, Rhizoplaca haydenii subsp. arbuscula is elevated to specific rank as Rhizoplaca arbuscula. For the enigmatic collection, we were able to assemble the nearly complete nrDNA cistron and over 50 Mb of the mitochondrial genome. Using these data, we identified this specimen as a morphologically deviant form representing Xanthoparmelia aff. subcumberlandia. This study highlights the power of high-throughput metagenomic shotgun sequencing in generating larger and more comprehensive genetic data from taxonomically important herbarium specimens

Reproduction and Dispersal of Biological Soil Crust Organisms

Biological soil crusts (BSCs) consist of a diverse and highly integrated community of organisms that effectively colonize and collectively stabilize soil surfaces. BSCs vary in terms of soil chemistry and texture as well as the environmental parameters that combine to support unique combinations of organisms—including cyanobacteria dominated, lichen-dominated, and bryophyte-dominated crusts. The list of organismal groups that make up BSC communities in various and unique combinations include—free living, lichenized, and mycorrhizal fungi, chemoheterotrophic bacteria, cyanobacteria, diazotrophic bacteria and archaea, eukaryotic algae, and bryophytes. The various BSC organismal groups demonstrate several common characteristics including—desiccation and extreme temperature tolerance, production of various soil binding chemistries, a near exclusive dependency on asexual reproduction, a pattern of aerial dispersal over impressive distances, and a universal vulnerability to a wide range of human-related perturbations. With this publication, we provide literature-based insights as to how each organismal group contributes to the formation and maintenance of the structural and functional attributes of BSCs, how they reproduce, and how they are dispersed. We also emphasize the importance of effective application of molecular and microenvironment sampling and assessment tools in order to provide cogent and essential answers that will allow scientists and land managers to better understand and manage the biodiversity and functional relationships of soil crust communities

Electrically conductive polyimides containing silver trifluoroacetylacetonate

Polyimides with enhanced electrical conductivity are produced by adding a silver ion-containing additive to the polyamic acid resin formed by the condensation of an aromatic dianhydride with an aromatic diamine. After thermal treatment the resulting polyimides had surface conductivities in the range of 1.7.times.10.sup.-3 4.5 .OMEGA..sup.-1 making them useful in low the electronics industry as flexible, electrically conductive polymeric films and coatings

Pleistocene Speciation in North American Lichenized Fungi and the Impact of Alternative Species Circumscriptions and Rates of Molecular Evolution on Divergence Estimates

Pleistocene climatic fluctuations influenced patterns of genetic variation and promoted speciation across a wide range of species groups. Lichens are commonly found in habitats that were directly impacted by glacial cycles; however, the role of Pleistocene climate in driving speciation in most lichen symbionts remains unclear. This uncertainty is due in part to limitations in our ability to accurately recognize independently evolving lichen-forming fungal lineages and a lack of relevant fossil calibrations. Using a coalescent-based species tree approach, we estimated divergence times for two sister clades in the genus Xanthoparmelia (Parmeliaceae) restricted to western North America. We assessed the influence of two different species circumscription scenarios and various locus-specific rates of molecular evolution on divergence estimates. Species circumscriptions were validated using the program BP&P. although speciation was generally supported in both scenarios, divergence times differed between traditional species circumscriptions and those based on genetic data, with more recent estimates resulting from the former. Similarly, rates of evolution for different loci resulted in variable divergence time estimates. However, our results unambiguously indicate that diversification in the sampled Xanthoparmelia clades occurred during the Pleistocene. Our study highlights the potential impact of ambiguous species circumscriptions and uncertain rates of molecular evolution on estimating divergence times within a multilocus species tree frameworkPeer reviewe

Multiple, distinct intercontinental lineages but isolation of Australian populations in a cosmopolitan lichen-forming Fungal Taxon, Psora decipiens (Psoraceae, Ascomycota)

Multiple drivers shape the spatial distribution of species, including dispersal capacity, niche incumbency, climate variability, orographic barriers, and plate tectonics. However, biogeographic patterns of fungi commonly do not fit conventional expectations based on studies of animals and plants. Fungi, in general, are known to occur across exceedingly broad, intercontinental distributions, including some important components of biological soil crust communities (BSCs). However, molecular data often reveal unexpected biogeographic patterns in lichenized fungal species that are assumed to have cosmopolitan distributions. The lichen-forming fungal species Psora decipiens is found on all continents, except Antarctica and occurs in BSCs across diverse habitats, ranging from hot, arid deserts to alpine habitats. In order to better understand factors that shape population structure in cosmopolitan lichen-forming fungal species, we investigated biogeographic patterns in the cosmopolitan taxon P. decipiens, along with the closely related taxa P. crenata and P. saviczii. We generated a multi-locus sequence dataset based on a worldwide sampling of these taxa in order to reconstruct evolutionary relationships and explore phylogeographic patterns. Both P. crenata and P. decipiens were not recovered as monophyletic; and P. saviczii specimens were recovered as a monophyletic clade closely related to a number of lineages comprised of specimens representing P. decipiens. Striking phylogeographic patterns were observed for P. crenata, with populations from distinct geographic regions belonging to well-separated, monophyletic lineages. South African populations of P. crenata were further divided into well-supported sub-clades. While well-supported phylogenetic substructure was also observed for the nominal taxon P. decipiens, nearly all lineages were comprised of specimens collected from intercontinental populations. However, all Australian specimens representing P. decipiens were recovered within a single well-supported monophyletic clade consisting solely of Australian samples. Our study supports up to 10 candidate species-level lineages in P. decipiens, based on genealogical concordance and coalescent-based species delimitation analyses. Our results support the general pattern of the biogeographic isolation of lichen-forming fungal populations in Australia, even in cases where closely related congeners have documented intercontinental distributions. Our study has important implications for understanding factors influencing diversification and distributions of lichens associated with BSC.This research was funded, in part, by a start-up grant from BYU College of Life Sciences to SL; MarW’s and MatW’s work was done within the European Soil Crust Project SCIN (Büdel et al., 2014) funded by the ERA-Net BiodivERsA program, with the national funder The Swedish Research Council for Environment, Agricultural Sciences and Spatial Planning (FORMAS)

Unexpected diversity in socially synchronized rhythms of shorebirds

The behavioural rhythms of organisms are thought to be under strong selection, influenced by the rhythmicity of the environment. Such behavioural rhythms are well studied in isolated individuals under laboratory conditions, but free-living individuals have to temporally synchronize their activities with those of others, including potential mates, competitors, prey and predators. Individuals can temporally segregate their daily activities (for example, prey avoiding predators, subordinates avoiding dominants) or synchronize their activities (for example, group foraging, communal defence, pairs reproducing or caring for offspring). The behavioural rhythms that emerge from such social synchronization and the underlying evolutionary and ecological drivers that shape them remain poorly understood. Here we investigate these rhythms in the context of biparental care, a particularly sensitive phase of social synchronization where pair members potentially compromise their individual rhythms. Using data from 729 nests of 91 populations of 32 biparentally incubating shorebird species, where parents synchronize to achieve continuous coverage of developing eggs, we report remarkable within-and between-species diversity in incubation rhythms. Between species, the median length of one parent's incubation bout varied from 1-19 h, whereas period length-the time in which a parent's probability to incubate cycles once between its highest and lowest value-varied from 6-43 h. The length of incubation bouts was unrelated to variables reflecting energetic demands, but species relying on crypsis (the ability to avoid detection by other animals) had longer incubation bouts than those that are readily visible or who actively protect their nest against predators. Rhythms entrainable to the 24-h light-dark cycle were less prevalent at high latitudes and absent in 18 species. Our results indicate that even under similar environmental conditions and despite 24-h environmental cues, social synchronization can generate far more diverse behavioural rhythms than expected from studies of individuals in captivity. The risk of predation, not the risk of starvation, may be a key factor underlying the diversity in these rhythms.</p

Contribution of copy number variants to schizophrenia from a genome-wide study of 41,321 subjects

Copy number variants (CNVs) have been strongly implicated in the genetic etiology of schizophrenia (SCZ). However, genome-wide investigation of the contribution of CNV to risk has been hampered by limited sample sizes. We sought to address this obstacle by applying a centralized analysis pipeline to a SCZ cohort of 21,094 cases and 20,227 controls. A global enrichment of CNV burden was observed in cases (OR=1.11, P=5.7×10−15), which persisted after excluding loci implicated in previous studies (OR=1.07, P=1.7 ×10−6). CNV burden was enriched for genes associated with synaptic function (OR = 1.68, P = 2.8 ×10−11) and neurobehavioral phenotypes in mouse (OR = 1.18, P= 7.3 ×10−5). Genome-wide significant evidence was obtained for eight loci, including 1q21.1, 2p16.3 (NRXN1), 3q29, 7q11.2, 15q13.3, distal 16p11.2, proximal 16p11.2 and 22q11.2. Suggestive support was found for eight additional candidate susceptibility and protective loci, which consisted predominantly of CNVs mediated by non-allelic homologous recombination

Gene expression imputation across multiple brain regions provides insights into schizophrenia risk

Transcriptomic imputation approaches combine eQTL reference panels with large-scale genotype data in order to test associations between disease and gene expression. These genic associations could elucidate signals in complex genome-wide association study (GWAS) loci and may disentangle the role of different tissues in disease development. We used the largest eQTL reference panel for the dorso-lateral prefrontal cortex (DLPFC) to create a set of gene expression predictors and demonstrate their utility. We applied DLPFC and 12 GTEx-brain predictors to 40,299 schizophrenia cases and 65,264 matched controls for a large transcriptomic imputation study of schizophrenia. We identified 413 genic associations across 13 brain regions. Stepwise conditioning identified 67 non-MHC genes, of which 14 did not fall within previous GWAS loci. We identified 36 significantly enriched pathways, including hexosaminidase-A deficiency, and multiple porphyric disorder pathways. We investigated developmental expression patterns among the 67 non-MHC genes and identified specific groups of pre- and postnatal expression

Mapping genomic loci implicates genes and synaptic biology in schizophrenia

Schizophrenia has a heritability of 60-80%1, much of which is attributable to common risk alleles. Here, in a two-stage genome-wide association study of up to 76,755 individuals with schizophrenia and 243,649 control individuals, we report common variant associations at 287 distinct genomic loci. Associations were concentrated in genes that are expressed in excitatory and inhibitory neurons of the central nervous system, but not in other tissues or cell types. Using fine-mapping and functional genomic data, we identify 120 genes (106 protein-coding) that are likely to underpin associations at some of these loci, including 16 genes with credible causal non-synonymous or untranslated region variation. We also implicate fundamental processes related to neuronal function, including synaptic organization, differentiation and transmission. Fine-mapped candidates were enriched for genes associated with rare disruptive coding variants in people with schizophrenia, including the glutamate receptor subunit GRIN2A and transcription factor SP4, and were also enriched for genes implicated by such variants in neurodevelopmental disorders. We identify biological processes relevant to schizophrenia pathophysiology; show convergence of common and rare variant associations in schizophrenia and neurodevelopmental disorders; and provide a resource of prioritized genes and variants to advance mechanistic studies