International Team Examines Origins and Impact of Copy Number Variation in the Human Genome

7 04 2010

The study, published April 1, in the journal Nature, used some 42 million probes to identify more than 11,000 copy number variations.  Following is the abstract from the study:

Abstract

Structural variations of DNA greater than 1 kilobase in size account for most bases that vary among human genomes, but are still relatively under-ascertained. Here we use tiling oligonucleotide microarrays, comprising 42 million probes, to generate a comprehensive map of 11,700 copy number variations (CNVs) greater than 443 base pairs, of which most (8,599) have been validated independently. For 4,978 of these CNVs, we generated reference genotypes from 450 individuals of European, African or East Asian ancestry. The predominant mutational mechanisms differ among CNV size classes. Retrotransposition has duplicated and inserted some coding and non-coding DNA segments randomly around the genome. Furthermore, by correlation with known trait-associated single nucleotide polymorphisms (SNPs), we identified 30 loci with CNVs that are candidates for influencing disease susceptibility. Despite this, having assessed the completeness of our map and the patterns of linkage disequilibrium between CNVs and SNPs, we conclude that, for complex traits, the heritability void left by genome-wide association studies will not be accounted for by common CNVs.

To view the complete article (with a subscription or by paying), please click the following URL: 

http://www.nature.com/nature/journal/v464/n7289/full/nature08516.html.

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Researchers find Evidence of Scavenging Behavior in a Velociraptor

6 04 2010
Velociraptor Teeth - Photo by David Hone

Velociraptor teeth, matching the bite marks on the Protoceratops, were found at the site.

An international team of researchers, working in upper Cretaceous deposits at Bayan Mandahu, in Inner Mongolia, China, has found evidence of scavenging behavior in Velociraptor.  The evidence, consisting of bite marks on the jaw of a Protoceratops along with Velociraptor teeth, was found by Dr. David Hone of the Chinese Academy of Sciences in Beijing.

The research, published in the journal Palaeogeography, Palaeoclimatology, Palaeoecology, provides insight into the behavior of animals that lived more than 65 million years ago, near the end of the age of dinosaurs.  It also provides evidence in a long-running debate over whether many theropod dinosaurs practiced scavenging along with their predatory ways.

“The marks were on and around bits of the jaw,” Dr Hone said in a recent interview with the BBC.  “Protoceratops probably weighed many times what a Velociraptor did, with lots of muscle to eat. Why scrape away at the jaws, where there’s obviously not much muscle, so heavily that you scratch the bone and lose teeth unless there was not much else there. In short, this looks like scavenging as the animal would be feeding on the haunches and guts first, not the cheeks.”

Scientists have long debated the relative extent to which predatory dinosaurs such as Velociraptor and Tyrannosaurus rex engaged in scavenging versus predatory behavior.  When a fossil was found (also in Inner Mongolia) a few years ago, showing a Velociraptor engaged in what appeared to be a fight with a Protoceratops in which they both died, it became clear that Velociraptor definitely engaged in actively hunting and killing at least some of the time.  With the addition of this new evidence, it also becomes clear that Velociraptor also engaged in scavenging, something that some paleontologists had disputed.

“Even the most dedicated predator won’t turn down a free meal if they chance across a dead animal with a few bits of meat still attached, and this looks like the case here,” Hone told the BBC.

Of course, this does nothing to settle the debate about relative frequencies of predatory versus scavenging behaviors.  While most scientists believe that Velociraptor was an active predator that only engaged in scavenging when the opportunity arose, many scientists are not as sure about T. rex.  Some see the “king of tyrants” as too big and slow to be anything but primarily a scavenger, while others point to its heavily-muscled hind quarters and see a powerful runner, capable of catching the large herbivores it likely fed on.

“Animals like Velociraptor were probably feeding on animals like Protoceratops regularly, probably including both predation and scavenging,” Hone said in the BBC interview.  “That is in line with the behaviour of many modern predators, as almost all living carnivores such as lions and jackals do both.  It’s a question of degree.  Lions mostly predate, jackals mostly scavenge.”

For the BBC article, please click the following URL:
http://news.bbc.co.uk/earth/hi/earth_news/newsid_8596000/8596568.stm.

For the Palaeogeography, Palaeoclimatology, Palaeoecology journal homepage, please click the following URL:
http://www.sciencedirect.com/science?_ob=PublicationURL&_cdi=5821&_pubType=J&_auth=y&_acct=C000050221&_version=1&_urlVersion=0&_userid=9182362&md5=74e4ce09feb43767eb457e97d065d91e&jchunk=289#289.





Cryptic Sex-Ratio Bias Provides Indirect Genetic Benefits Despite Sexual Conflict

5 04 2010
This image is courtesy of Wikipedia Commons and is in the public domain.

Anolis sagrei, was used in the study to demonstrate that sex-ratio bias can provide indirect genetic benefits despite sexual conflict

Two scientists from Dartmouth College have demonstrated a counterpoint to the long-held belief that sexual dimorphism causes high-fitness parents often to produce low-fitness progeny of the opposite sex.  According to the authors, this alleviates the evolutionary costs incurred, restoring the benefits of mate choice.

The article, by Robert M. Cox and Ryan Calsbeek, was published April 2, online in the journal Science.  Below is the abstract from the article.  To read the entire article (if you have a subscription), please click on the following URL:
http://www.sciencemag.org/cgi/content/abstract/sci;328/5974/92?maxtoshow=&hits=10&RESULTFORMAT=&fulltext=evolution&searchid=1&FIRSTINDEX=0&sortspec=date&resourcetype=HWCIT.

Abstract

When selection favors sexual dimorphism, high-fitness parents often produce low-fitness progeny of the opposite sex. This sexual conflict is thought to overwhelm the genetic benefits of mate choice because preferred males incur a cost through the production of low-fitness daughters. We provide a counterpoint in a lizard (Anolis sagrei) that exhibits sexual conflict over body size. By using mate-choice experiments, we show that female brown anoles produce more sons than daughters via large sires but more daughters than sons via small sires. Measures of progeny fitness in the wild suggest that maximal fitness payoffs can be achieved by shifting offspring production from daughters to sons as sire size increases. These results illustrate how the resolution of sexual conflict can restore the genetic benefits of mate choice.





Floral Symmetry Genes and the Origin and Maintenance of Zygomorphy in a Plant-Pollinator Mutualism

5 04 2010

This article, published online March 30, in the Proceedings of the National Academy of Science (PNAS) examines floral zygomorphy in light of pollinator selection.  Following is the abstract for the article.  To read the entire article (if you have a subscription), please click on the following URL:  http://www.pnas.org/content/early/2010/04/01/0910155107.abstract?abspop=1&related-urls=yes&legid=pnas;0910155107v1.

Abstract

The evolution of floral zygomorphy is an important innovation in flowering plants and is thought to arise principally from specialization on various insect pollinators. Floral morphology of neotropical Malpighiaceae is distinctive and highly conserved, especially with regard to symmetry, and is thought to be caused by selection by its oil-bee pollinators. We sought to characterize the genetic basis of floral zygomorphy in Malpighiaceae by investigating CYCLOIDEA2-like (CYC2-like) genes, which are required for establishing symmetry in diverse core eudicots. We identified two copies of CYC2-like genes in Malpighiaceae, which resulted from a gene duplication in the common ancestor of the family. A likely role for these loci in the development of floral zygomorphy in Malpighiaceae is demonstrated by the conserved pattern of dorsal gene expression in two distantly related neotropical species, Byrsonima crassifolia and Janusia guaranitica. Further evidence for this function is observed in a Malpighiaceae species that has moved to the paleotropics and experienced coincident shifts in pollinators, floral symmetry, and CYC2-like gene expression. The dorsal expression pattern observed in Malpighiaceae contrasts dramatically with their actinomorphic-flowered relatives, Centroplacaceae (Bhesa paniculata) and Elatinaceae (Bergia texana). In particular, B. texana exhibits a previously undescribed pattern of uniform CYC2 expression, suggesting that CYC2 expression among the actinomorphic ancestors of zygomorphic lineages may be much more complex than previously thought. We consider three evolutionary models that may have given rise to this patterning, including the hypothesis that floral zygomorphy in Malpighiaceae arose earlier than standard morphology-based character reconstructions suggest.





Simulation Study Indicates “Non-Negligible” Natural Selection on Alleles Affecting Human Longevity and Late-Life Disease

5 04 2010

This article, by Fotios Drenos and Thomas B. L. Kirkwood, both of the Institute for Ageing and Health at Newcastle University, Newcastle Upon Tyne, Tyne, United Kingdom, that appeared on March 31, 2010, in the online journal PloS One, uses computer simulation to show that the effects of natural selection on genes affecting health in old age can be significant.  Below is the abstract from the article.  To read the complete article, please see the following URL:  http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0010022.

Abstract

It is often claimed that genes affecting health in old age, such as cardiovascular and Alzheimer diseases, are beyond the reach of natural selection. We show in a simulation study based on known genetic (apolipoprotein E) and non-genetic risk factors (gender, diet, smoking, alcohol, exercise) that, because there is a statistical distribution of ages at which these genes exert their influence on morbidity and mortality, the effects of selection are in fact non-negligible. A gradual increase with each generation of the ε2 and ε3 alleles of the gene at the expense of the ε4 allele was predicted from the model. The ε2 allele frequency was found to increase slightly more rapidly than that for ε3, although there was no statistically significant difference between the two. Our result may explain the recent evolutionary history of the epsilon 2, 3 and 4 alleles of the apolipoprotein E gene and has wider relevance for genes affecting human longevity.





Scientists use Mitochondrial DNA to Identify Recently Diverged Mouse Lemur Lineages

5 04 2010
This image is copyrighted under the creative commons attribution license by Weisrock D.W., Rasoloarison R.M., Fiorentino I., Ralison J.M., Goodman S.M., et al. (2010) for the article “Delimiting Species without Nuclear Monophyly in Madagascar's Mouse Lemurs”. Appearing in PLoS ONE 5(3): e9883. doi:10.1371/journal.pone.0009883.

The island of Madagascar, showing the areas of sampling used in this study.

An international team of researchers has used mitochondrial DNA (mtDNA) to help distinguish between a group of Madagascar Mouse Lemurs who have recently begun to diverge.

One of the issues associated with delineating species that have recently diverged from common ancestors is that often there has not been sufficient time for the usual cues of speciation, such as morphological differences, reproductive isolation, and monophyly within the gene tree to have become settled and readily evident.  Writing in the online journal, PLoS One, seven scientists from the United States, Germany, and Madagascar used multiple lines of evidence from mtDNA and nuclear DNA (nDNA) to identify “cryptically diverged” population-level mouse lemur lineages from throughout Madagascar.  It is believed to represent the most thorough sample of mouse lemur species ever conducted.

The result was the identification of a large number of geographically-defined clades.  These were strongly supported by the initial mtDNA evidence, as well as additionally supported by nDNA patterns.  The clades thus identified, are also supported by population divergence estimates based on genealogical exclusivity estimates.  The paper concludes that “Mouse lemur lineage diversity is reflected in both a geographically fine-scaled pattern of population divergence within established and geographically widespread taxa, as well as newly resolved patterns of micro-endemism revealed through expanded field sampling into previously poorly and well-sampled regions.”

For more information, please see the original article at the following URL: http://www.plosone.org/article/info:doi/10.1371/journal.pone.0009883