Interspecies Aggression and Tolerance of Dogs Study Essay Write a short essay (500 words, 2 pages double spaced) from a particular paper AND the overall di

Interspecies Aggression and Tolerance of Dogs Study Essay Write a short essay (500 words, 2 pages double spaced) from a particular paper AND the overall discussion on the other three articles. Files are attached. 1 What is the objective of the study?
2 Materials and Methods:
a What is the sample or evidence used?
b What are the specific studies/research performed if any?
c Describe geographic location of the sample or evidence used.
3 What are the results of the study?
4 What are the conclusions reached?
5 How is the study contributing to our knowledge of the subject?
6 Are there stated limitations in the particular study?
7-Does the article answer or contribute to any of the main questions regarding dog
domestication including: when, where, or how?
a According to current evidence (archaeological/biological), when was dog
domestication first practiced?
b Is there convincing evidence to where domestication was first practiced?
c Are there studies that support some particular theories explaining the probable
processes that may have ‘produced’ domestication?
1 What is the objective of the study?
The objective of the study published by Range et al. (2015) was an investigation of
the interspecies aggression and tolerance of dogs and wolves which were raised and
kept under equal conditions. The investigation of interspecies aggression and
tolerance was carried out throughout the studying of dogs and wolves agonistic
behaviors in the situations which are directly associated with cooperation. Namely,
the authors investigated the competition of dogs and vowels during pair-wise food
competition tests by feeding the animals with a single bowl of meat pieces or a large
bone.
2 Materials and Methods:
a What is the sample or evidence used?
The total number of wolves involved in this study was 9 and they were originated
from North America. It is worth mentioning that the wolves were born in captivity.
The total number of dogs involved in this study was 8 and they were originated and
born in Hungary.
b What are the specific studies/research performed if any?
The data were collected from August do December 2009 and from April to July 2011
for wolves and dogs, respectively.
During the experiments, two conditions were used for each animal tested. Namely, (i)
meat conditions and (ii) bone conditions were evaluated. The meat conditions tests
were carried out in the special design bowls which were large enough to enable
simultaneously feeding of each animal. Additionally, the meat placed in bowls could
not be carried away. The second set of testing involved bones that could be carried
away and which were large enough for more than one animal. The maximum testing
period was set to 5 minutes and each animal was tested once per day.
c Describe geographic location of the sample or evidence used.
As it was previously mentioned the wolves originated from North America while the
dogs originated from Hungary.
3 What are the results of the study?
The results of the study can be separated into four groups. The first group represents
the results obtained for experiments dealing with the monopolization of food
resources. The results revealed that higher-ranged dogs were more likely to feed alone
than lower-ranked dogs. In experiments that were involved wolves this difference was
not found. The second group of tests represents the results of agonistic behaviors
between spices (dogs and wolves) and age, spices and dominance status, and spices
and conditions. The third set of experiments involved tests on silence during
co-feeding. The difference was observed between co-feeding with meat and bones.
Namely, dogs and wolves showed similar behavior in the meat conditions and dogs
showed lower “silence” than wolves during bones co-feeding. The difference in
lasting of co-feeding in silence was observed among wolves of different ages. The
fourth set of experiments involved co-feeding with agonistic signals. The difference in
aggressiveness was observed among the high- and the low-ranking dogs, while the
difference was not observed among the high- and the low-ranking wolves. The similar
results were obtained when the relative duration of co-feeding with agonistic signals
was investigated.
4 What are the conclusions reached?
The study revealed that wolves which belong to both dominant and subordinate
members of the dyads monopolized the food. Their agonistic behavior was equally
distributed. Opposite to the wolves, dogs showed behavior that was not equally
distributed. Namely, high-ranging individuals of the dogs showed the dominance. This
was reflected to the fact that dogs (subordinate dogs) rarely challenge their
high-ranging individuals, while subordinate wolves readily challenge their dominant
partners. The presented study demonstrated that wolves are tolerant enough for
within-species cooperation. The dogs showed a more rigid dominance of hierarchy in
comparison to wolves. The authors stated that across species interaction (dog-human
cooperation) is probably based on the interspecies (wolf-wolf) interactions which are
in accordance with the canine cooperation hypothesis.
5 How is the study contributing to our knowledge of the subject?
This study contributes to the subject as the authors clearly explained the experimental
part of the manuscript and its main drawbacks. Also, the conclusions that arose from
the results obtained in this study were supported by an appropriate literature review.
Additionally, the authors pointed out topics that should be clarified in further reach
related to this subject.
6 Are there stated limitations in the particular study?
Yes, the authors stated the limitation of the study. Namely, they clearly stated that the
number of tested animals was relatively small which were living in a few packs at the
same facilities. So they had a doubt about how their findings can be representative of
wolves and dogs generally.
7-Does the article answer or contribute to any of the main questions regarding dog
domestication including: when, where, or how?
The article by itself does not directly answer the questions regarding domestication
including when, where, or how? Some answers can be found in the literature which
was cited in the manuscript.
a According to current evidence (archaeological/biological), when was dog
domestication first practiced?
The earliest widely accepted archaeological dog remains date to about 15,000
years ago (Irving-Pease et al., 2018; Thalmann and Perri, 2018).
b Is there convincing evidence to where domestication was first practiced?
There is no convincing evidence to where domestication was first practiced
(Irving-Pease et al., 2018)
c Are there studies that support some particular theories explaining the probable
processes that may have ‘produced’ domestication?
The presented study supports the theory of wolf-wolf cooperation, which can be a
basis for the evolution of dog-human cooperation (Canine cooperation hypothesis).
The theory was supported by other citations in the presented manuscript [27,48,49].
References:
Thalmann O, Perri AR. Paleogenomic inferences of dog domestication. In: Lindqvist
C, Rajora OP, editors. Paleogenomics. Cham: Springer; 2018. p. 1–34.
Irving-Pease, Evan K.; Ryan, Hannah; Jamieson, Alexandra; Dimopoulos, Evangelos
A.; Larson, Greger; Frantz, Laurent A. F. (2018). “Paleogenomics of Animal
Domestication”. In Lindqvist, C.; Rajora, O. (eds.). Paleogenomics. Population
Genomics. Springer, Cham. pp. 225–272.
ARTICLE
Received 27 Feb 2017 | Accepted 25 May 2017 | Published 18 Jul 2017
DOI: 10.1038/ncomms16082
OPEN
Ancient European dog genomes reveal continuity
since the Early Neolithic
Laura R. Botigué1,*, Shiya Song2,*, Amelie Scheu3,4,*, Shyamalika Gopalan1, Amanda L. Pendleton5,
Matthew Oetjens5, Angela M. Taravella5, Timo Seregély6, Andrea Zeeb-Lanz7, Rose-Marie Arbogast8,
Dean Bobo1, Kevin Daly4, Martina Unterländer3, Joachim Burger3, Jeffrey M. Kidd2,5 & Krishna R. Veeramah1
Europe has played a major role in dog evolution, harbouring the oldest uncontested
Palaeolithic remains and having been the centre of modern dog breed creation. Here we
sequence the genomes of an Early and End Neolithic dog from Germany, including a sample
associated with an early European farming community. Both dogs demonstrate continuity
with each other and predominantly share ancestry with modern European dogs, contradicting
a previously suggested Late Neolithic population replacement. We find no genetic evidence to
support the recent hypothesis proposing dual origins of dog domestication. By calibrating
the mutation rate using our oldest dog, we narrow the timing of dog domestication to
20,000–40,000 years ago. Interestingly, we do not observe the extreme copy number
expansion of the AMY2B gene characteristic of modern dogs that has previously been
proposed as an adaptation to a starch-rich diet driven by the widespread adoption of
agriculture in the Neolithic.
1 Department of Ecology and Evolution, Stony Brook University, Stony Brook, New York 11794-5245, USA. 2 Department of Computational Medicine and
Bioinformatics, University of Michigan, Ann Arbor, Michigan 48109, USA. 3 Palaeogenetics Group, Johannes Gutenberg-University Mainz, 55099 Mainz,
Germany. 4 Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland. 5 Department of Human Genetics, University of Michigan, Ann Arbor,
Michigan 48109, USA. 6 Department of Prehistoric Archaeology, Institute of Archaeology, Heritage Sciences and Art History, University of Bamberg,
96045 Bamberg, Germany. 7 Generaldirektion Kulturelles Erbe Rheinland-Pfalz, Direktion Landesarchäologie, Auenstelle Speyer, 67346 Speyer, Germany.
8 CNRS UMR 7044-UDS, 5 Allée du Général Rouvillois F 67083 Strasbourg, France. * These authors contributed equally to this work. Correspondence and
requests for materials should be addressed to K.R.V. (email: krishna.veeramah@stonybrook.edu).
NATURE COMMUNICATIONS | 8:16082 | DOI: 10.1038/ncomms16082 | www.nature.com/naturecommunications
1
ARTICLE
NATURE COMMUNICATIONS | DOI: 10.1038/ncomms16082
E
urope has been a critically important region in the history
and evolution of dogs, with most modern breeds sharing
predominantly European ancestry1. Furthermore, the oldest
remains that can be unequivocally attributed to domestic dogs
(Canis lupus familiaris) are found on this continent, including
an Upper Palaeolithic 14,700-year-old jaw-bone from the
Bonn–Oberkassel site in Germany2 (older specimens from
Siberia and the Near East that have been proposed remain
highly controversial3,4). While ancient mitochondrial DNA
(mtDNA) suggests a European centre of dog domestication5,
analyses of mitochondrial and genomic data from modern dogs
have suggested East Asia6,7, the Middle East8 and Central Asia9.
The Neolithic period in Central Europe ranges from B7,500 to
4,000 BP and can be further subdivided based on specific features
of human culture10 (Supplementary Table 1). Multiple studies have
found evidence of a prehistoric turnover of canid mtDNA lineages
sometime between the Late Neolithic and today, with haplogroup
C, which appears in almost all Neolithic dogs but in less than 10%
of modern dogs, being replaced by haplogroup A in most of
Europe5,11,12. By analyzing genomic data from modern dogs and a
Late Neolithic (B5,000 years old) Irish dog from Newgrange
(hereafter referred to as NGD), Frantz et al.12 argue that this
matrilineal turnover was a consequence of a major population
replacement during the Neolithic. However, NGD primarily shares
ancestry with modern European dogs, implying the proposed
population replacement had largely already occurred before
this individual lived. Frantz et al.12 also estimate a relatively
recent east–west dog divergence (14,000–6,000 years ago), which,
placed within the context of existing archaeological data, they
explain with a dual origin of dog domestication.
The characterization of samples from earlier in the Neolithic
and from continental Europe is necessary to examine whether
and to what extent a large-scale demographic replacement
occurred during this period. This would be evidenced by a
distinct ancestry absent in modern dog genomes that was more
prominent in dogs from earlier in the Neolithic, as opposed to
genomic continuity from the Early Neolithic to today. Therefore,
we present analysis of B9 coverage whole genomes of two dog
samples from Germany dating to the Early and End Neolithic
(B7,000 years old and B4,700 years old, respectively). We
observe genetic continuity throughout this era and into the
present, with our ancient dogs sharing substantial ancestry with
modern European dogs. We find no evidence of a major
population replacement; instead, our results are consistent with
a scenario where modern European dogs emerged from a
structured Neolithic population. Furthermore, we detect an
additional ancestry component in the End Neolithic sample,
consistent with admixture from a population of dogs located
further east that may have migrated concomitant with steppe
people associated with Late Neolithic and Early Bronze age
cultures, such as the Yamnaya and Corded Ware culture13. We
also show that most autosomal haplotypes associated with
domestication were already established in our Neolithic dogs,
but that adaptation to a starch-rich diet likely occurred later.
Finally, we obtain divergence estimates between Eastern and
Western dogs of 17,000–24,000 years ago, consistent with a single
geographic origin for domestication, the timing of which we
narrow down to between B20,000 and 40,000 years ago.
Results
Archaeological samples and ancient DNA sequencing.
The older specimen, which we refer to hereafter as HXH, was
found at the Early Neolithic site of Herxheim and is dated to
5,223–5,040 cal. BCE (B7,000 years old) (Supplementary Fig. 1).
The younger specimen, which we refer to hereafter as CTC, was
2
found in Cherry Tree Cave and is dated to 2,900–2,632 cal. BCE
(B4,700 years old), which corresponds to the End Neolithic
period in Central Europe14 (Supplementary Fig. 2 and
Supplementary Notes 1–3).
We generated whole-genome sequence data for the two ancient
dogs and mapped over 67% of the reads to the dog reference
genome (CanFam3.1), confirming high endogenous canine DNA
content for both samples (Supplementary Table 2 and
Supplementary Note 4). MapDamage15 analysis demonstrated
that both samples possess damage characteristics typical of
ancient DNA16 (Supplementary Fig. 3). The final mean coverage
for both samples was B9 , while coverage on the X and Y
chromosome was B5 , indicating they both are male. We also
reprocessed the NGD data12 using the same pipeline as for CTC
and HXH. To call variants, we used a custom genotype caller
implemented in Python (see Supplementary Note 5) that
accounts for DNA damage patterns17. We found that our
approach eliminated many false positives that are likely due to
postmortem damage (Supplementary Fig. 4).
Modern canid reference data sets. We analysed these Neolithic
dogs within the context of a comprehensive collection of
5,649 canids, including breed dogs, village dogs and wolves that
had been previously genotyped at 128,743 single nucleotide
polymorphisms (SNPs)9,18 (Supplementary Table 3), as well as
99 canid whole genomes sequenced at medium to high coverage
(6–45 ) (Supplementary Table 4). To account for biases in variant
calling that might occur as a result of this variable coverage, we
ascertained variable sites in an outgroup (such that mutations are
known to have occurred in the root of all the populations being
analysed). We explored different ascertainment schemes for the
whole-genome data (Supplementary Note 6) and chose to use a call
set that includes sites variable in New World wolves (we note,
though, that our primary results are robust to changes in the
ascertainment scheme). This call set contains 1,815,911 variants
that are likely either private to New World wolves or arose in the
grey wolf (Canis lupus) ancestral population, and thus is the least
biased with regard to their ascertainment in Old World wolves and
dogs.
mtDNA analysis. We examined the phylogenetic relationship
of the entire mitochondrial genomes of HXH and CTC with a
comprehensive panel of modern dogs across four major clades
(A–D), modern wolves and coyotes, and previously reported ancient
wolf-like and dog-like whole mitochondrial sequences5,12. Like other
European Neolithic dogs, both HXH and CTC belong to haplogroup
C (Fig. 1a, Supplementary Fig. 5 and Supplementary Note 7)
together with NGD and the Upper Palaeolithic 12,500-year-old
Kartstein Cave dog (also from Germany). We note that
Bonn–Oberkassel also falls in the same haplogroup5 (Supplementary Figs 6 and 7), although analysis of this sample is complicated
by low mtDNA sequence coverage, pointing to some degree of
matrilineal continuity in Europe over B10,000 years, ranging from
the Late Palaeolithic to almost the entire Neolithic. The inclusion of
24 additional clade C samples19 in the phylogenetic analysis reveals
the expected C1 and C2 split (100% support) and that HXH, CTC,
NGD and the Kartstein Cave dog share a common lineage with C1
dogs (Supplementary Fig. 8). This topology suggests that these
ancient European dogs belong to an older sub-haplogroup that is
sister to the progenitor of the C1b and C1a sub-haplogroups and
possibly absent in modern dog populations.
Genomic clustering of the European Neolithic dogs. We
constructed a neighbour-joining (NJ) tree using the whole-genome
sequence data set (Fig. 1b and Supplementary Figs 9 and 10) to
NATURE COMMUNICATIONS | 8:16082 | DOI: 10.1038/ncomms16082 | www.nature.com/naturecommunications
ARTICLE
NATURE COMMUNICATIONS | DOI: 10.1038/ncomms16082
a
b
Clade A, USA (1,000), USA (8,500),
and Argentina (1,000)
92
Alaska (20,800)
100
Clade B
84
Village dogs from South China (6), Vietnam (6) Taiwan (1)
and Borneo (3), Dingo, Chow chow, Sharpei
100
100
100
58
89
49
100
94
71
99
29
97
50
100
94
Germany (12,500)
98
96
59
NGD (4,800)
CTC (5,000)
HXH (7,000)
NGD (4,800)
87
HXH (7,000)
100
77
100
CTC (5,000)
100
57
Village dogs from Portugal (3) and Lebanon (3), boxer
58
74
C1b
Village dogs from Sub-Saharan (3) and Egypt (2), Basenji
Qatar village dogs (2)
Saluki
Afghan hound
C1a
78
100
C2
Indian village dogs (5)
83
100
100
100
100
Russia (22,000)
Russia (33,500)
100
Middle Eastern wolves (3)
European wolves (5)
Switzerland3 (14,500)
100
55
Chinese wolf
100
100
Switzerland1 (14,500)
100
Clade D
100 100
Alaska (28,000)
100
100
New world wolves from Great Lakes
100
Russia (18,000)
Coyote(3)
100
Belgium (26,000)
100
Belgium (30,000)
New world wolves from Mexico (2)
New world wolves from Yellowstone (2)
Andean fox
Golden jackal
0.07
Figure 1 | Phylogeny of ancient and contemporary canids. (a) Phylogeny based on mtDNA. Age of the samples is indicated in parentheses, wolf samples
are shown in orange. (b) NJ tree based on pairwise sequence divergence from whole-genome data.
a
b
0.10
PC2 (1.88%)
0.05
Ancient breeds
Europe
Russia
Middle East
Central Asia
Afghanistan
Mongolia
NGD
Nepal
Europe
−0.10
0.3
HXH
0.2
CTC
0.00
−0.05
0.4
Southeast Asia
Thailand
Vietnam
Indonesia
China
India
Africa
Egypt
Islands
PNG
Arctic
CTC
HXH
NGD
−0.05
India
0.1
Mongolia
Kazakhstan
North China
South China
India
Vietnam
Africa
Europe
Middle East
Indonesia
PNG
Taiwan
Breed dog
CTC
HXH
NGD
CTC
0.0
Middle East
−0.1
Africa
0.00
0.05
PC1 (2.86%)
HXH
0.10
NGD
–0.20
–0.15
–0.10 –0.5
0.00
PC1 (8.45%)
0.05
0.10
Figure 2 | PCA between ancient and contemporary canids. (a) PCA of village dogs, with breed dogs and ancient dogs projected onto the PC space using
SNP array data. (b) PCA of village dogs, breed dogs and ancient dogs using whole-genome SNP data ascertained in the New World wolves.
determine which modern dog population shows the greatest
genetic similarity to the ancient samples (Supplementary Note 8).
We found that the Early Neolithic HXH and Late Neolithic NGD
grouped together as a sister clade to modern European village do…
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