This is the seventh school of a biennial series of international summer schools on mathematical ecology and evolution in Finland, organised by the Biomathematics Group of the University of Helsinki. The series of The Helsinki Summer School on Mathematical Ecology and Evolution is part of the EMS-ESMTB Schools in Applied Mathematics.

After the two-year break forced upon by the pandemic, we are looking forward to continue this series in August 2022, if only the covid situation permits.

The job description: "This research position focuses on the science
of bacterial evolution. It will consist of researching theoretical
principles, but could include translational applications. Phylogenomic
and bioinformatic analysis of bacterial populations in nature or
in laboratory experiments will be a key component of the work. Prior
experience is an asset though training will be possible at PMI.
Likewise, laboratory microbiological, molecular, and biochemical
skills are an asset though not essential. Communication and critical
thinking skills are essential for performing the work and for
communicating to the local and international scientific communities.
Participating in team or independent grant writing to obtain research
funding will be required. Student mentoring is a part of the NAU
mission and is a partial expectation."

https://hr.peoplesoft.nau.edu/psp/ph92prta/EMPLOYEE/HRMS/c/HRS_HRAM.HRS_APP_SCHJOB.GBL?Page=HRS_APP_JBPST&Action=U&FOCUS=Applicant&SiteId=1&JobOpeningId=608024&PostingSeq=1

Northern Arizona University is located in Flagstaff, Arizona, a
beautiful mountain town with a surprisingly vibrant restaurant
scene. Located a little over an hour from the Grand Canyon and ~45
min from Sedona, Flagstaff is a hiker's paradise. In fact, the city
of Flagstaff operates more than 50 miles of unpaved trails and there
are, on average, 266 sunny days per year with which to enjoy them.
At 7000 ft in elevation, Flagstaff experiences all four seasons,
but thesummers are mild and, in the winter, you can be on the ski
slopes within 30 min! https://www.flagstaffarizona.org/

As mentioned, joint projects with Professor Sheppard at Oxford
University are possible, including travel to his laboratory in the
United Kingdom. https://www.biology.ox.ac.uk/people/samuel-sheppard

Contact Information:
Paul.Keim@nau.edu

Paul S. Keim, Ph.D.
Regents Professor, &
Cowden Endowed Chair of Microbiology
Northern Arizona University
Flagstaff, AZ 86011-4073

Paul S Keim

The bones sat quietly in a fossil collection for years. One was part of a femur; the other, a tibia. They looked like the remains of an unusually large ancient human. But who did they belong to?

The answer came from an unexpected source: ancient proteins.

Using palaeoproteomic analysis, researchers found a molecular signature in both bones that matches the Denisovan lineage. The discovery identifies the two Penghu fossils as Denisovan and, more importantly, gives scientists their first substantial glimpse of the Denisovans' body size.

And the picture is striking.

One individual is estimated to have been about 1.8 metres tall and weighed around 83 kilograms. The other may have reached 1.9 metres and about 91 kilograms. Their leg bones rank among the largest known from Pleistocene Homo.

These were not small or fragile people.

They were powerful, heavily built humans moving through Ice Age eastern Asia.

But the bones tell an even more intriguing story. The femur has a pronounced ridge called a femoral pilaster—a feature particularly associated with modern human hunter-gatherers and increased mechanical strength during terrestrial movement. Why would a Denisovan, with an otherwise strongly archaic skeleton, possess this modern-looking feature?

Perhaps these Denisovans travelled extensively across the landscape. Perhaps their bodies were shaped by a demanding hunting lifestyle. Or perhaps, the researchers suggest, genetic exchange with early modern humans contributed to some of these features.

Their extraordinary size raises another mystery. A common expectation in human evolution is that populations living closer to the tropics tend to be smaller. Yet these Denisovans lived around 23°N latitude and were exceptionally large. The researchers argue that cold climate alone cannot explain their size, pointing instead toward lifestyle and diet—including evidence that at least one Penghu individual relied heavily on meat.

So, piece by piece, the Denisovans are becoming less mysterious.

What was once a shadowy population known mainly from DNA is beginning to take physical form: large, robust, mobile humans who lived across eastern Asia and whose bodies carried a fascinating mixture of ancient and modern traits.

And perhaps the most remarkable part of this story is where it began—not in a spectacular cave discovery, but with two weathered bones lying among thousands of fossils.

The Denisovans may have left no written history. But their bones are beginning to tell one.

*Note: This research is currently a bioRxiv preprint and has not yet undergone peer review.  Detail at https://www.biorxiv.org/content/10.64898/2026.08.07.743438v1.full.pdf

More @ http://www.ncbs.res.in/sowdhamini/groups_sowdhamini.htm

Address of the bookmark: https://sourceforge.net/projects/mimicree2/

Daniel A Dalquen, Maria Anisimova, Gaston H Gonnet, Christophe Dessimoz: ALF - A Simulation Framework for Genome Evolution. Mol Biol Evol, 29(4):1115-1123, April 2012.
http://mbe.oxfordjournals.org/content/29/4/1115

Address of the bookmark: http://alfsim.org/#index

Once a query gene has been entered, it is displayed in its genomic context in parallel to the genomic context of all its orthologous and paralogous copies in all the other sequenced metazoan genomes. Moreover, Genomicus stores and displays the predicted ancestral genome structure in all the ancestral species within the phylogenetic range of interest.

All the data on extant species displayed in this browser are from Ensembl.

Summary statistics of Genomicus version 105.01: (view species tree in pdf or newick)

Address of the bookmark: https://www.genomicus.bio.ens.psl.eu/genomicus-105.01/cgi-bin/search.pl

Key Findings of the Study:

1. Alu Insertion and Tail Loss:
   The researchers discovered an Alu-mediated genetic change in a common ancestor of modern apes and humans. This change disrupted the normal function of a gene involved in tail development, leading to the suppression of tail formation.

2. Gene Disruption Mechanism:
   The Alu insertion was found within a regulatory region of the TBXT gene (also known as T or Brachyury), which is crucial for tail development in vertebrates. This insertion likely altered the gene's expression patterns, leading to tail reduction over evolutionary time.

3. Functional Evidence from Model Organisms:
   To test their hypothesis, the researchers introduced similar genetic modifications in mice. The modified mice exhibited shortened or absent tails, supporting the idea that the identified mutation played a role in tail loss in hominoids.

4. Evolutionary Implications:
   The findings suggest that small, random genomic changes—such as transposable element insertions—can have profound effects on body morphology. This study provides evidence that mobile DNA elements (like Alu) can drive major evolutionary transitions.

5. Relevance to Human Evolution:
   Understanding the genetic basis of tail loss helps in reconstructing the evolutionary history of hominins (the lineage that includes humans and our extinct relatives). It also sheds light on how genetic variations contribute to anatomical diversity among primates.

Significance of the Study:

This research highlights the role of transposable elements in shaping evolutionary traits and provides a concrete genetic explanation for a defining characteristic of humans and great apes. It also demonstrates how mutations in regulatory regions of developmental genes can lead to significant anatomical changes.

Link:

http://www.nytimes.com/2013/11/21/science/two-surprises-in-dna-of-boy-found-buried-in-siberia.html?_r=0

http://www.nature.com/nature/journal/vaop/ncurrent/full/nature12736.html