Becoming Human Part 1

Our understanding of the evolution of us modern humans has changed dramatically in the last few years as ancient genomes are decoded and we discover that humans, Neanderthals and Denisovans interbred, and also in the remote past interbred with previously unknown “superarchaic” human groups.  Scientists are also discovering new species of extinct hominids, and no doubt will continue to shed further light on our origins. Just to try to sort out the big picture in my own mind and to put these various discoveries in context, I’ve tried to summarize what we think we know, or at least what the evidence available to date suggests. This will no doubt continue to change.

This is the first of two posts and summarizes the evolution of pre-human species from the first monkeys around 35 million years ago (Mya) to the appearance of the first human species around 2 Mya. A following post will summarize the evolution of humans from the appearance of the first human species Homo habilis 2 Mya to the appearance of anatomically modern Homo sapiens sapiens around 250 thousand years ago and  mitochondrial Eve, who lived around 178,000 years ago.

The evolution of mammals and the monkeys

Although the earliest true mammals evolved during the late Triassic period towards the end of the age of the dinosaurs, they remained small and relatively inconspicuous until around 65 Mya, the time of the disappearance of the dinosaurs. The first modern monkeys evolved in Africa or Asia around 35 Mya and around 23 Mya they split into two lines: the Old World Monkeys (which led to many species including baboons, macaques and colobus monkeys) and the Hominoids (which led to gibbons, orangutangs, apes and humans).

The split of gibbons and then gorillas from hominines

The split of the Hominoid superfamily (apes) into the Hylobatids (gibbons) and Hominids (great apes) families occurred in the early Miocene, roughly 20 to 16 million years ago. Recent research suggests that the last common ancestor of gibbons and apes — including humans — was much smaller than previously thought, about the size of a gibbon [1]. Mark Grabowski and co-authors compared body size data from modern primates, including humans, to those estimated from a wide range of fossil hominins and primates. They found that the common ancestor of apes and gibbons was likely small, probably weighing about 5.5 kg (12 pounds), which goes against previous suggestions of a chimpanzee-sized, chimpanzee-like ancestor. Our last common ancestor with the gibbons was very likely gibbon-like, a small and nimble tree-dweller.

The last common ancestor of the hominoids was likely a small tree-dwelling and gibbon-like primate.

Among living primates, humans are most closely related to bonobos and chimpanzees and gorillas. The following diagram shows evolution of the hominoid family and the dates at which the major hominoid genera split off from the lines that eventually became humans. The gibbons and then the orangutans were the first groups to split from the line leading to the hominins, including humans—followed by gorillas around 10 Mya, and, ultimately, by the chimpanzees (genus Pan).

With the sequencing of both the human and chimpanzee genome, as of 2012 estimates of the similarity between their DNA sequences range between 95% and 99%. By estimating the frequency of mutations and thus the time required for the number of divergent mutations to accumulate between two lineages, the approximate date for the split between lineages can be calculated.

The split between chimpanzees and humans

The split between hominin and chimpanzee lineages is placed by some between 4 to 8 million years ago, that is, during the Late Miocene. Speciation appears to have been unusually drawn out. Initial divergence occurred sometime between 7 to 13 million years ago, but ongoing hybridization blurred the separation and delayed complete separation during several millions of years. Patterson et al in 2006 [2] dated the final divergence at 5 to 6 million years ago.

Model of the speciation of Hominini and Gorillini over the past 10 million years; the hybridization process within Hominini is indicated as ongoing during roughly 8 to 6 Mya. Credit Wikipedia.

Species close to the last common ancestor of gorillas, chimpanzees and humans may be represented by Nakalipithecus fossils for an ape species that lived in Kenya around 10 Mya  and Ouranopithecus found in Greece and dated to 9 — 8 Mya.

Human evolution began in Africa around 7 million years ago when a now extinct ancestral ape population split and gave rise to the chimpanzee and bonobo family trees, and the hominin or human family tree due to climatic and geological activity pertaining to the formation of the Great Rift Valley in East Africa. The word “human” encompasses many upright walking bipedal apes, not just Homo sapiens (which is the only member left on the hominin family tree). This means that “human” can apply to any species that evolved on the hominin family after the split from the now extinct common ape ancestor we shared with chimpanzees and bonobos around 7 million years ago in Africa.

The evidence suggests that there was a quite long-drawn-out speciation process rather than a clean split between two lineages. The above diagram shows the speciation process lasting from 8 Mya to 5.5 Mya and others have argued that it may have lasted up to 4 million years. Different chromosomes appear to have split at different times, possibly over as much as a 4 million year period. While it has been generally assumed that the last common ancestor of humans and chimpanzees was chimpanzee-like, Sayers et al [3] have argued that many of the behavioural and anatomical characteristics of humans may have evolved in the common ancestral species and that the characteristics of chimanzees evolved subsequent to the split. They also argue that the social and sexual behaviour of humans is closer to that of bonobos than chimpanzees, and that chimpanzee behaviours are what diverged most.

The Australopithecines

Following the split, the human branch evolved into many Australopithecine genera and species, and there is much debate and ongoing revision of the classification of Australopithecine fossil remains into separate species. Most of them lived in Africa, many at the same time, over the period from around 7 Mya to 1 Mya. As shown in the diagram above, there were many evolutionary offshoots that went extinct. There were many species that belonged to various genuses such as Sahelanthropus, Ardipithecus, Australopithecus, Paranthropus, Kenyanthropus, and our own genus, Homo. Most of the African fossils have been found within and near the Great Rift in east Africa, in countries such as Ethiopia, Kenya, and Tanzania. But others have also been discovered in countries such as Chad, South Africa, Zambia, and Morocco.

Reconstruction of Lucy, Moersgaard Museum, Denmark

The genus Australopithecus evolved in eastern Africa around 4 million years ago before spreading throughout the continent and eventually becoming extinct 2 million years ago. There were a number of species, including Australopithecus afarensis. Fossilized bones of a female of this species were discovered in Ethiopia in 1974, dated to 3.2 Mya and became famous as “Lucy”. Lucy walked upright, weighed around 29 kg and 1.1 m tall, and looked somewhat like a chimpanzee. She is thought to be a young mature female around 12 years old. Lucy lived around the same time as the earliest known stone tools dating to around 3.3 to 3.4 million years old. These were discovered near Lake Turkana in Kenya and were likely made by Australopithecus afarensis.

The brain size of Lucy and other Australopithecus afarensis was in the range of around 375 to 500 cc, similar to that of modern chimpanzees. Around 2.8 Mya [4], the first species of a new genus Homo with around double that brain size evolved in Africa from an Australopithecine species, quite likely Australopithecus afarensis. The evolution of Homo will be summarized in a following post.

References

[1] Mark Grabowski, William L. Jungers. Evidence of a chimpanzee-sized ancestor of humans but a gibbon-sized ancestor of apes. Nature Communications, 2017; 8 (1) DOI: 10.1038/s41467-017-00997-4

[2] Patterson N, Richter DJ, Gnerre S, Lander ES, Reich D (June 2006). Genetic evidence for complex speciation of humans and chimpanzees. Nature. 441 (7097): 1103–8. doi:10.1038/nature04789

[3] Sayers, Ken; Raghanti, Mary Ann; Lovejoy, C. Owen (October 2012). Human Evolution and the Chimpanzee Referential Doctrine. Annual Review of Anthropology. 41: 119–138. doi:10.1146/annurev-anthro-092611-145815.

[4] Ghosh, Pallab (March 4, 2015). “‘First human’ discovered in Ethiopia”. BBC News. London.

My maternal ancestors – from Eve via ice age Europe to Victorian England

In an early post on this blog, I summarized my maternal-line ancestors and where and when they lived. In the last 6 years, there have been substantial revisions to estimates of the dates associated with these mitochondrial DNA (mtDNA) haplogroup founders, and revisions to the mtDNA haplogroup tree (deep-maternal-ancestry-and-mtdna) and this post provides an update. I am a member of mtDNA haplogroup U5, which is one of nine native European haplogroups stemming from haplogroup U which most likely arose in the Near East, and spread into Europe in a very early expansion. The presence of haplogroup U5 in Europe pre-dates the last ice age and the expansion of agriculture in Europe. Today, about 11% of modern Europeans are the direct maternal descendants of the founder U5 woman. They are particularly well represented in western Britain and Scandinavia. My more recent maternal ancestors were part of the population that tracked the retreat of ice sheets from Europe at the end of the last ice age and re-colonized Britain about 12,000 years ago.

The mtDNA sequence at the root of each haplogroup arose from one or more mutations in the mtDNA of just one woman, and the age of the associated haplogroup gives the time in the past when this specific woman lived. To emphasise that the maternal clan founders were real individuals, I have used the names given to them by Sykes [1] and Oppenheimer [2] and given my own names to the more recent subgroup founders. The Table below summarizes these founders, dates and locations and is followed by brief biographies. The haplogroups are identified by the labels used in Build 17 of the ISOGG mtDNA tree which can be accessed at http://phylotree.org/ [3]. Dates in the table below have been updated using most recent available dating estimates as described in my previous post deep-maternal-ancestry-and-mtdna.

The migration path out of Africa into Europe of the “grandmothers” linking mitochondrial Eve through to Ursula (U5) is shown on a map in my previous post deep-maternal-ancestry-and-mtdna. The subsequent migration from Europe to Britain is shown in the map below.

Figure 1. Migration path of my maternal ancestors from Ursula (U5) to Viviane (410 CE). A map of the earlier migration from mitochondrial Eve to U5 is included in an earlier post.

Updated biographies of my maternal haplogroup great* grandmothers follow below.

Continue reading

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