Like Mice Off a Not So Sinking Ship

19 03 2012
House_mouse_Mus_musculus

The humble house mouse (Mus musculus), traveling the globe with man. Image is courtesy of Wikimedia Commons and is in the public domain.

An international team of researchers led by scientists at the University of York in the United Kingdom have used mitochondrial DNA to show that the timeline of house mice migration across the upper north Atlantic through Scotland and the Scottish Islands, to Iceland, Greenland, and Newfoundland closely matches that of the Viking invasion.

The Vikings, who fought, raided, and explored their way across the north Atlantic from the late eighth to the mid-tenth centuries were the scourge of most of Europe at that time, raiding, killing, and pillaging large swaths of the continent, not just the areas above, but also parts of England, Wales, the Isle of Man, and Ireland.  They established the first cities in Ireland.  They founded the duchy of Normandy, in France, and they even established a kingdom in Sicily in the Mediterranean Sea.

It seems that where they went, their house mice (scientific name Mus musculus) went with them, at least on the northern part of their journey.

According to a press release (see here) the research team, made up of members from the UK, US, Iceland, Denmark, and Sweden, used techniques designed to characterize genetic similarity, and thereby infer the relatedness of one population, or one individual, with another, in order to determine a mouse colonisation timeline.

They obtained modern samples of house mic DNA and compared them to ancient samples dating mostly from the 10th to 12th centuries.  Samples were collected from nine sites in Iceland, Narsaq in Greenland, and four sites near the Viking archaeological site, L’Anse aux Meadows, in Newfoundland.  Ancient samples came from the Eastern and Western settlements in Greenland and four archaeological sites in Iceland.

When analyzed, the samples showed that house mice traveled with the Vikings to Iceland in the early 10th century , either from Norway or the northern part of the British Isles.  From Iceland the mice continued their journey on Viking ships to settlements in Greenland.  However, while descendants of these stowaways can still be found in Iceland, the early colonizers in Greenland have become extinct and their role has been filled by Danish house mice (same species) brought much later by a second wave of European human immigrants.

Of significance is the fact that no evidence of house mice was found in the Viking settlement in Newfoundland, nor was there any evidence of ancestral Viking house mice DNA in modern house mice there.  So, it seems that if the mice made if as far as Newfoundland, they became extinct before they could contribute to the modern house mice lineage on the island.

Replica of a Viking Long Ship

Replica of a Viking long ship. Photograph by archiwum własne wikingów, Jarmeryk, from Wikimedia Commons.





Ancient Horse Mother Found

1 02 2012

A team of geneticists, paleontologists, and archaeologists have identified the ancient mother of all the horses alive today, according to a paper (link here) published in the Proceedings of the National Academy of Sciences, January 30.

The study, led by Alessandro Achilli, of the Dipartimento di Biologia Cellulare e Ambientale, at the Università di Perugia, in Perugia, Italy, determined that the common ancestral mare to all living horses trotted the earth between 130,000 and 160,000 years ago, with a date of approximately 140,000 years being most likely.  More importantly, the study also identified 18 major clusters of genes called haplogroups, that were involved in the domestication of horses.

Torroni and his colleagues examined 83 modern horse genomes from the Americas, Asia, Europe, and the Middle East.  While the generalities of horse domestication are broadly understood, the specifics of time and location are not.  This study sheds significant light on these aspects of the horse’s natural history.

The study indicates that horses were domesticated over a broad area of Eurasia with multiple incidents of domestication occurring at different times.  This differs from many other domestic animals, such as cattle and sheep, which were domesticated from a handful of animals at very specific locations and then spread through trade and capture.  At least one of these domestication events took place in Europe, with Iberia being a possible location for it.

Horses have an extended and close relationship with humans.  They have played a major role in human history.  Horses were widely used in warfare until the end of World War I, and were still used to some extent even in World War II.  In civilian use, millions of horses were engaged for transportation and to haul goods until the 1920s, when they were largely replaced by trucks and automobiles.  They were still a common sight on many American roads until the 1940s.

In addition to its general scientific interest, the paper points out that the results of the study can also be used to classify fossil horse remains, identifying where they belong on the horse family tree; better define and understand modern horse breeds and their ancestry; and evaluate the role of maternal ancestry in racehorse performance.

Bhimbetka_Rock_Paintng_Man_Riding_Horse

A 30,000 year old rock painting from Bhimbetka in north central India, showing a man riding a horse. This image comes from Wiki Commons and is used under the GNU Free Documentation License





Mendel’s Manuscript Mess

1 06 2010
Image of Gregor Mendel (1822-1884) the father of modern genetics

Gregor Mendel (1822-1884) the father of modern genetics

One of the most important manuscripts in modern science, long thought lost, has resurfaced in the middle of an ownership dispute.

The original manuscript of Gregor Mendel’s pea-breeding experiments, that allowed him to deduce the laws of heredity, thereby laying the foundations of modern genetics, has turned up in Germany after being missing for more than 50 years.

At the time it was published, Mendel was an Augustinian monk in the Abbey of St. Thomas, in the Austro-Hungarian city of Brünn, now Brno in the Czech Republic.

The importance of Mendel’s work was unrecognized by the international scientific community until 1900 (16 years after Mendel’s death).  The was due mostly to the fact that it was published in the rather obscure Journal of the Brünn Natural History Society.

Once discovered, however, it quickly became one of the most important articles in modern science.  This was because it was the first publised article to describe in detail how genetics operated, even though Mendel (and the rest of the world for that matter) knew nothing about DNA or other elements of genetics.  Indeed, it was Mendel’s paper that set the world on the road to discovering the whole of genetic theory.  In addition, Mendel’s experiment is often cited as one of the most elegant scientific experiments in history.

In an article published on Monday (June 31) in The New York Times, writer Nicholas Wade describes what happened to the orignal manuscript after it was published 1865.  According to Wade, the manuscript, the title of which translates into English as Experiments on Plant Hybridization, has been through a lot in the last 145 years.  It languished in the Brünn Natural History Society’s library until 1911, when it was discarded.  Saved from the trash by a local high school teacher, it was returned to the society’s files.  During World War II, a German botany professor (apparently part of the occupying force, who was in chage of the library) keep it in his briefcase.  Afterward, when Soviet forces occupied the area, it disappeared and was presumed destroyed.  Only in 1988 did it resurace, in the hands of a descendent of Mendel’s, who is also an Augustinian monk.  Since then, there have been competing claims to its ownership, with the monk’s order threatening to throw him out and even the German government getting involved.

For the complete story and the details of  the ownership controversy, please see the NY Times article, here.





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.





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





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.





Study Shows Most European Paternal Lineages Originated in Neolethic Times

16 03 2010

A study published in PLoS Biology indicates that the ancestery of most Europeans started from a single Neolethic source in the near east during Neolethic times.

For the complete study, please see PLoS Biology at http://www.plosbiology.org/article/info%3Adoi%2F10.1371%2Fjournal.pbio.1000285. The abstract is as follows:

 

Abstract

The relative contributions to modern European populations of Paleolithic hunter-gatherers and Neolithic farmers from the Near East have been intensely debated. Haplogroup R1b1b2 (R-M269) is the commonest European Y-chromosomal lineage, increasing in frequency from east to west, and carried by 110 million European men. Previous studies suggested a Paleolithic origin, but here we show that the geographical distribution of its microsatellite diversity is best explained by spread from a single source in the Near East via Anatolia during the Neolithic. Taken with evidence on the origins of other haplogroups, this indicates that most European Y chromosomes originate in the Neolithic expansion. This reinterpretation makes Europe a prime example of how technological and cultural change is linked with the expansion of a Y-chromosomal lineage, and the contrast of this pattern with that shown by maternally inherited mitochondrial DNA suggests a unique role for males in the transition.