Multivariate complexity analysis of 3D surface form and function of centric diatoms at the Eocene–Oligocene transition

Complexity is important in the course of evolution, but consensus of what complexity analysis entails is elusive. In this study, multivariate complexity is measured and analyzed in terms of magnitude of change and the trends behind those changes. Multivariate morphological and functional complexities were analyzed using 3D surface models of centric diatom genera from the Eocene to Oligocene, a transitional time when temperatures cooled, sea levels rose, and glaciation increased. Diatoms were chosen for study because of their importance in biostratigraphy, biogeochemical cycling, productivity, food web dynamics, and sensitivity to environmental conditions. Probabilistic analysis using aMarkov chain indicated an increase in total complexity across the Eocene–Oligocene transition (EOT). Causal inference via structural equation modeling indicated weakly driven functional and morphological complexity trends over the EOT.Morphological and functional complexity trends differed with respect to predation resistance as responses to ecological complexity as environmental and climate change occurred across the EOT. Macroevolutionary patterns of morphological and functional complexity with respect to ecological complexity did not necessarily coincide over time.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/116860/1/2016JLP-MARMIC.pdfDescription of 2016JLP-MARMIC.pdf : main articl

QUANTITATIVE METHOD FOR DETERMINING A REPRESENTATIVE ALGAL SAMPLE COUNT 1

A method for determining a representative count of a sample dependent on number of species is presented for application to various algal communities. Constant species curves are calculated as efficiency = (number of individuals–number of species)/number of individuals and diagrammed on a plot of efficiency versus number of individuals counted. Efficiency is defined as the probability that a new species encountered is minimal. That is, as the ratio of number of species to number of individuals approaches 1, more individuals will need to be counted in order to achieve a representative count. Data and calculations of efficiency from two algal communities are presented for illustration.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/66065/1/j.0022-3646.1996.00693.x.pd

Collecting microfossils: Diatoms as science and art

This presentation was given by Janice L. Pappas at the Friends of the University of Michigan Museum of Palontology meeting on April 11, 2014.http://deepblue.lib.umich.edu/bitstream/2027.42/106589/1/JLP-Friends Apr 2014 talk 5-8-14-Annotated.pd

Quantitative morphometric methods in diatom research

Morphometric methods have been used in diatom research for decades. We present a review of the history of usage of morphometric methods of outline shape analysis, pattern recognition, and landmarkbased analysis. In addition, we present how morphometric methods are important in diatom taxonomy and classifi cation and what connections exist between morphometric methods and biologically meaningful results. Next, we present some details about calculating shape descriptors and using them in analysis of shape variation, the issues to be aware of, and what such results mean when defi ning shape groups as species groups. Finally, we provide a glimpse of the future in using morphometric methods in diatom research.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/117649/1/bibl_diatom_62_strelnikova.pdfDescription of bibl_diatom_62_strelnikova.pdf : Main articl

Effects of Inorganic Nitrogen Enrichment on Lake Huron Phytoplankton: An Experimental Study

Factorial experimental study analyzed using multivariate statistics.Effects of inorganic nitrogen (N03) enrichment on phytoplankton were studied using a factorial design experiment. Using species assemblages from Lake Huron waters, the effects of NO3 and total phosphorus (TSP) additions on species abundance and composition were monitored. The species-nutrient relationship was determined by canonical correspondence analysis (CCA). In addition, divisional differences were related to nutrient additions using correspondence analysis (CA). These techniques were instrumental in developing species relationships to N03 and TSP gradients and, by partialling out the effect of TSP to determine the primary species- NO3 relationship. Nitrate-phosphorus (N:P) effects were also analyzed at the species and divisional levels. Gross changes in biomass, as represented by chlorophyll a concentrations, were not evident from N03 enrichment. However, species composition did change, particularly for a few species. Most evident were increases in relative abundance of Cyclotella comensis. Cyclotella stelligera, Fragilaria capucina, F. pinnata, and flagellates showed similar increased proportional abundance. Flagellates responded positively to both N03 additions and N:P interactions. Overall, there were not great changes at the level of major algal divisions. All major groups maintained their abundances relative to one another throughout the experimental period. The results from this study showed that increased NO3 levels in the Great Lakes would affect species composition.Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/140715/1/Pappas and Stoermer 1995-nitrate study.pdfDescription of Pappas and Stoermer 1995-nitrate study.pdf : Main articl

Graph matching a skeletonized theoretical morphospace with a cladogram for gomphonemoid-cymbelloid diatoms (Bacillariophyta)

A three-dimensional (3D) theoretical morphospace of gomphonemoid and cymbelloid diatoms was skeletonized using concepts from extended Reeb graph analysis and Morse theory. The resultant skeleton tree was matched to a cladogram of the same group of related taxa using adjacency matrices of the trees and ordinated with multidimensional scaling (MDS) of leaf nodes. From this, an unweighted path matrix based on the number of branches between leaf nodes was ordinated to determine degree of matched tree structures. A constrained MDS of the path matrix, weighted by ranked MDS leaf node groups as facets, was used to interpret taxon environmental tolerances and habitat preferences with respect to adaptive value. The methods developed herein provided a way to combine results from morphological and phylogenetic analyses and interpret those results with respect to an aspect of evolutionary process, namely, adaptation.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/83675/1/JLP-JBS2011.pdf-

QUANTITATIVE ANALYSIS OF SHAPE VARIATION IN TYPE AND MODERN POPULATIONS OF MERIDION (BACILLARIOPHYCEAE)

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/65187/1/j.1529-8817.2001.037001175.x.pd

QUANTIFYING AND ANALYZING SURFACE FEATURES IN FOSSILS USING 3D DATA

Published abstract with citation.QUANTIFYING AND ANALYZING SURFACE FEATURES IN FOSSILS USING 3D DATA MILLER, Daniel J. and PAPPAS, Janice L., University of Michigan Museum of Paleontology, The University of Michigan, 1109 Geddes Ave, Ann Arbor, MI 48109-1079, [email protected] Characterizing the surface features of organisms can be useful for addressing a wide range of questions in paleontology and neontology. The ability to do so in a quantitative and explicit way permits analysis both within and across data sets. In this study, we use digital close-range photogrammetry to extract 3D coordinates that are then used to characterize surfaces. We use standard statistical parameters used in metrology, such as general surface roughness (average), degree of surface roughness (root mean square), preponderance of either peaks or valleys present on the surface (skewness), and degree of peakedness (kurtosis), as well as direction of change in surface roughness (root mean square slope). All of these parameters incorporate height and spacing information about the peaks on the surfaces of specimens. In addition, we also explore the potential application of spatial series analyses to characterize surfaces where spatial series take the form of sequential changes in surface features of a specimen. All calculations can be performed at different scales and on single or multiple patches from each specimen’s surface. Degree of continuity between patches or matching patches on a specimen surface is another potential way to quantitatively characterize surface features. We characterize the surfaces of a variety of fossil invertebrates from different phyla and demonstrate the use of these metrics in quantitatively comparing surfaces in different specimens regardless of their taxonomic position. Surface statistics are also used to explore features and patterns at a variety of spatial and size scales. Although these metrics are statistical summaries of surface features, they nevertheless provide a more precise quantitative means of comparing widely disparate morphologies when compared to qualitative approaches. The use of explicit and easily compared surface statistics potentially facilitates the exploration of a wide variety of hypotheses pertaining to biomechanics, development, biogeography, systematics, and taphonomy. 2010 GSA Denver Annual Meeting (31 October –3 November 2010) Geological Society of America Abstracts with Programs, Vol. 42, No. 5, p. 140http://deepblue.lib.umich.edu/bitstream/2027.42/85394/1/DJM-JLP-GSA2010citation.pd

Genotype-phenotype correlation at codon 1740 ofSETD2

The SET domain containing 2, histone lysine methyltransferase encoded by SETD2 is a dual-function methyltransferase for histones and microtubules and plays an important role for transcriptional regulation, genomic stability, and cytoskeletal functions. Specifically, SETD2 is associated with trimethylation of histone H3 at lysine 36 (H3K36me3) and methylation of α-tubulin at lysine 40. Heterozygous loss of function and missense variants have previously been described with Luscan-Lumish syndrome (LLS), which is characterized by overgrowth, neurodevelopmental features, and absence of overt congenital anomalies. We have identified 15 individuals with de novo variants in codon 1740 of SETD2 whose features differ from those with LLS. Group 1 consists of 12 individuals with heterozygous variant c.5218C>T p.(Arg1740Trp) and Group 2 consists of 3 individuals with heterozygous variant c.5219G>A p.(Arg1740Gln). The phenotype of Group 1 includes microcephaly, profound intellectual disability, congenital anomalies affecting several organ systems, and similar facial features. Individuals in Group 2 had moderate to severe intellectual disability, low normal head circumference, and absence of additional major congenital anomalies. While LLS is likely due to loss of function of SETD2, the clinical features seen in individuals with variants affecting codon 1740 are more severe suggesting an alternative mechanism, such as gain of function, effects on epigenetic regulation, or posttranslational modification of the cytoskeleton. Our report is a prime example of different mutations in the same gene causing diverging phenotypes and the features observed in Group 1 suggest a new clinically recognizable syndrome uniquely associated with the heterozygous variant c.5218C>T p.(Arg1740Trp) in SETD2

Association between community health center and rural health clinic presence and county-level hospitalization rates for ambulatory care sensitive conditions: an analysis across eight US states

<p>Abstract</p> <p>Background</p> <p>Federally qualified community health centers (CHCs) and rural health clinics (RHCs) are intended to provide access to care for vulnerable populations. While some research has explored the effects of CHCs on population health, little information exists regarding RHC effects. We sought to clarify the contribution that CHCs and RHCs may make to the accessibility of primary health care, as measured by county-level rates of hospitalization for ambulatory care sensitive (ACS) conditions.</p> <p>Methods</p> <p>We conducted an ecologic analysis of the relationship between facility presence and county-level hospitalization rates, using 2002 discharge data from eight states within the US (579 counties). Counties were categorized by facility availability: CHC(s) only, RHC(s) only, both (CHC and RHC), and neither. US Agency for Healthcare Research and Quality definitions were used to identify ACS diagnoses. Discharge rates were based on the individual's county of residence and were obtained by dividing ACS hospitalizations by the relevant county population. We calculated ACS rates separately for children, working age adults, and older individuals, and for uninsured children and working age adults. To ensure stable rates, we excluded counties having fewer than 1,000 residents in the child or working age adult categories, or 500 residents among those 65 and older. Multivariate Poisson analysis was used to calculate adjusted rate ratios.</p> <p>Results</p> <p>Among working age adults, rate ratio (RR) comparing ACS hospitalization rates for CHC-only counties to those of counties with neither facility was 0.86 (95% Confidence Interval, CI, 0.78–0.95). Among older adults, the rate ratio for CHC-only counties compared to counties with neither facility was 0.84 (CI 0.81–0.87); for counties with both CHC and RHC present, the RR was 0.88 (CI 0.84–0.92). No CHC/RHC effects were found for children. No effects were found on estimated hospitalization rates among uninsured populations.</p> <p>Conclusion</p> <p>Our results suggest that CHCs and RHCs may play a useful role in providing access to primary health care. Their presence in a county may help to limit the county's rate of hospitalization for ACS diagnoses, particularly among older people.</p