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	<title>DNALC Blogs &#187; Oscar Pineda-Catalan</title>
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		<title>DNA sequencing helps discover cavemen’s tools and diet</title>
		<link>http://blogs.dnalc.org/2012/02/17/dna-sequencing-helps-discover-cavemen%e2%80%99s-tools-and-diet/</link>
		<comments>http://blogs.dnalc.org/2012/02/17/dna-sequencing-helps-discover-cavemen%e2%80%99s-tools-and-diet/#comments</comments>
		<pubDate>Fri, 17 Feb 2012 20:57:58 +0000</pubDate>
		<dc:creator><![CDATA[Oscar Pineda-Catalan]]></dc:creator>
				<category><![CDATA[DNA Barcoding]]></category>
		<category><![CDATA[anthropology]]></category>
		<category><![CDATA[barcoding]]></category>
		<category><![CDATA[dna]]></category>
		<category><![CDATA[elephant]]></category>
		<category><![CDATA[mammoth]]></category>
		<category><![CDATA[mastodon]]></category>
		<category><![CDATA[radiocarbon]]></category>
		<category><![CDATA[Sequencing]]></category>

		<guid isPermaLink="false">http://blogs.dnalc.org/?p=4564</guid>
		<description><![CDATA[In the 1970s a team of archaeologists led by Carl Gustafson unearthed the remains of a single, 3-ton, male mastodon (Mammut americanum, a close relative of mammoths and elephants), hunted and butchered by a group of men at the Manis site in the state of Washington, USA (Gustafson 1979). Among the mastodon remains they found&#8230;]]></description>
				<content:encoded><![CDATA[<p>In the 1970s a team of archaeologists led by Carl Gustafson unearthed the remains of a single, 3-ton, male mastodon (<em>Mammut americanum</em>, a close relative of mammoths and elephants), hunted and butchered by a group of men at the Manis site in the state of Washington, USA (<a href="http://www.jstor.org/pss/41102203">Gustafson 1979</a>). Among the mastodon remains they found a spear point that pierced a rib bone. Luckily for us the hunters did not recover the projectile weapon. We thus have evidence of the technology that cavemen in the Americas used to secure their food.</p>
<p>Originally Gustafson and his colleagues dated the mastodon hunting at Manis to more than 13,500 years ago. This was nearly 1,000 years before the Clovis culture, long considered to be the first culture in the New World. Their research was heavily criticized, due to limitations in the <a href="http://www.c14dating.com">radiocarbon methodology</a> used for dating the archaeological findings. However a recent publication supported their finding; an international group of researchers led by Michael Waters of Texas A&amp;M University used a refined radiocarbon dating methodology and DNA analyses to demonstrate that the projectile found at the site came from <a href="http://www.sciencemag.org/content/334/6054/351.short">a mastodon bone shaped as a spear point, handcrafted 13,800 years ago</a>.</p>
<p>After careful DNA extractions of the hunted mastodon rib and the bone projectile found, the researchers successfully amplified a 69 base pair DNA fragment from the mitochondrial control region. Both samples produced identical sequences to mastodon DNA obtained previously, but distinct from other proboscideans (mammoth or elephant) by nine single nucleotide polymorphisms (SNPs).</p>
<p>These findings support the hypothesis that <a href="http://www.sciencemag.org/content/331/6024/1599.short">humans had permanent settlements in the Americas earlier than the Clovis culture (11,500 years ago)</a>. The bone projectile also shows that humans actively hunted megafauna (i.e., animals bigger than 50 kg) in this region. In addition, it suggests that the slow process of extinction of the biggest mammals inhabiting the Americas after the last glacial period (approximately 15,000 years ago), such as mammoths and mastodons, may have begun earlier than the time of the Clovis people.</p>
<p>Find out more about all these fascinating discoveries:</p>
<ul>
<li>Gustafson, C. E., et al. (1979). The Manis mastodon site: early man on the Olympic Peninsula. Canadian Journal of Archaeology, 3: 157-164.</li>
<li>Radiocarbon dating methodology:
<ul>
<li><a href="http://www.c14dating.com">www.c14dating.com</a></li>
<li><a href="http://en.wikipedia.org/wiki/Radiocarbon_dating">http://en.wikipedia.org/wiki/Radiocarbon_dating</a></li>
</ul>
</li>
<li>Waters, M. R., et al. (2011). Pre-Clovis mastodon hunting 13,800 years ago at the Manis Site, Washington. Science 334, 6054: 351-353.</li>
<li>Waters, M. R. et al. (2011). The Buttermilk Creek complex and the Origins of the Clovis at the Debra L. Friedkin Site, Texas. Science, 331, 6024: 1599-1603.</li>
</ul>
<p>&nbsp;</p>
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		<title>A virus in my meal?</title>
		<link>http://blogs.dnalc.org/2012/01/19/a-virus-in-my-meal/</link>
		<comments>http://blogs.dnalc.org/2012/01/19/a-virus-in-my-meal/#comments</comments>
		<pubDate>Thu, 19 Jan 2012 21:28:10 +0000</pubDate>
		<dc:creator><![CDATA[Oscar Pineda-Catalan]]></dc:creator>
				<category><![CDATA[DNA Barcoding]]></category>
		<category><![CDATA[barcoding]]></category>
		<category><![CDATA[dna]]></category>
		<category><![CDATA[hunting]]></category>
		<category><![CDATA[meat]]></category>
		<category><![CDATA[pathogen]]></category>
		<category><![CDATA[urban barcode project]]></category>
		<category><![CDATA[wildlife]]></category>

		<guid isPermaLink="false">http://blogs.dnalc.org/?p=4467</guid>
		<description><![CDATA[Could the meat in your plate pose a health risk for you? If the animal where it came from was properly raised and handled, and the meat went through a sanitary inspection before reaching your plate, there is little chance it can cause you a health problem. But, what could happen if a sanitary authority has&#8230;]]></description>
				<content:encoded><![CDATA[<p>Could the meat in your plate pose a health risk for you? If the animal where it came from was properly raised and handled, and the meat went through a sanitary inspection before reaching your plate, there is little chance it can cause you a health problem. But, what could happen if a sanitary authority has not inspected it?</p>
<p>Your meat indeed could be a high risk for your health. In some cases this can be a public concern, because meat can be a source of pathogens that could cause a disease outbreak. In fact, it has been documented that close interaction among wildlife, domestic animals, and humans could provide the perfect environment for pathogen exchange.<a href="#_ftn1">[1]</a> Even more alarmingly, almost 75% of diseases that have recently emerged in humans have their origin in animals, a process technically known as zoonosis.<a href="#_ftn2">[2]</a> Hunting and butchering of wild animals has been increasingly recognized as a source of disease emergence. The most common zoonotic pathogens are RNA viruses, such as the severe acute respiratory syndrome (SARS) coronavirus,<a href="#_ftn3">[3]</a> and the H5N1 influenza virus, that causes flu.<a href="#_ftn4">[4]</a> Wildlife products that have not been inspected for sanitary conditions could thus be a serious threat to public health.</p>
<p>The United States is one of the world’s largest importers of wildlife and wildlife products.<a href="#_ftn5">[5]</a> Every year approximately 120 million live wild animals and 25,000 tons of wildlife products are imported into the US. New York City is the busiest port of entry into the US, and in combination with the Los Angeles and Miami international airports, accounts for more than 50% of all wildlife imports. One of the main concerns with importation of wild animals and wildlife products is the introduction of pathogens that are associated with them. Examples of diseases introduced to the US by wildlife include amphibian chytridiomycosis, exotic Newcastle’s disease, and monkey pox.</p>
<p>In a study published this month in <em>PLoS ONE</em>, a large collaborative team composed by researchers from EcoHealth Alliance, Columbia University, the American Museum of Natural History, the US Centers for Disease Control and Prevention (CDC), the US Geological Survey, and the Wildlife Conservation Society tested samples from approximately 44 different meat products confiscated at five US international airports, the majority coming from JFK Airport.<a href="#_ftn6">[6]</a> Using DNA barcoding they identified that the bushmeat (term used to define product obtained from hunting and butchering of wild animals) came from chimpanzees, mangabeys, and green monkeys, among other animals. Both simian foamy viruses (SFV) and herpes viruses were detected in the wildlife products. Both type of viruses have been associated with infections and diseases in humans, such as malignant catarrhal fever or herpes B virus.<a href="#_ftn7">[7]</a> This is yet another study highlighting the manifold applications of DNA barcoding.</p>
<p>This <em>PLoS ONE</em> study<sup>6</sup> was the first to conduct surveillance for zoonotic viruses in bushmeat products illegally imported into the US and establishes a precedent of the threat these products could represent for our public health.</p>
<div>
<hr size="1" />
<div>
<p><a href="#_ftnref1">[1]</a> Karesh, W.B., et al. (2005). Wildlife trade and global disease emergence. Emerging Infectious Diseases, Vol. 11, No. 7: 1000-1002.</p>
</div>
<div>
<p><a href="#_ftnref2">[2]</a> Cleaveland, S., et al. (2007). Overview of pathogen emergence: Which pathogens emerge, when, and why. Current Topics in Microbiology and Immunology, Vol. 35: 85-111.</p>
</div>
<div>
<p><a href="#_ftnref3">[3]</a> Xu, R.H., et al. (2004). Epidemiologic clues to SARS origin in China. Emerging Infectious Diseases, Vol. 10, No. 6: 1030-1037.</p>
</div>
<div>
<p><a href="#_ftnref4">[4]</a> Li, K.S., et al. (2004). Genesis of a highly pathogenic and potentially pandemic H5N1 influenza virus in eastern Asia. Nature, Vol. 430, No. 6996: 209–213.</p>
</div>
<div>
<p><a href="#_ftnref5">[5]</a> US Fish and Wildlife Service Office of Law Enforcement Intelligence Unit. US wildlife trade: An overview for 1997-2003. Available at: <a href="http://www.fws.gov/le/pdffiles/Wildlife%20Trade%20Overview%20Report.pdf">http://www.fws.gov/le/pdffiles/Wildlife%20Trade%20Overview%20Report.pdf</a></p>
</div>
<div>
<p><a href="#_ftnref6">[6]</a> Smith, K.M., et al. (2012). Zoonotic viruses associated with illegal imported wildlife products. PLoS ONE, Vol. 7, Issue 1.</p>
</div>
<div>
<p><a href="#_ftnref7">[7]</a> Schrenzel, M.D. (2008). New host for equine herpesvirus 9. Emerging Infectious Diseases, Vol. 14, No. 10: 1616-1619.</p>
</div>
</div>
<p>&nbsp;</p>
]]></content:encoded>
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		<title>Farwell to Baiji, the Yangtze River Dolphin</title>
		<link>http://blogs.dnalc.org/2011/12/19/farwell-to-baiji-the-yangtze-river-dolphin/</link>
		<comments>http://blogs.dnalc.org/2011/12/19/farwell-to-baiji-the-yangtze-river-dolphin/#comments</comments>
		<pubDate>Mon, 19 Dec 2011 19:05:55 +0000</pubDate>
		<dc:creator><![CDATA[Oscar Pineda-Catalan]]></dc:creator>
				<category><![CDATA[DNA Barcoding]]></category>

		<guid isPermaLink="false">http://blogs.dnalc.org/?p=4383</guid>
		<description><![CDATA[A few years ago there were four species of dolphins living in freshwater ecosystems or estuaries in the world. Two of them are still distributed in South America – the Amazon River and the Plata River dolphins (Inia gophrensis and Pontoporia blainvillei, respectively) – and two lived in Asia – the Ganges and Indus River&#8230;]]></description>
				<content:encoded><![CDATA[<p>A few years ago there were four species of dolphins living in freshwater ecosystems or estuaries in the world. Two of them are still distributed in South America – the Amazon River and the Plata River dolphins (<em>Inia gophrensis</em> and <em>Pontoporia blainvillei</em>, respectively) – and two lived in Asia – the Ganges and Indus River dolphin (<em>Platanista gangetica</em>), and the Yangtze River Dolphin, or Baiji (<em>Lipotes vexillifer</em>). These species were highly adapted to live in freshwater ecosystems with distinctive anatomical characteristics that differentiated them from their marine relatives, such as larger snouts (almost four times larger than the snout size of seawater dolphins), movable cervical vertebrae, and small eyes as a possible adaptation to live in muddy water.</p>
<p>Regrettably, the International Union for Conservation of Nature considers the Baiji the most threatened cetacean (i.e. Marine mammals commonly known as whales, dolphins and porpoises) in the world, and it is likely already extinct (<a href="http://www.iucnredlist.org/">IUCN Red List of Threatened Species, 2011</a>). In 2006, a large international expedition of scientists tried to estimate the total population of this species living across its vast natural distributional area along the Yangtze River (<a href="http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2391192/?tool=pmcentrez">Turvey et al. 2007</a>). Unfortunately, after three months of intensive searches the scientists came back with absolute negative results: there was not a single sight of a Baiji. The team had to report thus the virtual or effective extinction of this species.</p>
<p>The implications of this possible extinction are substantial. It represents the loss of a complete lineage of mammalian evolutionary history with a geological record of approximately 20 million years of age (<a href="http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0000296">Isaac et al. 2007</a>). It is also the fourth recorded extinction of an entire taxonomic family since AD 1500 and it represents the first documented global extinction of a large vertebrate (on average adults greater than 100kg) for more than 50 years, since the disappearance of the Caribbean monk seal (<em>Monachus tropicalis</em>) in the 1950s (<a href="http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2391192/?tool=pmcentrez">Turvey et al. 2007</a>). Interestingly, the continuous decline of Baiji populations was not caused directly by human exploitation; the collapse was the mainly the result of incidental mortality caused by fishing activities and by large perturbations of habitats.</p>
<p>Unfortunately, many other sympatric species [two species are considered sympatric when they exist in the same geographic area] face the same dark future as the Baiji; for example, the Chinese paddlefish (<em>Psephurus gladius</em>), one of the largest freshwater fish in the world, and the Yangtze finless porpoise (<em>Neophocaena phocaenoides</em>), which has been classified as Endangered by IUCN since 1996 (IUCN Red List, 2011).</p>
<p>If you are interested in knowing more about these species, or more about other endangered species, there is a wealth of information on the <a href="http://www.iucnredlist.org/">IUCN Red List of Threatened Species</a> and the <a href="eol.org">Encyclopedia of Life</a> web pages.</p>
<p>&nbsp;</p>
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		<title>The Encyclopedia of Life</title>
		<link>http://blogs.dnalc.org/2011/10/14/the-encyclopedia-of-life/</link>
		<comments>http://blogs.dnalc.org/2011/10/14/the-encyclopedia-of-life/#comments</comments>
		<pubDate>Fri, 14 Oct 2011 20:00:59 +0000</pubDate>
		<dc:creator><![CDATA[Oscar Pineda-Catalan]]></dc:creator>
				<category><![CDATA[DNA Barcoding]]></category>
		<category><![CDATA[G2C Online]]></category>

		<guid isPermaLink="false">http://blogs.dnalc.org/?p=4192</guid>
		<description><![CDATA[Documenting the biological diversity of our planet is a challenging task. It implies information collection and organization of millions of species, their genetic diversity and their interactions in biological communities and ecosystems. It also implies coordination among multiple institutions and thousands of scientists, environmentalists, and professionals working with biodiversity. In 2007, Dr. Edward O. Wilson’s&#8230;]]></description>
				<content:encoded><![CDATA[<p>Documenting the biological diversity of our planet is a challenging task. It implies information collection and organization of millions of species, their genetic diversity and their interactions in biological communities and ecosystems. It also implies coordination among multiple institutions and thousands of scientists, environmentalists, and professionals working with biodiversity.</p>
<p>In 2007, Dr. Edward O. Wilson’s speech as the recipient of the TED Prize potentiated the creation of the Encyclopedia of Life (EOL), an international effort to gather together all human knowledge of Earth’s biodiversity.  EOL’s mission is “to increase awareness and understanding of living nature through an encyclopedia that gathers, generates, and shares knowledge in an open, freely accessible, and trusted digital resource.”</p>
<p>The EOL website went public in February 2008 (http://eol.org/). At present, there are more than 750,000 individual pages organized per species. The focus of the EOL is now to collect information relating to taxa of particular public interest, such as commercially valuable species, invasive organisms, disease agents or vectors, food sources, charismatic animals and plants, and newly discovered species. To set priorities, the EOL team has created the RedHotList, an inventory of taxa requiring the most urgent analysis and evaluation (approximately 2,700 taxa), including the 100 worst invasive species on Earth, and the most important food resources, among other groups of organisms.</p>
<p>If you want to know more about the Encyclopedia of Life, please visit their <a title="Encyclopedia of Life" href="http://eol.org/" target="_blank">web page</a> and became a member!</p>
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		<title>How Many Species are on Earth?</title>
		<link>http://blogs.dnalc.org/2011/09/16/how-many-species-are-on-earth/</link>
		<comments>http://blogs.dnalc.org/2011/09/16/how-many-species-are-on-earth/#comments</comments>
		<pubDate>Fri, 16 Sep 2011 20:40:28 +0000</pubDate>
		<dc:creator><![CDATA[Oscar Pineda-Catalan]]></dc:creator>
				<category><![CDATA[DNA Barcoding]]></category>

		<guid isPermaLink="false">http://blogs.dnalc.org/?p=4037</guid>
		<description><![CDATA[For several years scientists have tried to estimate the number of species living on Earth. This is not an easy question to answer and multiple approaches have been developed to calculate how large Earth’s biodiversity is. All of the estimates obtained so far have a large prediction range, hundreds of thousands or even millions of&#8230;]]></description>
				<content:encoded><![CDATA[<p>For several years scientists have tried to estimate the number of species living on Earth. This is not an easy question to answer and multiple approaches have been developed to calculate how large Earth’s biodiversity is. All of the estimates obtained so far have a large prediction range, hundreds of thousands or even millions of species from the smallest estimates to the largest ones. On top of this shaming ignorance, our planet’s biodiversity is highly threatened. Solid evidence indicates that we are facing a massive extinction event, driven unfortunately by our own activities. The most recent evidence indicates that a large portion of extent species, approximately a third of them, is facing a high risk of extinction (See www. iucnredlist.org). Technically a high risk of extinction means that if all variables affecting the demography and ecology of those species continue as they are now, they are going to disappear in 100 years or less. Therefore, it is crucial to estimate more accurately how many species live on our planet; otherwise it is going to be impossible to develop efficient strategies for protecting this diversity.</p>
<p>On a recent publication, Camilo Mora and collaborators estimated how many species are on Earth, using a novel approach based on the predictable pattern of diversity observed in the hierarchical taxonomic classification system. Their results indicate that there are approximately 8.7 million (± 1.3 million) of eukaryote species. If we considered that 1.2 million species have been catalogued, more than 85% of existing species on Earth have not been scientifically described.</p>
<p>I encourage you to read the whole paper and know more about this fundamental question in science:</p>
<p>Mora C, Tittensor DP, Adl S, Simpson AGB, Worm B (2011) How Many Species Are There on Earth and in the Ocean? PLoS Biol 9(8): e1001127. doi:10.1371/journal.pbio.1001127</p>
<p>&nbsp;</p>
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