Evolutionary Inference from Admixed Genomes: Implications of Hybridization for Biodiversity Dynamics and Conservation

Hybridization as a macroevolutionary mechanism has been historically underappreciated among vertebrate biologists. Yet, the advent and subsequent proliferation of next-generation sequencing methods has increasingly shown hybridization to be a pervasive agent influencing evolution in many branches of the Tree of Life (to include ancestral hominids). Despite this, the dynamics of hybridization with regards to speciation and extinction remain poorly understood. To this end, I here examine the role of hybridization in the context of historical divergence and contemporary decline of several threatened and endangered North American taxa, with the goal to illuminate implications of hybridization for promoting—or impeding—population persistence in a shifting adaptive landscape. Chapter I employed population genomic approaches to examine potential effects of habitat modification on species boundary stability in co-occurring endemic fishes of the Colorado River basin (Gila robusta and G. cypha). Results showed how one potential outcome of hybridization might drive species decline: via a breakdown in selection against interspecific heterozygotes and subsequent genetic erosion of parental species. Chapter II explored long-term contributions of hybridization in an evolutionarily recent species complex (Gila) using a combination of phylogenomic and phylogeographic modelling approaches. Massively parallel computational methods were developed (and so deployed) to categorize sources of phylogenetic discordance as drivers of systematic bias among a panel of species tree inference algorithms. Contrary to past evidence, we found that hypotheses of hybrid origin (excluding one notable example) were instead explained by gene-tree discordance driven by a rapid radiation. Chapter III examined patterns of local ancestry in the endangered red wolf genome (Canis rufus) – a controversial taxon of a long-standing debate about the origin of the species. Analyses show how pervasive autosomal introgression served to mask signatures of prior isolation—in turn misleading analyses that led the species to be interpreted as of recent hybrid origin. Analyses also showed how recombination interacts with selection to create a non-random, structured genomic landscape of ancestries with, in the case of the red wolf, the ‘original’ species tree being retained only in low-recombination ‘refugia’ of the X chromosome. The final three chapters present bioinformatic software that I developed for my dissertation research to facilitate molecular approaches and analyses presented in Chapters I–III. Chapter IV details an in-silico method for optimizing similar genomic methods as used herein (RADseq of reduced representation libraries) for other non-model organisms. Chapter V describes a method for parsing genomic datasets for elements of interest, either as a filtering mechanism for downstream analysis, or as a precursor to targeted-enrichment reduced-representation genomic sequencing. Chapter VI presents a rapid algorithm for the definition of a ‘most parsimonious’ set of recombinational breakpoints in genomic datasets, as a method promoting local ancestry analyses as utilized in Chapter III. My three case studies and accompanying software promote three trajectories in modern hybridization research: How does hybridization impact short-term population persistence? How does hybridization drive macroevolutionary trends? and How do outcomes of hybridization vary in the genome? In so doing, my research promotes a deeper understanding of the role that hybridization has and will continue to play in governing the evolutionary fates of lineages at both contemporary and historic timescales

The biodiversity benefit of native forests and mixed-species plantations over monoculture plantations

Aim: China's Grain for Green Program (GFGP) is the largest reforestation programme in the world and has been operating since 1999. The GFGP has promoted the establishment of tree plantations over the restoration of diverse native forests. In a previous study, we showed that native forests support a higher species richness and abundance of birds and bees than do GFGP plantations and that mixed-species GFGP plantations support a higher level of bird (but not bee) diversity than do any individual GFGP monocultures (although still below that of native forests). Here, we use metabarcoding of arthropod diversity to test the generality of these results. Location: Sichuan, China. Methods: We sampled arthropod communities using pan traps in the land cover types concerned under the GFGP. These land use types include croplands (the land cover being reforested under the GFGP), native forests (the reference ecosystem as the benchmark for the GFGP’s biodiversity effects) and the dominant GFGP reforestation outcomes: monoculture and mixed-species plantations. We used COI-amplicon sequencing (“metabarcoding”) of the arthropod samples to quantify and assess the arthropod community profiles associated with each land cover type. Results: Native forests support the highest overall levels of arthropod species diversity, followed by mixed-species plantations, followed by bamboo and other monocultures. Also, the arthropod community in native forests shares more species with mixed-species plantations than it does with any of the monocultures. Together, these results broadly corroborate our previous conclusions on birds and bees but show a higher arthropod biodiversity value of mixed-species plantations than previously indicated by bees alone. Main conclusion: In our previous study, we recommended that GFGP should prioritize the conservation and restoration of native forests. Also, where plantations are to be used, we recommended that the GFGP should promote mixed-species arrangements over monocultures. Both these recommendations should result in more effective protection of terrestrial biodiversity, which is an important objective of China's land-sustainability spending. The results of this study strengthen these recommendations because our policy prescriptions are now also based on a dataset that includes over 500 species-resolution taxa, ranging across the Arthropoda

Annual Report: 2009

I submit herewith the annual report from the Agricultural and Forestry Experiment Station, School of Natural Resources and Agricultural Sciences, University of Alaska Fairbanks, for the period ending December 31, 2009. This is done in accordance with an act of Congress, approved March 2, 1887, entitled, “An act to establish agricultural experiment stations, in connection with the agricultural college established in the several states under the provisions of an act approved July 2, 1862, and under the acts supplementary thereto,” and also of the act of the Alaska Territorial Legislature, approved March 12, 1935, accepting the provisions of the act of Congress. The research reports are organized according to our strategic plan, which focuses on high-latitude soils, high-latitude agriculture, natural resources use and allocation, ecosystems management, and geographic information. These areas cross department and unit lines, linking them and unifying the research. We have also included in our financial statement information on the special grants we receive. These special grants allow us to provide research and outreach that is targeted toward economic development in Alaska. Research conducted by our graduate and undergraduate students plays an important role in these grants and the impact they make on Alaska.Financial statement -- Grants -- Students -- Research Reports: Partners, Facilities, and Programs; Geography; High-Latitude Agriculture; High-Latitude Soils; Management of Ecosystems; Natural Resources Use and Allocation; Index to Reports -- Publications -- Facult

Molecular investigations in date palm genetic structure and diversity among commercially important date palm cultivars (Phoenix dactylifera L.)

2019 Fall.Includes bibliographical references.The date palm, Phoenix dactylifera L. is the notable palm which produces a nutrient-rich edible fruit (the date), well known for its unique attributes of medicine and healthy energy. It is a species that has been cultivated since early civilizations in the fertile crescent and later in the Middle East. It is typically cloned with many cultivars (over 3000). A means of accurately identifying specific clones and an understanding of the relationships among major commercial cultivars would provide valuable information for the maintenance, potentially an improvement and continued conservation of superior genotypes. Phylogenetic relationships amid commercial date cultivars are poorly understood, despite their importance. This research aimed at providing applicable knowledge through an expedient technique, by developing an exclusively tailored Simple Sequence Repeat (SSR) panel, custom-made for date palm fingerprinting and molecular identification also named as 'Dates PalmàPrinting'. This assembled modified genotyping by microsatellite markers provides a standardized approach to cultivar identification and a quality control application in date palm micropropagation production. A deeper understanding and relationship of today's major commercial cultivars is incomplete. Improving the development and productivity of this tree species is restricted due to few genetic resources. Only regionally narrowed studies have been conducted but it is more important to have a broader base of such knowledge. The present research reports on 20 selected, commercially important date palm cultivars, consisting of 18 females and 2 males, which are grown throughout the world. The knowledge of relationships among these cultivars is needed, although the date palm genome has been mostly sequenced (90.2 %) with 41,660 gene models representing an 82,354 scaffold. The relationships among the major cultivars remain unclear. Presently, the information on the characterization of these cultivars requires an assessment to better understand the relationships among the superior genotypes. The use of microsatellites, due to their accuracy and high polymorphic capability, have led to fine scaled phylogenies. The phylogenetic relationships were determined using neighbor joining un-rooted trees correlated with genetic structure clustering. Primer selections were achieved from evaluation of 14 nuclear SSR loci isolated from P. dactylifera. Results revealed a high degree of polymorphism observed in the 20 cultivars with fewer common alleles than anticipated. Within the cultivars studied, a broad heterozygosity across base pair (bp) amplification data has led to an understanding of limited inbreeding, accounting for possible adaptation to environmental changes and revealing conserved extensive array of genomic structure. Population structure analysis suggests a large genetic boundary between Northwest African and Middle Eastern cultivars with 6 subpopulations that represent divergences and fragments of admixture in cultivars present in these regions. The possible selection of potential and good quality parents is achievable for improving cultivars by generating population and structure maps. This analysis documents patterns of relationship and provides genetic structure and diversity of gene pool specificity complexes of date palm cultivars. This study provides insights about the relationships that exist among cultivars of interest through genetic sequence analysis using SSRs, facilitating the development of a standard approach to identification and enhancements to the micropropagation process. Keywords: Microsatellites, Phoenix dactylifera L., Simple sequence repeats, Phylogenetics, Genetic structure, Date palm, Genetic diversit

Giant reverse transcriptase-encoding transposable elements at telomeres

Author Posting. © The Author(s), 2017. This is the author's version of the work. It is posted here by permission of Oxford University Press for personal use, not for redistribution. The definitive version was published in Molecular Biology and Evolution 34 (2017): 2245–2257, doi:10.1093/molbev/msx159.Transposable elements are omnipresent in eukaryotic genomes and have a profound impact on chromosome structure, function and evolution. Their structural and functional diversity is thought to be reasonably well-understood, especially in retroelements, which transpose via an RNA intermediate copied into cDNA by the element-encoded reverse transcriptase, and are characterized by a compact structure. Here we report a novel type of expandable eukaryotic retroelements, which we call Terminons. These elements can attach to G-rich telomeric repeat overhangs at the chromosome ends, in a process apparently facilitated by complementary C-rich repeats at the 3’-end of the RNA template immediately adjacent to a hammerhead ribozyme motif. Terminon units, which can exceed 40 kb in length, display an unusually complex and diverse structure, and can form very long chains, with host genes often captured between units. As the principal polymerizing component, Terminons contain Athena reverse transcriptases previously described in bdelloid rotifers and belonging to the enigmatic group of Penelope-like elements, but can additionally accumulate multiple co-oriented ORFs, including DEDDy 3’-exonucleases, GDSL esterases/lipases, GIY-YIG-like endonucleases, rolling-circle replication initiator (Rep) proteins, and putatively structural ORFs with coiled-coil motifs and transmembrane domains. The extraordinary length and complexity of Terminons and the high degree of inter-family variability in their ORF content challenge the current views on the structural organization of eukaryotic retroelements, and highlight their possible connections with the viral world and the implications for the elevated frequency of gene transfer.This work was supported by the National Institutes of Health (grant GM111917 to I.A.).2018-05-3

Comparative genomics of early animal evolution

The explosion of genomics permits investigations into the origin and early evolution of the Metazoa at the molecular level. In this thesis, I am particularly interested in investigating the molecular foundation of the animal senses (i.e. how animals perceive their world). To understand the directionality of evolutionary innovation a well-developed phylogenetic framework is necessary. On one hand, the combination of molecular and morphological data sets has revolutionized our views of metazoan relationships over the past decades, but on the other hand, a number of nodes on the metazoan tree remain uncertain. Uncertainty is particularly high with reference to the taxa generally named “early branching metazoans”. Unfortunately, understanding the relationships among these taxa is key to understanding the evolution of sensory perception (Nielsen 2008). In this thesis I will investigate both animal phylogenetics (to attempt to resolve the phylogeny among the early branching Metazoa) and the evolution of the metazoan sensory receptors. The G-protein coupled receptor superfamily (GPCR) superfamily is the main family of metazoan surface receptors. In this thesis, after an initial introduction (Chapter 1), I address and substantially clarify the relationship among the early branching animals (Chapter 2) using novel genomic data and publicly available expressed sequence tags (ESTs). I then move forward (Chapter 3) to use network-based methods to study the early evolution of the GPCR superfamily in Eukaryotes and animals. Finally (Chapter 4), I focus on the study of a specific subset of GPCRs (the a-group, Rhodopsin-like receptors). This GPCR group is particularly interesting as it includes the best studied and, arguably, one of the most interesting among the GPCR families: the Opsin family. Opsins are key proteins used in the process of light detection, and the origin and early evolution of this family are still substantially unknown. Chapter 4 addresses both these problems. The thesis is then concluded by a general discussion (Chapter 5) and a future directions (Chapter 6) section. Overall, this thesis provides new insights into the origin and early evolution of the Metazoa and their senses

Increased somatic mutation burdens in normal human cells due to defective DNA polymerases.

Funder: Wellcome PhD StudentshipFunder: Jean Shank/Pathological Society Intermediate FellowshipFunder: Wellcome Clinical PhD fellowshipMutation accumulation in somatic cells contributes to cancer development and is proposed as a cause of aging. DNA polymerases Pol ε and Pol δ replicate DNA during cell division. However, in some cancers, defective proofreading due to acquired POLE/POLD1 exonuclease domain mutations causes markedly elevated somatic mutation burdens with distinctive mutational signatures. Germline POLE/POLD1 mutations cause familial cancer predisposition. Here, we sequenced normal tissue and tumor DNA from individuals with germline POLE/POLD1 mutations. Increased mutation burdens with characteristic mutational signatures were found in normal adult somatic cell types, during early embryogenesis and in sperm. Thus human physiology can tolerate ubiquitously elevated mutation burdens. Except for increased cancer risk, individuals with germline POLE/POLD1 mutations do not exhibit overt features of premature aging. These results do not support a model in which all features of aging are attributable to widespread cell malfunction directly resulting from somatic mutation burdens accrued during life

Sulfate reducing communities in aquifer systems can be reliably stimulated by addition of complex nutrients

The disseration presented below is the summation of research into the potential roles of microbial communities associated with aquifers of Bangladesh contaminated with naturally occuring arsenic. These investigations also included experimental microcosm experiments to assess the role of nutrients supplementation of complex carbon sources (molasses), and inorganic sulfate (MgSO4), on both the solubility of arsenic to determine the feasibility of this method for the goal of performing in situ bioremediation. Community structure and functional gene profiling was performed on all samples, as well as detection of community shifts following amendments predicted to encourage the growth of sulfate reducting microorganisms (SRM). This included community profiling via 16S analysis, as well as presence and quantification of a number of genes involved in respiratory sulfate reduction and genes involved in arsenic cycling. Investigation of samples gathered from contaminated aquifers seems to indicate that even in a community with relatively simple distribution of organisms, there is no distinct linkage between examined functional genes and concentrations of any detected elements in the aquifers. Examination of the effects of nutrient supplementation on sediments gathered from one impacted aquifer shows that stimulation of the system with either nutrient tested is sufficient to stimulate growth of sulfate reducing microbes, as indicated by conserved genes in the respiratory sulfate reduction pathway. These shifts can be closely associated with an initial decrease in detectable soluble arsenic levels, as well as a commensurate decrease in soluble metals. However, only the addition of both a complex carbon source and magnesium sulfate in equal molar portions seemed to show prolonged removal of these elements from the soluble phase. Community shifts appear to have occurred by 14 days of incubation, and were coupled with expected changes in the color and consistency of sediment as black particulate can serve as an indicator of sulfidic minerals formed as a result of excess sulfides produced by SRM. Increased SRM numbers were maintained through 96 days of incubation. Due to the ability of any perturbation of a microcosm system to produce increased density of SRM in the samples, a bioinformatic investigation of the identified subsystems encoded by all sequenced and finished bacteria capable of carrying out the most conserved steps in sulfate reduction was performed. These analyses indicated that there are a number of SRM capable of directly reducing complex carbon sources, both in syntrophic communities, as well as without additional aid from the environment. These results indicate that sulfate reducing microbes are present, detectable and easily stimulated to grow in aquifer sediment, and that these communities of SRM are able to create conditions capable of removing arsenic from the soluble phase. The rate of growth and ability to maintain this immobilization supports the theory that SRM detected in the environment are capable of growth on complex nutrients, and require additional nutrients to successfully remediate arsenic for long periods of time