Mammal Phylogeny based on Multispecies Coalescent analysis of 447 genes (Song et al 2012 Proc. Nat. Acad. Sci. USA)

Size: px

Start display at page:

Download "Mammal Phylogeny based on Multispecies Coalescent analysis of 447 genes (Song et al 2012 Proc. Nat. Acad. Sci. USA)"

Primrose Kelley
5 years ago
Views:

1 Modern Primates

2 Mammal Phylogeny based on Multispecies Coalescent analysis of 447 genes (Song et al 2012 Proc. Nat. Acad. Sci. USA)

3 Primate Phylogeny based on 8 Mb DNA sequence (Perelman et al PLoS Genet)

5 Primates (extant Euprimates ) Strepsirhini 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

6 Primates Strepsirhini pro-simians Haplorhini Lorisiformes Lemuriformes Tarsiiformes simians or anthropoids Platyrrhini New World monkeys and marmosets Catarrhini Old World monkeys and apes Hominoidea apes Cercopithecoidea Old World monkeys Family Hylobatidae lesser apes (gibbons) Family Hominidae great apes Subfamily Homininae Genus Homo and extinct relatives

7 Scandentia Tree Shrews 20 species Southeast Asia

8 Dermoptera Colugos or Flying Lemurs 2 species Phillipines, Southeast Asia

9 Purgatorius - earliest Paleocene Montana earliest known possible primate known (with certainty) only from isolated cheek teeth

10 Plesiadapiformes questionably primates ~9 families, many highly derived e.g., Carpolestidae Paleocene-Eocene North America

11 Plesiadapis Paleocene-Eocene North America/Europe

12 Teihardina early Eocene China earliest Euprimate (true primate) Evidence that early euprimates were arboreal, diurnal, predators

13 Strepsirhini Lemuriformes Lemurs Madagascar

14 Strepsirhini Lorisiformes Galagos or bush babies Africa Lorises India SE Asia

15 Middle Eocene Adapidae stem Strepsirhines Darwinius Adapis Notharctus

16 Haplorhini Tarsiiformes Tarsier SE Asia

17 Afrotarsius and Afroasia late middle Eocene to Oligocene Egypt, Lybia, Myanmar presumed earliest Haplorhines known only from isolated cheek teeth

18 Earliest Catarrhines Late Eocene to Oligocene Africa Aegyptopithecus MY Victoriapithecus MY Catopithecus MY

19 Earliest possible Hominoids Proconsul Miocene MY East Africa

20 Earliest Hominoids Dryopithecus Miocene 12-9 MY Africa, Eurasia

21 Earliest Hominoids Sivapithecus (Ramapithecus) Miocene 12.2 MY India

22 Earliest Hominoids Oreopithecus Miocene 9-7 MY Italy

23 Phylogeny of Hominoidea guenons gibbons orang gorilla chimps human Hylobatidae Ponginae Hominidae Homininae Cercopithecoidea Hominoidea

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.

25 Possible earliest Homininae Miocene Africa inferred habitual bipedality some with reduced canines Sahelanthropus Chad 7-6 MY inferred habitual bipedality reduced canines Orrorin Kenya MY inferred habitual bipedality Ardipithecus kadabba Ethiopia MY obligate bipedality reduced canines Ardipithecus ramidus Ethiopia MY obligate bipedality reduced canines

26 Possible earliest Homininae Miocene Africa inferred habitual bipedality some with reduced canines Sahelanthropus Chad 7-6 MY Orrorin Kenya MY Ardipithecus kadabba Ethiopia MY Ardipithecus ramidus Ethiopia MY

27 Some key hominine taxa listed in reverse order of age Sahelanthropus tchadensis 7-6 MYA Ardipithecus ramidus MY Australopithecus afarensis MY Australopithecus africanus MY Homo habilis MY Homo ergaster MY Homo erectus 1.9 MY - 70,000 yrs Homo naledi 335, ,000 yrs Homo neanderthalensis 230,000-30,000 years Homo floresiensis 94,000-13,000 yrs

29 Sahelanthropus tchadensis 7-6 MYA Africa, bipedal? Gorilla

30 Australopithecus anamensis MY Kenya, Ethiopia probably partly arboreal

31 Australopithecus afarensis MY Ethiopia cranial capacity cc, bipedal, possibly partly arboreal

32 Australopithecus africanus MY Africa cranial capacity cc, bipedal, partly arboreal Chimpanzee

33 Paranthropus spp. robust australopithecines Africa, evolutionary off-shoot, specialized for nut-cracking

34 Key finding bipedalism came first increased brain size came later

35 Homo habilis MY Africa, possibly Asia cranial capacity cc, Oldowan tool culture

Homo ergaster (possibly African Homo erectus) 1.9-1.

36 Homo ergaster (possibly African Homo erectus) MY Southern Africa, possibly central Europe possibly the first hominin to vocalize, Oldowan and Achuelean tool cultures

37 Homo erectus 1.8 MY - 300,000 years, Africa and Asia Cranial capacity cc Acheulean tool culture, fire use

38 Homo heidelbergensis (rhodesiensis) archaic Homo sapiens 900,00-200,000 years, Africa, Europe Probable funerary practice, Achuelean tool culture

39 Homo neanderthalensis 230,000-30,000 years Europe, Middle East Cranial capacity cc

40 Homo neanderthalensis multiple tool technologies Mousterian Keilmessergruppen Levallois

41 Homo neanderthalensis Introgressive hybridization with modern Homo sapiens

42 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 sterility Denisovan Introgression 4-6% Denisovan in Melanesians (Reich et al Nature Nature 468, (23 December 2010)

43 Homo neanderthalensis funerary practice cannabalism care for the invalid use of pigments body ornamentation

44 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)

45 Discoveries still being made Homo floresiensis discovered in 2003 estimated 18,000 years, Indonesia, 1 meter tall

46 Discoveries still being made Denisovan discovered 2010 in cave in Siberia from which Neanderthals were already known originally only a phalanx (finger bone), now teeth of three other individuals Introgression 17% of Denisovan genome is of Neanderthal origin 3-5% of modern aboriginal Australian and Melanesian genomes are Denisovan

47 Discoveries still being made Homo naledi thousands of bones discovered in 2013 in South Africa

49 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 (approximately coeval with first fossil occurrence of Homo and marked increases in brain size) the 2.4 MY duplication is approximately coeval with first fossil occurrence of archaic Homo sapiens (i.e, Homo heidelbergensis)

50 modern Homo sapiens 160,000 - present 40,000 30,000 yrs painting, jewelry, carving 11,000 yrs agriculture, 6,000 yrs metallurgy

51 Timeline of Human Dispersal

52 Africa All modern human genotypes coalesce to ,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: 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

53 African populations are genetically the most diverse and earliest divergences among modern humans (based on 1327 microsatellite and indel loci). Tishkoff et al Science May 22; 324(5930):

54 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

55 Anzick-1 Clovis gene flow from Siberian Upper Palaeolithic Mal ta into Native American ancestors before 12,600 years BP Rasmussen et al. Nature 506, (2014)

56 Relationships of Anzick-1 Clovis

57 Principal components analysis of individual genotypes. (A) Global data set and (B) African data set. Tishkoff et al Science May 22; 324(5930):

58 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

59 Relationships of Anzick-1 Clovis

Human populations are highly differentiated but also highly introgressed above, SNP Polymorphisms private to a population, private to a continental

60 Human populations are highly differentiated but also highly introgressed 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

61 Human populations are highly differentiated but also highly introgressed 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 1000 Genomes Project Consortium Nature 2015 Oct 1;526(7571):68-74

62 Mapped Structural Variants among 2,504 living humans Deletions (biallelic) 42,279 Duplications (biallelic) 6,025 Copy number variants (CNV) 2,929 Inversions 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

63 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 LINE1 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 variants per genome implicated in rare disease 1000 Genomes Project Consortium Nature 2015 Oct 1;526(7571):68-74

64 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 <1,500) between 15,000 to 20,000 years ago, while African populations experienced a less-severe bottleneck during the same time period (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

66 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

67 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.

68 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, ) Nurhaci, grandson of Giocangga.

69 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: ) 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 Jun;24(6): ) 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

70 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)

71 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

27-40,000 years ago Cattle were domesticated from wild

years ago (Orlando Genome Biology (2015) 16:225) 30,000

first been domesticated in Eurasian steppes about 4,000

72 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) 30,000 yr old auroch painting in France Horses appear to have first been domesticated in Eurasian steppes about 4,000 years ago Ocellated turkey 12,000 yr old human dog burial in Israel

Americas (~9,000 yrs ago) squash, maize, beans,

73 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

74 Independent Centers of Plant Domestication Smith PNAS 2006;103:

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

76 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

77 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

78 Timeline of early civilizations

79 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

80 Language 7,106 registered languages worldwide

81 Origins of Major Languages

Long-Distance Trade Estimates as old as 150,000 yrs (Watson 2005. Ideas: A History of Thought and Invention from Fire to Freud.

82 Long-Distance Trade Estimates as old as 150,000 yrs (Watson Ideas: A History of Thought and Invention from Fire to Freud. New York: Harper Collins; Smith 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

83 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 BC in India, China, and Aegean Sea Chinese spade money BC

84 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

85 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

86 NASA data; Hansen et al 2006 Global temperature change. PNAS 103:

for undersea mineral and petroleum resources - increased frequency and severity of extreme climatic events (drought, fires,

87 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

Mammal Phylogeny based on Multispecies Coalescent analysis of 447 genes (Song et al 2012 Proc. Nat. Acad. Sci. USA)

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