Plants to People: the Swift Tempo of Spontaneous Mutation

Research published today in the journal Science serves to further calibrate the ticking clock of genetic mutation. By tediously analyzing the genomes from multiple generations of the plant Arabidopsis thaliana, scientists from the Max Planck Institute have shown that spontaneous mutations can arise rather frequently in the genome. Despite commonly held assumptions of minimally effectual rarity, the study demonstrates that the rate at which novel mutations occur have more than ample potency to drive evolution. Moreover, when considering the total population size of Arabidopsis, the tempo of mutation indicates that evolution likely proceeds much faster than previously suspected.

Although a single seed of Arabidopsis thaliana may only posses a single point mutation (i.e. a single base or ‘letter’ of DNA) relative to its parents, when multiplied by millions of individual plants over multiple generations, that single mutation quickly compounds to produce tens of new base pairs in only a few years time. The rate of genetic change revealed by the Max Planck study not only aids our understanding of how observed resistance to chemical herbicides rapidly evolves within the weedy plants combated by agriculture, its findings also point to possibly underestimated speeds of mutation in other organisms – like those of humans.

For example, back in September a team headed by Sanger scientists published work in which the rate of mutation in humans was estimated at around 1 mutation per 15 to 30 million nucleotides. Comparatively, this estimate translates to about 150 point mutations in every individual as measured against their parents; that’s a mutation tempo 100 times fold that of Arabidopsis thaliana.



Ossowski, S., Schneeberger, K., Lucas-Lledo, J., Warthmann, N., Clark, R., Shaw, R., Weigel, D., & Lynch, M. (2009). The Rate and Molecular Spectrum of Spontaneous Mutations in Arabidopsis thaliana Science, 327 (5961), 92-94 DOI: 10.1126/science.1180677

Xue, Y., Wang, Q., Long, Q., Ng, B., Swerdlow, H., Burton, J., Skuce, C., Taylor, R., Abdellah, Z., & Zhao, Y. (2009). Human Y Chromosome Base-Substitution Mutation Rate Measured by Direct Sequencing in a Deep-Rooting Pedigree Current Biology, 19 (17), 1453-1457 DOI: 10.1016/j.cub.2009.07.032

Human Evolution Hampered by History

In a earlier post (available HERE), the ability to track ancient Neanderthal geographical distributions and migration patterns through DNA sequencing was discussed in light of recent research by Fabre, Condemi & Degioanni; now, a new study published at PLoS Genetics examines the genome of modern humans in an attempt to gauge rates of selection and correlate geographic patterns over more recent time periods.

In the paper The Role of Geography in Human Adaptation, Graham Coop (et al.) moves beyond expressed phenotypes and investigates the traces of human adaptation found in the genomes of extant and geographically diverse populations. By analyzing nonsynonymous SNPs, the study found that signals expressed in the genome can be used to predict the patterns found within specific loci. Essentially, the patterns they identified demonstrated that closely related populations possessed fewer genetic differences than would be expected having been subject to differing ecological pressures over the past 100,000 years. These apparently resilient genetic patterns - they suggest - are indicative of a selection pressure that “has been strongly constrained by the historical relationships and gene flow between populations.”

(Image from Article)

From the Introduction:
“…Humans have spread out of Africa to colonize almost all of the world's land mass, and in the process have experienced a vast range of new climates, diets and ecosystems. Humans have also encountered new pathogens as they moved around the globe and moved into close proximity with domesticated animals, and as human population densities increased.
These changes in human ecology suggest that there has been ample scope for the action of natural selection in recent human evolution. Moreover, most species, including humans, probably face various additional selection pressures on a persistent basis: e.g., due to sexual competition, viability selection and resistance to evolving pathogens. Hence, it seems reasonable that our genomes would show evidence for recent selection…”

Evidence for natural selection is exactly what they find, however they also conclude that the power of selection on humans can be very weak and therefore easily influenced by historic patterns of migration and genetic drift.

The paper is well worth a look…

Coop, G., Pickrell, J., Novembre, J., Kudaravalli, S., Li, J., Absher, D., Myers, R., Cavalli-Sforza, L., Feldman, M., & Pritchard, J. (2009). The Role of Geography in Human Adaptation PLoS Genetics, 5 (6) DOI: 10.1371/journal.pgen.1000500

The Blitzkrieg of Ungulates in Levant

The region of the Middle East referred to as “Levant” includes modern day Israel, Palestine and Jordon, and there are few places on earth more intensely studied by archaeologists than the birthplace of monotheistic religion. In addition to yielding a vast record of human occupation, culture and war, the archaeological sites within this region also document the decimation of several mammalian species. A couple of days ago (April 29), several Israeli scientists published an article in PLoS One in which they identified human driven overkill as the primary cause of regional extinction in several species of ungulates.

Through examination of vertebrate remains associated with the archaeological sites of Levant, scientists were able to piece together patterns of ungulate biogeography that point to over hunting and environmental degradation as the impetus for the extinction of hartebeests, aurochs, hippopotami and several species of deer. Additionally, a direct correlation was found between the body mass of the hunted species and the rate at which the animal went extinct – presumably, larger animals were of greater value (provided more meat) and were easier to hunt (bigger = slower).

Figure: Body mass of ungulates that became extinct at end of Iron Age (by 586 BCE), at end of Mamluk period (12th century CE), at end of 19th century CE, as well as body mass of extant ungulate species. Three species became extinct during the Iron Age (1,Hippopotamus amphibius; 2, Bos primigenius; 3, Alcelaphus buselaphus), one species during the 12th century CE (4, Cervus elaphus), and six species during the 19th century CE (5, Dama mesopotamica; 6, Capra aegagrus; 7, Capreolus capreolus; 8, Gazella subgutturosa; 18 9, Equus hemionus; 10, Oryx leucoryx). Four species still exist (11, Sus scrofa; 12,Gazella gazelle; 13, Capra ibex nubiana; 14, Gazella dorcas). Because only one species become extinct during the 12th century this period could not be included in the ANOVA analysis. Horizontal broken line indicates average body mass of the 14 ungulates in Natufian Period (13,000–9,500 years BCE). Letters above bars indicate a significant difference between groups (Bonferroni Multiple Comparison Test, P,0.05). doi:10.1371/journal.pone.0005316.g011

According to the researchers, “It thus appears that during the Holocene period in the southern Levant, the most important causes of ungulate extinctions were habitat destruction and uncontrolled hunting.” They further detail, “Based on the data of this study we assume that overkill in the southern Levant operated in two stages: 1) slow overkill by ancient hunting methods, that caused the disappearance of the larger species and 2) modern blitzkrieg, which was made possible by the use of modern firearms, such blitzkrieg differed drastically from the prehistoric hunting of naive large fauna in other continents and islands, where human hunters were never encountered.”

Tsahar, E., Izhaki, I., Lev-Yadun, S., & Bar-Oz, G. (2009). Distribution and Extinction of Ungulates during the Holocene of the Southern Levant PLoS ONE, 4 (4) DOI: 10.1371/journal.pone.0005316

New Study Merges Genetics, Demography and Paleoanthropology

Mitochondrial DNA from twelve Neanderthal fossil assemblages was sequenced, compared and correlated with morphological data from fossil skulls, limbs and dentary remains to render evidence for multiple demes of Neanderthals from across Asia and Europe.

According to the authors, this “…approach to Neanderthal variability, based on nucleotide sequences analysis, confirms from a genetic point of view the morphological variations between western and eastern Neanderthals and the existence of a southern group…”

The mtDNA portion of the study therefore supports prior determinations based on morphological analysis that at least three separate Neanderthal sub-groups (and possibly a fourth group from western Asia) emerged from an ancestral population approximately 130,000 years ago. Furthermore, there is evidence that these populations existed in a dynamic state of migration.

Figure 2. Neanderthal Group Distribution

Abstract:
The Neanderthals are a well-distinguished Middle Pleistocene population which inhabited a vast geographical area extending from Europe to western Asia and the Middle East. Since the 1950s paleoanthropological studies have suggested variability in this group. Different sub-groups have been identified in Western Europe, in southern Europe and in the Middle East. On the other hand, since 1997, research has been published in paleogenetics, carried out on 15 mtDNA sequences from 12 Neanderthals. In this paper we used a new methodology derived from different bioinformatic models based on data from genetics, demography and paleoanthropology. The adequacy of each model was measured by comparisons between simulated results (obtained by BayesianSSC software) and those estimated from nucleotide sequences (obtained by DNAsp4 software). The conclusions of this study are consistent with existing paleoanthropological research and show that Neanderthals can be divided into at least three groups: one in western Europe, a second in the Southern area and a third in western Asia. Moreover, it seems from our results that the size of the Neanderthal population was not constant and that some migration occurred among the demes.


In case you were wondering about genetic links to modern Homo sapiens, the study was limited to “…what occurred previous to the arrival of modern humans in the Neanderthal landscape and we therefore do not consider the potential phylogenetic relationship between Neanderthals and modern Humans.”

The article, in its entirety, is available at the below referenced link.

Fabre, V., Condemi, S., & Degioanni, A. (2009). Genetic Evidence of Geographical Groups among Neanderthals PLoS ONE, 4 (4) DOI: 10.1371/journal.pone.0005151

The Rise of “Homo egocentricis”

Although it was literally a dark and stormy night, such weather conditions were but a novelty to the speaker – a scientist whom had spent the majority of his life scanning barren rocks and desiccated landscapes for fragments of fossil bone beneath the unrelenting and scorching sun of an East African desert. Yet, I can’t help but think that some level of instinctual fear naggingly tickled at his stomach as he approached the waiting crowd…

There was little doubt that villains - the arch enemies of reason and deniers of fact– concealed themselves among the many upstanding community members and university staff in attendance. This was, after all, Tallahassee, Florida. A city of the Southeastern Unite States, geographically located near the eastern extent of the so called “Bible belt.”

How would they react to being told that biological evolution is fact? Moreover, how would they respond to learning that Homo sapiens, despite an egocentric view of the world, have shared a common ancestry with other primates, and in fact, a common lineage with all life on Earth?

Actually, they responded remarkably well, much to the credit of Dr. Don Johanson.

By all accounts, the talk on Human Origins was a success. Dr. Johanson spoke with the confidence and familiarity that has made him a highly sought, world renowned lecturer and scientist.



He began the talk by discussing the development of his personal interest in anthropology as a child and quickly moved through a summary of the major fossil discoveries made during his lifetime - a true story of adventure and discovery. The lecture was given at an IMAX theater and included some fantastic images of hominid fossils and African landscapes; the presentation can be viewed in its entirety by going to the FSU Origins webpage HERE and clicking on the red-highlighted “Webcast” text to the right of Dr. Johanson’s photograph.

As a further suggestion, I’d recommend a quick look at a recent article by Kaye E. Reed of the Institute of Human Origins (which Don Johanson runs in Arizona) discussing the paleoecology of the Hadar hominin site in Ethiopia. The article discusses speciation and environmental transitions associated with Australopithecus afarensis.

Reed, K. (2008). Paleoecological patterns at the Hadar hominin site, Afar Regional State, Ethiopia Journal of Human Evolution, 54 (6), 743-768 DOI: 10.1016/j.jhevol.2007.08.013