Thursday, July 31, 2014

Smoking the Shield

















Smoking the Shield, as painted by George Catlin, 1837-39

“The Sioux shield [is] made of the skin of the buffalo's neck, hardened with the glue extracted from the hoofs and joints of the same animal . . . This skin is at first, twice as large as the size of the required shield; but having got his particular and best friends (who are invited on the occasion) into a ring, to dance and sing around it, and solicit the Great Spirit to instill into it the power to protect him harmless against his enemies, [the young man] spreads over it the glue, which is rubbed and dried in, as the skin is heated; and a second busily drives other and other pegs, inside of those in the ground, as they are gradually giving way and being pulled up by the contraction of the skin. By this curious process, which is most dexterously done, the skin is kept tight whilst it contracts to one-half of its size, taking up the glue and increasing in thickness until it is rendered as thick and hard as required.” (Catlin, Letters and Notes, vol. 1, no. 30, 1841; reprint 1973)

Smithsonian American Art Museum
(Link)

Tuesday, July 29, 2014

Kotz-a-tó-ah, Smoked Shield, Distinguished Warrior

   Kotz-a-tó-ah, Smoked Shield, a Distinguished Warrior
   Painting of George Catlin, painted 1834
 
" . . . another of the extraordinary men of this tribe [Kiowa], near seven feet in stature, and distinguished, not only as one of the greatest warriors, but the swiftest on foot, in the nation. This man, it is said, runs down a buffalo on foot, and slays it with his knife or his lance, as he runs by its side!” (Catlin, Letters and Notes, vol. 2, no. 43, 1841, reprint 1973; Gurney and Heyman, eds., George Catlin and His Indian Gallery, 2002)
 
Smithsonian American Art Museum
(Link)

Friday, July 25, 2014

Comparative Performance of Two Whole Genome Capture Methodologies on Ancient DNA Illumina Libraries

, , , , , , , ,



(Link) open access

Abstract

1. The application of whole genome capture (WGC) methods to ancient DNA (aDNA) promises to increase the efficiency of ancient genome sequencing.

2. We compared the performance of two recently developed WGC methods in enriching human aDNA within Illumina libraries built using both double-stranded (DSL) and single-stranded (SSL) build protocols. Although both methods effectively enriched aDNA, one consistently produced marginally better results, giving us the opportunity to further explore the parameters influencing WGC experiments.

3. Our results suggest that bait length has an important influence on library enrichment. Moreover, we show that WGC biases against the shorter molecules that are enriched in SSL preparation protocols. Therefore application of WGC to such samples is not recommended without future optimization. Lastly, we document the effect of WGC on other features including clonality, GC composition and repetitive DNA content of captured libraries.

4. Our findings provide insights for researchers planning to perform WGC on aDNA, and suggest future tests and optimization to improve WGC efficiency.


Fig. 1. WGC preferentially retrieves longer fragments in sequencing libraries. The read length distribution of pre-capture and post-capture libraries is shown for (a) double-stranded libraries (DSL) and (b) single-stranded-libraries. In (a) the x axis is split in <90 bp and >90 bp to adjust the scale and better illustrate the higher concentration of short reads in the pre-capture libraries (pink line) and the bias observed against these in capture experiments (green and blue lines) where longer fragments are preferentially retrieved. (b) Illustrates that the relative gain of shorter fragments obtained by building a SSL, is lost by capturing these types of libraries. The plot shown in (c) depicts the bioanalyzer profile of the bait libraries revealing that for WISC a wider tail is observed for longer baits, which might explain the stronger bias in favor of longer fragments by this particular method.


Discussion

By comparing the performance of WISC and MYbaits in enriching for endogenous human DNA in ancient DNA extracts, we have been able to pinpoint potential factors influencing the dynamics of WGC experiments. The assessment of the subtle differences between both approaches to in-WGC enables us to draw insights on two variables that may the affect capture efficiency – bait length distribution and hybridization time. Our data furthermore provides insights into the effect of blocking agents, and first insights into the performance of whole-genome enrichment methods on SSL.

Although the experimental design and parameters used in this study seem to suggest an apparent benefit of one of the methods over the other, we strongly caution that batch effects could be playing an important role under these settings, hence discourage such interpretation from our results. Likewise, it is worth considering that even though there is a certain convenience in using a pre-made kit (MYbaits), our observations point to specific factors that can be optimized in the in house method (WISC) namely bait length distribution and hybridization parameters. Knowing the relevance of such parameters in WGC, gives users the flexibility of customizing their capture experiment to match the particularities of each aDNA library (see below).

Role of bait length distribution on the efficiency of WGC

Bait length distributions (Fig. 1c) differ mainly in that WISC shows a wider range and longer bait lengths. This in principle could account for the marked retrieval of longer reads in the WISC compared with the MYbaits experiments (Figs. 1a-b).  Following this rationale, the higher success of the latter could be explained by its ability to better access a fraction of the sequencing library, specifically that with the smaller fragments, while this fraction remains inaccessible due to the higher concentration of longer baits used in WISC. An important consequence of this feature was the poor and even unsuccessful outcome of capturing SSL, which include a higher fraction of short fragments, with either method. At the same time, this limitation reveals an important area for future development in the context of WGC experiments.

Although there was a small, yet consistent, benefit in the MYbaits over the WISC, it would be rash to conclude that the MYbaits method always outperforms WISC.  These results were generated using a single batch of WISC bait versus a single batch of MYbaits. Given that (i) bait lengths will likely vary between batches as a result of initial template DNA fragmentation, and (ii) our hypothesis that bait length may play a key role in retaining shorter DNA fragments, we believe it is more than likely our results simply reflect the fact that in these batches tested the WISC bait were slightly longer than the MYbaits. Future studies that examine the role of bait length in capture success will be needed to further examine this hypothesis.

Wednesday, July 23, 2014

The Resettlement of Northern Europe

Felix Riede
The Oxford Handbook of the Archaeology and Anthropology of Hunter-Gatherers
Edited by Vicki Cummings, Peter Jordan and Marek Zvelebil
Print Publication Date: April 2014
(Link)

Abstract

As the climate began to ameliorate after the last Ice Age, pioneer plants, animals, and people began to resettle northern Europe. The recolonization of the North European Plain and the maritime and mountainous landscapes of Scandinavia is associated with variants of the Magdalenian techno-complex. Structured by the successive maturation of landforms as well as by a number of catastrophic environmental changes, this process took the form of a series of colonization pulses followed by contractions and renewed colonization efforts. With the introduction of important new technologies such as the bow and arrow, watercraft, and fishing technology as well as domesticated dogs, this demographically and environmentally dynamic period saw the expansion of the geographic as well the behavioural dimensions of the hunter-gatherer niche. Underwritten by extensive mobility, trade, and exchange networks, these forager populations were able to explore and settle even the most remote parts of Arctic northern Europe early during the Holocene.

Tuesday, July 22, 2014

Dusk at a small lake, Lassen Volcanic National Park

Dusk at a small lake, Lassen Volcanic National Park, California
 
 
Nurse's Song
 
1757-1827

When the voices of children are heard on the green,
And laughing is heard on the hill,
My heart is at rest within my breast,
And everything else is still.

‘Then come home, my children, the sun is gone down,
And the dews of night arise;
Come, come leave off play, and let us away
Till the morning appears in the skies.’

‘No, no, let us play, for it is yet day,
And we cannot go to sleep;
Besides, in the sky the little birds fly,
And the hills are all cover'd with sheep.’

‘Well, well, go and play till the light fades away,
And then go home to bed.’
The little ones leapèd, and shoutèd, and laugh'd
And all the hills echoed.

Sunday, July 20, 2014

Margaret Hamilton, Mathematician and Computer Scientist, Played Key Role in Space Program



Hamilton as Lead Apollo Flight Software Designer
 
(Link) Wikipedia
(Link) NASA Office of Logic Design
 
Margaret Hamilton (born 1938) is an American former NASA scientist, and founder and CEO of software development company Hamilton Technologies, Inc. At NASA she was Director of the Software Engineering Division of the MIT Instrumentation Laboratory, later the Charles Stark Draper Laboratory, which played a key role in the success of the Apollo space program.


NASA Research

At NASA Hamilton was responsible for helping pioneer the Apollo on-board guidance software required to navigate to/from and land on the moon, and its multiple variations used on numerous missions (including the subsequent Skylab.) She worked to gain hands-on experience during a time when computer science and software engineering courses or disciplines were non-existent.

In the process, she produced innovations in the fields of system design and software development, enterprise and process modelling, preventative systems design, development paradigm, formal systems (and software) modelling languages, system-oriented objects for systems modelling and development, automated life-cycle environments, methods for maximizing software reliability and reuse, domain analysis, correctness by built-in language properties, open-architecture techniques for robust systems, full life-cycle automation, quality assurance, seamless integration (including systems to software), distributed processing systems, error detection and recovery techniques, man/machine interface systems, operating systems, end-to-end testing techniques, and life-cycle management techniques.

These in turn led her to develop concepts of asynchronous software, priority scheduling, and man-in-the-loop decision capability, which became the foundation for modern, ultra-reliable software design.


Apollo 11

Preventing an abort of the Apollo 11 mission has been attributed to her work. Just three minutes before the Lunar lander reached the Moon's surface several computer alarms were triggered. The cause of the alarms was an overload of incoming to the Apollo Guidance Computer (AGC). Due to its robust architecture, the computer was able to keep running, as the Apollo onboard flight software was developed using an asynchronous executive so that higher priority jobs (e.g. important for landing) could interrupt lower priority jobs. A 2005 re-analysis concluded that a hardware design error in the rendezvous radar provided the computer with faulty information even while in standby mode.

Margaret Hamilton, on the design of the Apollo 11 Guidance Computer software:
". . . the computer was being asked to perform all of its normal functions for landing while receiving an extra load of spurious data which used up 15% of its time. The computer (or rather the software in it) was smart enough to recognize that it was being asked to perform more tasks than it should be performing. It then sent out an alarm, which meant to the astronaut, I'm overloaded with more tasks than I should be doing at this time and I'm going to keep only the more important tasks; i.e., the ones needed for landing ... Actually, the computer was programmed to do more than recognize error conditions. A complete set of recovery programs was incorporated into the software. The software's action, in this case, was to eliminate lower priority tasks and re-establish the more important ones ... If the computer hadn't recognized this problem and taken recovery action, I doubt if Apollo 11 would have been the successful [M]oon landing it was.
—Margaret Hamilton, Letter to Datamation, March 1, 1971
 
Today
 
Margaret's current activities as of February 2010 include fulfilling her role as the founder and CEO of Hamilton Technologies, Inc., a business developed around the Universal Systems Language (USL) which is in turn based upon her Development Before The Fact (DBTF) paradigm for systems and software design.
 
 
Publications
 
Margaret Hamilton has published 130 papers, proceedings and reports concerned with the 60 projects and 6 major programs in which she has been involved.

A selection:
  • M. Hamilton, S. Zeldin (1976) "Higher order software—A methodology for defining software" IEEE Transactions on Software Engineering, vol. SE-2, no. 1, Mar. 1976.
  • M. Hamilton (1994), “Inside Development Before the Fact,” cover story, Editorial Supplement, 8ES-24ES. Electronic Design, Apr. 1994.
  • M. Hamilton, Hackler, W.R.. (2004), Deeply Integrated Guidance Navigation Unit (DI-GNU) Common Software Architecture Principles (revised dec-29-04), DAAAE30-02-D-1020 and DAAB07-98-D-H502/0180, Picatinny Arsenal, NJ, 2003-2004.
  • M. Hamilton and W.R. M. Hackler (2007), “Universal Systems Language for Preventative Systems Engineering,” Proc. 5th Ann. Conf. Systems Eng. Res. (CSER), Stevens Institute of Technology, Mar. 2007, paper #36.


Forty Five Years Ago Today


David Woods, video editor
(his books)

Apollo 11 Lunar Surface Journal, The First Lunar Landing
Corrected Transcript and Commentary Copyright © 1995 by Eric M. Jones
All rights reserved.
(Link)

Blog notes:

The first moon landing was forty five years ago, today.  As a child, I watched many of the moon landings and was fascinated with the details of the radio communication.  In this video, you can hear the challenges the Apollo 11 mission faced with radio communication and with different kinds of background noise.  (Some of it is also engine noise.  Today, with radio and telephony, you rarely hear radio noise because it is filtered out using digital and analog filters and other noise and error rejection schemes.)

For most of the descent, the Eagle lunar lander is controlled by the flight computer, the Apollo Guidance Computer (AGC), which among other things, is fed data by a radar system which can "see" the lunar surface. 

The full transcript of the lunar descent is available at the NASA site Apollo 11 Lunar Surface Journal, The First Lunar Landing (see above for the link).

The video starts at 102:32:35 into the transcript.

At about 5:17 into the video, or 102:38:04 into the transcript, you can hear Aldrin say "we got good lock on", meaning that the radar and AGC have acquired information about the lunar surface and are flying under computer control with the radar information.

The "P" annotations on the video refer to the computer programs that are being run during the descent.  The AGC programs were:

P63 - Landing maneouver braking program
P64 - Landing maneouver approach phase
P65 - Landing phase - auto
P66 - Rate of descent landing
P67 - Manual landing phase

From the Apollo Guidance Computer wiki page:

At about 5:40 in the video, "Buzz Aldrin gave the Apollo Guidance Computer (AGC) the command '1668' which instructed it to calculate and display DELTAH (the difference between altitude sensed by the radar and the computed altitude). This added an additional 10% to the processor work load causing executive overflow and a '1202' alarm. After being given the "GO" from Houston Aldrin entered '1668' again and another '1202' alarm occurred. When reporting the second alarm Aldrin added the comment "It appears to come up when we have a 1668 up". "

"Luckily for Apollo 11, the AGC software had been designed with priority scheduling. Just as it had been designed to do, the software automatically recovered, deleting lower priority tasks including the '1668' display task, to complete its critical guidance and control tasks."

"The problem was not a programming error in the AGC, nor was it pilot error. It was a peripheral hardware design bug that was already known and documented by Apollo 5 engineers. However because the problem had only occurred once during testing they concluded that it was safer to fly with the existing hardware that they had already tested, than to fly with a newer but largely untested radar system. In the actual hardware, the position of the rendezvous radar was encoded with synchros excited by a different source of 800 Hz AC than the one used by the computer as a timing reference. The two 800 Hz sources were frequency locked but not phase locked, and the small random phase variations made it appear as though the antenna was rapidly "dithering" in position even though it was completely stationary. These phantom movements generated the rapid series of AGC cycle steals."

Again at about 9:30 into the video, there are low priority alarms, '1201' and '1202', which are again over-ridden by the AGC.  The AGC continues to control the flight profile, processing high priority tasks, and ignoring low priority tasks.

At 10:30 into the video, Armstrong takes the AGC out of the controlled P64 approach phase program and into a P66 rate of descent manually controlled landing.  He pitches the profile of the Eagle forward, to maintain speed, in order to fly across Crater West boulder field.  Once across the boulder field, at about 11:05, he pitches back to slow down.

They land with 20 seconds of fuel remaining.

Thursday, July 17, 2014

Ithaka

C.P. Cavafy
Collected Poems.
Translated by Edmund Keeley and Philip Sherrard.
Edited by George Savidis. Revised Edition.
Princeton University Press, 1992
(Link)


As you set out for Ithaka
hope the voyage is a long one,
full of adventure, full of discovery.
Laistrygonians and Cyclops,
angry Poseidon—don’t be afraid of them:
you’ll never find things like that on your way
as long as you keep your thoughts raised high,
as long as a rare excitement
stirs your spirit and your body.
Laistrygonians and Cyclops,
wild Poseidon—you won’t encounter them
unless you bring them along inside your soul,
unless your soul sets them up in front of you.

Hope the voyage is a long one.
May there be many a summer morning when,
with what pleasure, what joy,
you come into harbors seen for the first time;
may you stop at Phoenician trading stations
to buy fine things,
mother of pearl and coral, amber and ebony,
sensual perfume of every kind—
as many sensual perfumes as you can;
and may you visit many Egyptian cities
to gather stores of knowledge from their scholars.

Keep Ithaka always in your mind.
Arriving there is what you are destined for.
But do not hurry the journey at all.
Better if it lasts for years,
so you are old by the time you reach the island,
wealthy with all you have gained on the way,
not expecting Ithaka to make you rich.

Ithaka gave you the marvelous journey.
Without her you would not have set out.
She has nothing left to give you now.

And if you find her poor, Ithaka won’t have fooled you.
Wise as you will have become, so full of experience,
you will have understood by then what these Ithakas mean.

Ocean Beach

Sea Fever

John Masefield
1878-1967
(Link) (poetry foundation)

I must go down to the seas again, to the lonely sea and the sky,
And all I ask is a tall ship and a star to steer her by;
And the wheel’s kick and the wind’s song and the white sail’s shaking,
And a grey mist on the sea’s face, and a grey dawn breaking,

I must go down to the seas again, for the call of the running tide
Is a wild call and a clear call that may not be denied;
And all I ask is a windy day with the white clouds flying,
And the flung spray and the blown spume, and the sea-gulls crying.

I must go down to the seas again, to the vagrant gypsy life,
To the gull’s way and the whale’s way where the wind’s like a whetted knife;
And all I ask is a merry yarn from a laughing fellow-rover,
And quiet sleep and a sweet dream when the long trick’s over.

Wednesday, July 16, 2014

Ocean Beach

Posterior predictive checks to quantify lack-of-fit in ADMIXTURE models of latent population structure

David Mimno, David M Blei, Barbara E Engelhardt
submitted 30 Jun 2014
http://arxiv.org/abs/1407.0050

Abstract

Admixture models are a ubiquitous approach to capture latent population structure in genetic samples.  Despite the widespread application of admixture models, little thought has been devoted to the quality of the model fit or the accuracy of the estimates of parameters of interest for a particular study. Here we develop methods for validating admixture models based on posterior predictive checks (PPCs), a Bayesian method for assessing the quality of a statistical model. We develop PPCs for ve population-level statistics of interest: within-population genetic variation, background linkage disequilibrium, number of ancestral populations, between-population genetic variation, and the downstream use of admixture parameters to correct for population structure in association studies. Using PPCs, we evaluate the quality of the model estimates for four qualitatively different population genetic data sets: the POPRES European individuals, the HapMap phase 3 individuals, continental Indians, and African American individuals. We found that the same model fitted to different genomic studies resulted in highly study-specific results when evaluated using PPCs, illustrating the utility of PPCs for model-based analyses in large genomic studies.
 


 
 
 

Discussion

We have developed posterior predictive checks (PPCs) for analyzing genomic data sets with the admixture model. We have demonstrated that the PPC-|estimating the posterior predictive distribution and checking the likelihood of the true observed data under this distribution-|gives a valuable perspective on genetic data beyond statistical inference of model parameters. In the research literature, fitted admixture models are often accompanied by a 'just so' story to explain the inferred parameters and how they are reflective of ancestral truth [13]. The model may suggest these hypotheses, but only conditioned on the model being a good fit for the observed data. PPCs check this assumption of good fit, giving weight to the hypotheses by confirming that the underlying assumptions do not oversimplify the existing structure in the observed data.  In this paper, we developed PPCs for the admixture model, designing biological discrepancy functions to quantify the effect of the model assumptions on interpreting and using the estimated parameters for downstream analyses.

Statistical modeling of genetic data requires us to balance the complexity of the model with its capacity to capture the data at hand. As examples of limitations, we may not have enough data to support an overly complex model, or the model class that that we want to fit may be too complex given our computational constraints. Thus, we support the iterative practice of fitting the simplest model (i.e., the one we fit here), checking whether a higher resolution model is needed, and then improving the model only in the ways that result in more reliable interpretations of the results. PPCs can drive this process of targeted model development, pointing us towards enriched Bayesian admixture models along gradients that quantifiably improve their performance for the exploratory tasks that matter. With this practice in mind, we revisit the PPCs described above and discuss how we might enrich the simple admixture model to address its misspecified assumptions.

Many population studies have applied admixture models to explore and quantify genetic variation between individuals within and across ancestral populations [13,45,46]; these analyses may benefit from the inter-individual PPC. For studies where this PPC indicates misfit, prior work has adapted the admixture model to control admixture LD by explicitly modeling haplotype blocks for each ancestral population instead of modeling each SNP separately [30]. In particular, the SNP-specific ancestry assignment z variables for each individual are modeled by a Markov chain, where the probability of transitioning to a different ancestral population from one position to the next has an exponential distribution. This specifies a Poisson process describing the length of haplotype blocks across the chromosome, with global rate parameter r.

Many studies have noted that background LD may lead to phantom ancestral populations [37]; applying admixture models to genomic data that contain background LD may find the SNP autocorrelation PPC useful. After identifying model misspecification using our background LD discrepancy function, we could extend the admixture model to explicitly capture background LD. Above we described a Markov model on the z variables. It assumes that, conditional on ancestral population assignment, genotypes are independent. Extending this idea, SABER [47] implements a Markov hidden Markov (MHMM) model to capture both haplotype blocks and background LD by adding a Markov chain across the population-specific allele frequencies in beta.  Others have further extended this model in various ways, including estimating recombination events explicitly in the MHMM [48].

Methods and statistics have been proposed to evaluate the proper number of latent ancestral populations, often motivated by FST [6, 49]; additionally, nonparametric Bayesian models estimate the posterior probability for each K [50, 51]. We propose a PPC with the FST discrepancy for general use in evaluating appropriate ranges of the number of ancestral populations for a specific study. A simple adaptation of the model to correct for a failure of this PPC is to change the number of ancestral populations K (Figure S3).

There are also explicit model adaptations that will affect the FST of the inferred ancestral populations.  For example, one can build hierarchical models that allow the sharing of allele frequencies across populations for some SNPs; this was implemented in the structure 2.0 model, which includes a hierarchical component to allow similar allele frequencies across ancestral populations (the so-called F model) [30]. A second example is from the topic model literature (similar models applied to modeling text documents), where the ancestral populations are captured in a tree-structured hierarchy [52, 53].  In the corresponding admixture models, the root node would include SNPs that have shared allele frequencies across all ancestral populations; at the leaves, the population-specific allele frequencies would include SNPs that have a frequency in that population that is different than the frequency in all other ancestral populations (referred to as ancestry informative markers [20]).

Previous population studies have explored and interpreted the population-specific SNP frequencies estimated by admixture models [54-56]; almost all applications of this admixture model have used MAP estimates of ancestry assignments to determine the proportion of admixture in individuals [14, 20]. The average entropy PPC will check model misspecification for ancestry assignment, and has implications for interpreting estimates of SNP frequencies. To adapt the model to this misspecification, the hyperparameters for the Dirichlet-distributed allele-specific ancestry assignments may be changed. (We and others set to alpha = 1 [6], giving equal weight to all possible contribution across ancestries for each SNP.) In particular, we might give higher weight to admixture proportions near 0 and 1 by setting alpha < 1 for studies where we expect low levels of admixture (e.g., the HapMap data). The equivalent change for the hyperparameters in the population-specific allele frequency parameters would encourage for allele frequency spectrums that more closely match what we find in natural populations [57]. Another relevant model adaptation would be to modify the distribution of a SNP to be not Bernoulli but instead Poisson [58], normal [59], or something more sophisticated [60, 61]. We emphasize that, though these extensions seem reasonable, the PPC with this discrepancy found little need to modify the admixture model assumptions in our current studies. The exception to this point is the ASW study, although we hypothesize that correcting for background LD as suggested above will address this misspecification.

We believe that all model-based methods to control for population stratification in association mapping will benefit from application of the mapping PPC, including linear mixed models and non-generative methods such as EIGENSTRAT [2, 62]. Failure of the association mapping PPC indicates that the estimates of population structure are insuffi cient to correct for the confounding latent structure in the individuals. There are many directions to consider for mitigating this type of model misspecification.  As examples, one may use larger numbers of estimated principal components or ancestral populations, use alternative approaches to specifying the latent structure variables, or correct for structure that are estimated on local regions of the genome. This same discrepancy function - replacing z with the estimated random effect from linear mixed models - would be useful in quantifying model misspecification for these alternative methods for association mapping in the presence of confounding population structure [63-65].

Applied statisticians develop models to capture the biological complexity of their data. To form hypotheses from these models, however, we need assurances that the data can support them. PPCs provide a simple mechanism to quantify when a model is suffi cient or when it needs additional structure to support downstream analysis. While we have focused on the admixture model, the PPC methodology applies to any probabilistic model of data. For example, we believe there could be a substantial role for PPCs in evaluating demographic models. As we continue to collect complex genomic data, we continue to develop complex models to explain them. Equally important to building our repertoire of statistical models for analyzing genomic data is to build our repertoire of ways to check those analyses.

Tuesday, July 15, 2014

Arlington Man of the Channel Islands


    National Park Service
    (Link)

     "Arlington Springs Man lived at the end of the Pleistocene when the
     four northern Channel Islands were all still united together as one
     mega-island, and the climate was much cooler than today. The evidence
     that people had arrived on that island by 13,000 years ago demonstrates
     that watercraft were in use along the California coast at that early date
     and lends support for a theory that the earliest peoples to enter the
     Western Hemisphere may have migrated along the Pacific coast from
     Siberia and Alaska using boats. Recent radiocarbon dating by Dr. Larry
     Agenbroad of pygmy mammoth fossils from Santa Rosa Island suggests
     that the last of these unique mammals may have been present on the
     island at the time the first humans arrived."

The Pygmy Mammoths of the Channel Islands

 
   National Park Service
   (Link)
 
   "Found only on the California Channel Islands and nowhere
   else in the world, the pygmy mammoth was probably a small
   form of the Columbian mammoth found on the mainland.
   Pygmy mammoths varied from 4.5 to 7 feet high at the shoulders
   and may have weighed only about 2,000 pounds, compared to the
   14-foot tall, 20,000 pound Columbian mammoth. In other respects,
   they were probably similar, with short fur, a typical mammoth
   body form, and a relatively large head."

    Map showing the location of Sonora, Mexico, South western
    California and the Channel Islands of California.

Meet the gomphothere: Archaeologists discover bones of elephant ancestor

 
   Phys.org
   July 14th, 2014
   (Link)
 
   Archaeologists have discovered artifacts of the prehistoric Clovis
   culture mingled with the bones of two gomphotheres – an ancient
   ancestor of the elephant – at an archaeological site in northwestern
   Mexico [Sonora].
 
    Map showing the location of Sonora, Mexico, South western
    California and the Channel Islands of California

Monday, July 14, 2014

Why all medical professionals need to study evolution

Jonathan Eisen
Blog post
(Link)

Jonathan, great old post, which I'm "reblogging" here.  I'd say that not only medical professionals, but also members of the public at large would greatly benefit from a better understanding of evolution and phylogenomics.  In addition to your list, a better understanding of these would help us comprehend the challenges we are facing with the environment.

I would also say that, esthetically, an understanding of phylogeny can be a source of personal enjoyment.

My Dad was a forestry major and later, a professor of forestry.  Because of this, he knew many of the phylogenic names of the plants, animals and insects of the British Columbia and Alberta forests.  When I was old enough, he would take me tree seedling specimen collecting in the Coast Ranges of British Columbia and also in the Canadian Rockies.  He was a fast walker and as a girl, I could hardly keep up with him.  He could name off the phylogenic names of these tree seedlings and understood whole ecosystems . . . he would describe the watershed, precipitation, temperature and elevation zones for trees and grasslands.  To me, there seemed to be more meaning when you could see the whole picture of plants in a forest or grassland zone.

He loved bugs.  When we lived in Ghana, he trapped, collected and pinned hundreds of insects.  Many of them were huge, exotic and fantastically colored.

Another passion was growing colorful flowers.  Foxglove (Digitalis purpurea) was a favourite.  He spent many summers collecting their seeds, trying to see how tall he could make them.  Other treasures were California poppy (Eschscholzia californica) and Clarkia.  Dahlias, too.

His father was the chief beef inspector for the government of Alberta for many years, so my Dad also knew a lot about livestock genetics.  I remember him taking me to agricultural fairs, including the Calgary Stampede.  Cows and pigs are quite interesting animals.

So . . . esthetically, as a way to appreciating plants and insects in the natural world, and even farm animals, it is tremendously enriching to understand phylogeny.

Sunday, July 13, 2014

RIP for a key Homo species?

Michael Balter
Science

Vol. 345 no. 6193 p. 129
DOI: 10.1126/science.345.6193.129   
(Link)
                     
Blog note:  If you don't have institutional access to Science, you can purchase the full text of this article for one day for $20 (yes, quite expensive for non-institutional access!)  In any case, here's the second half of the article, which concerns a concise synopsis of the current and still undecided status of the Homo species H. heidelbergensis:

"H. heidelbergensis has a history of controversy. The species is based on a single lower jaw found in 1907 at Mauer, near Heidelberg, in Germany. Estimated at about 600,000 years old, the jaw has an unusually thick ramus—the vertical projection that hinges to the skull—and nothing quite like it has been found since. For decades, the name failed to catch on, until anthropologists including Rightmire and Chris Stringer of the Natural History Museum in London noted distinctive thick brow ridges and large faces in skulls of roughly similar age from sites including Arago; Petralona in Greece; Broken Hill in Zambia; Yunxian in China; and Bodo in Ethiopia. All of these skulls also housed much larger brains than H. erectus, about 1200 cubic centimeters, within range of modern human brains, which average about 1400 cc. (Neandertal brains may be slightly larger.)

"In the 1970s, Stringer and others postulated a single species spanning Europe, Africa, and Asia, and resurrected the H. heidelbergensis name to describe it. The species' larger brain was reflected in the complex tools attributed to it, such as wooden spears at Schöningen in Germany (Science, 6 June, p. 1080).
                 
"Some researchers were skeptical, arguing that the African fossils were a separate species called H. rhodesiensis, which led to our ancestors. H. heidelbergensis got a big boost when researchers working at the site of Sima de los Huesos in Spain attached the name to the remains of 28 hominins found there. But in a paper last month in Science (20 June, p. 1358), the Sima team, led by Juan Luis Arsuaga of the Complutense University of Madrid, argued that these 430,000-year-old hominins were more closely related to Neandertals and don't belong in H. heidelbergensis.

"At the meeting, Arsuaga went a big step further and proposed eliminating H. heidelbergensis altogether. He argued that the Mauer jaw, the type specimen on which the species is based, cannot be closely matched with any other fossil, in part because few other jaws are preserved. To keep the species alive, researchers need to find and designate a new type specimen that has both a jaw and skull, but such a specimen would surely spark new debates, Arsuaga said. The better course “would be to let the species die.”
                 
"Anthropologist Yoel Rak of Tel Aviv University in Israel supported this argument by comparing the Mauer jaw with the few jaws claimed to be H. heidelbergensis fossils, including three partial jaws from Arago. “The Mauer specimen is one of a kind,” Rak concluded in his talk.
                 
"But others fought vigorously to save both the species and the simpler, more straightforward view of human evolution that it represents. Rightmire analyzed 34 H. erectus and 11 potential H. heidelbergensis skulls, and found that their similarities—including massive brow ridges, large faces, and flattened frontal bones—stemmed from true relatedness, rather than convergent evolution. “Calling them H. heidelbergensis is the correct position,” he said.
                 
"And paleoanthropologist Ian Tattersall of the American Museum of Natural History in New York City argued that the Mauer jaw isn't so singular after all: He found close affinities between it and the Arago jaws, especially in the teeth. Specimens from Arago preserve both the face and jaws, Tattersall notes, and the face resembles those of other claimed members of H. heidelbergensis, thus completing the link between the type specimen and skulls from several continents.
                 
"New fossils from this mysterious time period would help. At the meeting, paleontologist Berhane Asfaw of the Rift Valley Research Service in Addis Ababa offered a rare glimpse of new finds from Ethiopia's Middle Awash region. His team has found partial skulls and jaws from 32 hominin individuals, roughly dated by animal bones to 300,000 years ago. These as-yet-unpublished fossils may link the Bodo skull from Ethiopia, which resembles Arago, and modern human skulls from the Middle Awash site of Herto. Expect fresh debate when these key fossils make it into print."

Saturday, July 12, 2014

Culture-Genetic Models of Information Exchange in Humans: Integrating Genetic, Skeletal and Archaeological Data

Marc Kissel
PhD Thesis
(Advisor:  John Hawks)
University of Wisconsin-Madison
2014
(Link)

Abstract

Here, I test a model that attempts to explain the low genetic diversity and low effective population size of Homo sapiens though a model of Culturally Mediated Migration (CMM). This model posits that human genetic diversity has been reduced throughout the Pleistocene by an interaction of culture and gene flow. According to the CMM model, humans inevitably develop cultural practices that reduce gene flow between culturally different groups. In this restricted gene flow population, natural selection cannot spread favorable genes by simple diffusion across populations. Instead, favorable genes spread when the populations that carry them expand; displacing or replacing other populations. This process may reduce genetic diversity across the genome as a function of the successive replacements of most ancient populations. However, the model is untested. I derive expectations as to how the anthropological data (osteological, genetic, ethnographic, and archaeological) should be pattern if CMM is an accurate depiction for human behavior. I show that the archaeological data is patterned in the expected way: information follows between populations in ways expected based upon mediated migration. However, neither the skeletal data, the ethnographic, nor the genetic results support the tested hypothesis. I further investigate the force of natural selection in Neandertal populations, to assess the extent to which morphological characters may inform about ancient population sizes as opposed to natural selection. Models predicated on effective population size often misuse this genetic parameter. I further demonstrate that any model that limits the power of natural selection is inherently flawed, as Neandertals were subjected to this force to a greater extent than is often realized. This study uses multiple lines of anthropological data to test a genetic model of human evolution. Low human genetic diversity is symptomatic of the early human population as a whole and models explicating this genetic anomaly must take into account all of these factors. I show that information (both genetic and cultural) moved between regional populations to a greater degree than often recognized.

Friday, July 11, 2014

The open-air site of Tolbor 16 (Northern Mongolia): Preliminary results and perspectives

Nicolas Zwyns, Sergei A. Gladyshev, Biamba Gunchinsuren, Tsedendorj Bolorbat, Damien Flas, Tamara Dogandsic, Andrei V. Tabarev, J. Christopher Gillam, Arina M. Khatsenovich, Shannon McPherron, Davakhuu Odsuren, Cleantha H. Paine, Khovor-Erdene Purevjal, John R. Stewart

Quaternary International xxx (2014) (in press)
(Link) open access

Abstract

Numerous questions remain regarding the timing and the context of Upper Paleolithic emergence inNortheast Asia. Available data allow the recognition of a form of Initial Upper Paleolithic (IUP) docu-mented in the Altai circa 45-40 ka 14C BP, and in the Cis- and Transbaikal around -37 ka 14C BP. In Northern Mongolia, a series of assemblages show intriguing similarities with IUP laminar assemblages from South Siberia and suggest long distance contact/movements of population during the first half of MIS3. These contacts are potentially enabled by the main river that drains into Lake Baikal, the Selenga.  By cutting through the Sayan and the Yablonovy mountain ranges, the Selenga drainage system provides a potential corridor connecting South Siberia with the plains of Mongolia. The Tolbor 16 site (Ikh Tulberiin Gol, Northern Mongolia) is located circa 13 km from the confluence with the Selenga. The first results presented here suggest that the lithic assemblage and the ornaments discovered at Tolbor 16 document the early appearance of Upper Paleolithic in the region. This newly discovered site offers the possibility to generate high-resolution contextual data on the first appearance of the blade Mongolia and to test the ‘Selenga corridor hypothesis’.


 

The timing of ostrich existence in Central Asia: AMS C14 Age of Eggshells from Mongolia and southern Siberia (a pilot study)

Evgeny N. Kurochkin, Yaroslav V. Kuzmin, Igor V. Antoshchenko-Olenev, Vladimir I. Zabelin, Sergey K. Krivonogov, Tatiana I. Nohrina, Ludmila V. Lbova, G.S. Burr, Richard J. Cruz

Nuclear Instruments and Methods in Physics Research B 268 (2010) 1091–1093
Available online 7 October 2009
(Link) open access

Abstract

The presence of Asiatic ostrich in Central Asia in the later Cenozoic time is well-documented; nevertheless, few direct age determinations existed until recently. We performed AMS C14 dating of ostrich egg-shells found in Mongolia, Transbaikal, and Tuva. It shows that ostriches existed throughout the second part of Late Pleistocene, until the Late Glacial time (ca. 13,000–10,100 BP). It seems that Asiatic ostrich went extinct in Central Asia just before or even in the Holocene.

Related Posts:

The open-air site of Tolbor 16 (Northern Mongolia): Preliminary results and perspectives

Ostriches

Ostriches



Related Posts

The timing of ostrich existence in Central Asia: AMS C14 Age of Eggshells from Mongolia and southern Siberia (a pilot study)

The open-air site of Tolbor 16 (Northern Mongolia): Preliminary results and perspectives

Nomads of South Siberia: the pastoral economies of Tuva: HUNTING TECHNIQUES

Pipes and Hunting Calls of the South Siberian Tuva

The Case for Low Frequency Sound Production by Palaeolithic Hunters as an Aid to Mammoth Hunting

Karkur Talh: Addax, Ostrich, Wild Dog, Gazelle

Karkur Talh: Archers, Ostriches, Giraffes, Bovids, Dogs, Oryx

Karkur Talh:  An Ancient Cattle Trail

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Karkur Talh Rock Art

Wednesday, July 9, 2014

The atlas of King George

A 250-year-old promise to indigenous peoples still binds

The Economist
July 5th, 2014
(Link)

WHEN King George III proclaimed in 1763 that Canada’s indigenous peoples had rights to their ancestral lands, it bought peace with the locals who outnumbered and sometimes outfought the British colonists. But as the balance of inhabitants shifted—indigenous people now account for only 4.3% of the population—governments took an increasingly narrow view of that promise. In some cases they ignored it completely. On June 26th the Supreme Court of Canada provided a sharp reminder that King George’s word is still law.

(read more)

Stuff of Fairy Tales: Stepping into Europes Last Old Growth Forest

Jeremy Hance
mongabay.com
July 09, 2014
tweeted by Nicki Whitehouse
(Link) to story.

This is an amazing article about old growth forest in Poland.  Elk, bison and wolves still are endemic.

Tuesday, July 8, 2014

"Dance Of Human Evolution Was Herky-Jerky, Fossils Suggest" (NPR's Morning Edition)

 
Christopher Joyce (interviewer)
NPR's Morning Edition
July 4th, 2014
(Link) audio and transcript

Evolution of early Homo: An integrated biological perspective

Susan C. Antón, Richard Potts, Leslie C. Aiello
Science 4 July 2014:
Vol. 345 no. 6192
DOI: 10.1126/science.1236828
(Link)

Abstract

Integration of evidence over the past decade has revised understandings about the major adaptations underlying the origin and early evolution of the genus Homo. Many features associated with Homo sapiens, including our large linear bodies, elongated hind limbs, large energy-expensive brains, reduced sexual dimorphism, increased carnivory, and unique life history traits, were once thought to have evolved near the origin of the genus in response to heightened aridity and open habitats in Africa. However, recent analyses of fossil, archaeological, and environmental data indicate that such traits did not arise as a single package. Instead, some arose substantially earlier and some later than previously thought. From ~2.5 to 1.5 million years ago, three lineages of early Homo evolved in a context of habitat instability and fragmentation on seasonal, intergenerational, and evolutionary time scales. These contexts gave a selective advantage to traits, such as dietary flexibility and larger body size, that facilitated survival in shifting environments.

Introduction [quoting from the paper]

The evolution of the genus Homo has long been linked to the onset of African aridity, and the evolution of key features such as increased carnivory, brain enlargement, long-distance mobility, and prolonged life history. These features have been explained as a response to the progressive expansion of open, grassland habitats (1, 2). However, new environmental data challenge this interpretation, and archaeological research has identified behaviors in early toolmakers that aided flexible responses to dynamic environments (3, 4). Furthermore, comparative studies of mammalian development, energetics, ecology, and behavior offer new interpretive models. In this context, new fossils have also expanded the known range of morphological variation, raising questions about the number of species of early Homo and the distinction between inter- and intraspecific adaptations (5, 6, 7, 8, 9, 10).
                 
The East African fossil record continues to command much attention because of a unique combination of factors. The history of East African rift volcanism enables precise geochronological analyses through long stratigraphic sequences rich in fossil and archaeological remains. The temporal sequence of morphological and behavioral innovations in early Homo is thus more finely resolved in East Africa than elsewhere. Environmental indicators can also be measured in lengthy stratigraphic order, enabling researchers to assess climate and habitat dynamics at a variety of time scales rather than relying on more limited environmental snapshots or broadly time-averaged portraits of the environment. Uncertainties over stratigraphic correlation and dating have arisen that directly affect an understanding of early Homo, yet East African rift basins typically offer opportunities to resolve the geological debates [e.g., (11, 12)]. Beyond this region, important recent finds pertinent to the evolution of Homo have been made at Malapa, South Africa (6, 7, 9, 13), and Dmanisi, Georgia (8), which expand how hominin morphological variation and the dispersal of early Homo beyond Africa are understood. This review begins with a focus on morphological variation and environmental dynamics because these topics have strongly affected analyses of the adaptive shifts distinctive to early Homo (Fig. 1). [below]

Fig. 1   Hominin evolution, diet, landscape vegetation, and climate dynamics from 3.0 to 1.5 Ma.
(A) Currently known species temporal ranges for Pa, Paranthropus aethiopicus; Pb, P. boisei; Pr, P. robustus; Aafr, Australopithecus africanus; Ag, A. garhi; As, A. sediba; H sp., early Homo > 2.1 Ma; 1470 and 1813 groups, see text for definitions (traditionally classified as H. rudolfensis and H. habilis, respectively); and He, H. erectus. The temporal position of Dmanisi H. erectus, He (D), is indicated. (B) Icons representing the first appearance of (from bottom) Oldowan technology (~2.6 Ma), Homo dispersal to Eurasia (~1.85 Ma), and Acheulean technology (~1.76 Ma). Horizontal pale green lines mark these times across (A) to (D). (C) Homo tooth δ13C. Carbon isotopic values measured on tooth enamel of East African specimens assigned to Homo and P. boisei (21); the mean and range of dental δ13C for A. africanus is also shown (22). (D) East African paleosol δ13C: compilation of δ13C values for East African fossil soil carbonates [data compiled in (74)]. Values range from those typical of woodland (40 to 80% woody cover) to wooded grassland (10 to 40% woody cover) to grassland (0 to 10% woody cover). Woody cover estimates based on (2). (E) Climate variability. Alternating intervals of high (lighter color bands) and low (darker color bands) climate variability based on predicted insolation resulting from the modulation of orbital precession by eccentricity, where low variability is defined by eccentricity ε ≤ 0.0145, (i.e., 1 SD below mean ε for the past 5 million years) (67). White circles show the standard deviations for terrigenous dust flux values at Ocean Drilling Project sites 721 and 722, western Arabian Sea (64, 69). Change between eolian dust standard deviations (adjacent white circles) follows the predicted direction between alternating high (larger SD, further to the right) and low (smaller SD, further to the left) climate variability for 13 of the 16 variability transitions. For example, the large SD in the two predicted high climate variability intervals, 2.79 to 2.47 and 2.37 to 2.08 Ma, is further to the right of the plot than is the intervening small SD in the predicted low-variability interval 2.47 to 2.37 Ma.


[ Body of the paper (blog comments):

The body of the paper includes sections "Who was early Homo?", "Environmental instability as an evolutionary paradigm", and "The paleobiology of early Homo" . These sections are important toward understanding the conclusions of the paper.  However, as the paper is currently not open access, I have not included them here.

There are also two important "box" discussions in the body of the paper:

Box 1: Anatomical features of early Homo groups (which details the methods used to classify the 1470 and 1813 groups, and early H. erectus discussed in Figure 1), and

Box 2:  Sympathry and niche partitioning in early Homo.

Key points from the box discussions:

Box 1: Anatomical features of early Homo groups: "Key members of Early H. erectus are from Africa and Georgia: crania and calvaria KNM-ER 3733, KNM-ER 3883, and KNM-ER 42700, OH 9, and Dmanisi 2280; crania and associated mandibles Dmanisi 2282/211, 2700/2735, and 3444/3900; crania and associated postcrania KNM-ER 1808 and 15000."

Box 2: Sympathry and niche partitioning in early Homo:  "carbon isotopic values for teeth of broadly sympatric representatives of early Homo in the Turkana Basin, Kenya (~1.99 to 1.46 Ma), call into question the idea that tool use precludes niche differentiation."

] (end of blog comments)


Conclusion: New frameworks and unresolved questions
[quoting from the paper]

A suite of morphological and behavioral traits once considered to define the origin of the genus Homo or of earliest H. erectus evolved not as an integrated package but over a prolonged time frame that encompassed species of Australopithecus, early Homo, H. erectus, and later Homo. The idea of an integrated package of traits in early Homo has been thought to anticipate the adaptive characteristics of H. sapiens and to include reduced face and teeth, a substantial increase in brain size, body proportions characterized by an elongated hind limb and shortened forelimb, essentially modern hand functional morphology, dependence on toolmaking and culture with incipient language capabilities, dietary expansion, persistent carnivory and systematic hunting, narrow hips with implications for the birth of altricial young, prolonged life history compared with extant apes, and cooperative food-sharing focused at a home base (15, 122, 123, 124, 125). New fossil and archaeological data summarized here allow refined perspectives on the morphological variation and pacing of evolutionary change in the Homo clade. These empirical findings, coupled with interpretive models drawn from developmental and comparative biology and behavioral ecology, now require the disentangling of this package of traits (Fig. 3). [below]


Fig. 3. Evolutionary timeline of important anatomical, behavioral, and life history characteristics that were once thought to be associated with the origin of the genus Homo or earliest H. erectus.

An important, continuing goal is to develop a more refined understanding of exactly what adaptive features did originate with early Homo. According to present data, facial and dental reduction defines the earliest members of the genus between 2.4 and 2.0 Ma. Cranial capacity expanded by 2.0 Ma. A greater yet varied degree of brain enlargement correlated with body size increase is expressed in early H. erectus between 1.9 and 1.5 Ma, although estimates of the degree of encephalization overlap with those of Australopithecus. However, brain expansion independent of body size appears to be most strongly expressed later, between 800 and 200 thousand years ago. A relatively elongated hind limb is present in A. afarensis (by 3.9 Ma) and in later Australopithecus (A. africanus, A. garhi, and A. sediba) but not in Ardipithecus (4.4 Ma). Absolutely longer and strongly built femora evolved between 1.9 and 1.5 Ma, coinciding with early H. erectus. Stone technology at ~2.6 Ma may predate the origin of Homo, whereas cultural capabilities of the early Pleistocene led to highly persistent traditions of toolmaking rather than an innovative, cumulative culture linked to symbolic behavior typical of the latter part of the Pleistocene. Transversely oriented hips and a broad pelvis persisted until H. sapiens, although a brain consistently >700 cm3, which occurred after ~1.8 Ma, connotes altricial neonates and heightened cooperation among H. erectus adults. Based on first molar dental histology and eruption, the tempo of life history was slower in H. erectus than in Australopithecus yet was similar to that of extant great apes. Far more prolonged phasing of growth typical of H. sapiens, with implications for intensive social cooperation, is evident in the middle Pleistocene, which is also when definitive evidence of hearths and shelters occurs in the archaeological record, implying strong centrally located social cooperation. The traits associated with the origin of Homo and of H. erectus thus evidently did not approximate the integrated complex of adaptations found in H. sapiens.

The evolution of early Homo, moreover, was associated with recurrent periods of intensified moist-dry variability (Fig. 1E). Dynamic environments favored evolutionary experimentation and the coupling and uncoupling of biological variables (71, 126), which governed against any simple transition from Australopithecus to Homo. We maintain that the East African record to date preserves three distinct taxa of early Homo, including H. erectus, although the issues that arise from recent discoveries elsewhere at Malapa and Dmanisi hint at the intriguing shuffling of derived and plesiomorphic traits and biological variables that likely characterized the early evolution of Homo.

Developmental plasticity and ecological versatility were at a premium in the habitats in which early Homo evolved. Although plasticity across biological levels (molecular to behavioral) was favored in dynamic habitats, both extrinsic (e.g., environmental) factors as well as biological and social feedback mechanisms were complexly entwined in the evolution of Homo and can no longer stand as alternative explanatory hypotheses (4, 61). Understanding the processes by which adaptability evolved in Homo and exactly how various traits contributed to plasticity during the evolution of the genus are important future challenges.

Critical foci for future research on the paleobiology of early Homo are numerous. To cite four examples, first, the field is always well served by new fossil and archaeological finds. Larger fossil samples between 2.5 and 1.5 Ma will be necessary to assess the taxonomic diversity of early Homo and to determine the temporal and spatial integrity of the morphological groups. Second, comparative mammalian studies focused on population structure, genetic isolation, niche differentiation, and the variables enabling the coexistence of congeneric taxa will help build more effective models for understanding morphological groups and diversity in early Homo. Third, much remains to be learned about encephalization in early Homo, the degree of plasticity in body and brain size, and how these variables were related to paleoenvironmental variables (e.g., shifting resource abundance). Last, interpretations concerning early Homo rely on the comparative biology of a wide range of mammals (including humans) in order to test and develop robust models of the intricate relationships between energetics, life history, brain and body size, diet, mortality, and resource variability across temporal and spatial scales. A refined understanding of these relationships will enable the union of many disciplines to yield a deeper understanding of human evolution.

Thursday, July 3, 2014

Smithsonian Scientist and Collaborators Revise Timeline of Human Origins

New Synthesis of Research Links Changing Environment with Homo’s Evolutionary Adaptability

Richard Potts, Smithsonian
Susan Antón, New York University
Leslie Aiello, Wenner-Gren Foundation for Anthropological Research
News Release
July 3, 2014
(Link)

Many traits unique to humans were long thought to have originated in the genus Homo between 2.4 and 1.8 million years ago in Africa. Although scientists have recognized these characteristics for decades, they are reconsidering the true evolutionary factors that drove them.

A large brain, long legs, the ability to craft tools and prolonged maturation periods were all thought to have evolved together at the start of the Homo lineage as African grasslands expanded and Earth’s climate became cooler and drier. However, new climate and fossil evidence analyzed by a team of researchers, including Smithsonian paleoanthropologist Richard Potts, Susan Antón, professor of anthropology at New York University, and Leslie Aiello, president of the Wenner-Gren Foundation for Anthropological Research, suggests that these traits did not arise as a single package. Rather, several key ingredients once thought to define Homo evolved in earlier Australopithecus ancestors between 3 and 4 million years ago, while others emerged significantly later.

(read more)