A phylogenomic perspective on the radiation of ray-finned fishes based upon targeted sequencing of ultraconserved elements

Ray-finned fishes constitute the dominant radiation of vertebrates with over 30,000 species. Although molecular phylogenetics has begun to disentangle major evolutionary relationships within this vast section of the Tree of Life, there is no widely available approach for efficiently collecting phylogenomic data within fishes, leaving much of the enormous potential of massively parallel sequencing technologies for resolving major radiations in ray-finned fishes unrealized. Here, we provide a genomic perspective on longstanding questions regarding the diversification of major groups of ray-finned fishes through targeted enrichment of ultraconserved nuclear DNA elements (UCEs) and their flanking sequence. Our workflow efficiently and economically generates data sets that are orders of magnitude larger than those produced by traditional approaches and is well-suited to working with museum specimens. Analysis of the UCE data set recovers a well-supported phylogeny at both shallow and deep time-scales that supports a monophyletic relationship between Amia and Lepisosteus (Holostei) and reveals elopomorphs and then osteoglossomorphs to be the earliest diverging teleost lineages. Divergence time estimation based upon 14 fossil calibrations reveals that crown teleosts appeared ~270 Ma at the end of the Permian and that elopomorphs, osteoglossomorphs, ostarioclupeomorphs, and euteleosts diverged from one another by 205 Ma during the Triassic. Our approach additionally reveals that sequence capture of UCE regions and their flanking sequence offers enormous potential for resolving phylogenetic relationships within ray-finned fishes

Applying Conservation Genomic Techniques to Guide Management of the Reticulated Flatwoods Salamander (Ambystoma bishopi)

The Reticulated flatwoods salamander (Ambystoma bishopi) is a federally endangered amphibian endemic to the longleaf-pine ecosystem of the southeastern U.S. This study used analyses of single-nucleotide polymorphism (SNP) data, collected from 2,255 unique individuals across 5 breeding seasons, spread across the known extant range of A. bishopi, to characterize the genetic diversity and demographics of populations, genetic relationships among populations, and patterns and spatial extents of gene flow, and to evaluate potential effects of management on A. bishopi’s resiliency. Population structure was strongly hierarchical, with individual breeding ponds (n = 38) acting as semi-connected subpopulations within five regional metapopulations (Mayhaw in Georgia; Oglesby, Eastbay, Garcon, and Escribano in Florida). Likewise, gene flow among populations was scale-dependent: negligible genetic differentiation, indicative of high gene flow, was observed only between pairs of ponds separated by \u3c 0.5 km, whereas between 0.5 and 5 km I observed steep genetic isolation by distance, and beyond 5 km genetic differentiation was generally high and only weakly related to distance. Across several breeding seasons, the effective number of breeders (Nb) per pond per year averaged 26 individuals (range 4 to 104). Larger-area, slower-drying ponds located closer to other occupied ponds exhibited larger Nb and greater genetic diversity. Based on genetically-reconstructed pedigrees, the ongoing headstarting program at Escribano successfully captured 97.9% of the estimated total number of alleles, but only 63% of the total number families, in each cohort. Based on these results, I recommend the following: 1) Given its genetic distinctiveness, Georgia populations merit elevated priority for protection and restoration. 2) Resiliency and redundancy (a la the species’ recovery plan) should be assessed at the spatial grain of individual breeding ponds. 3) Attempts to restore habitat connectivity should consider dispersal over distances \u3e 500 m to be relatively unlikely. 4) Finally, to the extent that headstarted individuals are used to augment existing or introduce new populations, managers should consider the potential risks of founder effects, and reduce these risks by creating genetically and demographically diverse headstart samples, for example by maximizing the diversity of egg/larva collections over time and space within ponds

American Mastodon Mitochondrial Genomes Suggest Multiple Dispersal Events in Response to Pleistocene Climate Oscillations

Pleistocene glacial-interglacial cycles are correlated with dramatic temperature oscillations. Examining how species responded to these natural fluctuations can provide valuable insights into the impacts of present-day anthropogenic climate change. Here we present a phylogeographic study of the extinct American mastodon (Mammut americanum), based on 35 complete mitochondrial genomes. These data reveal the presence of multiple lineages within this species, including two distinct clades from eastern Beringia. Our molecular date estimates suggest that these clades arose at different times, supporting a pattern of repeated northern expansion and local extirpation in response to glacial cycling. Consistent with this hypothesis, we also note lower levels of genetic diversity among northern mastodons than in endemic clades south of the continental ice sheets. The results of our study highlight the complex relationships between population dispersals and climate change, and can provide testable hypotheses for extant species expected to experience substantial biogeographic impacts from rising temperatures

Microbial diversity drives carbon use efficiency in a model soil

© The Author(s), 2020. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Domeignoz-Horta, L. A., Pold, G., Liu, X. A., Frey, S. D., Melillo, J. M., & DeAngelis, K. M. Microbial diversity drives carbon use efficiency in a model soil. Nature Communications, 11(1), (2020): 3684, doi:10.1038/s41467-020-17502-z.Empirical evidence for the response of soil carbon cycling to the combined effects of warming, drought and diversity loss is scarce. Microbial carbon use efficiency (CUE) plays a central role in regulating the flow of carbon through soil, yet how biotic and abiotic factors interact to drive it remains unclear. Here, we combine distinct community inocula (a biotic factor) with different temperature and moisture conditions (abiotic factors) to manipulate microbial diversity and community structure within a model soil. While community composition and diversity are the strongest predictors of CUE, abiotic factors modulated the relationship between diversity and CUE, with CUE being positively correlated with bacterial diversity only under high moisture. Altogether these results indicate that the diversity × ecosystem-function relationship can be impaired under non-favorable conditions in soils, and that to understand changes in soil C cycling we need to account for the multiple facets of global changes.Funding for this project was provided by the Department of Energy grant DE-SC0016590 to K.M.D. and S.D.F., and an American Association of University Women Dissertation fellowship to G.P. We would also like to thank Stuart Grandy and Kevin Geyer for the fruitful discussions and Mary Waters, Courtney Bly and Ana Horta for their help with samples processing

The microbial ecology of bacterial lignocellulosic degradation in the ocean

The overarching theme of my dissertation is to study the role of bacteria in lignocellulose degradation. In recent years, more research has investigated the biodegradability of lignocellulose for biofuel production. The components of the lignocellulosic plant cell wall are considered intrinsically recalcitrant due to their structure. However, we hypothesize that these components are not intrinsically recalcitrant but their biodegradation is contingent on the environmental conditions, particularly the bacterial diversity. We believe bacteria will become especially important in lignocellulose degradation in conditions that are unfavorable for white-rot fungi. Therefore, we investigated the potential for lignin degradation by bacteria in the ocean where fungi would likely be rare. This knowledge would gather insight into allochthonous terrestrial organic carbon cycling in the ocean, a basic science knowledge gap in the complex ocean carbon cycle. Also, our investigation into the microbial ecology of marine lignocellulolytic bacteria may find new hosts of stress-tolerant commercial enzymes for biofuels and lignin valorization

Global radiation in a rare biosphere soil diatom

Soil micro-organisms drive the global carbon and nutrient cycles that underlie essential ecosystem functions. Yet, we are only beginning to grasp the drivers of terrestrial microbial diversity and biogeography, which presents a substantial barrier to understanding community dynamics and ecosystem functioning. This is especially true for soil protists, which despite their functional significance have received comparatively less interest than their bacterial counterparts. Here, we investigate the diversification of Pinnularia borealis, a rare biosphere soil diatom species complex, using a global sampling of >800 strains. We document unprecedented high levels of species-diversity, reflecting a global radiation since the Eocene/Oligocene global cooling. Our analyses suggest diversification was largely driven by colonization of novel geographic areas and subsequent evolution in isolation. These results illuminate our understanding of how protist diversity, biogeographical patterns, and members of the rare biosphere are generated, and suggest allopatric speciation to be a powerful mechanism for diversification of micro-organisms

Rapid biodiversity monitoring of freshwater ponds using environmental DNA : traversing the aquatic-terrestrial boundary in pondscapes

Environmental DNA (eDNA) analysis is transforming biodiversity monitoring in aquatic ecosystems with immense potential to inform their conservation and management. eDNA analysis is rapid, non-invasive, cost-efficient, and often more accurate and sensitive than conventional monitoring tools for single species detection and community survey. Ponds are extremely diverse yet understudied freshwater habitats that require novel tools to enable comprehensive, systematic, long-term monitoring. eDNA monitoring could radically improve assessments of pond biodiversity, but the applications and methodical constraints of this tool in ponds are largely unexplored. In this thesis, eDNA analysis was examined as a tool for monitoring biodiversity associated with ponds, including aquatic, semi-aquatic, and terrestrial taxa. eDNA analysis using metabarcoding was shown to have comparable detection sensitivity for Triturus cristatus to targeted eDNA analysis using quantitative PCR, depending on species detection thresholds applied. Using the community data generated by this method comparison, eDNA metabarcoding was validated as a tool for ecological hypothesis testing, specifically biotic and abiotic determinants of T. cristatus and vertebrate species richness. A novel eDNA assay was designed and validated for targeted survey of the threatened Carassius carassius, a fish species characteristic of ponds. Furthermore, eDNA metabarcoding was compared to established methods of freshwater invertebrate assessment, and all methods used to evaluate the impact of stocking C. carassius for conservation purposes. Finally, eDNA metabarcoding was vindicated as a tool to monitor semi-aquatic and terrestrial mammals associated with ponds, and investigate the spatiotemporal distribution of their eDNA signals in these water bodies as a function of behaviour. These results combined emphasise the biological and scientific importance of ponds, and the prospects of eDNA analysis - targeted and community approaches - for enhanced conservation, management, monitoring, and research of these valuable ecosystems

Building catalogues of genetic variation in Poplar

La tesi descrive l\u2019analisi della variazione genetica a livello di sequenza in due specie di pioppo (Populus nigra e Populus detoides) con l\u2019utilizzo di tecnologie di sequenziamento di nuova generazione e di analisi bioinformatiche. \uc8 stata analizzata sia la variazione a livello di singolo nucleotide in un numero ristretto di geni ma in un campione molto esteso di individui, sia la variazione strutturale nell\u2019intero genoma in un campione limitato di individu

Molecular analysis of fungal communities and laccase genes in decomposing litter reveals differences among forest types but no impact of nitrogen deposition

The fungal community of the forest floor was examined as the cause of previously reported increases in soil organic matter due to experimental N deposition in ecosystems producing predominantly high-lignin litter, and the opposite response in ecosystems producing low-lignin litter. The mechanism proposed to explain this phenomenon was that white-rot basidiomycetes are more important in the degradation of high-lignin litter than of low-lignin litter, and that their activity is suppressed by N deposition. We found that forest floor mass in the low-lignin sugar-maple dominated system decreased in October due to experimental N deposition, whereas forest floor mass of high-lignin oak-dominated ecosystems was unaffected by N deposition. Increased relative abundance of basidiomycetes in high-lignin forest floor was confirmed by denaturing gradient gel electrophoresis (DGGE) and sequencing. Abundance of basidiomycete laccase genes, encoding an enzyme used by white-rot basidiomycetes in the degradation of lignin, was 5–10 times greater in high-lignin forest floor than in low-lignin forest floor. While the differences between the fungal communities in different ecosystems were consistent with the proposed mechanism, no significant effects of N deposition were detected on DGGE profiles, laccase gene abundance, laccase length heterogeneity profiles, or phenol oxidase activity. Our observations indicate that the previously detected accumulation of soil organic matter in the high-lignin system may be driven by effects of N deposition on organisms in the mineral soil, rather than on organisms residing in the forest floor. However, studies of in situ gene expression and temporal and spatial variability within forest floor communities will be necessary to further relate the ecosystem dynamics of organic carbon to microbial communities and atmospheric N deposition.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/72825/1/j.1462-2920.2007.01250.x.pd