Pattern and process of biotic homogenization in the New Pangaea.

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Pattern and process of biotic homogenization in the New Pangaea.

Proc Biol Sci. 2012 Oct 10;

Authors: Baiser B, Olden JD, Record S, Lockwood JL, McKinney ML

Abstract
Human activities have reorganized the earth’s biota resulting in spatially disparate locales becoming more or less similar in species composition over time through the processes of biotic homogenization and biotic differentiation, respectively. Despite mounting evidence suggesting that this process may be widespread in both aquatic and terrestrial systems, past studies have predominantly focused on single taxonomic groups at a single spatial scale. Furthermore, change in pairwise similarity is itself dependent on two distinct processes, spatial turnover in species composition and changes in gradients of species richness. Most past research has failed to disentangle the effect of these two mechanisms on homogenization patterns. Here, we use recent statistical advances and collate a global database of homogenization studies (20 studies, 50 datasets) to provide the first global investigation of the homogenization process across major faunal and floral groups and elucidate the relative role of changes in species richness and turnover. We found evidence of homogenization (change in similarity ranging from -0.02 to 0.09) across nearly all taxonomic groups, spatial extent and grain sizes. Partitioning of change in pairwise similarity shows that overall change in community similarity is driven by changes in species richness. Our results show that biotic homogenization is truly a global phenomenon and put into question many of the ecological mechanisms invoked in previous studies to explain patterns of homogenization.

PMID: 23055062 [PubMed – as supplied by publisher]

via pubmed: school of aquatic an… http://www.ncbi.nlm.nih.gov/PubMed/23055062?dopt=Abstract

Characterizing short read sequencing for gene discovery and RNA-Seq analysis in Crassostrea gigas.

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Characterizing short read sequencing for gene discovery and RNA-Seq analysis in Crassostrea gigas.

Comp Biochem Physiol Part D Genomics Proteomics. 2012 Jun;7(2):94-9

Authors: Gavery MR, Roberts SB

Abstract
Advances in DNA sequencing technology have provided opportunities to produce new transcriptomic resources for species that lack completely sequenced genomes. However, there are limited examples that rely solely on ultra-short read sequencing technologies (e.g. Solexa, SOLiD) for transcript discovery and gene expression analysis (i.e. RNA-Seq). Here we use SOLiD sequencing to examine gene expression patterns in Pacific oyster (Crassostrea gigas) populations exposed to varying degrees of anthropogenic impact. Novel transcripts were identified and RNA-Seq analysis revealed several hundred differentially expressed genes. Gene enrichment analysis determined that in addition to biological processes predicted to be associated with anthropogenic influences (e.g. immune response), other processes play important roles including cell recognition and cell adhesion. To evaluate the effectiveness of restricting characterization solely to short read sequences, mapping and RNA-Seq analysis were also performed using publicly available transcriptome sequence data as a scaffold. This study demonstrates that ultra-short read sequencing technologies can effectively generate novel transcriptome information, identify differentially expressed genes, and will be important for examining environmental physiology of non-model organisms.

PMID: 22244882 [PubMed – indexed for MEDLINE]

via pubmed: school of aquatic an… http://www.ncbi.nlm.nih.gov/PubMed/22244882?dopt=Abstract