Session 17: Episode 5(2) —

Genomics, our African genesis and family tree

William P. Hall President Kororoit Institute Proponents and Supporters Assoc., Inc. - http://kororoit.org william-hall@bigpond.com http://www.orgs-evolution-knowledge.net

Access my research papers from Google Citations

Tonight

Now that our ancient ancestors and close relatives have been introduced we will consider the historical facts so far as they can be determined.

– From comparing fossils and genomic information we can construct a more-or-less detailed family tree going back a million years or so

– From fossils and toolkits we can reconstruct geographic distributions

Fossils, tools, genomics and human migrations Oldowan origins in the crucible of the Rift valley “Out of Africa 1 (and 2?)” – what hominins from Dmanisi and Flores tell us Origin and spread of the Acheulean toolkit through Africa and Asia Fossil hominins in Europe prior to Homo sapiens Proliferation and genomics of the heidelbergensis species complex Triumph of anatomically modern Homo sapiens out of Africa to the world

Fossils & toolkits (“hardware”)

Earliest stone tools associated with hominin fossils found in East African & Ethiopian Rifts

Australopithecine tool making? – 3.4 mya, cut marked (i.e.

butchered) bones found at Dikika (McPherron Et Al 2010) – Ethiopian Rift

– 3.3 mya, oldest stone tools like Oldowan but larger, found in West Turkana area (Harmand et al. 2015) – East African Rift

Prior to above discoveries, oldest tools plausibly associated with Homo were found around

– Gona (2.6 mya) & Hadar (2.36 mya) – Ethiopian Rift

– Omo (2.34)– referenced in Harmand et al., and Lokalalei 2C between Omo and West Turkana (2.34 mya) in the East African Rift (Roche et al. 2009)

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Species IDed from the fossil record

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naledi newly discovered, small brained, mosaic of primitive and modern features from South Africa

Dmanisi Georgia - Variation in Dmanisi specimens show erectus, ergaster, & probably also rudolfensis and habilis might form one chronospecies persisting through time

floresiensis (Hobbit) lived up to a few thousand years ago on Flores (Indonesia) probably derived from Dmanisi erectus (Kubo et al. 2013) or possibly even Australopithecus (Stringer 2014)

erectus longest lived Homo, spread widely through Africa and (via Dmanisi?) Eurasia

antecessor fossils from N central Spain associated with Mode 1 tools – pre heidelbergensis ?

(rhodesiensis ) name sometimes applied to African branch of heidelbergensis probably ancestral to “out of Africa” sapiens

heidelbergensis Eurasian stock probably ancestral to neanderthalensis and Denisovans, probably derived from erectus – via antecessor ?

sapiens, neanderthalensis & Denisovans (Prüfer et al 2014) modern sibling species deriving from heidelbergensis - all using Denisova cave ad different times

After Wood, B. 2012.

H. naledi

?

?

H. erectus/rhodesiensis

Geographic spread of Homo away from E Africa based on fossil sites

Shows distribution of fossil sites attributed to Homo

– Bräuer is a “lumper”, does not recognize H. heidelbergensis as different from “primitive homo”

– ⓢ speciation events Brauer recognizes

Early exits from Africa – Dmanisi, Georgia –

possibly via Strait of Hormuz

– Sangiran, Indonesia – possibly along Indian Ocean coast

– Atapuerca, Spain – possibly two separate times via Strait of Gibralter 6 Bräuer (2008, 2012)

i.e., Indonesia

How do we know they are made tools?

“Refits” of pieces show clear evidence of intentional flaking.

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Increasingly complex/sophisticated tools help map spread of humans out of Africa

Mode 1 = Oldovan sharp edged pebbles & stones (on core)

Mode 2 = Acheulean bi-facial hand axes & cutting tools shows planned manufacturing (on flake)

Mode 3 = Mousterian industry (primarily used by Neanderthals)

Mode 4 = Arignacian industry – Variety of sophisticated stone &

bone tools (scrapers, bladelets) Mode 5 = Microlithic industries

making blades, points, etc. for use as parts of compound tools (arrows, sickles, awls, etc.)

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Temporal distribution of stone tools by putative species

9 Brooks 2000; Shea 2011, 2011a

Foley & Lahr 1997

Ocean currents affecting floresiensis colonization of Flores

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H. erectus

Biogeography: out of Africa

Alternative hypotheses for early exits from Africa (after Rightmire & Lordkipanidze 2010).

– Top: one species (H. erectus) evolved in Africa and spread through Eurasia. floresensis was an early

offshoot of erectus – Bottom: an early African Homo

spread to Eurasia, giving rise to erectus in Asia, that then returned to Africa. floresiensis ancestors may

have exited Africa prior to erectus

Common ancestor to sapiens, neanderthalensis, & denisovans may be erectus or another independent exit from Africa 11

After Rightmire & Lordkipanidze 2010

In this our direct ancestors’ first landfall in Eurasia?

Dating early human occupation of Eurasia (Dennell 2010) by fossils and/or tools

– Black bars = no evidence – Bold type = widely accepted – Light ? = controversial

Did erectus spread from Asia

Minor (Dennell 2010a) ? – Version 2

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Possible paths for early Homo to reach Western Europe

13 (Sirakov et al. 2010)

Most detailed record of fossils from early Homo out of Africa is from Europe

Earliest tools from western Europe (no hominin fossils found) – Biostratigraphically dated to 1.6-1.3 mya from Pirro Nord in

southern Italy (Arzarello & Peretto 2010; Pavia et al. 2012) – Radiometrically dated dated to 1.57 mya from Lezignan-la-Cebe,

France (Crochet et al. 2009). No hominin fossils have been found with these tools.

Earliest fossils are from Spain, H. antecessor (Bermudez de Castro et al. 1997, 2013),

– Dated from 1.22 mya and around 800 kya (Carbonell et al. 2008; Manzi 2011, 2012; MacDonald et al. 2012).

– Both dates ssociated with Mode 1 (Oldowan) tools. Few fossils are available between ~ 800 kya and ~ 700 kya

– most earlier and later specimens are fragmentary – difficult to define clear boundaries and infer genealogical

relationships among the various species based solely on morphological traits preserved by the fragments.

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Temporal and geographic distribution of homo in the strict sense based more or less on fossils & tools

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Genomics (“software”)

- Allows much more

precise reconstruction of relations & migrations of

H. sapiens and our closest relatives

What does genomics tell us

Data universe vastly larger than provided by fossils – Nuclear genomes: ~3 x 109 potential base-pair differences – Y-chromosome DNA: ~ 9 M male-specific base-pairs – Mitochondrial genome: matrilineally inherited 16,600 base-pairs

Analytical tools – Phyletic genealogies

Each mutation is a potential point of bifurcation – Genetic distances (i.e., % different) x estimated mutation rates

Accuracy improves with increasing numbers of data points – Linkage & genetic disequilibrium

Gene loci close together on a chromosome stay together longer and thus tend to be inherited as a package

Mitochondrial & Y-chromosome genes do not recombine – Measures of heterozygosity

Variability lost in small populations Reduced adaptability

– Comparative analysis 17

Latest genomics gives accurate genealogy for heidelbergensis siblings, splits and interspecific hybridization

High quality whole genomic DNA (Prüfer, K., et al. 2014)

mDNA from 300-400 kya fossil Homo (Meyer, et al. 2014) Nuclear DNA dates sapiens/Neanderthal separation to 700 kya and Neanderthal/ Denisovan to 500 kya (Gibbons 2015. Science 349, p. 1270)

Red arrows show inter-specific hybridization with introgression of genes and proportion of genome introgressed

4500 kya

Mitochondrial DNA shows stepwise genealogical derivation based on sequence of single nucleotide mutations 18

Genes not found in Neanderthal genomes H. erectus ?

700 kya

500 kya

Genetic distances from 2.3 M SNPs

19 Schlebusch et al. 2012, Lombard et al. 2013

Phyletics of 24,402 autosomal markers

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Southern African pops. show greatest diversity & variability

Variability reduced as distance increases from s. Africa

Probable consequence of selection & small population sizes of pops. on the leading edge of expansion

(Petersen et al. 2013)

mitochondrial DNA phylogeny of the “L” branchs in Africa

21 Behar et al. 2008

Time scale 200 kya+ years; LSA = Lower Stone Age

The “L” branch includes the most primitive mDNA sequences in human pops

Turquois shade comprise speakers of the Khoisan dialect

Lavender comprises all other Africans

Pink comprises most branches in the rest of the world mostly deriving from M & N – 7 major bifurcations down from the common ancestor with L0

Human migrations as mapped by mitochondrial DNA mutations

22 Wikipedia

Dating Y-chromosomal DNA lineage branches from 200 kya common ancestor Eurasian stocks down 5 branches

23 Scozzari et al. 2014

B2, E, C, & F found outside of Africa

Detailed Y-chromosome phylogeny

24 Hallast et al. 2015

Oldest known patrilineal bifurcation between any humans (A00 and A0, with 75 derived mutational differences in 180 kb) is estimated to be 239,000 years ago with a 95% CI of 188,000–296,000 years ago, not too different from that of 170,000–180,000 years ago for mitochondrial DNA (Helgason et al. 2015)

Human migrations based on uniparental DNA

25 Oppenheimer 2012

The spread of heidelbergensis derivatives as recorded in Neanderthal, Denisovan & sapiens’ nuclear genomes

“heidelbergensis” spreads across Africa & Eurasia. Mid Pleistocene split of Eurasian branch into Neanderthal & Denisovan. Denisovan lineage hybridizes with surviving “erectus”. Denisovan hybridizes with Neanderthal. African heidelbergensis directly ancestral to sapiens (Eurasians trace genetic ancestry to S. African lines). First sapiens crossing(s) into Levant ~190 kya(?) and 133-80 kya didn’t survive. Next crossing 70-60 kya hybridized with Neanderthals in Levant & spread across Eurasia. Early southern migrants to Australian shelf & Pacific islands hybridized with Denisovans but were replaced by more modern sapiens in Eurasia. Later dispersal of sapiens into Asia hybridized a second time with Neanderthals. H. sapiens remaining in Africa mix around ~35 kya with surviving separate Homo species that had diverged around 700 kya. 26

Veeramah & Hammer 2014

Next session begins to explore our first five million years “How did we become who we are now?”

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To this point I have summarized a vast array of evidence about the physical evidence for reconstructing hominin history leading to domination of the world by Homo sapiens (ourselves).

In the next session I begin to reconstruct the evolutionary circumstances that led humans to diverge from their close primate relatives to become something so completely new that our capacity to dominate our physical and biological environment has grown to the point where we are on the way to consuming the entire planetary biosphere.

– How and why did the divergence begin? – How has this shaped who we are today and are likely to become?

An Evolutionary Hypothesis: - Our First Five Million Years or “How Did We Get Here?” Life in the primeval forest The end of Eden and adapting to a hard life in a drier world with fewer trees What Can We Learn About Early Hominins from Chimpanzees and Capuchin Monkeys Cultural versus hereditary transmission of technological knowledge Where hominins have gone beyond chimpanzees and capuchins.

Next session starts in the Garden of Eden

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