Modern Primates - New Mexico State Universitylithornis.nmsu.edu/~phoude/human evolution_GoH.pdf ·...
Transcript of Modern Primates - New Mexico State Universitylithornis.nmsu.edu/~phoude/human evolution_GoH.pdf ·...
-
Modern Primates
-
Mammal Phylogeny based on Multispecies Coalescent analysis of 447 genes (Song et al 2012 Proc. Nat. Acad. Sci. USA)
-
Primate Phylogeny based on 8 Mb DNA sequence (Perelman et al. 2011 PLoS Genet)
-
Primates (extant “Euprimates”)
Strepsirrhini
Lemuriformes - lemurs
Lorisiformes - lorises and galagos
Haplorhini
Tarsiiformes - tarsiers
Anthropoidea or Simiiformes - monkeys and apes
Platyrrhini - New World monkeys and marmosets
Catarrhini - Old World monkeys and apes
Cercopithecoidea - Old World monkeys
Hominoidea - humans and apes
Hylobatidae - gibbons, siamangs
Hominidae
Ponginae - Orangutan
Homininae - Human, Chimps, Gorillas
-
Primates
Strepsirhini “pro-simians”
Haplorhini
Platyrrhini New World monkeys and marmosets
Catarrhini Old World monkeys and apes
Family Hominidae “great apes”
Lorisiformes Tarsiiformes
Lemuriformes
“simians” or
“anthropoids”
Cercopithecoidea Old World monkeys
Hominoidea apes
Subfamily Homininae Genus Homo and extinct relatives
Family Hylobatidae “lesser apes” (gibbons)
-
Scandentia – Tree Shrews 20 species Southeast Asia
-
Dermoptera – Colugos or “Flying Lemurs” 2 species Phillipines, Southeast Asia
-
Purgatorius - earliest Paleocene Montana
earliest known possible primate
known (with certainty) only from isolated cheek teeth
-
“Plesiadapiformes” – questionably primates
~9 families, many highly derived
e.g., Carpolestidae Paleocene-Eocene North America
-
Pesiadapis Paleocene-Eocene North America/Europe
-
Teihardina
early Eocene China
earliest Euprimate (true primate)
Evidence that early euprimates
were arboreal, diurnal,
predators
-
Strepsirrhini Lemuriformes Madagascar
-
Strepsirrhini Lorisiformes
Lorises India, SE Asia
Galagos Africa
-
Tarsier SE Asia
-
Adapis
Darwinius
Middle Eocene Adapidae –
stem Strepsirrhines
Notharctus
-
Afrotarsius and Afroasia
late middle Eocene to Oligocene
Egypt, Lybia, Myanmar
presumed Earliest Haplorrhines
known only from isolated cheek teeth
-
Victoriapithecus
Catopithecus
Aegyptopithecus Earliest Catarrhines
Late Eocene to Oligocene
Africa
-
Earliest possible Hominoids
Proconsul Miocene 25-23 MY East Africa
-
Earliest Hominoids
Dryopithecus
Miocene Africa, Eurasia
-
Earliest Hominoids
Sivapithecus (Ramapithecus)
Miocene 12.2 MY India
-
Earliest Hominoids
Oreopithecus
Miocene 9-7 MY Italy
-
Phylogeny of Hominidae
guenons gibbons orang gorilla chimps human
-
Possible earliest Homininae
Miocene Africa
inferred habitual bipedality
some with reduced canines
Sahelanthropus Chad 7 - 6 MY
inferred habitual bipedality
reduced canines
Orrorin – Kenya 6.0 - 5.7 MY
inferred habitual bipedality
Ardipithecus kadabba Ethiopia
5.77 - 5.54 MY
obligate bipedality
reduced canines
Ardipithecus ramidus Ethiopia
4.51 - 4.32 MY
obligate bipedality
reduced canines
-
Possible earliest Homininae
Miocene Africa
inferred habitual bipedality
some with reduced canines
Sahelanthropus Chad 7 - 6 MY
Orrorin – Kenya 6.0 - 5.7 MY
Ardipithecus kadabba Ethiopia
5.77 - 5.54 MY
Ardipithecus ramidus Ethiopia
4.51 - 4.32 MY
-
Some Key Homininae Taxa listed in reverse order of age
Ardipithecus ramidus 4.51 - 4.32 MY
Australopithecus afarensis 3.9 - 2.9 MY
Australopithecus africanus 3.8 - 2.0 MY
Homo habilis 2.8 – 1.5 MY
Homo ergaster 1.9 – 1.4 MY
Homo erectus 1.9 MY – 70,000 yrs
Homo neanderthalensis 230,000 – 30,000 years
Homo floresiensis 94,000 – 13,000 yrs
Homo naledi – age unknown
-
Sahelanthropus tchadensis 6-7 MYA
Africa, bipedal?
Gorilla
-
Australopithecus anamensis 4.2 – 3.9 MY Kenya, Ethiopia
probably partly arboreal
-
Australopithecus afarensis 3.9 – 2.9 MY Ethiopia
cranial capacity 380-430 cc, bipedal, possibly partly arboreal
-
Australopithecus africanus 2 - 3.3 MYA Africa
cranial capacity 420-500 cc, bipedal, partly arboreal
Chimpanzee
-
Paranthropus spp. – robust australopithecines
Africa, evolutionary off-shoot, specialized for nut-cracking
-
Key finding bipedalism came first
increased brain size came later
-
Homo habilis 1.5-2.4 MYA Africa, possibly Asia
cranial capacity 500-800 cc, Oldowan tool culture
-
Homo ergaster (possibly African Homo erectus)
1.9 – 1.4 MY MYA Southern Africa, possibly central Europe
possibly the first hominin to vocalize, Oldowan and Achuelean tool cultures
-
Homo erectus 1.8 MY – 300,000 years, Africa and Asia
Cranial capacity 750-1225 cc Acheulean tool culture, fire use
-
Homo heidelbergensis (rhodesiensis) – “archaic Homo sapiens”
900,00 - 200,000 years, Africa, Europe
Probable funerary practice, Achuelean tool culture
-
Homo neanderthalensis 230,000 – 30,000 years Europe, Middle East
Cranial capacity 1350-1450 cc
http://images.google.com/imgres?imgurl=http://www.nature.com/nature/journal/v395/n6702/images/395539aa.eps.2.gif&imgrefurl=http://www.nature.com/nature/journal/v395/n6702/fig_tab/395539a0_F1.html&usg=__kEr8AOLs-Ec_ajM0n-airKLe7jY=&h=554&w=600&sz=232&hl=en&start=21&tbnid=vSsIZYA8dy1DXM:&tbnh=125&tbnw=135&prev=/images%3Fq%3Dneanderthal%2Bskull%26start%3D20%26gbv%3D2%26ndsp%3D20%26hl%3Den%26sa%3DNhttp://images.google.com/imgres?imgurl=http://karmak.org/archive/2003/01/westasia_files/amudrt.jpg&imgrefurl=http://karmak.org/archive/2003/01/westasia.htm&usg=__Zqrh6JqOaqi2kGOULW_tglUXQOU=&h=288&w=340&sz=20&hl=en&start=30&tbnid=MJTmXHRIV1L00M:&tbnh=101&tbnw=119&prev=/images%3Fq%3Dneanderthal%2Bskull%26start%3D20%26gbv%3D2%26ndsp%3D20%26hl%3Den%26sa%3DNhttp://images.google.com/imgres?imgurl=http://www.mnh.si.edu/anthro/humanorigins/ha/images/Bh3.jpg&imgrefurl=http://ahotcupofjoe.wordpress.com/page/12/&usg=__8-48faMG6vF0Lbp9VPnH_aqyB-A=&h=255&w=383&sz=11&hl=en&start=32&tbnid=dqhCpHI9so71vM:&tbnh=82&tbnw=123&prev=/images%3Fq%3Dneanderthal%2Bskull%26start%3D20%26gbv%3D2%26ndsp%3D20%26hl%3Den%26sa%3DN
-
Homo neanderthalensis multiple tool technologies
Mousterian Keilmessergruppen Levallois
-
Homo neanderthalensis
Introgressive hybridization
with modern Homo sapiens
-
Neanderthal Introgression
Up to 2% Neanderthal in non-Africans, highest in East Asians
presumably due to smaller populations (Sankararaman et al Nature 2014 Mar 20;507(7492):354-7)
Neanderthal alleles that affect skin and hair may have helped
modern humans to adapt to non-African environments
Multiple Neanderthal-derived alleles confer risk for disease, i.e.,
lupus, biliary cirrhosis, Crohn’s disease, optic-disk size, smoking
behavior, type 2 diabetes, suggesting that Neanderthal alleles
continue to shape human biology
Neanderthal-derived sex-linked genes are reduced 5-fold
compared to autosomal genes, suggesting strong selection for
hybrid sterilty
Denisovan Introgression
4-6% Denisovan in Melanesians (Reich et al Nature Nature 468, 1053–1060 (23 December 2010)
-
Homo neanderthalensis
funerary practice
cannabalism
care for the invalid
use of pigments
body ornamentation
-
Discoveries still being made
Homo floresiensis estimated 18,000 years, Indonesia
1 meter tall
Other recent discoveries include Homo naledi and Denisova
-
from left to right: Australopithecus africanus, 2.5 million years old; Homo rudolfensis,
1.9 million years old; Homo erectus, ~ 1 million years old; Homo heidelbergensis,
~350,000 years old; Homo sapiens, ~ 4,800 years old (Photo Credit: Chip Clark, Jim DiLoreto, & Don Hurlbert, Smithsonian Institution)
-
SRGAP2 gene
duplicated in humans but not in other primates
slows the rate of synaptic maturation and increases the density of synapses in
the cerebral cortex
duplicated in the human genome three times: 3.4, 2.4 MY, and 1 million years
ago.
the 2.4 MY duplication is present in 100% of all humans
-
modern Homo sapiens 160,000 - present
40,000 – 30,000 yrs painting, jewelry, carving
11,000 yrs agriculture, 6,000 yrs metallurgy
-
Timeline of Human Dispersal
-
African populations are genetically the
most diverse and earliest divergences
among modern humans (based on 1327
microsatellite and indel loci).
Tishkoff et al Science. 2009 May 22; 324(5930): 1035–1044.
-
Africa
All modern human genotypes coalesce to 150-200,000 years ago
Central and Northern Asia
Mitochondrial haplogroups A, B, and G originated about 50,000 years ago, and
bearers subsequently colonized Siberia, Korea, and Japan by about 35,000 years
ago
Newly discovered teeth date modern humans in southern China 80,000 years ago (Liu et al Nature 526: 696 29 October 2015)
Americas
Paleo-Indians originated from Central Asia, crossing the Bering Land Bridge
between eastern Siberia and present-day Alaska. Humans lived throughout the
Americas by the end of the last glacial period. Dates for Paleo-Indian migration
out of Beringia range from 40,000 to around 16,500 years ago
-
Migration of modern humans into Europe
It may have taken 15-20,000 yrs for Europe to be colonized
37,500 yrs 35,000 yrs 32,500 Yrs 30,000 yrs
https://en.wikipedia.org/wiki/File:Cro-Magnon_range_37,500_ybp.svghttps://en.wikipedia.org/wiki/File:Cro-Magnon_range_35,000_ybp.svghttps://en.wikipedia.org/wiki/File:Cro-Magnon_range_32,500_ybp.svghttps://en.wikipedia.org/wiki/File:Cro-Magnon_range_30,000_ybp.svg
-
Native Americans represent at least three waves of
migrants from Asia
Nearly all the populations from Aleut people in Alaska to the Yaghan in
Chile originated from a single migration across the Bering land bridge
Southern populations have less genetic diversity than northern,
suggesting that their ancestors travelled quickly, probably along the
West Coast, winnowing down diversity as they moved
two later migrations from Asia gave rise to Inuit people of
Greenland and Chipewyan people from west of Hudson Bay in northern
Canada
-
Rasmussen et al. Nature 506, 225-229 (2014)
Anzick-1 Clovis gene flow from Siberian Upper Palaeolithic Mal’ta into Native American
ancestors before 12,600 years BP
-
Relationships of Anzick-1 Clovis
-
Relationships of Anzick-1 Clovis
-
above, SNP Polymorphisms private to a population, private to a continental
area, shared across continental areas, and shared across all continents
right, the number of
variant sites per
genome Sherry et al Nature 526 Oct 2015
Human populations are highly differentiated but also highly introgressed
-
Principal components analysis of individual
genotypes. (A) Global data set and (B) African
data set.
Tishkoff et al Science. 2009 May 22; 324(5930): 1035–1044.
-
Geographic and genetic
structure of populations within
Africa.
(A) Geographic discontinuities
among African populations
assuming no population
admixture.
(B) Genetic structure showing
admixture of 14 ancestral
population clusters that
correlate with self-described
ethnicity and shared cultural
and/or linguistic properties.
High levels of mixed ancestry in
most populations reflect
historical migration events
across the continent.
Tishkoff et al Science. 2009 May 22; 324(5930): 1035–1044.
-
Human populations are highly differentiated but also highly
introgressed
Mapped Structural Variants among 2,504 living humans
Deletion (biallelic) 42,279
Duplication (biallelic) 6,025
Copy number variants (CNV) 2,929
Inversion 786
Mobile element insertions (MEI) 16,631
Nuclear mitochondrial translocations(NUMT) 168
Collapsing multiple copies of CNVs and homozygous SVs onto the haploid
reference assembly, a median of 8.9Mbp of sequence are affected by SVs,
compared to 3.6Mbp for SNPs
median 18.4 Mbp of SVs per diploid genome (CNVs 11.3 Mbp, biallelic
deletions 5.6Mbp)
65% of structural variants occur at a frequency of 0.2% and are specific to
individual continental groups
nearly all structural variants with frequency >2 % are shared across
continents Sudmant et al Nature 2015 Oct 1;526(7571):75-81
-
1000 Genomes Project Consortium Nature 2015 Oct 1;526(7571):68-74
Unmapped Variants among 2,504 living humans from 26 populations
single nucleotide polymorphisms (SNPs) 84.7 million
short insertions/deletions (indels) 3.6 million
structural variants 60,000
The typical human genome
99.9% of variants consist of SNPs and short indels
2,100 to 2,500 structural variants (1,000 large deletions, 160 copy-number
variants, 915 Alu insertions, 128 L1 insertions, 51 SVA insertions, 4
NUMTs, and 10 inversions) total ~20 million bases of sequence
differs from the reference human genome at 4.1 million to 5.0 million sites
~2,000 variants per genome associated with complex traits
24–30 variants per genome implicated in rare disease
-
Human populations are highly differentiated but also highly
introgressed
1000 Genomes Project Consortium Nature 2015 Oct 1;526(7571):68-74
86% of rare variants restricted to a single continental group
but most variants in any individual are common and shared among continents
east–west clines exist in Africa and East Asia
north–south cline exists in Europe, Europe, and Africa
Native-American admixture exists in the Americas
-
Population Bottlenecks
There is evidence that the first human bottleneck occurred ~50,000 years ago
when founding populations emigrated from Africa
Europeans, Asians, and Americans appear to share a strong and sustained
bottleneck (Ne 4,250) (1000 Genomes Project Consortium Nature 2015 Oct 1;526(7571):68-74)
Evidence from Y-chromosomes suggest another bottleneck occurred only in
males between 4-8,000 years ago during a period of global growth
There was a dramatic decline in genetic diversity in male lineages with the
advent of agriculture, likely the result of the accumulation of material wealth
In contrast, female genetic diversity (based on the mitochondrial chromosome)
was on the rise during this same period
This genetic structure may predispose some populations to certain types of
genetic disorders
-
Hereditary inequality began over 7,000 years ago in
Europe in the early Neolithic era
The Neolithic era introduced heritable property (land and livestock) into
Europe and that wealth inequality got underway when this happened
Strontium isotope analysis of >300 skeletons
indicated that men buried with stone adzes
had less variable isotope signatures than men
buried without adzes
Early Neolithic women were more likely to
have originated from other areas, indicating
a male-centered kinship system in which
females move to reside in the location of the
males when they marry
-
64% of European Men are Descended from
just Three Bronze Age Warlords between
3,500 to 7,300 years ago (Batini et al Nature Communications 6: 7152 (2015)
-
11 dynastic leaders
believed contributed
disproportionately to
the genetic legacy of
Asia
Genghis Khan 12-13th century, with
~16 million descendants
Giocangga 16th century, with ~1.5
million descendants
nine other dynastic leaders of Asia
dating from 2100 BC and 700 AD
(Balaresque et al European Journal of Human
Genetics (2015) 23, 1413–1422)
Nurhaci, grandson of Giocangga.
-
Are humans still evolving?
10%–20% of amino acid changes have been adaptive, i.e.,
show signatures of selection, in human evolution (Messer & Petrov 2013 Proc Natl Acad Sci 110: 8615–8620)
There have been approximately 100 strong selective sweeps
in humans in the past 100,000 years; these occurred primarily
in regulatory rather than coding regions (Enard et al Genome Res. 2014 Jun;24(6):885-95 )
The signals of positive selection are evident in all human
populations, but stronger in the “out-of-Africa” populations,
although this could be artifactual due to demographic or other
reasons
-
The agricultural revolution 8,500 years ago in
Eurasia witnessed the appearance of genetic
variants associated with height, lactase
persistence, fatty acid metabolism, vitamin D
levels, light skin pigmentation and blue eye color,
and immunity
Two variants appear on genes that have been
linked to higher risk of coeliac disease but that may
have been important in adapting to an early
agricultural diet (Mathieson et al Nature 30 October 2015)
-
Lactase Persistence in Europeans
Ancient hunter-gatherers in Europe could not digest milk 8,000
years ago
The ability to do so only came about 4,300 years ago
Skin color in Europeans
7,700 year old remains from Sweden had light skin, blonde hair,
and blue eyes
8500 year old hunter-gatherers in Spain, Luxembourg, and
Hungary had dark skin and hair but a 7,000 yr old Spaniard had
dark hair and the dark-skinned genes of an African but blue
eyes
Central and Southern Europeans acquired genes for light skin
at about 5,800 yrs ago with admixing from the Near East
-
Domestication of Livestock
Estimates on the age of domestication of
dogs varies from 11-16,000 years ago to
27-40,000 years ago
Cattle were domesticated from wild
aurochs in the Anatolian Fertile Crescent
around 10,500 years ago (Orlando Genome Biology (2015) 16:225)
Horses appear to have first been
domesticated in Eurasian steppes about
4,000 years ago
12,000 yr old human dog burial in Israel
30,000 yr old auroch painting in France
Ocellated turkey
-
Domestication of Plants
Earliest evidence in Southwest Asia and the Middle East to about 11,050
years ago
Americas (~9,000 yrs ago) – squash, maize, beans, cassava, potatoes
East Asia – millet, rice, soy
Middle East – peas, wheat
-
Independent Centers of Plant Domestication
Smith PNAS 2006;103:12223-
12228
-
Metallurgy
Technology that facilitated agriculture, warfare, transport, cooking, and
industrialization
Native copper fashioned into knives and sickles from about 7000 BC in Anatolia
Copper ore mined from deep shafts and smelted since 4000 BC at Rudna Glava in
the Balkans and by about 3800 BC in the Sinai
peninsula
Bronze (alloy of copper and tin) first developed
in the Middle East around 2800 BC
Egyptians made weapons of native meteoric iron
from about 3000 BC
Hittites first smelted iron in Anatolia from about
1500 BC
Cast iron historically recorded in China to 513 BC
-
Conquerors and Imperialism – has and continues to shape human evolution through
genocide, both concentration and deprivation of resources,
migration and introgression, socialization, and cultural
phenomena (e.g., language, technology, religion, hygiene,
education) that have changed selective pressures and
paradoxically increased
civilization
-
Timeline of early civilizations
-
Throughout human evolution there has been a
proliferation of social groups, languages, and religions
from just a few ancestral forebears
In general this is manifested as social bonding within
groups and competition between groups
Bases for social identity
Language – 7,106 registered languages worldwide
Religion – roughly 4,200 religions worldwide
Political boundaries – there are currently 196 countries and
roughly 5,000 indigenous tribes worldwide
Wealth
-
Language – 7,106 registered languages worldwide
http://www.sil.org/
-
Origins of Major Languages
http://www.linguisticsociety.org/
-
Long-Distance Trade
Estimates as old as 150,000 yrs (Watson 2005. Ideas: A History of Thought and Invention from Fire to Freud. New York: Harper Collins; Smith 2008. Premodern trade in World History. Taylor and Francis)
Trade in flint and obsidian in Africa from 17,000 BC, in North America from
10,000 BC
-
Money
Native gold nuggets have been found in archaeological context from
40,000 years ago
Earliest forms of commodity money (i.e., obsidian, grains, cattle, cowry
shells) to at least 9,000 BC
2400 BC in the kingdom of Ur in Mesopotamia, accounts were being kept
using weights of silver
Gold has been considered valuable since at least 4000 BC. In about 1500
BC in Egypt, gold became the recognized standard medium of exchange
for international trade.
Earliest coinage (bronze spade money) from about 1000 BC
in China and manufactured coins from 700-500 BC in India,
China, and Aegean Sea
Chinese spade money 1200-800 BC
-
Will Humans Continue to Evolve? – with the advent of medical interventions, gene editing to correct
hereditary disease, and our ability to modify our environment in
ways that remove preexisting selective pressures?
Biological evolution is the change in frequency of heritable
characteristics, i.e., genotype frequency (and epigenetic factors,
as we are now coming to realize)
In the absence of continued selection, mutation and drift are
expected to alter allele and genotype frequency and thus erode
existing adaptations – indeed, this would be evolution albeit
nonadaptive
It is also relevant that not all people have equal access to the
aforementioned benefits of society due to social, economic, and
political factors that are themselves selective agents
There are and will continue to be new technology-driven skills,
social, economic, political, and environmental (nutrition,
environmental toxins) selective pressures
-
Will Humans Continue to Evolve?
Based on NOAA record-keeping beginning in 1880
• The three hottest years on record have occurred in the last 10 years
• Nine of the 10 hottest years on record have occurred in the 21st century
• Thirteen of the 15 the hottest years on record have occurred in the last 15
years
• All 15 years from 2000 on have been among the top 20 warmest years on
record
• The last 358 months in a row have been warmer than the 20th-century
average
Based on fossil foraminifera
• It took 4,000 years for the world to warm about 1.25 degrees from the end
of the ice age to about 7,000 years ago. A similar level of warming occurred
from the 1920s to the 1940s (Marcott Science)
• There is no precedent for this heat spike as far back as 11,000 years
• It may have been 125,000 years since there have been temperatures
rivaling today's
-
NASA data; Hansen et al 2006 Global temperature change. PNAS 103: 14288-14293
-
Global Warming already has
- caused changes in fisheries industries by increased temperature and
acidification, resulting in changes in distribution, poisonous algal blooms,
and die-offs
- begun opening arctic ice sheets leading to increased political tension
vying for undersea mineral and petroleum resources
- increased frequency and severity of extreme climatic events (drought,
fires, flooding, storms) leading to increased spending on disaster relief
- increased coastal flooding that is making low-lying areas uninhabitable