LING337: Assignment 2 Option 1
1
Use the three texts below to describe how the language of science changes with changes in audience
purpose and mode.
You should comment on:
 Genre(s)


Technical language





Lexical density
Nominal groups and nominalisation
Information organisation
Relationship between writer and
readers

Text 1 is taken from New Scientist, Text 2 is from a popular science website and Text 3 was published
in the journal Nature.
Length:
Due date:
2000 words
Friday April 20th 2018 11.55pm
(NB: This is the end of the first week of the mid-semester break. If you are going
away, you will need to submit your assignment earlier than the due date, or make sure
that you can submit on-line from your holiday destination.)
Weighting: 40%
Marking criteria
Your lecturer will use the following criteria to assess your assignment:
The student:
 identifies key features of each text with regard to each of the 7 nominated areas
 identifies and discusses changes in the texts from text 1 – text 3


relates the analysis to the readings studied in weeks 1-6 of the unit. You must make explicit
reference to at least five readings.
structures the assignment as an information report (see handout on iLearn in folder named
Improving you academic writing)
gives adequate attention to cohesive argument, grammatical construction and technical
conventions (grammar, spelling, punctuation)
uses APA referencing procedures and includes a reference list







Assignment submission and return


This assignment needs to be submitted to Turnitin using the link in the Assessments file on
iLearn
Add a footer to each page of the assignment, with page numbering and the unit code in the
footer
Type double-spaced





Marked assignments will be available on iLearn, and the mark registered in Grademark (on iLearn)
usually 4 weeks after submission. An announcement will be posted on iLearn when marking is
completed.
Late Submissions
Late submissions may incur a penalty of 5% daily. If you wish to avoid this then you must
apply for special consideration via ask@mq.edu.au. Neither Louise nor I (Caroline) can give
you an extension without this documentation.
LING337: Assignment 2 Option 1
2
Ancient European hunter-gatherer was a blue-eyed
boy
New Scientist, 26 January 2014 by Catherine de Lange

An ancient hunter-gatherer whose remains
were found in a Spanish cave has a genome
surprisingly similar to modern humans. The
male, who lived 7000 years ago, had blue
eyes and a host of immunity genes that were
thought to have evolved later.
In 2006, two exceptionally preserved human
skeletons were found in a cave in Leon,
Spain. Carles Lalueza-Fox of Pompeu Fabra
University in Barcelona extracted DNA
from one of the skeleton’s teeth, and his
team has now sequenced the whole genome.
“This is the first pre-agricultural European
genome we have,” says Lalueza-Fox. “It
will help us to understand how the arrival of
the Neolithic era – farming, new diet and
new diseases related to animals – has shaped
the genome of modern Europeans.”
Farming came to Europe 7500 years ago,
but didn’t reach Spain until 1500 years later,
says Lalueza-Fox. With it came livestock
Blue-eyed boy (Image: CSIC)

breeding and fixed settlements, replacing the hunter-gatherer lifestyle.
Farming genes
Genetic analyses have already hinted at some of the changes caused by the rise of farming, as
people evolved to deal with shifts in diet and exposure to animal diseases. For instance,
lactose tolerance – the ability to drink milk as an adult – probably evolved when farming
spread.
The new genome backs this up: the Spanish hunter-gatherer seems to have been lactoseintolerant. But other aspects of his genome took Lalueza-Fox by surprise. “My predictions
were completely wrong,” he says.
For instance, the hunter-gatherer had the genes for darkly pigmented skin and hair like his
African ancestors, but also blue eyes, which are a more European trait. “This suggests eye
colour came first,” says Lalueza-Fox, rather than lighter skin.
It makes sense that lighter skin evolved in cooler climates, perhaps to deal with a lack of
vitamin D, says Mark Thomas of University College London. Light eye colour is harder to
LING337: Assignment 2 Option 1
3
explain. “What’s the use?” he asks. It may be that blue eyes evolved by sexual selection, in
which one or both sexes preferred partners with blue eyes for some cultural reason.
Healthy genome
The other surprise lay in the hunter-gatherer’s immune system. His immune system genes,
and genes that affect the risk of bacterial infection, were similar to those of modern humans.
Previously, it was thought that many immunity genes evolved in farmers – partly to cope with
diseases that spread due to close contact with animals, and partly because farmers lived in
large, stationary populations through which disease could spread more easily.
Lalueza-Fox speculates that these hunter-gatherers may have been exposed to diseases like
cholera, which are not spread by animals.
It’s not the first time that changes thought to be brought about by farming have been shown to
precede it. Earlier this year, it emerged that rotten teeth were common in some huntergatherers long before farming, and sugar-rich diets, became common.
Journal reference: Nature, DOI: 10.1038/nature12960
LING337: Assignment 2 Option 1
4
Text 2:
Science
http://www.news.com.au/technology/science/ancient-europeans-had-dark-skin-and-blueeyes-researchers-say/story-fn5fsgyc-1226810985900
http://www.news.com.au/
Ancient Europeans had dark skin and blue
eyes, researchers say
 7 days ago January 27, 2014 5:52AM
Researchers say light-skinned Europeans, like actress Tilda Swinton, emerged “much later” than once
believed – possibly only in the Neolithic era when erstwhile hunter-gatherers became farmers. Picture:
AFP Source: AFP
THE DNA of a hunter-gatherer who lived in Spain some 7,000 years ago suggests that
Europeans were dark-skinned until much more recently than previously thought,
according to researchers.
Genetic material recovered from a tooth of La Brana 1, an ancient man whose skeleton was
dug up in a deep cave system in Spain in 2006, revealed a strange combination of dark skin
and blue eyes, according to a study in the journal Nature.
Europeans from the Mesolithic Period between 10,000 and 5,000 years ago, when La Brana
lived, were thought to have already been fair-skinned due to low ultraviolet radiation levels at
these high latitudes.
LING337: Assignment 2 Option 1
5
“Until now, it was assumed that light skin colour evolved quite early in Europe, (during) the
Upper Palaeolithic… But this is clearly not the case,” study co-author Carles Lalueza-Fox
from Spain’s Evolutionary Biology Institute, told AFP.
“This individual had the African variants for the pigmentation genes.”
The Upper Palaeolithic or Late Stone Age stretched from 50,000-10,000 years ago, followed
by the Mesolithic or Middle Stone Age that lasted until about 5,000 years ago, when it was
followed in Europe by the Neolithic or New Stone Age.
Lalueza-Fox said light-skinned Europeans emerged “much later” than once believed –
possibly only in the Neolithic era when erstwhile hunter-gatherers became farmers.
The cause, he said, may have been a change in diet and lower vitamin D intake associated
with this lifestyle change.
In the absence of natural vitamin D, the human skin can produce its own in contact with the
sun – but dark skins synthesise much less than fair ones – creating an evolutionary incentive
for change.
In La Brana 1, Lalueza-Fox and his team also found the genetic signature for blue eyes and
dark hair.
While the exact hue of skin cannot be determined, the scientists say its combination with blue
eyes was not to be found in modern Europeans today.
It is widely accepted that Man’s oldest common forefather was dark skinned, and that people
became more pale as they moved further north out of Africa into colder climates with less
sunlight.
Subsequent migrations and mixing created the wide range of hues we have today.
La Brana’s genome is the first of a European hunter-gatherer to be fully sequenced.
When compared to today’s humans, it was found to be most closely genetically related to
northern Europeans like the Swedes or Fins.
The probe also found that La Brana 1 had not yet acquired the genetic mutation that allowed
later humans to digest milk and starch more easily – an adaptation that probably coincided
with the birth of agriculture in the Neolithic age.
The authors said more Mesolithic genomes will have to be analysed to determine how
widespread La Brana’s genomic traits really were.
LING337: Assignment 2 Option 1
6
Text 3:
Derived immune and ancestral pigmentation alleles
in a 7,000-year-old Mesolithic European
Iñigo Olalde, Morten E. Allentoft, Federico Sánchez-Quinto, Gabriel Santpere,
Charleston W. K. Chiang, Michael DeGiorgio, Javier Prado-Martinez, Juan Antonio
Rodríguez, Simon Rasmussen, Javier Quilez, Oscar Ramírez, Urko M. Marigorta, Marcos
Fernández-Callejo, María Encina Prada, Julio Manuel Vidal Encinas, Rasmus Nielsen,
Mihai G. Netea, John Novembre, Richard A. Sturm, Pardis Sabeti, Tomàs MarquèsBonet, Arcadi Navarro, Eske Willerslev & Carles Lalueza-Fox
Nature (2014)
doi:10.1038/nature12960
Ancient genomic sequences have started to reveal the origin and the demographic
impact of farmers from the Neolithic period spreading into Europe1, 2, 3. The adoption of
farming, stock breeding and sedentary societies during the Neolithic may have resulted
in adaptive changes in genes associated with immunity and diet4. However, the limited
data available from earlier hunter-gatherers preclude an understanding of the selective
processes associated with this crucial transition to agriculture in recent human
evolution. Here we sequence an approximately 7,000-year-old Mesolithic skeleton
discovered at the La Braña-Arintero site in León, Spain, to retrieve a complete preagricultural European human genome. Analysis of this genome in the context of other
ancient samples suggests the existence of a common ancient genomic signature across
western and central Eurasia from the Upper Paleolithic to the Mesolithic. The La Braña
individual carries ancestral alleles in several skin pigmentation genes, suggesting that
the light skin of modern Europeans was not yet ubiquitous in Mesolithic times.
Moreover, we provide evidence that a significant number of derived, putatively
adaptive variants associated with pathogen resistance in modern Europeans were
already present in this hunter-gatherer.
Main
Next-generation sequencing (NGS) technologies are revolutionizing the field of ancient DNA
(aDNA), and have enabled the sequencing of complete ancient genomes5, 6, such as that of
Ötzi, a Neolithic human body found in the Alps1. However, very little is known of the genetic
composition of earlier hunter-gatherer populations from the Mesolithic period (circa 10,000–
5,000 years before present, bp; immediately preceding the Neolithic period).
The Iberian site called La Braña-Arintero was discovered in 2006 when two male skeletons
(named La Braña 1 and 2) were found in a deep cave system, 1,500 m above sea level in the
Cantabrian mountain range (León, Northwestern Spain) (Fig. 1a). The skeletons were dated
to approximately 7,000 years bp (7,940–7,690 calibrated bp)7. Because of the cold
environment and stable thermal conditions in the cave, the preservation of these specimens
proved to be exceptional (Fig. 1b). We identified a tooth from La Braña 1 with high human
DNA content (48.4%) and sequenced this specimen to a final effective genomic depth-ofcoverage of 3.40× (Extended Data Fig. 1).
LING337: Assignment 2 Option 1
7
Figure 1: Geographic location and genetic affinities of the La Braña 1 individual.
a, Location of the La Braña-Arintero site (Spain). b, The La Braña 1 skeleton as discovered in 2006. c, PCA
based on the average of the Procrustes transformations of individual PCAs with La Braña 1 and each of the five
Neolithic samples1, 3. The reference populations are the Finnish HapMap, FINHM and POPRES. Population
labels with labelling of ref. 12 with the addition of FI (Finns) or LFI (late-settlement Finns). Ajv70, Ajv52, Ire8
and Gok4 are Scandinavian Neolithic hunter-gatherers and a farmer, respectively3. Ötzi is the Tyrolean Ice
Man1.
We used several tests to assess the authenticity of the genome sequence and to determine the
amount of potential modern human contamination. First, we observed that sequence reads
from both the mitochondrial DNA (mtDNA) and the nuclear DNA of La Braña 1 showed the
typical ancient DNA misincorporation patterns that arise from degradation of DNA over
time8 (Extended Data Fig. 2a, b). Second, we showed that the observed number of human
DNA fragments was negatively correlated with the fragment length (R2 > 0.92), as expected
for ancient degraded DNA, and that the estimated rate of DNA decay was low and in
agreement with predicted values9 (Extended Data Fig. 2c, d). We then estimated the
contamination rate in the mtDNA genome, assembled to a high depth-of-coverage (91×), by
checking for positions differing from the mtDNA genome (haplogroup U5b2c1) that was
previously retrieved with a capture method2. We obtained an upper contamination limit of
1.69% (0.75–2.6%, 95% confidence interval, CI) (Supplementary Information). Finally, to
generate a direct estimate of nuclear DNA contamination, we screened for heterozygous
positions (among reads with >4× coverage) in known polymorphic sites (Single Nucleotide
Polymorphism Database (dbSNP) build 137) at uniquely mapped sections on the X
chromosome6 (Supplementary Information). We found that the proportion of false
LING337: Assignment 2 Option 1
8
heterozygous sites was 0.31%. Together these results suggest low levels of contamination in
the La Braña 1 sequence data.
To investigate the relationship to extant European samples, we conducted a principal
component analysis (PCA)10 and found that the approximately 7,000-year-old Mesolithic
sample was divergent from extant European populations (Extended Data Fig. 3a, b), but was
placed in proximity to northern Europeans (for example, samples from Sweden and
Finland)11, 12, 13, 14. Additional PCAs and allele-sharing analyses with ancient Scandinavian
specimens3 supported the genetic similarity of the La Braña 1 genome to Neolithic huntergatherers (Ajv70, Ajv52, Ire8) relative to Neolithic farmers (Gok4, Ötzi) (Fig. 1c, Extended
Data Figs 3c and 4). Thus, this Mesolithic individual from southwestern Europe represents a
formerly widespread gene pool that seems to be partially preserved in some modern-day
northern European populations, as suggested previously with limited genetic data2, 3. We
subsequently explored the La Braña affinities to an ancient Upper Palaeolithic genome from
the Mal’ta site near Lake Baikal in Siberia15. Outgroup f3 and D statistics16, 17, using different
modern reference populations, support that Mal’ta is significantly closer to La Braña 1 than to
Asians or modern Europeans (Extended Data Fig. 5 and Supplementary Information). These
results suggest that despite the vast geographical distance and temporal span, La Braña 1 and
Mal’ta share common genetic ancestry, indicating a genetic continuity in ancient western and
central Eurasia. This observation matches findings of similar cultural artefacts across time
and space in Upper Paleolithic western Eurasia and Siberia, particularly the presence of
anthropomorphic ‘Venus’ figurines that have been recovered from several sites in Europe and
Russia, including the Mal’ta site15. We also compared the genome-wide heterozygosity of the
La Braña 1 genome to a data set of modern humans with similar coverage (3–4×). The overall
genomic heterozygosity was 0.042%, lower than the values observed in present day Asians
(0.046–0.047%), Europeans (0.051–0.054%) and Africans (0.066–0.069%) (Extended Data
Fig. 6a). The effective population size, estimated from heterozygosity patterns, suggests a
global reduction in population size of approximately 20% relative to extant Europeans
(Supplementary Information). Moreover, no evidence of tracts of autozygosity suggestive of
inbreeding was observed (Extended Data Fig. 6b).
To investigate systematically the timing of selection events in the recent history of modern
Europeans, we compared the La Braña genome to modern populations at loci that have been
categorized as of interest for their role in recent adaptive evolution. With respect to two
recent well-studied adaptations to changes in diet, we found the ancient genome to carry the
ancestral allele for lactose intolerance4 and approximately five copies of the salivary amylase
(AMY1) gene (Extended Data Fig. 7 and Supplementary Information), a copy number
compatible with a low-starch diet18. These results suggest the La Braña hunter-gatherer was
poor at digesting milk and starch, supporting the hypotheses that these abilities were selected
for during the later transition to agriculture.
To expand the survey, we analysed a catalogue of candidate signals for recent positive
selection based on whole-genome sequence variation from the 1000 Genomes Project13,
which included 35 candidate non-synonymous variants, ten of which were detected uniquely
in the CEU (Utah residents with northern and western European ancestry) sample 19. For each
variant we assessed whether the Mesolithic genome carried the ancestral or derived
(putatively adaptive) allele.
Of the ten variants, the Mesolithic genome carried the ancestral and non-selected allele as a
homozygote in three regions: C12orf29 (a gene with unknown function), SLC45A2
(rs16891982) and SLC24A5 (rs1426654) (Table 1). The latter two variants are the two
LING337: Assignment 2 Option 1
9
strongest known loci affecting light skin pigmentation in Europeans20, 21, 22 and their ancestral
alleles and associated haplotypes are either absent or segregate at very low frequencies in
extant Europeans (3% and 0% for SLC45A2 and SLC24A5, respectively) (Fig. 2). We
subsequently examined all genes known to be associated with pigmentation in Europeans22,
and found ancestral alleles in MC1R, TYR and KITLG, and derived alleles in TYRP1, ASIP
and IRF4 (Supplementary Information). Although the precise phenotypic effects cannot
currently be ascertained in a European genetic background, results from functional
experiments20 indicate that the allelic combination in this Mesolithic individual is likely to
have resulted in dark skin pigmentation and dark or brown hair. Further examination revealed
that this individual carried the HERC2 rs12913832*C single nucleotide polymorphism (SNP)
and the associated homozygous haplotype spanning the HERC2–OCA2 locus that is strongly
associated with blue eye colour23. Moreover, a prediction of eye colour based on genotypes at
additional loci using HIrisPlex24 produced a 0.823 maximal and 0.672 minimal probability
for being non-brown-eyed (Supplementary Information). The genotypic combination leading
to a predicted phenotype of dark skin and non-brown eyes is unique and no longer present in
contemporary European populations. Our results indicate that the adaptive spread of light
skin pigmentation alleles was not complete in some European populations by the Mesolithic,
and that the spread of alleles associated with light/blue eye colour may have preceded
changes in skin pigmentation.
Table 1: Mesolithic genome allelic state at 10 nonsynonymous variants recently selected
in Europeans
Figure 2: Ancestral variants around the SLC45A2 (rs16891982, above) and SLC24A5
(rs1426654, below) pigmentation genes in the Mesolithic genome.
The SNPs around the two diagnostic variants (red arrows) in these two genes were analysed. The resulting
haplotype comprises neighbouring SNPs that are also absent in modern Europeans (CEU) (n = 112) but present
in Yorubans (YRI) (n = 113). This pattern confirms that the La Braña 1 sample is older than the positiveselection event in these regions. Blue, ancestral; red, derived.
For the remaining loci, La Braña 1 displayed the derived, putatively adaptive variants in five
cases, including three genes, PTX4, UHRF1BP1 and GPATCH1 (ref. 19), involved in the
immune system (Table 1 and Extended Data Fig. 8). GPATCH1 is associated with the risk of
LING337: Assignment 2 Option 1
10
bacterial infection. We subsequently determined the allelic states in 63 SNPs from 40
immunity genes with previous evidence for positive selection and for carrying
polymorphisms shown to influence susceptibility to infections in modern Europeans
(Supplementary Information). La Braña 1 carries derived alleles in 24 genes (60%) that have
a wide range of functions in the immune system: pattern recognition receptors, intracellular
adaptor molecules, intracellular modulators, cytokines and cytokine receptors, chemokines
and chemokine receptors and effector molecules. Interestingly, four out of six SNPs from the
first category are intracellular receptors of viral nucleic acids (TLR3, TLR8, IFIH1 (also
known as MDA5) and LGP2)25.
Finally, to explore the functional regulation of the genome, we also assessed the La Braña 1
genotype at all expression quantitative trait loci (eQTL) regions associated to positive
selection in Europeans (Supplementary Information). The most interesting finding is arguably
the predicted overexpression of eight immunity genes (36% of those with described eQTLs),
including three Toll-like receptor genes (TLR1, TLR2 and TLR4) involved in pathogen
recognition26.
These observations suggest that the Neolithic transition did not drive all cases of adaptive
innovation on immunity genes found in modern Europeans. Several of the derived haplotypes
seen at high frequency today in extant Europeans were already present during the Mesolithic,
as neutral standing variation or due to selection predating the Neolithic. De novo mutations
that increased in frequency rapidly in response to zoonotic infections during the transition to
farming should be identified among those genes where La Braña 1 carries ancestral alleles.
To confirm whether the genomic traits seen at La Braña 1 can be generalized to other
Mesolithic populations, analyses of additional ancient genomes from central and northern
Europe will be needed. Nevertheless, this genome sequence provides the first insight as to
how these hunter-gatherers are related to contemporary Europeans and other ancient peoples
in both Europe and Asia, and shows how ancient DNA can shed light on the timing and
nature of recent positive selection.
Methods
DNA was extracted from the La Braña 1 tooth specimen with a previously published
protocol2. Indexed libraries were built from the ancient extract and sequenced on the Illumina
HiSeq platform. Reads generated were mapped with BWA27 to the human reference genome
(NCBI 37, hg19) after primer trimming. A metagenomic analysis and taxonomic
identification was generated with the remaining reads using BLAST 2.2.27+ and MEGAN4
(ref. 28) (Extended Data Fig. 9). SNP calling was undertaken using a specific bioinformatic
pipeline designed to account for ancient DNA errors. Specifically, the quality of
misincorporations likely caused by ancient DNA damage was rescaled using the
mapDamage2.0 software29, and a set of variants with a minimum read depth of 4 was
produced with GATK30. Analyses including PCA10, Outgroup f316 and D statistics17 were
performed to determine the population affinities of this Mesolithic individual (Supplementary
Information).
References
1. Keller, A. et al. New insights into the Tyrolean Iceman’s origin and phenotype as
inferred by whole-genome sequencing. Nature Commun. 3, 698 (2012)
LING337: Assignment 2 Option 1
11
2. Sánchez-Quinto, F. et al. Genomic affinities of two 7,000-year-old Iberian huntergatherers. Curr. Biol. 22, 1494–1499 (2012)
3. Skoglund, P. et al. Origins and genetic legacy of Neolithic farmers and huntergatherers in Europe. Science 336, 466–469 (2012)
4. Laland, K. N., Odling-Smee, J. & Myles, S. How culture shaped the human genome:
bringing genetics and the human sciences together. Nature Rev. Genet. 11, 137–148
(2010)
5. Rasmussen, M. et al. Ancient human genome sequence of an extinct Palaeo-Eskimo.
Nature 463, 757–762 (2010)
6. Rasmussen, M. et al. An Aboriginal Australian genome reveals separate human
dispersals into Asia. Science 334, 94–98 (2011)
7. Vidal Encinas, J. M. & Prada Marcos, M. E. Los hombres mesolíticos de La BrañaArintero (Valdelugueros, León) (León: Junta de Castilla y León, 2010)
8. Overballe-Petersen, S., Orlando, L. & Willerslev, E. Next-generation sequencing
offers new insights into DNA degradation. Trends Biotechnol. 30, 364–368 (2012)
9. Allentoft, M. E. et al. The half-life of DNA in bone: measuring decay kinetics in 158
dated fossils. Proc. R. Soc. B Biol. Sci. 279, 4824–4733 (2012)
10. Patterson, N., Price, A. L. & Reich, D. Population structure and eigenanalysis. PLoS
Genet. 2, e190 (2006)
11. Nelson, M. R. et al. The population reference sample, POPRES: a resource for
population, disease, and pharmacological genetics research. Am. J. Hum. Genet. 83,
347–358 (2008)
12. Novembre, J. et al. Genes mirror geography within Europe. Nature 456, 98–101
(2008)
13. An integrated map of genetic variation from 1,092 human genomes. Nature 491, 56–
65 (2012)
14. Surakka, I. et al. Founder population-specific HapMap panel increases power in
GWA studies through improved imputation accuracy and CNV tagging. Genome Res.
20, 1344–1351 (2010)
15. Raghavan, M. et al. Upper Palaeolithic Siberian genome reveals dual ancestry of
Native Americans. Nature 505, 87–91 (2014)
16. Reich, D., Thangaraj, K., Patterson, N., Price, A. L. & Singh, L. Reconstructing
Indian population history. Nature 461, 489–494 (2009)
17. Green, R. E. et al. A draft sequence of the Neandertal genome. Science 328, 710–722
(2010)
18. Perry, G. H. et al. Diet and the evolution of human amylase gene copy number
variation. Nature Genet. 39, 1256–1260 (2007)
19. Grossman, S. R. et al. Identifying recent adaptations in large-scale genomic data. Cell
152, 703–713 (2013)
20. Lamason, R. L. et al. SLC24A5, a putative cation exchanger, affects pigmentation in
zebrafish and humans. Science 310, 1782–1786 (2005)
21. Norton, H. L. et al. Genetic evidence for the convergent evolution of light skin in
Europeans and East Asians. Mol. Biol. Evol. 24, 710–722 (2007)