Speciation genomics and morphological evolution in an extraordinary avian radation, the Lonchura munias of New Guinea and Australia

Speciation, the evolution of morphologically, behaviorally and/or ecologically distinct lineages from a common ancestor, is the fundamental process generating biodiversity. The rapidly developing field of speciation genomics is challenging traditional views of speciation as a gradual, genome-wide process, and highlighting the role of divergent natural selection in the speciation process. This study investigates morphological evolution and the genomic architecture of speciation in a clade of 12 "munias" in the genus Lonchura, one of the most extraordinary cases of recent and rapid diversification in birds. With a diversity of plumage patterns and replicate examples of closely related species living in sympatry, this group is ideally suited for addressing fundamental questions about the genomics of speciation. In this study, I (1) test for evidence of character displacement between sympatric species using quantitative measurements of plumage coloration and morphology; (2) examine the structure of genome-wide variation using ddRAD-seq (double-digest Restriction Site Associated DNA sequencing); and (3) investigate the genomic structure of divergence using whole-genome sequencing. I find some evidence for character displacement, particularly in morphometrics and crown coloration. There is also a trend, however, for sympatric species to be more similar in coloration than allopatric species, particularly those that have come into contact more recently. Analysis of 7,043 ddRAD-seq loci reveals evidence of introgression among sympatric populations, with overall genomic variation corresponding more closely to geography than species identity. There is also substantial heterogeneity in genetic structure among mitochondrial, autosomal, and Z-linked markers. Finally, whole-genome sequencing reveals low overall genomic divergence while pinpointing "islands of differentiation" that exhibit elevated divergence between species. Two of these islands overlap genes known to be associated with coloration—Agouti signaling protein (ASIP) and Kit ligand (KITLG)—and allelic variation at these genes is associated with phenotypic traits. I also find evidence of a ~26 million base pair inversion on the Z chromosome, which groups the focal species differently than genome-wide variation. A strongly mosaic pattern of population structure among genomic regions supports a genic view of speciation, in which a small fraction of the genome is involved in the initial divergence of species

Decompositions of Triangle-Dense Graphs

High triangle density -- the graph property stating that a constant fraction of two-hop paths belong to a triangle -- is a common signature of social networks. This paper studies triangle-dense graphs from a structural perspective. We prove constructively that significant portions of a triangle-dense graph are contained in a disjoint union of dense, radius 2 subgraphs. This result quantifies the extent to which triangle-dense graphs resemble unions of cliques. We also show that our algorithm recovers planted clusterings in approximation-stable k-median instances.Comment: 20 pages. Version 1->2: Minor edits. 2->3: Strengthened {\S}3.5, removed appendi

Implicit presuppositions: an exercise in multidimensional scaling and hierarchical clustering

This working paper, like Humanities Working Papers 66 and 75, of which it is a further development, has two main aims. The first of these is to resolve a particular problem in art history. For this purpose the data already studied in Working Papers 66 and 75 are reanalyzed by means of multidimensional scaling and hierarchical clustering procedures, with results that support our earlier conclusion that sixteenth century Mannerism is best understood as an exaggeration of the High Renaissance style rather than as a distinct school. Our second aim, which in this paper takes precedence over the first, is to demonstrate to humanists that the quantitative methods of the social sciences can be used effectively to deal with some of the problems with which humanists are characteristically concerned, by replacing unresolved difference of opinion by judgments based on public procedures. Though this is a joint paper, the text is chiefly the responsibility of a psychologist and an anthropologist; the explanatory comments and Discussion section are chiefly the responsibility of a philosopher. Thus the authorship of the paper reflects the kind of cooperation between social scientists and humanists that we are recommending

Networks and Contexts: Variation in the Structure of Social Ties

A core axiom of sociology is that social structure affects and is affected by human behavior. The term "social structure" conveys two quite different meanings. One meaning is relational, involving networks of ties between individuals or groups of individuals. A second meaning refers to the contexts containing these individuals. Studies of neighborhood and community effects depend on variability in both types of social structure. Using data from multiple villages in Nang Rong, Thailand, this article documents substantial variability in network structure and shows that network structure covaries with context in meaningful ways, suggesting reciprocal effects of changes in both. Finally, it considers implications of variability in network structure, showing that social cohesion affects the likelihood of finding and interviewing former village residents

Social and spatial networks: Kinship distance and dwelling unit proximity in rural Thailand

We address a long hypothesized relationship between the proximity of individuals' dwelling units and their kinship association. Better understanding this relationship is important because of its implications for contact and association among members of a society. In this paper, we use a unique dataset from Nang Rong, Thailand which contains dwelling unit locations (GPS) and saturated kinship networks of all individuals living in 51 agricultural villages. After presenting arguments for a relationship between individuals’ dwelling unit locations and their kinship relations as well as the particulars of our case study, we introduce the data and describe our analytic approach. We analyze how kinship - considered as both a system linking collections of individuals in an extended kinship network and as dyadic links between pairs of individuals -patterns the proximity of dwelling units in rural villages. The results show that in general, extended kin live closer to one another than do unrelated individuals. Further, the degree of relatedness between kin correlates with the distance between their dwelling units. Close kin are more likely to co-reside, a fact which drives much of the relationship between kinship relatedness and dwelling unit proximity within villages. There is nevertheless suggestive evidence of a relationship between kinship association and dwelling unit proximity among kin who do not live together

The Iowa Homemaker vol.3, no.7

Table of Contents Home Economics Cleans House – Division Ready for New Year by Anna E. Richardson, page 1 Storing the Winter’s Supply of Vitamines by C. L. Fitch, page 2 First Hand Acquaintance With Tokyo’s Earthquake by Katherine Cranor, page 3 Hurrah for the Pumpkin Pie by Ruth Elaine Wilson, page 4 Choosing the Fall Hat by Florence Faust, page 5 Who is Responsible for the Child? by An “Old – Maid Aunt”, page 6 A Review of Farm Meats by Viola M. Bell, page 6 Color Hints From Gay October by Ruth Spencer, page 7 Paying Homage to the King of Fruits by Jeanette Beyer, page 8 Sheppard-Towner Bill by Lois Miller Herd, page 9 Buttons and _______ Buttons by Esther Ellen Rayburn, page 9 Candy Popularity by Esther Ellen Rayburn, page 13 Before the Bar of Science by Eda Lord Murphy, page 15 Gingered Pears by Elizabeth Storm, page 1

Phenotyping Metastatic Brain Tumors Applying Spectrochemical Analyses: Segregation of Different Cancer Types

Metastatic brain tumours represent a significant proprotion of tumours identified intraoperatively. A rapid diagnostic method, circumventing the need for histopathology studies could prove clinically useful. As many spectroscopic studies have shown ability to differentitate between different tumour types, this technique was evaluated for use within metastatic brain tumours. Spectrochemical approaches [Raman and attenuated total reflection Fourier-transform infrared spectroscopy (ATR-FTIR) spectroscopy] were applied to determine how readily it could identify the primary site from the metastatic tumour. Metastases were from primary adenocarcinomas of lung (n=7) and colorectum (n=7), and for comparison, metastatic melanoma (n=7). The objective was to determine if Raman or ATR-FTIR spectroscopy could delineate the origin of the primary tumour. The results demonstrate that there are marked similarities between the two adenocarcinoma groups and whilst Raman and ATR-FTIR can distinguish the three groups with limited success, classification accuracy is greatly improved when combining the adenocarcinoma groups. The use of such techniques in the clinical setting is more likely to be found intraoperatively, determining the presence of a tumour and suggesting the tumour class; however, traditional histopathology would still be needed to identify the primary origin of the tumour

Genomic approaches to understanding population divergence and speciation in birds

© 2016 American Ornithologists\u27 Union. The widespread application of high-throughput sequencing in studying evolutionary processes and patterns of diversification has led to many important discoveries. However, the barriers to utilizing these technologies and interpreting the resulting data can be daunting for first-time users. We provide an overview and a brief primer of relevant methods (e.g., whole-genome sequencing, reduced-representation sequencing, sequence-capture methods, and RNA sequencing), as well as important steps in the analysis pipelines (e.g., loci clustering, variant calling, whole-genome and transcriptome assembly). We also review a number of applications in which researchers have used these technologies to address questions related to avian systems. We highlight how genomic tools are advancing research by discussing their contributions to 3 important facets of avian evolutionary history. We focus on (1) general inferences about biogeography and biogeographic history, (2) patterns of gene flow and isolation upon secondary contact and hybridization, and (3) quantifying levels of genomic divergence between closely related taxa. We find that in many cases, high-throughput sequencing data confirms previous work from traditional molecular markers, although there are examples in which genome-wide genetic markers provide a different biological interpretation. We also discuss how these new data allow researchers to address entirely novel questions, and conclude by outlining a number of intellectual and methodological challenges as the genomics era moves forward