Mathematical Models and Biological Meaning: Taking Trees Seriously

We compare three basic kinds of discrete mathematical models used to portray phylogenetic relationships among species and higher taxa: phylogenetic trees, Hennig trees and Nelson cladograms. All three models are trees, as that term is commonly used in mathematics; the difference between them lies in the biological interpretation of their vertices and edges. Phylogenetic trees and Hennig trees carry exactly the same information, and translation between these two kinds of trees can be accomplished by a simple algorithm. On the other hand, evolutionary concepts such as monophyly are represented as different mathematical substructures are represented differently in the two models. For each phylogenetic or Hennig tree, there is a Nelson cladogram carrying the same information, but the requirement that all taxa be represented by leaves necessarily makes the representation less efficient. Moreover, we claim that it is necessary to give some interpretation to the edges and internal vertices of a Nelson cladogram in order to make it useful as a biological model. One possibility is to interpret internal vertices as sets of characters and the edges as statements of inclusion; however, this interpretation carries little more than incomplete phenetic information. We assert that from the standpoint of phylogenetics, one is forced to regard each internal vertex of a Nelson cladogram as an actual (albeit unsampled) species simply to justify the use of synapomorphies rather than symplesiomorphies.Comment: 15 pages including 6 figures [5 pdf, 1 jpg]. Converted from original MS Word manuscript to PDFLaTe

Genomic islands of divergence in the Yellow Tang and the Brushtail Tang Surgeonfishes.

The current ease of obtaining thousands of molecular markers challenges the notion that full phylogenetic concordance, as proposed by phylogenetic species concepts, is a requirement for defining species delimitations. Indeed, the presence of genomic islands of divergence, which may be the cause, or in some cases the consequence, of speciation, precludes concordance. Here, we explore this issue using thousands of RAD markers on two sister species of surgeonfishes (Teleostei: Acanthuridae), Zebrasoma flavescens and Z. scopas, and several populations within each species. Species are readily distinguished based on their colors (solid yellow and solid brown, respectively), yet populations and species are neither distinguishable using mitochondrial markers (cytochrome c oxidase 1), nor using 5193 SNPs (pairwise Φst = 0.034). In contrast, when using outlier loci, some of them presumably under selection, species delimitations, and strong population structure follow recognized taxonomic positions (pairwise Φst = 0.326). Species and population delimitation differences based on neutral and selected markers are likely due to local adaptation, thus being consistent with the idea that these genomic islands of divergence arose as a consequence of isolation. These findings, which are not unique, raise the question of a potentially important pathway of divergence based on local adaptation that is only evident when looking at thousands of loci

Laser ablation loading of a radiofrequency ion trap

The production of ions via laser ablation for the loading of radiofrequency (RF) ion traps is investigated using a nitrogen laser with a maximum pulse energy of 0.17 mJ and a peak intensity of about 250 MW/cm^2. A time-of-flight mass spectrometer is used to measure the ion yield and the distribution of the charge states. Singly charged ions of elements that are presently considered for the use in optical clocks or quantum logic applications could be produced from metallic samples at a rate of the order of magnitude 10^5 ions per pulse. A linear Paul trap was loaded with Th+ ions produced by laser ablation. An overall ion production and trapping efficiency of 10^-7 to 10^-6 was attained. For ions injected individually, a dependence of the capture probability on the phase of the RF field has been predicted. In the experiment this was not observed, presumably because of collective effects within the ablation plume.Comment: submitted to Appl. Phys. B., special issue on ion trappin

Population Structure Analyses Provide Insight into the Source Populations Underlying Rural Isolated Communities in Illinois

We have previously hypothesized that relatively small and isolated rural communities may experience founder effects, defined as the genetic ramifications of small population sizes at the time of a community’s establishment. To explore this, we used an Illumina Infinium Omni2.5Exome-8 chip to collect data from 157 individuals from four Illinois communities, three rural and one urban. Genetic diversity estimates of 999,259 autosomal markers suggested that the reduction in heterozygosity due to shared ancestry was approximately 0, indicating a randomly mating population. An eigenanalysis, which is similar to a principal component analysis but ran on a genetic coancestry matrix, conducted in the SNPRelate R package revealed that the majority of these individuals formed one cluster with a few putative outliers obscuring population variation. An additional eigenanalysis on the same markers in a combined data set including the 2,504 individuals in the 1000 Genomes database found that most of the 157 Illinois individuals clustered into one group in close proximity to individuals of European descent. A final eigenanalysis of the Illinois individuals with the 503 individuals of European descent (within the 1000 Genomes Project) revealed two clusters of individuals and likely two source populations; one British and one consisting of multiple European subpopulations. We therefore demonstrate the feasibility of examining genetic relatedness across Illinois populations and assessing the number of source populations using publicly available databases. When assessed, it becomes possible for population structure information to contribute to the understanding of genetic history in rural populations

Weight Loss Programs May Have Beneficial or Adverse Effects on Fat Mass and Insulin Sensitivity in Overweight and Obese Black Women

OBJECTIVE: Weight loss interventions have produced little change in insulin sensitivity in black women, but mean data may obscure metabolic benefit to some and adverse effects for others. Accordingly, we analyzed insulin sensitivity relative to fat mass change following a weight loss program. DESIGN AND METHODS: Fifty-four black women (BMI range 25.9 to 54.7 kg/m(2)) completed the 6-month program that included nutrition information and worksite exercise facilities. Fat mass was measured by dual-energy X-ray absorptiometry, and insulin sensitivity index (S(I)) was calculated from an insulin-modified intravenous glucose tolerance test using the minimal model. RESULTS: Baseline S(I) (range 0.74 to 7.58 l/mU(−1)•min(−1)) was inversely associated with fat mass (r = −0.516, p < 0.001), independent of age. On average, subjects lost fat mass (baseline 40.8 ± 12.4 to 39.4 ± 12.6 kg [mean ± SD], P < 0.01), but 17 women (32 %) actually gained fat mass. S(I) for the group was unchanged (baseline 3.3 ± 1.7 to 3.2 ± 1.6, P = 0.67). However, the tertile with greatest fat mass loss (−3.6 kg, range −10.7 to −1.7 kg) improved insulin sensitivity (S(I) +0.3 ± 1.2), whereas the tertile with net fat mass gain (+0.9 kg, range −0.1 to +3.8 kg) had reduced insulin sensitivity (S(I) −0.7 ± 1.3) from baseline values (P < 0.05 by ANOVA). CONCLUSIONS: Black women in a weight loss program who lose fat mass may have improved insulin sensitivity, but fat mass gain with diminished sensitivity is common. Additional support for participants who fail to achieve fat mass loss early in an intervention may be required for success

A depolarization and attenuation experiment using the COMSTAR and CTS satellites

Monthly and annual percent-of-time data on ground rain fall rate and attenuation on satellite downlinks at 11.7 GHz, 19.04 GHz, and 28.56 GHz is presented. Equal probability values of attenuation and rain rate are compared for monthly, quarterly, half-year periods and for the entire year. Regression equations relating cross polarization isolation to the logarithm of attenuation are also presented

Communicating Phylogeny: Evolutionary Tree Diagrams in Museums

Tree of life diagrams are graphic representations of phylogeny—the evolutionary history and relationships of lineages—and as such these graphics have the potential to convey key evolutionary ideas and principles to a variety of audiences. Museums play a significant role in teaching about evolution to the public, and tree graphics form a common element in many exhibits even though little is known about their impact on visitor understanding. How phylogenies are depicted and used in informal science settings impacts their accessibility and effectiveness in communicating about evolution to visitors. In this paper, we summarize the analysis of 185 tree of life graphics collected from museum exhibits at 52 institutions and highlight some potential implications of how trees are presented that may support or hinder visitors’ understanding about evolution. While further work is needed, existing learning research suggests that common elements among the diversity of museum trees such as the inclusion of anagenesis and absence of time and shared characters might represent potential barriers to visitor understanding

Tissue Sampling Methods and Standards for Vertebrate Genomics

The recent rise in speed and efficiency of new sequencing technologies have facilitated high-throughput sequencing, assembly and analyses of genomes, advancing ongoing efforts to analyze genetic sequences across major vertebrate groups. Standardized procedures in acquiring high quality DNA and RNA and establishing cell lines from target species will facilitate these initiatives. We provide a legal and methodological guide according to four standards of acquiring and storing tissue for the Genome 10K Project and similar initiatives as follows: four-star (banked tissue/cell cultures, RNA from multiple types of tissue for transcriptomes, and sufficient flash-frozen tissue for 1 mg of DNA, all from a single individual);three-star (RNA as above and frozen tissue for 1 mg of DNA); two-star (frozen tissue for at least 700 μg of DNA); and one-star (ethanol-preserved tissue for 700 μg of DNA or less of mixed quality). At a minimum, all tissues collected for the Genome 10K and other genomic projects should consider each species’ natural history and follow institutional and legal requirements. Associated documentation should detail as much information as possible about provenance to ensure representative sampling and subsequent sequencing. Hopefully, the procedures outlined here will not only encourage success in the Genome 10K Project but also inspire the adaptation of standards by other genomic projects, including those involving other biota

Developing User‐Friendly Habitat Suitability Tools from Regional Stream Fish Survey Data

We developed user‐friendly fish habitat suitability tools (plots) for fishery managers in Michigan; these tools are based on driving habitat variables and fish population estimates for several hundred stream sites throughout the state. We generated contour plots to show patterns in fish biomass for over 60 common species (and for 120 species grouped at the family level) in relation to axes of catchment area and low‐flow yield (90% exceedance flow divided by catchment area) and also in relation to axes of mean and weekly range of July temperatures. The plots showed distinct patterns in fish habitat suitability at each level of biological organization studied and were useful for quantitatively comparing river sites. We demonstrate how these plots can be used to support stream management, and we provide examples pertaining to resource assessment, trout stocking, angling regulations, chemical reclamation of marginal trout streams, indicator species, instream flow protection, and habitat restoration. These straightforward and effective tools are electronically available so that managers can easily access and incorporate them into decision protocols and presentations.Received April 9, 2010; accepted November 8, 2010Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/141005/1/nafm0041.pd