Browsing by Subject "phylogenetics"

Now showing 1 - 2 of 2
  • Thumbnail Image
    Item
    High-performance tools for precise microbiome characterization
    (2018-08) Al-Ghalith, Gabriel
    The microbiome, defined as the vast number of microorganisms inhabiting both human and non-human environments, has been associated with human disease as well as other important ecological phenomena. However, its quantitative study is complicated in part by measurement error and computational limitations, pointing to a need for more sensitive and reproducible DNA sequence analysis techniques. To this end, I have developed a variety of improved methods including a flexible short-read quality control pipeline, curated databases of marker genes and whole genomes, streamlined OTU picking software, and a high-throughput optimal aligner with taxonomy interpolation. Together, these methods represent advancements over traditional sequence analysis pipelines and may improve the quality of downstream statistical analyses.
  • Thumbnail Image
    Item
    Taxonomy and systematics: contributions to benthology and J-NABS
    (University of Chicago Press, 2010) Holzenthal, Ralph W.; Robertson, Desiree R.; Pauls, Steffen U.; Mendez, Patina K.
    Systematics, or taxonomy, is the study of the diversity of life on Earth. Its goals are to discover and describe new biological diversity and to understand its evolutionary and biogeographic origins and relationships. Here we review the contributions to the field of systematics and taxonomy published over the last 25 y in J-NABS and its predecessor Freshwater Invertebrate Biology (FIB). We examined a total of 64 studies that we considered to be largely taxonomic in nature. We classified these studies into 2 major categories: morphological (e.g., descriptive taxonomy, taxonomic revisions) and molecular (e.g., deoxyribonucleic acid [DNA] barcoding, population genetics). We examined studies in 5-y increments for J-NABS. We also studied the period 1982 to 1985, during which FIB was published. On average, 12 taxonomic studies were published within each 5-y period. Molecular studies first appeared in 1986 and have slowly increased, reaching their greatest number within the last 5 y. Studies also were classified by their individual attributes. Morphological studies were, by far, the most common, but studies also included molecular data, biological information, distributional data, keys, and biogeographical analyses. Most studies included .1 of these attributes. Overall, the role of J-NABS in the development of benthic taxonomy has been minimal in terms of number of publications, but as part of the nexus of taxomonic literature, all contributions have been important to the discipline. We discuss these contributions and their impact on the following subject areas: taxonomy and revisionary systematics, phylogenetic and molecular systematics, taxonomic resources, taxonomic resolution, conservation and taxonomy, professional training, taxonomic certification, and graduate education. We also give an overview of new developments in the taxonomists’ toolbox. These developments include DNA barcoding, online taxonomic resources, digital identification keys, cybertaxonomy, and modern museum collections and resources.