Evolutionary genetics

The composition of marine bacterial communities from South Florida beaches
were characterized using 16S rRNA sequence analysis. To compare cultivable and noncultured
populations, community genomic DNA was extracted directly from sand and
seawater samples and from two cultured equivalents. Only two ofthe 86 (2.3%) direct
extracted sequences and 79 of 150 (52.6%) culture sequences belong to known isolates in
Ribosomal Database (version 9.0) at 95% confidence level. At low stringency (p=0.70),
the populations cluster into several unknown clads with early divergence, indicating the
presence of novel well established bacterial groups. Members of phylum Bacteroidetes,
Firmicuites and Proteobacteria were identified, with the latter being the most prevalent in
culture. Diversity indices rank Hollywood beach > Fort Lauderdale > Hobie beach.
Taxonomic representation indicates marine water as more diverse compared to dry sand
and wet sand. A combination of phylogenetic markers will be needed to define the
immense diversity of this niche.

The Paranthropus head is characterized by features traditionally thought to be related to heavy chewing. McCollum [Science 284 (1999) : 301-305] proposed that palatal thickening is a response to developmental integration between the mandibular ramus, oral and nasal functional matrices, and the vomer, which inserts onto the premaxilla in Paranthropus and causes the palate to thicken instead of rotate during vertical expansion. I tested whether palate thickness increases as a byproduct of differential increases in the sizes of the oral and nasal functional matrices compared to growth in the mandibular ramus. To do so, I collected 3D volume and landmark data from computed tomography (CT) scans of extant (Homo sapiens, Pan troglodytes, Gorilla gorilla, Pongo pygmaeus) and extinct taxa (Australopithecus and Paranthropus), and tested counterpart relationships for bones in the cranium using scaling analyses. Results suggest that developmental constraints related to growth counterpart relationships in the skulll are unlikely to affect palate thickness in the genus Paranthropus.

Phylogenies constructed from skeletal data often contradict those built from genetic data. This study evaluates the phylogenetic utility of adult male, female, and juvenile hominoid cranial bones. First, I used geometric morphometric methods to compare the cranial bone shapes of seven primate genera (Gorilla, Homo, Hylobates, Macaca, Nomascus, Pan, and Pongo). I then coded these shapes as continuous characters and constructed cladograms via parsimony analysis for the adult male, female, and juvenile character matrices. Finally, I evaluated the similarity of these cladograms to one another and to the genetic phylogeny using topological distance software. Cladograms did not differ from one another or the genetic phylogeny less than comparisons of randomly generated trees. These results suggest that cranial shapes are unlikely to provide accurate phylogenetic information, and agree with other analyses of skeletal data that fail to recover the molecular phylogeny (Collard & Wood, 2000, 2001; Springer et al., 2007).

Carbohydrate Active Enzyme family 6 (CA6) glycosyltransferases (GTs) are type II transmembrane proteins localized in the Golgi apparatus. CA6 GTs have a GT-A fold, a type of structure that resembles the Rossman fold and catalyze the transfer either galactose (Gal) or N-acetylgalactosamine (GalNAc) from the UDP nucleotide sugar to an non-reducing terminal Gal or GalNAc on an acceptor via an a-1,3 linkage. In this reaction, the anomeric configuration of the sugar moiety of the donor is retained in the product. CA6 GTs includes the histo-blood group A and B GTs, a-galactosyltransferase (a3GT), Forssman glycolipid synthase (FS), isogloboside 3 synthase (iGb3) in mammals. a3GT and its products (a-Gal epitode) are present in most mammals but are absent in humans and old world primates because of inactivating mutations. The absence of a3GT and its products results in the production of anti-a-Gal epitope natural antibodies in these species.