Nectocaris pteryx Reinterpreted as a Cephalopod

26 05 2010

The middle Cambrian species Nectocaris pteryx has long puzzled paleontologists.  Originally described as “a shrimp with a chordate tail,” two Canadian scientists have reexamined the organism and come to the conclusion that it is a cephalopod.

The findings are published as a letter in the May 27 issue of the journal Nature.

Based on new material from the Burgess Shale, Martin R. Smith and Jean Bernard Caron of the University of Toronto have grouped N. pteryx along with Nectocaris, Petalilium, and (probably) Vetustovermis to form the clade Nectocaridae.

Smith and Caron describe the new clade as “characterized by an open axial cavity with paired gills, wide lateral fins, a single pair of long, prehensile tentacles, a pair of non-faceted eyes on short stalks, and a large, flexible anterior funnel.”  It pushes back the presence of cephalopods in the fossil record by more than 30 million years.  It also indicates that “[t]he explosive diversification of mineralized cephalopods in the Ordovician may have an understated Cambrian ‘fuse’.”

In addition, Smith and Caron conclude that “primitive cephalopods lacked a mineralized shell, were hyperbenthic, and were presumably carnivorous.”

They also conclude that “[t]he presence of a funnel suggests that jet propulsion evolved in cephalopods before the acquisition of a shell.”

To read an abstract of the article or to purchase the entire article, please use the following link:
http://www.nature.com/nature/journal/v465/n7297/full/nature09068.html.

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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.





Researchers Use DNA to Find New Human Species… Probably

24 03 2010

In a report published Wednesday in the journal Nature, Russian scientists report using mitochondrial DNA (mtDNA) to identify a new species.  While the identification is tentative, and awaits confirmation, it none-the-less represents an important new use of DNA technology.

The discovery occurred in the summer of 2008, when the scientists were digging in Denisova cave, in Siberia.  They were looking for the remains and artifacts of Neanderthals, who occupied the cave between 30,000 and 48,000 years ago.  During excavations, they found a small sliver of finger bone.  According to the scientists, it was considered unremarkable at the time.

However, when they sent it to German scientists to have the DNA extracted and sequenced, they were in for a surprise.  The results did not match Neanderthals.  Nor did it match modern humans, who were also living in the area at the time.

The conclusion was that the bone represented a here-to-fore unknown human species.  Based on the differences between the bone’s DNA and that of modern humans, it is estimated that the species diverged from human ancestors a million years ago, long before the split between modern humans and Neanderthals.  By inference, this means that the proposed species left Africa in a previously unknown migration, sometime between that of Homo erectus about 1.9 million years ago and that of the Neanderthal ancestor Homo heidelbergensis, 300,000 to 500,000 years ago.

But, as yet, none of this is entirely certain.  The use of mtDNA poses its own problems, and scientists also must examine the bone’s nuclear DNA to get a full picture.  While mtDNA comes through the mother’s lineage, nuclear DNA comes from through the father’s.  It is important to have both in order to make a proper assessment.

Researchers point out that it is possible that some modern humans or Neanderthals living in Siberia 40,000 years ago had unusual mtDNA.  Only by also examining the nuclear DNA will a complete enough picture of the person it belonged to come out, allowing scientists to make a determination.  Such a picture might also allow scientists to properly define this new relative’s position within the human family tree.

To read more about this find, please see the article in Nature News at the following URL:  http://www.nature.com/news/2010/100324/full/464472a.html.





Hominins on Flores, Indonesia, 1.0 to 1.04 Million Years Ago

18 03 2010
This image is courtesy of Wikipedia Commons and is within the public domain.

Map showing Flores island in yellow and the rest of Indonesia in green

A study published Wednesday, online in the journal Nature cites evidence for hominin presence on the island of Flores, Indonesia as early as one million years ago.  The abstract for the article, along with a link to it on the Nature site, follow:

Previous excavations at Mata Menge and Boa Lesa in the Soa Basin of Flores, Indonesia, recovered stone artefacts in association with fossilized remains of the large-bodied Stegodon florensis florensis. Zircon fission-track ages from these sites indicated that hominins had colonized the island by 0.88 ± 0.07 million years (Myr) ago. Here we describe the contents, context and age of Wolo Sege, a recently discovered archaeological site in the Soa Basin that has in situ stone artefacts and that lies stratigraphically below Mata Menge and immediately above the basement breccias of the basin. We show using 40Ar/39Ar dating that an ignimbrite overlying the artefact layers at Wolo Sege was erupted 1.02 ± 0.02 Myr ago, providing a new minimum age for hominins on Flores. This predates the disappearance from the Soa Basin of ‘pygmy’ Stegodon sondaari and Geochelone spp. (giant tortoise), as evident at the nearby site of Tangi Talo, which has been dated to 0.90 ± 0.07 Myr ago. It now seems that this extirpation or possible extinction event and the associated faunal turnover were the result of natural processes rather than the arrival of hominins. It also appears that the volcanic and fluvio-lacustrine deposits infilling the Soa Basin may not be old enough to register the initial arrival of hominins on the island.

 To view the entire article (if you have a subscription to Nature), please use the following link:

http://www.nature.com/nature/journal/vaop/ncurrent/full/nature08844.html.





Study Indicates Decline in Tasmanian Devil Populations Caused by Disease has Resulted in Changes to Genetic Structure

16 03 2010

 

A study published in the March 10 issue of Nature Heredity indicates that disease-mediated population decline in Tasmanian Devil populations resulting from The following abstract Devil facial tumour disease (DFTD) has caused significant changes in the species’ genetic structure as well as population dispersal patterns.  Following is the abstract to the study.  For the complete study, see Nature Heredity at:

http://www.nature.com/hdy/journal/vaop/ncurrent/full/hdy201017a.html.

Tasmanian Devil.  Photo courtesy Wikimedia Commons by Mike Lehmann.  Licensed under the terms of the GNU Free Documentation License, Version 1.2.

Tasmanian Devil

Infectious disease has been shown to be a major cause of population declines in wild animals. However, there remains little empirical evidence on the genetic consequences of disease-mediated population declines, or how such perturbations might affect demographic processes such as dispersal. Devil facial tumour disease (DFTD) has resulted in the rapid decline of the Tasmanian devil, Sarcophilus harrisii, and threatens to cause extinction. Using 10 microsatellite DNA markers, we compared genetic diversity and structure before and after DFTD outbreaks in three Tasmanian devil populations to assess the genetic consequences of disease-induced population decline. We also used both genetic and demographic data to investigate dispersal patterns in Tasmanian devils along the east coast of Tasmania. We observed a significant increase in inbreeding (FIS pre/post-disease −0.030/0.012, P<0.05; relatedness pre/post-disease 0.011/0.038, P=0.06) in devil populations after just 2–3 generations of disease arrival, but no detectable change in genetic diversity. Furthermore, although there was no subdivision apparent among pre-disease populations (θ=0.005, 95% confidence interval (CI) −0.003 to 0.017), we found significant genetic differentiation among populations post-disease (θ=0.020, 0.010–0.027), apparently driven by a combination of selection and altered dispersal patterns of females in disease-affected populations. We also show that dispersal is male-biased in devils and that dispersal distances follow a typical leptokurtic distribution. Our results show that disease can result in genetic and demographic changes in host populations over few generations and short time scales. Ongoing management of Tasmanian devils must now attempt to maintain genetic variability in this species through actions designed to reverse the detrimental effects of inbreeding and subdivision in disease-affected populations.