Skiing in the French Alps

I have just spent a week skiing in the French Alps with my younger son. We stayed in a chalet above the village of Les Gets in Les Portes du Soleil ski doman (the Gates of the Sun). Normally the snow is down to the village, but this February is the warmest I have experienced since I have lived in Geneva and the snow did not extend much lower than our chalet. Fortunately it snowed quite a bit after we arrived, and there was plenty of fresh powder for skiing. And enough to ski back to our chalet at the end of the day.

View from our chalet

Another view from the chalet after the snowfall

My son is now a better skier than me and he spent a lot of time off-piste on the very steep moountain slope behind him (the one in shadow).

He also likes to jump and get some air under his skis.

From the higher ridges above Les Gets are some great views towards Chamonix and the high Alps of the Mont Blanc region. Towards the mid-left of the skyline in the photo below are the Grandes Jorasses (4208m). The Aiguille du Midi (3842m) is on the skyline to the right of centre, it is the prominent spire. There is a cable car from Chamonix up to the top of the Aiguille du Midi which has spectacular views of the Mont Blanc massif. To the right of the Aiguille are Mont Blanc du Tacul (4248m) and Mont Maudit (4465m). Mont Blanc itself is to the right of this photo, and can be seen in the following photo.

View towards Chamonix and the Mont Blanc region.

The Mont Blanc massif.

Mont Blanc is centre right in the photo above. On the left skyline is the Aiguille du Midi. To the right of Mont Maudit is the main peak of Mont Blanc (4810m). Below Mont Blanc to its right are the Dome du Gouter (4305m) and below that is the Gouter Ridge.

A closer view of the Aiguille and the Arête des Cosmiques

The narrow ridge running down from the Aiguille du Midi to the right is the Arête des Cosmiques. This was the most technically challenging of the Alpine climbing trips I have done  (see my earlier post (arete-des-cosmiques).

A closer view of Mont Blanc

Using the telephoto lens, I got a very nice shot of the Gouter route to the summit of Mont Blanc. This was the route by which I climbed Mont Blanc in 2010 (mont-blanc). To the very right of the photo is the steep rocky Gouter Ridge. This is the most dangerous part of the climb as there are often rock falls and there is usually one or two deaths a year from rock falls on the Gouter Ridge. When we were descending it in the afternoon we kept out of the gullies and at one point several very large boulders fell down the gully beside us, barely missing some climbers lower down.  Above the Gouter Ridge is theDome du Gouter (4305m) and behind it leading up to the left is the summit ridge to the top. The other popular route is from the Aiguille du Midi across Mont Blanc du Tacul (4248m) and Mont Maudit (4465m) to Mont Blanc summit at 4810m (the Three Mont Blancs route).

View across Les Gets valley to Mont Chérie.

Heading down as the sun gets low.

 

Our Asgardian ancestors

I grew up reading northern European myths and legends, including tales of Odin, Thor, and the other gods of Asgard. I was largely unaware of the Marvel comics appropriation of Thor and other Asgardians as superheros until the Marvel cinematic universe started to hit the big screens in the last 12 years.

Loki, Thor and Odin (from the Marvel Cinematic Universe)

I have only recently come across the growing evidence that an Asgardian was one of our ancestors, way back near the beginning of the evolution of life, when the first eukaryotic cell appeared. Eukaryotes are organisms whose cells contain membrane-wrapped internal structures, such as a nucleus, unlike prokaryotes (Bacteria and Archaea), which have no membrane-bound internal structures.

In an earlier post on mitochondrial DNA, I mentioned that the mitochondria are thought to have arisen when a primitive cell incorporated a bacteria inside it. Increasing evidence is being found to suggest that an Asgardian was responsible for this. Mitochondria have a separate circular ring of DNA, like bacteria, which is separate to the nuclear DNA comprising the chromosomes.

Fifty years ago, scientists split life on Earth into two categories: eukaryotes; and prokaryotes, single-celled organisms that generally lack internal membranes. Bacteria were the only prokaryotes that biologists knew about. Then, in 1977, evolutionary biologist Carl Woese and his colleagues described archaea as a third, distinct form of life — one that reached back billions of years. Archaea are also prokaryotes that are somewhat like bacteria, in that they lack nuclei and membrane-bound organelles, and get around using flagella. But there are a few key differences. They divide differently. Their cell walls are made of slightly different stuff. And their RNA is different enough to separate them on the phylogenetic tree. Archaea are able to survive in very harsh environments, such as those found in undersea volcanic vents, and to derive energy from hydrocarbons such as methane or butane.

In 2015, A Spang and colleagues [1] recovered several unusual Archaea from the sea floor near a “black smoker” hydrothermal vent between Greenland and Norway. This vent field had been discovered seven years earlier and had been named Loki’s Castle as its shape reminded its discoverers of a fantasy castle. Loki is the trickster god of Norse mythology, son of the giant Farbauti [2]. He is a friend of Thor and the blood brother of Odin, not the adopted son of Odin as in the Marvel Cinematic Universe.

Loki’s Castle, the field of deep sea vents between Norway and Greenland, is home to sediments containing DNA from the newly discovered archaea.

The unusual archaea discovered near Loki’s Castle were named Lokiarchaeota and share several genetic features with us, the Eukaryotes. DNA analysis of these organisms suggests that modern eukaryotes belong to the same archaeal group. According to Spang and colleagues, the ancestor of the Asgard archaea probably fed on carbon-based molecules, such as methane and butane. This diet would have generated byproducts that could nourish partner bacteria. Such food-sharing agreements — common among microbes — could have evolved into a more intimate relationship. An archaeon might have snuggled up next to its bacterial partner to ease nutrient exchanges, leading eventually to the ultimate embrace.

This has been an area of controversy and sometimes bitter argument, but I will review recent evidence below that indeed suggests we are descendants of ancient Asgardian archaea.  In the five years since the discovery of the Lokiarchaeota, several other archaea were discovered that had eukaryotic characteristics [3]. These archaea were named after other Norse gods: Thorarchaeota, Odinarchaeota and Heimdallarchaeota. The entire grouping of new phyla was named Asgard after the realm of the Norse gods. When these Asgardian gods are included in the tree of life, eukaryotes do not cluster anymore as a separate domain. Instead, they fall within the domain of archaea.

Phylogenomics of the Asgard archaea. Reproduced from Zaremba-Niedzwiedzka K (2017) [3].

Eukaryotes are thought to have arisen when two types of single cell merged, with one engulfing the other. A cell from the Asgardian domain of archaea is proposed to have engulfed a bacterial cell of a type know as alphaproteobacterium, and the engulfed bacterium evolved into the energy generating mitochondria of eukaryotes, which later evolved into multicelled organisms, among which are humans. This event is estimated to have occurred 1.8 to 2 billion years ago [4]

Ancient Asgardians are thought to be the archaea who took this step, because many of the Asgardian genes involved in DNA transcription and replication share a common ancestor with (are genetically similar to) the corresponding eukaryotic genes.  And the Lokiarchaeota are the closest living relatives.

Asgard (Marvel Cinematic Universe)

Last week’s issue of Nature reports the growth of an Asgardian in the laboratory for the first time ever. Imachi and colleagues [5,6] report that they have cultured an Asgardian from the Lokiarchaeota phylum that they have named Prometheoarchaeum syntrophicum. Although Prometheoarchaeum was obtained from deep ocean sediments, Imachi and colleagues found that it grew best at 20° C with amino acids, peptides and even baby-milk powder for food.

They found that Prometheoarchaeum would only grow in the presence of one or two other microbes, the archaeon Methanogenium and the bacterium Halodesulfovibrio. Prometheoarchaeum breaks down amino acids into hydrogen, which the other microbes eat. But the hydrogen-producing process requires the breakdown of sulphates into sulphides which only the other two microbes can do. So these organisms have a syntrophic relationship in which they are all needed for mutual survival.

Prometheoarchaeum develops lengthy appendages with multiple branches, and suggest the microbe may have used the tentacles to grab hold of oxygen-producing organisms. Imachi and coauthors speculate that the origin of mitochondria was a result of the need for the host cell to adapt to oxygen use as a consequence of rising oxygen levels on ancient earth, and that a bacterial partner became entangled with and then engulfed by an ancestral Asgardian.

The diagram below gives a more detailed summary of the tree of life showing the family relationships between bacteria, archaea and eukaryotes. It is from a 2016 paper, and does not include all the Asgardian phyla now discovered (see previous diagram for those).

Domains of life showing the Asgardian archaea and the Eukaryotes (among which humans belong). Cropped from Fig. 2 in Hug et al. [7] Here each major lineage represents the same amount of evolutionary distance.

I cannot resist concluding with a picture of Heimdall from the first of Marvel’s Asgardian movies.

Heimdall (played by Idris Elba in the Marvel Cinematic Universe)

References

  1. Spang, A., Saw, J. H., Jørgensen, S. L., Zaremba-Niedzwiedzka, K., Martijn, J., Lind, A. E., … Ettema, T. J. G. (2015). Complex archaea that bridge the gap between prokaryotes and eukaryotes. Nature, 521(7551), 173–179. doi:10.1038/nature14447
  2. Neil Gaiman. Norse Mythology. Bloomsbury: London, 2017.
  3. Zaremba-Niedzwiedzka K,  Caceres EF, Saw JH, et al. Asgard archaea illuminate the origin of eukaryotic cellular complexity. Nature 2017, 541:XXX. doi10.1038/nature21031
  4. Betts HC, Puttick MN, Clark JW, Williams TA, Donoghue PCJ, Pisani D. Integrated genomic and fossil evidence illuminates life’s early evolution and eukaryote origin. Nat Ecol Evol. 2018;2(10):1556–1562. doi:10.1038/s41559-018-0644-x
  5. Imachi H, Nobu MK et al. Isolation of an archaeon at the prokaryote-eukaryote interface. Nature 577, 519–525 (2020)
  6. Schleper C, Sousa FL. Meet the relatives of our cellular ancestors. Nature 2020, 577: 478-479.
  7. Hug LA, Baker BJ, Anantharaman K, Brown CT, Probst AJ, Castelle CJ et al. (2016). A new view of the tree of life. Nat Microbiol 1: 16048.

Powerlifting

Approaching retirement from full-time work, the last thing I would have foreseen doing was to take up powerlifting and get involved in competitions. I had plans to spend more time walking and climbing in the Alps, but increasing knee problems (osteoarthritis) around 2014-2015 put that on hold. I stopped doing Crossfit classes in 2015 and instead started to focus on weight training apart from squats.

I had also been reading various books and research relating to exercise and ageing, and became convinced that to maximise my health and functioning into older age I needed to maintain and improve my strength, and that this was probably more important than the endurance cardiovascular training that I had been doing for many years.

I found that I really enjoyed training with heavy weights and low repetitions (usually in range 3-6) and that my knees felt a lot better after a workout. With some coaching on good technique, I was able to substantially increase the weight and volume I was working with and would often leave the gym with an endorphin high and pain-free knees. Occasional lower back pain (related to an old injury during jujutsu training) also became rarer.

So in 2016 and in my sixties, I got into strength training more seriously and also went to the weekly Strongman training at my gym, where I not only learnt a whole range of fun strength training techniques involving kettlebells, axles, logs, yokes, sleds and other strongman equipment, but I also got excellent coaching on training for the three main powerlifting techniques (squat, bench press, deadlift) from a coach who was a very experienced powerlifter as well as a strongman.

There are three strength athletics sports with a primary focus on strength: Olympic weightlifting, powerlifting and Strongman competition. Olympic weightlifting has two competition lifts: the snatch and the clean and jerk, both of which involve getting the loaded bar completely overhead.  Powerlifting has three competition lifts: the squat below parallel, the benchpress (with a pause of the bar on the chest), and the deadlift. The objective in competition is to maximise the sum of the weight lifted in each of the three lifts, with three attempts allowed for each lift.

Strongman involves a wide range of strength challenges with events such as the log lift, atlas stones, vehicle pull, deadlift, farmer’s walk, and weight throw. Whereas Olympic weightlifting and powerlifting competitions have age and weight classes and athletes choose the weights they will attempt to lift, Strongman events use fixed weights or equipment for all competitors, and aim to achieve maximum distance, time or repetitions as appropriate.

None of the strength sports should be confused with bodybuilding where the focus of training is on muscle hypertrophy and the aesthetics of appearance. While bodybuilders are generally strong, they are not training to maximise strength. Some powerlifters and strongmen may look like bodybuilders, many do not. And in fact some of the strongest lifters in powerlifting competitions do not look particularly muscular, at least in the weight categories below the top open-ended category.

When I started doing strongman class, I added the squat to my training, initially quite lightly loaded (around 50 kg) and worked very hard on achieving good technique.  To my surprise, I found that when the squat was done with good technique to below parallel (hips lower than the position where the top of the thigh is parallel to the floor) I had no knee pain,  even on days when my knees were playing up walking around. My current personal best squat in competition is 107.5 kg (237 lb) which is relatively low compared to my bench press and deadlift, but I am very happy to be able to squat again. I hope to work on lower body mobility and continue to improve my squat.

Opening squat of 95 kg in a powerlifting competition, December 2019

In 2017, I decided to enter the SDFPF Single Lift competition in the bench press and deadlift events, for the fun of it, and to see what was involved in competition.  I also thought it might potentially add to my motivation to train regularly. I was competing in the Masters 5 age category (60-64 years) and the under 100 kg weight class. In the deadlift, my opening lift was a relatively safe 130 kg (in the sense that I was sure that was within my capacity) When I went out for my second attempt at 140 kg, the official told the crowd that this would be a new Swiss record for my age-weight class.  I achieved that and went on to successfully lift 150 kg.  That gave me quite a thrill with the crowd cheering me on, and I was hooked on competing again.

Performing a 100 kg benchpress at the SDFPF Single Lift Championships 2017

Powerlifting competition is very different to most other physical activities in that the goal is to achieve 100% effort in a single lift that typically takes around 5 seconds or less. To achieve that requires the ability to recruit every muscle in your body and maintain maximum tension by “getting tight” through your entire body. This requires training your central nervous system to send signals to your muscles to contract at the limit of their capacities. But beyond this, it requires extreme mental focus and intention. Distraction during the lift, for example starting to think about whether you went low enough in the squat, can result in loss of tension and the failure of the lift, or forgetting to wait for a command to rack the bar (which will disqualify you).

A major appeal of powerlifting training for me is this integration of mind-body training and the intellectual challenge of learning and maximising skill and technique. Somewhat similar to the appeal that the martial arts and alpine climbing have had for me. I have always sought out activities that challenge me mentally and get me to “lean beyond my edge” on a regular basis. Through powerlifting, I am still doing that.

At the 2019 Swiss Drug Free Powerlifting Federation (SDFPF) Championships in  Zuchwil, I set records for my age-weight category (Masters 6, u100 kg, unequipped) for all three lifts and for the total of 390 kg. I was particularly pleased with a personal best of 175 kg for the deadlift, and 100 kg for the bench press, though my squat was a less satisfying 85 as I failed to achieve acceptable depth in the following two attempts.  A month later, at the SDFPF Single Lift Championships (Unequipped) I set two more Swiss records for the squat (100 kg) and the deadlift (180 kg).

Performing a 175 kg deadlift at the SDFPF Powerlifting Championship 2019

More recently in December 2019, I set a new personal best for the deadlift at 190 kg, at a Geneva powerlifting competition, the “Coupe de l’Escalade”. There were no age-weight categories in this competition, with the powerlifting total being adjusted for body weight and age using Wilk/McCulloch coefficients. The McCulloch age coefficient was 1.51 for my age, which was more than 25 years older than the next oldest competitor. Based on these weighted scores, I came 2nd overall in the men’s competition. The following video shows my 190 kg deadlift, equivalent to a lift of 287 kg ( 633 lbs) by a man aged less than 40.

 

Deep maternal ancestry and mtDNA

In February 2014, I did a series of posts on my deep maternal ancestors, identified through a test of mutations on my mitochondrial DNA (mtDNA) which is inherited only from the mother. This test was carried out by Ancestry.com, who have since discontinued tests of mtDNA and Y-chromosome DNA. Costs of DNA tests have dropped dramatically since then, and late last year I ordered an mtDNA test from FamilyTreeDNA (www.familytreedna.com) which carried out a full sequencing of the mitochondrial DNA.

As well as the DNA that makes up the chromosomes in the nuclei of our cells, we also have another type of DNA called mitochondrial DNA (mtDNA). The mitochondria are organs located outside the cell nucleus which convert sugars into energy.  Mitochondria have a small circular loop of DNA, containing only approximately 16,569 base pairs in humans. The circular mtDNA is similar to the DNA of bacteria, and it is thought that mitochondia evolved from symbiotic bacteria that were once free living.

In humans, as in other higher organisms, a DNA molecule consists of two strands that wrap around each other in the well known double helix structure. Each strand contains a linear arrangement of four different bases: adenine (A), thymine (T), guanine (G), and cytosine (C).  Specific sequences of three bases make a DNA “word” which codes for an amino acid. A string of DNA “words” strung together in a sequence provides the instructions to make a particular protein. The base-pairs on the circular mtDNA loop are numbered from 1 to 16,569 and different portions of the loop have been given different names as shown in the following diagram. The first and second portions, called hypervariable control region 1 (HRV1) and hypervariable control region 2 (HRV2) are regions of the mtDNA that accumulate mutations (changes in base-pairs) relatively quickly and thus tend to be hyper-variable between people who are not closely related. The third portion, the coding region, accumulates far fewer changes and contains the base-pair sequences for mitochondrial genes [1].

mtDNA molecule (Credit: Debbie Parker Wayne)

One type of mutation, called a single nucleotide polymorphism (SNP), is a single base pair in a DNA sequence that has been replaced by a different base pair. My mtDNA test results identified 68 SNPs, 13 in HRV1, 17 in HRV2, and 38 in the coding region through comparison of my base sequences with those of the Reconstructed Sapiens Reference Sequence (RSRS). The RSRS is a recent effort to reconstruct a single ancestral genome for all living humans, using both a global sampling of modern human samples and samples from ancient hominids. It was introduced in early 2012 as a replacement for the rCRS (revised Cambridge Reference Sequence).

Mitochondrial DNA is inherited from the mother alone, rather than being inherited from the father and the mother. Additionally, recombination (or crossing over) does not occur in mitochondrial DNA (mtDNA). For both of these reasons, the sequence of mitochondrial DNA stays largely the same over generations, and thus is a useful tool for looking at maternal ancestry.

Over a period of nearly 180,000 years, SNPs have steadily accumulated on different human mtDNA molecules being passed down from mothers to their children. SNPs thus provide a cumulative dossier of our own maternal prehistory. We can use these mutations to reconstruct a genetic tree of mtDNA, because each new SNP in a prospective mother’s ovum will be transferred in perpetuity to all her descendants down the female line.

When a group of people share similar SNPs, they are part of the same “haplogroup”. For example, over 95% of native-born Europeans fit into seven haplogroups, which in turn derive from an older haplogroup that arose in the Middle East. Other regions of the world are associated with different haplogroups. Each of these groups trace their maternal ancestry back to just one woman, the common maternal ancestor of everyone in her haplogroup, or clan. Not everyone in the same clan has exactly the same mtDNA, because DNA accumulates additional mutations gradually over the generations. However, everyone in the clan shares a set of common mutations, which are the signature of the mtDNA of their founding maternal ancestor.

By averaging the numbers of mutations found in the mtDNA of modern members of a haplogroup, and knowing the average mutation rate for mtDNA, as well as the dating of ancient human remains whose mtDNA has been sequenced,  it is possible to estimate how old each clan is, or in other words, when the common maternal ancestor of the clan lived (see below). By studying features of the geographical distribution of their present-day descendants, as well as the locations of ancient human remains whose mtDNA has been sequenced, it is possible to work out where they most likely lived as well. Generally speaking, the likely geographic origin for a clan is not necessarily the place where it is most common today, but the place where it is the most varied.

It is thus possible to trace migration routes by observing the branching points in an ancestral map containing all known haplogroups (see map below). Mitochondrial DNA in humans of African origin show the most diversity in the world. This supports the concept that ancient humans first existed in Africa and stayed in Africa for thousands of years.  The humans who left Africa around 70,000 years age took two major routes, to Asia (haplogroup M) and to Europe (haplogroup N).

Migration routes of human beings dating back to 170,000 years ago. All humans originated in Africa and migrated out, branching into the two main out of Africa haplogroups, M and N. Individuals in haplogroup M headed west to Asia and later to the Americas, while haplogroup N moved into Europe.

The clan mothers were not the only people alive at the time, of course, but they were the only ones to have direct maternal descendants living right through to the present day. The other women around, or their descendants, either had no children at all or had only sons, who could not pass on their mtDNA. And, of course, the clan mothers had ancestors themselves. Everyone alive on the planet today can trace their maternal ancestry back to just one woman, the founder of haplogroup L. According to recent studies, she lived in Africa nearly 180,000 years ago and is known as “Mitochondrial Eve” (see my previous post  mitochondrial eve )

Age Estimates

The age estimates for haplogroup founders in my 2014 posts were based on estimating average mutation rates for mtDNA SNPs, assuming an average constant mutation rate [2, 3]. There have been several more recent studies that have updated these estimates using not only samples from living humans but also analyses of mtDNA from ancient humans.

My previous post on mitochondrial Eve used dates from Behar et al. 2012 [4]. Comparing these with the dates given on the FamilyTreeDNA site and on the site  snpTracker, as well as as two other more recent papers [5, 6], there is considerable variation in some of these. I revised the date for mitochondrial Eve based on the average of the dates from Behar et al [4] and Fu et al [5], and the dates for L3 and U based on the average of the dates from Behar et al [4], Fu et al [5] and Soares et al [6]. Dates from these three papers were reasonably consistent. Dates for other haplogroups from Behar et al were adjusted accordingly. 90% uncertainty ranges were estimated using the relative uncertainty ranges Behar et al. [4]. Because of the random nature of individual mutations (they may not occur at exactly the average time to next mutation), there is an uncertainty range around dates (which is also statistically estimated).

The following map summarizes the revised timeline for the migration of the ancestors of maternal haplogroup U5 out of Africa.

Ancestral migration path of maternal ancestors for haplogroup U5

In following posts, I will update the previous posts summarizing my maternal haplogroup ancestors and placing them in the context of the human expansion out of Africa and across Europe, as well as the context of the ice ages and the evolution of human cultures.

References

[1] Blaine T. Bettinger (2016). The Family Tree Guide to DNA Testing and Genetic Genealogy. Family Tree Books: Cincinnati.

[2] Behar D, Villems R, Soodyall H, Blue-Smith J, Luisa Pereira L, Ene Metspalu E, Rosaria Scozzari R, Heeran Makkan H, Shay Tzur, David Comas, Jaume Bertranpetit, Lluis Quintana-Murci, Chris Tyler-Smith, R. Spencer Wells, Saharon Rosset (2008). The Dawn of Human Matrilineal Diversity. American Journal of Human Genetics, 82(5):1130-1140.

[3] Soares P, Ermini L, Thomson N, Mormina M, Rito T, Röhl A, Salas A, Oppenheimer S, Macaulay V, Richards MB (2009). Correcting for purifying selection: an improved human mitochondrial molecular clock American Journal of Human Genetics, 84(6):740-59.

[4] Behar D, van Oven M, Rosset S, et al. A “Copernican” Reassessment of the Human Mitochondrial DNA Tree from Its Root. Am J Hum Genet. 2012;90(5):936. doi:10.1016/j.ajhg.2012.04.007 Open ArchiveDOI:https://doi.org/10.1016/j.ajhg.2012.03.002

[5] Fu Q, Mittnik A, Johnson PLF, et al. A revised timescale for human evolution based on ancient mitochondrial genomes. Curr Biol. 2013;23(7):553–559. doi:10.1016/j.cub.2013.02.044 https://www.cell.com/current-biology/fulltext/S0960-9822(13)00215-7?code=cell-site

[6] Soares S, Alshamali F, Pereira JB, Fernandes V, Silva NM, Afonso C, Costa MD, Musilová E, Macaulay V, Richards MB, Černý V, Pereira L, The Expansion of mtDNA Haplogroup L3 within and out of Africa, Molecular Biology and Evolution, Volume 29, Issue 3, March 2012, Pages 915–927, https://doi.org/10.1093/molbev/msr245

Australia appears to be committing climate suicide

Media across the world have been publishing articles and photos on the catastrophic bushfires in Australia. Richard Flanagan, a well-known Australian author, published an opinion piece in the New York Times two days ago, which fairly accurately summarized the impact of the fires and the complete inadequacy of the government and political response (Australia Is Committing Climate Suicide).

Mogo, a town on the NSW south coast has been devastated by bushfires. One Mogo resident watched his 92 year old father’s house burning next door. At the time of taking this photo, he wasn’t sure where his father was. Credit: James Brickwood

Here are some quotes from the article:

“Australia today is ground zero for the climate catastrophe. Its glorious Great Barrier Reef is dying, its world-heritage rain forests are burning, its giant kelp forests have largely vanished, numerous towns have run out of water or are about to, and now the vast continent is burning on a scale never before seen.       …….

“The fires have already burned about 14.5 million acres — an area almost as large as West Virginia, more than triple the area destroyed by the 2018 fires in California and six times the size of the 2019 fires in Amazonia. Canberra’s air on New Year’s Day was the most polluted in the world partly because of a plume of fire smoke as wide as Europe.

“Scientists estimate that close to half a billion native animals have been killed and fear that some species of animals and plants may have been wiped out completely. Surviving animals are abandoning their young in what is described as mass “starvation events.” At least 18 people are dead and grave fears are held about many more. …..”

A deceased horse on a property on the outskirts of Cobargo, a town on the NSW south coast that was devastated by bushfires at New Year. Credit: James Brickwood

Other impacts not mentioned by this article include the more than 1500 houses burnt down or the growing number of towns across NSW and Victoria devastated. The last couple of days have probably increased the number of deaths to around 30. Record temperatures were recorded in Canberra and Sydney, with the temperature in Penrith reaching 48.9 degrees, the highest ever recorded in the Sydney region. A cool change yesterday brought strong winds of up to 104 km/hour.

Dead livestock on a property south west of Cobargo. Credit: James Brickwood

The article goes on to draw a parallel between Australia’s situation and that of the Soviet Union in the 1980s when an all-powerful political clique demented on its own fantasies faced a monstrous reality which it had neither the ability or will to confront.

Batemans Bay residents surrounded by thick smoke wait on the beach on New Year’s Eve (Picture: 9News)

Residents of coastal towns in NSW and Victoria have sheltered on beaches, and in some cases taken to the water to escape the fires. The Australian Government belatedly sent three naval ships to evacuate residents from some beaches.  Families with young babies were left stranded in Mallacoota when the navy ship refused to take children under 5 (apparently because they would have to climb a ladder onto the ship) and told the families to wait for an aircraft to evacuate them. When the aircraft arrived, it was unable to land because of the zero visibility and the families were left stranded and trapped.  Fuel is running low in many of the towns affected and people are unable to leave.

An 11 year old boy navigates a boat through thick smoke at Mallacoota, as fire advanced on the seaside Victorian town on December 31, 2019.

Some further quotes from the article:

“And yet, incredibly, the response of Australia’s leaders to this unprecedented national crisis has been not to defend their country but to defend the fossil fuel industry, a big donor to both major parties — as if they were willing the country to its doom. While the fires were exploding in mid-December, the leader of the opposition Labor Party went on a tour of coal mining communities expressing his unequivocal support for coal exports. The prime minister, the conservative Scott Morrison, went on vacation to Hawaii.

“Since 1996 successive conservative Australian governments have successfully fought to subvert international agreements on climate change in defense of the country’s fossil fuel industries. Today, Australia is the world’s largest exporter of both coal and gas. It recently was ranked 57th out of 57 countries on climate-change action.

“This posture seems to be a chilling political calculation: With no effective opposition from a Labor Party reeling from its election loss and with media dominated by Rupert Murdoch — 58 percent of daily newspaper circulation — firmly behind his climate denialism, Mr. Morrison appears to hope that he will prevail as long as he doesn’t acknowledge the magnitude of the disaster engulfing Australia.     ……

“The situation is eerily reminiscent of the Soviet Union in the 1980s, when the ruling apparatchiks were all-powerful but losing the fundamental, moral legitimacy to govern. In Australia today, a political establishment, grown sclerotic and demented on its own fantasies, is facing a monstrous reality which it has neither the ability nor the will to confront.     …..

“As Mikhail Gorbachev, the last Soviet leader, once observed, the collapse of the Soviet Union began with the nuclear disaster at Chernobyl in 1986. In the wake of that catastrophe, “the system as we knew it became untenable,” he wrote in 2006. Could it be that the immense, still-unfolding tragedy of the Australian fires may yet prove to be the Chernobyl of climate crisis?”

Day turns to a blood red sky in Mallacoota with the South Westerly change sparking up fire activity in the area on Saturday 28 December. Credit: Justin McManus

Mitochondrial Eve – an update

A recently published paper in Nature (Oct 18) has analysed the mitochondrial DNA of 1,200 indigenous Africans living in the southern part of Africa and identified the ancestral homeland of all humans alive today, the place where mitochondrial Eve lived nearly 200,000 years ago. More on that below, but first some background.

In February 2014, I did a series of posts on my deep maternal ancestors, identified through a test of mutations on my mitochondrial DNA (mtDNA) which is inherited only from the mother. These mutations allowed me to track back through time to mitochondrial Eve, the single woman from whom all humans alive today descended through their female line (mother to mother to mother….).  Specific mutations on the mtDNA define maternal haplogroups, and the founder of a given haplogroups is the specific individual woman in which the defining mutation occurred. All members of a given haplogroup trace their maternal ancestry back to this founder.

DNA tests have become much less expensive, and can include much more detailed testing. In the last three months, I’ve redone a test on my mtDNA and also on my Y DNA, which is inherited only down the male line (father to father to father….). I am still digesting the results of these tests, and will post on them in the near future.  One of the first things I discovered was that the dates associated with haplogroup founders have been revised over time, and as more and more test results are available, and that the terminology used for identifying haplogroups has also evolved.  I also came across very recent research which has pinned down the location where mitochondrial Eve lived, as well as revised estimates of the time period in which she lived.

Haplogroup U5 – the oldest of seven native European haplogroups

My mtDNA haplogroup is U5, the oldest of the seven native European haplogroups. Haplogroup U most likely arose in the Near East, and spread into Europe in a very early expansion, giving rise to seven native European haplogroups, including U5. The presence of haplogroup U5 in Europe pre-dates the last ice age and the expansion of agriculture in Europe. Today, about 10% of modern Europeans are the direct maternal descendants of the founder U5 woman, who has been given the nickname Ursula*. They are particularly well represented in western Britain and Scandinavia.

Ancestral migration path of maternal ancestors for haplogroup U5

Haplogroup U in turn is descended via haplogroups R and N from haplogroup L3, which is associated with a migration of humans out of Africa around 70,000 to 50,000 years ago. The dominant theory of human origins, the “recent African origin” theory, proposes that all modern non-African populations are substantially descended from populations of H. sapiens that left Africa after during that time period. H. sapiens most likely developed in Africa between 300,000 and 200,000 years ago, and there were at least several “out-of-Africa” migrations of modern humans, possibly beginning as early as 270,000 years ago. These early dispersals may have died out or retreated, although some paleoanthropologists argue that they possibly interbred with various other local hominid species and with later humans from “recent-out-Africa” and it just so happens that all the maternal lineages trace back to “recent-out-Africa”. Of all the lineages present in Africa, only the female descendants of Lara*, founder of the L3 haplogroup, are found outside Africa. If there had been several migrations, one would expect descendants of more than one lineage to be found.  Of course, all this could be upturned if descendants of other African lineages are found outside Africa, and can be traced back to earlier migrations.

Mitochondrial Eve (haplogroup L)

Mitochondrial Eve (mt-Eve) is a member of Haplogroup L and lived just before the divergence of macro-haplogroup L into L0 and L1–6 (see diagram below). Today the haplogroup L0 and its offshoots are found mainly in southern and eastern Africa, with particularly high frequencies among the San people (bushmen) of Botswana, Namibia and other countries of southern Africa.

Haplogroup L1 is found in West and Central sub-Saharan Africa. The descendants of haplogroup L1 are also African haplogroups L2 and L3, the latter of which gave rise to all non-African haplogroups.

Phylogenetic tree for mtDNA Haplogroup L, commencing with mitochondrial Eve, the most recent common maternal ancestor (MRCA) of all humans.

A recent paper by Chan et al. in Nature (October 2019) [1] analysed the genomes of more than 1,200 indigenous Africans living in southern Africa and claim to have identified precisely where and when the L haplogroup split into L0 and L1 and when these groups migrated from their homeland.

Chan et al. identified this homeland as Makgadikgadi, a vast wetland some 120,000 square kilometers in area, or roughly twice the area of Lake Victoria, Africa’s largest lake today. Mitochondrial Eve and her descendants lived in this region for about 30,000 years (from 200,000 to 170,000 years ago) before the L0 lineage split into its first subgroup. Today, Makgadikgadi is one of the largest salt flats in the world. Climate models suggest that, 200,000 years ago, it was a fertile oasis.  The map  shows the overall location of Makgadikgadi in southern Africa, and the following map shows  a more detailed view.

Satellite view of the Makgadikgadi salt pans. This area is located about 250 km south of Victoria Falls close to the borders of Zambia, Zimbabwe and Botswana.

Chan et al [1] date the deepest rooting L0 branch to 200,000 years ago (with 95% confidence interval 165,000 – 240,000 years ago).  I have reviewed the most recent comprehensive dating of maternal haplogroups and found that the dates in Fu et al (2012)  [2] and Behar et al [2013] were in reasonably good agreement.  I have used dates from Behar et al, which give a date of  176,700 years ago (confidence interval ± 11,300 years) for mitochondrial Eve, and 136,300 (± 11,700) years ago for L1. This is substantially earlier than the date of the recent out-of-Africa dispersal of L3 around 65,000 years ago.

The Okavango delta, in north-west Botswana, looks very similar to how Makgadikgadi would have looked 170,000-200,000 years ago. Credit: Diego Delso, CC BY-SA 4.0, https://commons.wikimedia.org/w/index.php?curid=75769486

Migrations from the Makgadikgadi homeland

The Makgadikgadi wetlands were large, wet, and lush with vegetation. They would have provided an ideal home for wildlife and for early humans, including mt-Eve. So why did some migrate?  Around 130,000 years ago, there was a major climatic shift associated with the end of the penultimate glacial period. This led to higher rainfall and created “green corridors” leading to the northeast and to the southwest.  In particular, it appears that the ancestral founder of the L1 haplogroup lived around 136,000 years ago among a group that had migrated north into Zambia, and by around 70,000 years ago her descendents had made their way north to the horn of Africa, where Lara (L3 haplogroup founder live).

The “green corridors” proposed by Chan et al [1] helped lead humans out of the ancestral homeland

Chan and his group have extrapolated the likely location of mt-Eve’s homeland from the present-day distribution of the L haplgroup in Southern Africa, and it is always possible that future data may lead to revisions of this conclusion. However, multiple sets of evidence lead to the conclusion that mt-Eve was among the ancestors of the San people of southern Africa, although of course we likely will never know for sure exactly where she lived. And this was not the only ancestral human homeland. Y-DNA evidence suggests that Y-Adam lived in West Africa in a time period even further in the past (this will be subject of a future post) and of course, there may be other ancestral homelands associated with the many other ancestral lines than the purely maternal and paternal.

The San people of southern Africa have one of the most oldest maternal DNA lineages on Earth. They share the Haplogroup L with mitochondrial Eve who lived in northern Botswana nearly 200,000 years ago.


* Bryan Sykes in his 2001 book The seven daughters of Eve gave names to each of the women who founded the seven native European haplogroups, and also names to some of their ancestral haplogroups. He chose names that began with the letter by which the haplogroup was identified. Oppenheimer (The Origins of the British: A Genetic Detective Story, 2006) followed this example and also gave names to both mtDNA and Y-DNA haplogroups. To emphasise that the maternal clan founders were real individuals, who were my ancesters, I have used these names and given my own names to the more recent subgroup founders.

References

[1] Chan EKF, Hardie RA, Petersen DC, Beeson K, Bornman RMS, et al. (2015) Revised Timeline and Distribution of the Earliest Diverged Human Maternal Lineages in Southern Africa. PLOS ONE 10(3): e0121223.
https://doi.org/10.1371/journal.pone.0121223

[2] Fu Q, Mittnik A, Johnson PLF, et al. A revised timescale for human evolution based on ancient mitochondrial genomes. Curr Biol. 2013;23(7):553–559. doi:10.1016/j.cub.2013.02.044
https://www.cell.com/current-biology/fulltext/S0960-9822(13)00215-7?code=cell-site

[3] Behar D, van Oven M, Rosset S, et al. A “Copernican” Reassessment of the Human Mitochondrial DNA Tree from Its Root. Am J Hum Genet. 2012;90(5):936. doi:10.1016/j.ajhg.2012.04.007
Open ArchiveDOI:https://doi.org/10.1016/j.ajhg.2012.03.002

Australian bushfires and global warming

At the beginning of December, 118 forest fires were burning in NSW, 48 of them out of control. The bushfire season started much earlier this year, with more than 140 fires in northern New South Wales (NSW) and Queensland, which destroyed over 600 homes and killed six people. One of these fires destroyed the Binna Burra resort in the Lamington National Park, as well as surrounding rainforest. This was followed by another outbreak of bushfires in November, with more than 129 bushfires in NSW and Queensland. At least 200 houses were destroyed and four people killed.

By the end of November, around 2 million hectares (5 million acres) of bushland had been burnt, and all this before the start of summer and the traditional bushfire season  According to the Climate Council of Australia, the catastrophic, unprecedented fire conditions currently affecting NSW and Queensland have been aggravated by climate change. Bushfire risk was exacerbated by record breaking drought, very dry fuels and soils, and record breaking heat. Since the mid-1990s, southeast Australia has experienced a 15% decline in late autumn and early winter rainfall and a 25% decline in average rainfall in April and May. Across Australia average temperature has increased leading to more record breaking hot weather. Extreme fire danger days have increased.

Extensive fires currently burning in the Blue Mountains

I was in Australia in November to visit family at Noosa. A couple of days before my trip, I was stunned to read on the web that Tewantin, the suburb next to Noosaville where I was headed, was being evacuated because of the threatening bushfire.

While I was in Noosa, the residents of Noosa North Shore were evacuated because of another fire, as were the people who lived around Lake Cooroibah, about 10 km upstream on the Noosa River. Some days later, I drove up to Cooroibah where I saw extensive burnt areas of bush.  The photos below show the fire damage. Most of the trees are evergreen eucalypts (gum trees) and the dead leaves from the heat are orange or brown. Though it may look like autumn colours to those from the Northern Hemisphere, it is actually dead leaves. Most of the larger trees will regenerate, as the ecucalypt forests of Australia have evolved to adapt to fire, with thick bark, an ability to resprout along their entire trunks, and in some cases depend on fire to open their seed pods.  Animals such as the koala bear and other threatened species do not do so well, particularly when the fires are widespread and have significant impact on populations.

Bushland near Lake Cooroiba

Around 2,500 people were evacuated from about 440 homes in this area, but only one house and some sheds were destroyed. A teenage boy on his own in the house that was destroyed managed to make it into the nearby lake as the fire came over.

Burnt forest on the shore of Lake Cooroiba

The fire came quite close to this house.

There is a small housing development here, and the fire came within 50 metres of the houses. I spoke to one resident who told me he and his dog stayed, and hid when the police came to evacuate everyone.

Years ago when I lived in Sydney, there were regularly bushfires in the nearby Blue Mountains where increasing numbers of people were living. Those who stayed with their homes were able to put out spot fires, fill gutters with water, and deal with floating embers. Those who left their houses often returned to find the houses burnt down. Of course, those who underestimated the intensity of the fire and stayed sometimes paid with their lives.

So it’s a difficult call whether to stay or leave. One time in the 1980s, I went up to the Blue Mountains to help some friends during a bushfire. We stayed with the house and fought the spot fires successfully. The house was on a ridge and the wind drove the fire up the side of the ridge and over the house. As the fire approached, the heat increased and it became very difficult to breathe due to smoke. We all wrapped ourselves in wet towels and lay flat in the gutter of the road where the air was clearer. The fire passed over us and we were OK, though somewhat terrified. Australian eucalypts have a lot of eucalyptus oil in the leaves, and the heat vaporises this into the air, so that fires will spread at tree height, and in the most intense fires will leap across the tops of the trees as the eucalyptus oil above the trees ignites.

Fire damaged bark on a tree trunk

Returning to 2019, although Australia has always had devastating bushfires in some years, scientists and fire service chiefs have stated that the fire risk this year is the highest ever. Back in August, the The Bushfire and Natural Hazard Cooperative Research Centre (BNHCR) warned that New South Wales and Queensland and some other parts of Australia faced higher than normal fire potential. The Australian Bureau of Meteorology publishes a Forest Fire Danger Index (FFDI) which combines measurement of temperature, humidity, rainfall, evaporation and wind speel. Their cumulative winter index for 2019 (BOM), published in September, shows the overwhelming majority of the country, with a few exceptions in Victoria, central Queensland and western Tasmania, is experiencing between “above average” and “highest on record” fire conditions when compared with the average since 1950 (see map below). The measured FFDI values were in the extreme category (over 75) across large areas, reaching the catastrophic category (FFDI values of 100 or above) at some locations in New South Wales.

In line with the measured rise in average annual surface temperature over recent decades, the FFDI has been increasing across most of eastern Australia. Projections by Bureau of Meteorology Scientists recently published in Nature (ref), continue to show an increase in FFDI values due to increasing greenhouse gas emissions over the course of the century. This result is robust across a range of climate projection models, methods and metrics. This means that the number of days in the year where the FFDI value represents “Very High” fire danger will increase substantially over the next 50 years.

What is the political response to all this?  The Australian Prime Minister Scott Morrison is a climate denialist and stated that there was no evidence to link the increased bushfire risk to climate change. He went further and stole a line from US poliiticians, telling the nation “Now is not the time to discuss possible causes of the fires, instead we must pray for the victims.”

Extinction Rebellion and other forms of climate protest have become more vocal recently, and Morrison recently announced hi intention to outlaw and criminalize protest by climate activists. The Queensland government is also fast-tracking laws to crack down on climate protesters.

The Australian government is also discussing how to outlaw consumer boycotts of businesses such as coal miners. They have a bit of a problem figuring out how to do that as some of the major banks and investment companies are also avoiding investment in fossil fuels.

Bushland burnt in September near Peregian Beach