Whole genome computational comparative genomics: A fruitful approach for ascertaining Alu insertion polymorphisms

Alu elements are the most active and predominant type of short interspersed elements (SINEs) in the human genome. Recently inserted polymorphic (for presence/absence) Alu elements contribute to genome diversity among different human populations, and they are useful genetic markers for population genetic studies. The objective of this study is to identify polymorphic Alu insertions through an in silico comparative genomics approach and to analyze their distribution pattern throughout the human genome. By computationally comparing the public and Celera sequence assemblies of the human genome, we identified a total of 800 polymorphic Alu elements. We used polymerase chain reaction-based assays to screen a randomly selected set of 16 of these 800 Alu insertion polymorphisms using a human diversity panel to demonstrate the efficiency of our approach. Based on sequence analysis of the 800 Alu polymorphisms, we report three new Alu subfamilies, Ya3, Ya4b, and Yb11, with Yb11 being the smallest known Alu subfamily. Analysis of retrotransposition activity revealed Yb11, Ya8, Ya5, Yb9, and Yb8 as the most active Alu subfamilies and the maintenance of a very low level of retrotransposition activity or recent gene conversion events involving S subfamilies. The 800 polymorphic Alu insertions are characterized by the presence of target site duplications (TSDs) and longer than average polyA-tail length. Their pre-integration sites largely follow an extended NT-AARA motif. Among chromosomes, the density of Alu insertion polymorphisms is positively correlated with the Alu-site availability and is inversely correlated with the densities of older Alu elements and genes. © 2005 Elsevier B.V. All rights reserved

Chimpanzee population structure in Cameroon and Nigeria is associated with habitat variation that may be lost under climate change

Background: The Nigeria-Cameroon chimpanzee (Pan troglodytes ellioti) is found in the Gulf of Guinea biodiversity hotspot located in western equatorial Africa. This subspecies is threatened by habitat fragmentation due to logging and agricultural development, hunting for the bushmeat trade, and possibly climate change. Although P. t. ellioti appears to be geographically separated from the neighboring central chimpanzee (P. t. troglodytes) by the Sanaga River, recent population genetics studies of chimpanzees from across this region suggest that additional factors may also be important in their separation. The main aims of this study were: 1) to model the distribution of suitable habitat for P. t. ellioti across Cameroon and Nigeria, and P. t. troglodytes in southern Cameroon, 2) to determine which environmental factors best predict their optimal habitats, and 3) to compare modeled niches and test for their levels of divergence from one another. A final aim of this study was to examine the ways that climate change might impact suitable chimpanzee habitat across the region under various scenarios. Results: Ecological niche models (ENMs) were created using the software package Maxent for the three populations of chimpanzees that have been inferred to exist in Cameroon and eastern Nigeria: (i) P. t. troglodytes in southern Cameroon, (ii) P. t. ellioti in northwestern Cameroon, and (iii) P. t. ellioti in central Cameroon. ENMs for each population were compared using the niche comparison test in ENMtools, which revealed complete niche divergence with very little geographic overlap of suitable habitat between populations. Conclusions: These findings suggest that a positive relationship may exist between environmental variation and the partitioning of genetic variation found in chimpanzees across this region. ENMs for each population were also projected under three different climate change scenarios for years 2020, 2050, and 2080. Suitable habitat of P. t. ellioti in northwest Cameroon / eastern Nigeria is expected to remain largely unchanged through 2080 in all considered scenarios. In contrast, P. t. ellioti in central Cameroon, which represents half of the population of this subspecies, is expected to experience drastic reductions in its ecotone habitat over the coming century

The time scale of recombination rate evolution in great apes

We present three linkage-disequilibrium (LD)-based recombination maps generated using whole-genome sequence data from 10 Nigerian chimpanzees, 13 bonobos, and 15 western gorillas, collected as part of the Great Ape Genome Project (Prado-Martinez J, et al. 2013. Great ape genetic diversity and population history. Nature 499:471-475). We also identified species-specific recombination hotspots in each group using a modified LDhot framework, which greatly improves statistical power to detect hotspots at varying strengths. We show that fewer hotspots are shared among chimpanzee subspecies than within human populations, further narrowing the time scale of complete hotspot turnover. Further, using species-specific PRDM9 sequences to predict potential binding sites (PBS), we show higher predicted PRDM9 binding in recombination hotspots as compared to matched cold spot regions in multiple great ape species, including at least one chimpanzee subspecies. We found that correlations between broad-scale recombination rates decline more rapidly than nucleotide divergence between species. We also compared the skew of recombination rates at centromeres and telomeres between species and show a skew from chromosome means extending as far as 10-15Mb from chromosome ends. Further, we examined broad-scale recombination rate changes near a translocation in gorillas and found minimal differences as compared to other great ape species perhaps because the coordinates relative to the chromosome ends were unaffected. Finally, on the basis of multiple linear regression analysis, we found that various correlates of recombination rate persist throughout the African great apes including repeats, diversity, and divergence. Our study is the first to analyze within- And between-species genome-wide recombination rate variation in several close relatives

Long-Term Urban Market Dynamics Reveal Increased Bushmeat Carcass Volume despite Economic Growth and Proactive Environmental Legislation on Bioko Island, Equatorial Guinea.

Bushmeat hunting is extensive in west and central Africa as both a means for subsistence and for commercial gain. Commercial hunting represents one of the primary threats to wildlife in the region, and confounding factors have made it challenging to examine how external factors influence the commercial bushmeat trade. Bioko Island, Equatorial Guinea is a small island with large tracts of intact forest that support sizeable populations of commercially valuable vertebrates, especially endemic primates. The island also has a low human population and has experienced dramatic economic growth and rapid development since the mid-1990's. From October 1997 - September 2010, we monitored the largest bushmeat market on Bioko in Malabo, recording over 197,000 carcasses for sale. We used these data to analyze the dynamics of the market in relation to political events, environmental legislation, and rapid economic growth. Our findings suggest that bushmeat hunting and availability increased in parallel with the growth of Equatorial Guinea's GDP and disposable income of its citizens. During this 13-year study, the predominant mode of capture shifted from trapping to shotguns. Consequently, carcass volume and rates of taxa typically captured with shotguns increased significantly, most notably including intensified hunting of Bioko's unique and endangered monkey fauna. Attempts to limit bushmeat sales, including a 2007 ban on primate hunting and trade, were only transiently effective. The hunting ban was not enforced, and was quickly followed by a marked increase in bushmeat hunting compared to hunting rates prior to the ban. Our results emphasize the negative impact that rapid development and unenforced legislation have had on Bioko's wildlife, and demonstrate the need for strong governmental support if conservation strategies are to be successful at preventing extinctions of tropical wildlife

Primate carcass rates raw data, fitted, and predicted values.

<p>Values are as estimated in the intervention analysis via ARIMA (2,0,0,)x(1,0,0)₁₂. Significant interventions are numbered at: 1) 2/1998 –political uprising; 2) 3/2002 –bushmeat roundtable; 3) 11/2003 –Law 7/2003; 4) 11/2007 –Decree 72/2007.</p

Primate carcass rates raw data, fitted, and predicted values.

<p>Values are as estimated in the intervention analysis via ARIMA (2,0,0,)x(1,0,0)₁₂. Significant interventions are numbered at: 1) 2/1998 –political uprising; 2) 3/2002 –bushmeat roundtable; 3) 11/2003 –Law 7/2003; 4) 11/2007 –Decree 72/2007.</p

Regression of average carcass rates for total, shotgunned, and trapped carcasses with oil prices as a proxy for income in Early, Pre-ban, and Post-ban periods.

<p>Regression of average carcass rates for total, shotgunned, and trapped carcasses with oil prices as a proxy for income in Early, Pre-ban, and Post-ban periods.</p

Time series plots of the carcass rates (carcasses/market day).

<p>Shown are the (A) total number of carcasses and the number of carcasses captured by shotgun or trap, (B) the number of domestic (island), and (C) the number of primate carcasses. Vertical lines delineate periods. The transition between Pre-ban and Post-ban also coincides with the passing of the October 2007 primate hunting ban.</p

Distribution of major human settlements, main roads, and protected areas on Bioko Island.

<p>Also shown is Ureca, the only permanent human settlement entirely within a protected area on Bioko.</p