Comparing genes across linguistic families

Comparing genes across

linguistic families

Guido Barbujani

Princeton, Institute of Advanced Study October 2014

“If we possessed a perfect pedigree of mankind, a genealogical arrangement of the races of man would afford the best classification of the various languages now spoken throughout the world...”

-Charles Darwin, The Origin of Species, 1859

In turn, language data are useful to help us understand biological diversity and migration processes

AC

B

History

A common language frequently signifies a common origin and a related language indicates a common origin further back in time. Such commonality of origin should be reflected by genetic relationship, despite several complicating factors.

Robert R. Sokal (1988) Proc. Natl. Acad. Sci. USA

Summary

1.Migrations are population, not molecular, processes

2.Classical comparisons of genes and languages

3.The trouble with the vocabulary and an alternative approach

4.Comparing genes across language families

Fig. 1. The first principal component of gene frequencies from 38 independent alleles at the human loci: ABO, Rh, MNS, Le, Fy, Hp, PGMi, HLA-A, and HLA-B. Shades indicate different intensities of the first principal component, which accounts for 27 percent of the total variation

It all began from this

P. Menozzi, A. Piazza & L.L. Cavalli-Sforza (1978) Science

Continentwide genetic gradients in Europe

L.L. Cavalli-Sforza et al. (1994) Science

Diffusion of Neolithic artifacts in Europe

P. Balaresque et al. (2010) PLoS Biology, interpolated from data by R. Pinhasi et al.

Rationale for the proposal of a Neolithic demic diffusionEuropean genetic diversity distributed in gradients. Only gene flow can generate such patterns on the continental scale

No documented migration in post-Neolithic times spanning the area from the Levant to the Atlantic coasts

Neolithic technologies may have spread by cultural contact or by migration (most likely, by a combination thereof)

Diffusion of Neolithic artifacts cannot produce genetic clines if it is caused only by cultural contacts

Demic diffusion: expanding Neolithic people carried in Europe their know-how, their genes, and perhaps their languages too.

E. Kitchen et al. (2009) Proc. R. Soc. B

Their languages too?

C. Renfrew (1987) Archaeology and language: The puzzle of Indo-European origins

Their languages too?

Conditions for the origin of genetic gradients by demic diffusion

1. Demographic growth of farmers

2. Diffusion, incomplete admixture

3. Farmers continue to grow in numbers, hunter-gatherers don’t

A.J. Ammerman & L.L. Cavalli-Sforza (1984) The NeolithicTransition and the Genetics of Populations in Europe

But…

0. Low population density

In the first DNA studies (mtDNA) very old ages are estimated for the

main European mutations

“Each cluster can be assigned, in its entirety, to one of the proposed migration phases; the age of each cluster approximates very closely the timing of the migratory event”

“The main mitochondrial variants in Europe predate the Neolithic expansion”

(M. Richards et al. (1996, 2000) Am. J. Hum. Genet.

Estimated ages of mitochondrial haplogroups (x 1000)

Richards Sykes Richards et al. 1996 1999 et al. 2000

H 23.5 11.0-14.0 15.0 - 17.2 J 23.5 8.5 6.9 - 10.9 T 35.5 11.0-14.0 9.6 - 17.7 IWX 50.5 11.0-14.0

X: 20.0 I: 19.9 - 32.7 K 17.5 11.0-14.0 10.0 - 15.5 U 36.5 5: 50.0 44.6 - 54.4

Neolithic contribution overestimated in preDNA studies? Hans Bandelt

Haplogroup H, “the signature of the Paleolithic expansion in Europe”

Two basic models

Palaeolithic model Neolithic model (Cultural diffusion of food- (Demic diffusion of food- production technologies production technologies

G. Barbujani (2012) Curr. Biol.

Ok folks, all those with haplogroup H come with me, let’s do the Paleolithic

migration. No way Steve, not you. You’re a J, damn it, a J! Wait until the Neolithic!

“Each cluster can be assigned, in its entirety,to one of the proposed migration phases; the age of each cluster

approximates very closely the timing of the migratory event”

Ancient DNA evidence: Neolithic Europeans did not only carry the J hg, no evidence of the H hg in Paleolithic Europeans

20,00055,00045,0007,70022,70013,60012,000

Haplogroup estimated age

21 pre-neolithic hunter-gatherers 105 Nolithic farmers

Post Pr (Model B): 1,655 to 2,691 folds as high as Post Pr (Model A)

Genetic continuity since Paleolithic times very unlikely in ABC analyses of mtDNA

2 individuals from the Upper Paleolithic, 43 from the Mesolithic (including the two La Braña specimens) and 121 from the Neolithic

It is people who migrate, not haplogroupsHaplogroup ages are not estimates of migration times

Summary

1.Migrations are population, not molecular, processes

2.Classical comparisons of genes and languages

3.The trouble with the vocabulary and an alternative approach

4.Comparing genes across language families

Often, genetic isolates are also linguistic isolates

F. Calafell & J. Bertranpetit (1993) Am. J. Phys. Anthropol.

In Europe, linguistically-related populations are genetically closer than unrelated populations separated by the same geographic distance

Correlations Positive, significant • GEO,LANG 26 / 26• GEO,GEN 22 / 26• GEN,LANG 16 / 26• GEN,LANG.GEO 11 / 26

R.R. Sokal (1988) Proc. Natl. Acad. Sci USA

In agreement with Renfrew’s predictions, four African-Eurasian gradients corresponding to four language families

G. Barbujani & A. Pilastro (1993) Proc. Natl. Acad. Sci .USA

R.D. Gray & Q.D. Atkinson (2003) Nature

In agreement with Renfrew’s predictions, estimated

divergence between Indo-European languages

between 7,800 and 9,500 years BP

R. Bouckaert et al. (2012) Science

In agreement with Renfrew’s predictions, geographic origin of the Indo-European family inferred in Anatolia

But no gene-language correlation in the Americas

A simple, global correspondence between genetic and linguistic

diversity?

1. Do we speak different languages because our genes influence language learning?

2. Do we carry different alleles because we speak different languages?

L.L. Cavalli-Sforza et al. (1988) Proc. Natl. Acad. Sci. USA

Summary

1.Migrations are population, not molecular, processes

2.Classical comparisons of genes and languages

3.The trouble with the vocabulary and an alternative approach

4.Comparing genes across language families

Many linguists disagree

Controversial linguistic classifications

Random similarities due to the limited number of sounds humans can produce

Impossibility to tell random from significant correspondences if etimologies cannot be traced

Overlapping cultural boundaries

The trouble with vocabulary comparisons

An alternative to vocabulary comparisons: Structural features of languages in grammar and syntax

Word order Englishequivalent

Proportionof languages

Examplelanguages

SOV "She him loves." 45% Pashtoon, Japanese, Afrikaans

SVO "She loves him." 42% English, Hausa, Mandarin

VSO "Loves she him." 9% Hebrew, Tuareg, Zapotec

VOS "Loves him she." 3% Malgasy, Baure

OVS "Him loves she." 1% Hixkaryana

OSV "Him she loves." <1% Warao

The Parametric Comparison MethodG. Longobardi & C. Guardiano (2009) Lingua

Summary

1.Migrations are population, not molecular, processes

2.Classical comparisons of genes and languages

3.The trouble with the vocabulary and an alternative approach

4.Comparing genes across language families

5,886 subjects genotyped at 500,568 loci using the Affymetrix 500K single nucleotide polymorphism (SNP) chip.

POPRES populations that match our linguistic database in Europe

Genetic data

Populations: England, France, Germany, Greece, Hungary, Ireland, Italy, Poland, Portugal, Romania, Russia, Serbia, Croatia, Spain

20 Spanish Basques

+ Basque

+ Finnish93 Finns

Final sample size:805 individuals for ~ 220,000 SNPs (MAF > 0.01 and genotyping rate > 98%)

Principal Component Analysis (PCA) of individual genotypes

A matrix summarizing structural variation in 15 European languages

PCAnalysis of languages

Language diversity

Genomic diversity

Common elements and differences between PCA plots of genomic and linguistic diversity

Main inconsistencies:1.Hungarians genomes close to those of Indo-European speakers2.Romanian genomes close to those of their geographical, non-Romance speaking, neighbours

Among Indo-European languages, distances inferred from vocabulary and syntax suggest similar clusterings

Vocabulary Syntax

In Europe, distances inferred from syntax and DNA suggest similar clusterings

Syntax Genetic distances

Path difference distance between linguistic and genetic UPGMA

Comparison with those obtained in 100,000 pairs of random topologies drawn, with replacement, from the total set of the possible topologies for 15 taxa

Probability to obtain smaller distance values than observed, P<0.004

The close relationship between trees inferred from linguistic and genetic distances is very unlikely to have arisen just by chance

Mantel correlations between distance matrices

Bonferroni P=0.0006

Mantel and partial Mantel correlations between distance matrices

Bonferroni P=0.006

Main inconsistencies:1.Hungarians genomes close to those of Indo-European speakers2.Romanian genomes close to those of their geographical, non-Romance speaking, neighbours

Recent admixture accounts for some PCA inconsistencies

To summarize:

1.Within the Indo-European family, similar trees inferred from vocabulary and

syntactic comparisons

2.European populations speaking similar languages also tend to resemble each

other at the genomic level

3.Syntax appears to offer a better prediction of genomic distances than geography

4.Contacts between populations after their separation from a common ancestor

can be recognized, and better accounted for, by comparing genomic and linguistic

patterns of variation

When did the main human populations

separate?

Henn et al. (2012) Proc Natl Acad Sci USA

Scally and Durbin (2012) Nature Rev Genet

Fossil, archaeological and genomic evidence place divergence among continental populations in the interval. 120-60 k years ago. When did the main language families diverge?

Correlation suggests, but does not prove, common causation. Would it be possible that the same geographic constraints led to parallel genetic and linguistic change, in different time moments?

Darwin had in mind population trees; but how sure are we that genetic evolution and linguistic change really occurred in a tree-like fashion?

Indoeuropean Documentation Center, Utexas at Austin

Several open questions

Silvietta Ghirotto

Francesca Tassi

Pino LongobardiYork University

Davide PettenerUniversity of Bologna

http://www.langelin.org/

Cristina GuardianoUniversity of Modena