Alu elements and primate genomics

Alu elements are a primate-specific non-autonomous retrotransposon of ~300 base pairs (bp). A Short INterspersed Element (SINE), Alu elements are found in high copy number in genomes across the primate radiation. Alu elements have a history of effective use as a phylogenetic marker due to the presence-absence nature of their retrotransposition, and have been implicated in the cause of a number of genetic diseases. Various subfamilies of Alu elements have gone through periods of increased activity during the history of the primate radiation, with the overwhelming majority of elements classified as genomic fossils which no longer propagate but can serve as useful markers in elucidating phylogenies. Lemurs (Infraorder: Lemuriformes) are a monophyletic radiation of strepsirrhine primates indigenous to the Island of Madagascar. The Lemuriformes are taxonomically subdivided into 5 families and \u3e100 species, with numerous questions remaining to be answered about evolutionary relationships at the family, genus, and species levels. We computationally examined the grey mouse lemur (Microcebus murinus) genome for the presence of informative Alu elements and constructed a phylogenetic tree of 22 lemur species and 2 out-group species using the 138 loci retrieved. Alu element activity level in primate genomes varies widely across species examined. The genome of the Western lowland gorilla (Gorilla gorilla gorilla) was sequenced in 2012 and made available for study. We examined this genome for the presence of AluY elements. AluY is the youngest Alu subfamily and the one most active in the hominid lineage. Our study elucidated 1,075 western lowland gorilla-specific AluY elements classified into 10 subfamilies based on diagnostic mutations in the sequence of the element

The Dinosauria: Baraminological and Multivariate Patterns

The Dinosauria pose both interesting and challenging questions for creationist systematists. One question is whether new dinosaur discoveries are closing morphospatial gaps between dinosaurian groups, revealing continuous morphological fossil series, such as between coelurosaurians and avialans. Questions such as these underscore the importance of systematics for resolving correct group memberships, including tools for visualizing morphospatial relationships. Baraminic distance correlation (BDC), three-dimensional multidimensional scaling (MDS), and a new method to baraminic studies – principal component analysis (PCA) – were applied to 18 character matrices from 2004. The data included saurischian and ornithischian dinosaur groups including (1) “basal” Saurischia, (2) Ceratosauria (including Coelophysidae), (3) “basal” Tetanurae, (4) Tyrannosauroidea, (5) “Prosauropoda”, (6) Sauropoda, (7) Maniraptoriformes, (8) Therizinosauroidea, and (9) Oviraptorosauria. The ornithischians included (10) “basal” Thyreophora, (11) Stegosauria, (12) Ankylosauria, (13) “basal” Ornithopoda, (14) “basal” Iguanodontia, (15) Hadrosauridae, (16) Pachycephalosauria, (17) “basal” Ceratopsia, and (18) Ceratopsidae. BDC and MDS revealed several potential holobaramins and apobaramins, and PCA identified some divisions not recognized by the traditional methods, but since the datasets are 14 years old, many important taxa are missing. As a result, we performed PCA on 19 newer datasets (from 2009 to 2018) and compared the results, which revealed a substantially clearer picture since only 2004. Dinosaur group ordinations commonly occur within morphospatial clusters or linear series. Holobaramins were revealed mainly as closely-spaced morphospatial series of taxa. Some series were additionally stratomorphic. Assuming holobaramins are discontinuity-bounded morphospatial series of taxa, we estimate 27 potential holobaramins within the newer data. PCA revealed that bird-dinosaur morphospatial relationships vary by dataset. Paravians likely contain two branching morphoseries, connected at the base by dromaeosaurs and avialans. The two morphoseries are functional/ecological, rather than evolutionary. Multivariate analysis offers the potential to improve our understanding of baramins and discontinuity, and provide a new perspective on questions in creation systematics such as bird-dinosaur relationships

Revision of Madagascar's Dwarf Lemurs (Cheirogaleidae:Cheirogaleus): Designation of Species, Candidate Species Status and Geographic Boundaries Based on Molecular and Morphological Data

The genus Cheirogaleus, the dwarf lemurs, is a radiation of strepsirrhine primates endemic to the island of Madagascar. The dwarf lemurs are taxonomically grouped in the family Cheirogaleidae (Infraorder: Lemuriformes) along with the genera Microcebus, Mirza, Allocebus, and Phaner. The taxonomic history of the genus Cheirogaleus has been controversial since its inception due to a paucity of evidence in support of some proposed species. In this study, we addressed this issue by expanding the geographic breadth of samples by 91 individuals and built upon existing mitochondrial (cytb and COII) and nuclear (FIBA and vWF) DNA datasets to better resolve the phylogeny of Cheirogaleus. The mitochondrial gene fragments D-loop and PAST as well as the CFTR-PAIRB nuclear loci were also sequenced. In agreement with previous genetic studies, numerous deep divergences were resolved in the C. major, C. minor and C. medius lineages. Four of these lineages were segregated as new species, seven were identified as confirmed candidate species, and four were designated as unconfirmed candidate species based on comparative mitochondrial DNA sequence data gleaned from the literature or this study. Additionally, C. thomasi was resurrected. Given the widespread distribution of the genus Cheirogaleus throughout Madagascar, the methodology employed in this study combined all available lines of evidence to standardize investigative procedures in a genus with limited access to type material and a lack of comprehensive sampling across its total distribution. Our results highlighted lineages that likely represent new species and identified localities that may harbor an as-yet undescribed cryptic species diversity pending further field and laboratory work.We are most grateful to the Ahmanson Foundation, the Theodore F. and Claire M. Hubbard Family Foundation, the Primate Action Fund / Conservation International, the Margot Marsh Biodiversity Foundation, and the National Geographic Society, for financial assistance

Arts and Culture Policy and Creative Placemaking in Detroit

This report focused on arts and culture policy and creative placemaking. It was an investigation of community-based arts and culture in Detroit and its economic benefits, with recommendations to foster creative placemaking. The research included: (1) compiling an inventory of neighborhood arts and culture in Detroit, (2) creating a map to identify existing clusters, (3) conducting case studies, and (4) interviewing subject-matter experts such as artists, arts entrepreneurs, business owners, the former Director of the Detroit Planning Commission, a former state Representative, and an Associate Program Officer of Community Development at the Kresge Foundation

Analysis of western lowland gorilla (Gorilla gorilla gorilla) specific Alu repeats

Abstract Background Research into great ape genomes has revealed widely divergent activity levels over time for Alu elements. However, the diversity of this mobile element family in the genome of the western lowland gorilla has previously been uncharacterized. Alu elements are primate-specific short interspersed elements that have been used as phylogenetic and population genetic markers for more than two decades. Alu elements are present at high copy number in the genomes of all primates surveyed thus far. The AluY subfamily and its derivatives have been recognized as the evolutionarily youngest Alu subfamily in the Old World primate lineage. Results Here we use a combination of computational and wet-bench laboratory methods to assess and catalog AluY subfamily activity level and composition in the western lowland gorilla genome (gorGor3.1). A total of 1,075 independent AluY insertions were identified and computationally divided into 10 subfamilies, with the largest number of gorilla-specific elements assigned to the canonical AluY subfamily. Conclusions The retrotransposition activity level appears to be significantly lower than that seen in the human and chimpanzee lineages, while higher than that seen in orangutan genomes, indicative of differential Alu amplification in the western lowland gorilla lineage as compared to other Homininae.http://deepblue.lib.umich.edu/bitstream/2027.42/112762/1/13100_2013_Article_86.pd

Analysis of western lowland gorilla (Gorilla gorilla gorilla) specific Alu repeats

Background: Research into great ape genomes has revealed widely divergent activity levels over time for Alu elements. However, the diversity of this mobile element family in the genome of the western lowland gorilla has previously been uncharacterized. Alu elements are primate-specific short interspersed elements that have been used as phylogenetic and population genetic markers for more than two decades. Alu elements are present at high copy number in the genomes of all primates surveyed thus far. The AluY subfamily and its derivatives have been recognized as the evolutionarily youngest Alu subfamily in the Old World primate lineage. Results: Here we use a combination of computational and wet-bench laboratory methods to assess and catalog AluY subfamily activity level and composition in the western lowland gorilla genome (gorGor3.1). A total of 1,075 independent AluY insertions were identified and computationally divided into 10 subfamilies, with the largest number of gorilla-specific elements assigned to the canonical AluY subfamily. Conclusions: The retrotransposition activity level appears to be significantly lower than that seen in the human and chimpanzee lineages, while higher than that seen in orangutan genomes, indicative of differential Alu amplification in the western lowland gorilla lineage as compared to other Homininae. © 2013 McLain et al.; licensee BioMed Central Ltd