Improving College Access and Completion for Low-Income and First-Generation Students: The Role of College Access and Success Programs

Resequencing of Agaricus bisporus herbarium specimen 99817338

Genomic Treasure Troves: Complete Genome Sequencing of Herbarium and Insect Museum Specimens

Unlocking the vast genomic diversity stored in natural history collections would create unprecedented opportunities for genome-scale evolutionary, phylogenetic, domestication and population genomic studies. Many researchers have been discouraged from using historical specimens in molecular studies because of both generally limited success of DNA extraction and the challenges associated with PCR-amplifying highly degraded DNA. In today's next-generation sequencing (NGS) world, opportunities and prospects for historical DNA have changed dramatically, as most NGS methods are actually designed for taking short fragmented DNA molecules as templates. Here we show that using a standard multiplex and paired-end Illumina sequencing approach, genome-scale sequence data can be generated reliably from dry-preserved plant, fungal and insect specimens collected up to 115 years ago, and with minimal destructive sampling. Using a reference-based assembly approach, we were able to produce the entire nuclear genome of a 43-year-old Arabidopsis thaliana (Brassicaceae) herbarium specimen with high and uniform sequence coverage. Nuclear genome sequences of three fungal specimens of 22–82 years of age (Agaricus bisporus, Laccaria bicolor, Pleurotus ostreatus) were generated with 81.4–97.9% exome coverage. Complete organellar genome sequences were assembled for all specimens. Using de novo assembly we retrieved between 16.2–71.0% of coding sequence regions, and hence remain somewhat cautious about prospects for de novo genome assembly from historical specimens. Non-target sequence contaminations were observed in 2 of our insect museum specimens. We anticipate that future museum genomics projects will perhaps not generate entire genome sequences in all cases (our specimens contained relatively small and low-complexity genomes), but at least generating vital comparative genomic data for testing (phylo)genetic, demographic and genetic hypotheses, that become increasingly more horizontal. Furthermore, NGS of historical DNA enables recovering crucial genetic information from old type specimens that to date have remained mostly unutilized and, thus, opens up a new frontier for taxonomic research as well

From morphological nightmare to molecular conundrum : phylogenetic evolutionary and taxonomic studies on Guatteria (Annonaceae)

The Neotropics (Mexico to South Brazil) contains c. 30% of the world's plant diversity, but the origin of this diversity remains unclear. Several recent studies have suggested that a substantial portion of this diversity has resulted from the dispersal of taxa into that region. However, more data are needed to substantiate this claim. Guatteria (Annonaceae) is with c. 290 species the third largest genus of Neotropical trees. Its widespread distribution and frequent occurrence makes the genus an excellent model taxon to study diversification patterns. This dissertation reconstructed the evolutionary history of Guatteria and inferred three major events in the history of this genus: 1) A migration across the ocean from Central into South America before the closing of the Isthmus of Panama; 2) a major diversification of the lineage within South America; and 3) several migrations of South American lineages back into Central America via the closed Panamanian land bridge. Therefore, most of the species of Guatteria resulted from a major radiation that followed its dispersal into South America over 6 million years ago. This study provides further evidence that migration into the Neotropics was an important factor in the historical assembly of its biodiversity. Next to this, the accepted classification of the species within Guatteria as well as the relationship between Guatteria and its small satellite genera (Guatteriopsis, Guatteriella and Heteropetalum) was investigated. Current classification of Guatteria is based on morphology and species are often difficult to tell apart. Because of this morphological complexity researchers have been reluctant to study these plants. Therefore, the last thorough study of this genus as a whole dates back to 1939. In this dissertation, an evolutionary tree containing c. 40% of the species of Guatteria was constructed. This was done on the basis of chloroplast DNA. Unfortunately, clear insight in most of the evolutionary relationships between species was not achieved. Therefore, a completely new classification of Guatteria would be premature. However, it is clear that the largest part of the currently accepted classification should be abandoned. Notwithstanding this, conclusions could be drawn on the morphological evolution of the genus. Furthermore, the closest relative of Guatteria could not be determined with certainty. This knowledge is necessary in order to understand the origin of the genus. A morphological nightmare for taxonomists in the past decades proves to some extent to be a mystery for molecular biologists, even today. The Central American species of Guatteria are in general easier to tell apart than the South American representatives. In order to study these species, field work in Costa Rica and Panama was carried out. During this fieldwork five new species of Guatteria were discovered and named. These species were studied together with all the already known Central American species of Guatteria and the resulting Flora treatment is included in this dissertation. The descriptions of the species, accompanied by photographs, can be used by specialists and non-specialists to identify herbarium material of Central American Guatteria's. Finally, the use of herbarium specimens in this molecular phylogenetic study was evaluated

A method for making Red List assessments with herbarium data and distribution models for species-rich plant taxa: Lessons from the Neotropical genus Guatteria (Annonaceae)

Societal Impact Statement Despite its importance, biodiversity is declining rapidly. To adequately prioritise conservation efforts, we need to know how threatened species actually are. The International Union for the Conservation of Nature (IUCN) Red List is the most widely recognised tool for assessing extinction risk. Unfortunately, many lesser-known species are not yet represented, such as those that are rarely collected or are in species-rich taxon groups. This is potentially due to low data availability, although Red List assessments can still be made with little data. We present a method to rapidly assess the conservation status of species that have low data availability, which will speed up the inclusion of species from large groups into the IUCN Red List. center dot The International Union for the Conservation of Nature (IUCN) Red List is the most widely recognised tool to assess the extinction risk of species. For it to be effective in directing conservation effort, it is important that as many species as possible are represented, but many are unfortunately not. A lack of data is often the main reason for this, especially for lesser-studied species. However, this does not mean assessments cannot be made. center dot We examine the use of georeferenced herbarium data in combination with species distribution modelling for assessing plants on the IUCN Red List, with Guatteria (Annonaceae), a genus of Neotropical trees, as a case study. We focus on differences between preliminary and officially published assessments, show the final conservation status of all Guatteria species and provide a roadmap for compiling Red List assessments for species-rich plant groups in the future. center dot We found that species-distribution models aid in compiling Red List assessments, especially for taxa that lack data, but expert opinion remains an important source of information. Half of Guatteria species (48.0%) are Least Concern, and 13.1% of species are near threatened or threatened. The remaining species are Data Deficient or Not Evaluated. Most of our preliminary assessments remained unchanged upon review and publication on the IUCN Red List. center dot Our method allows for assessing a large group of taxa in a relatively short amount of time. We argue that this benefit outweighs the potential disadvantage of a lack of detail in these assessments, emphasising the potential of this method for future Red List assessments

A concise bibliographic overview of Annonaceae

It is important that taxonomic knowledge is disseminated by those who possess it. This can be carried out via online databases, printed publications or training in taxonomic practice. For Annonaceae, the online database AnnonBase includes all published names of Annonaceae at any rank worldwide. Recently, an updated index to genera, species and infraspecific taxa of Neotropical Annonaceae was published in hard copy. This manuscript contains a concise update to the Bibliography of Annonaceae published by the late E. A. Mennega in 1993. Since his publication, much work has been carried out on systematics and evolution of Annonaceae, with the advent of molecular phylogenetics providing an additional stimulus. Here, however, we concentrate only on taxonomic papers focusing specifically on the description and circumscription of taxa (e.g. revisions, monographs, floras, checklists, descriptions of new species or phylogenetic studies that show monophyly/polyphyly/paraphyly of genera). The index should provide an easy entrance into the most important taxonomic literature on Annonaceae from 1900 onwards for the trained and untrained taxonomist with an interest in Annonaceae