866550

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AVB0010.1177/1758155919866550Avian Biology ResearchPeñuela et al.

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Avian Biology Research

Transcontinental genetic inference of urban 2019, Vol. 12(4) 152­–162

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DOI: 10.1177/1758155919866550
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Mauricio Peñuela,1 Fernando Rondón,2 Ranulfo González1

and Heiber Cárdenas1

Abstract
Domestic pigeons have high polymorphism in plumage morphs and colours. The genes that affect colour and coat
patterns can be used to estimate genetic profiles that allow us to deduce the structures of populations, establish whether
they are in a population equilibrium and learn the genetic similarity among them. This article tested these population
components and the existing relationships among cities in northern South America, Western Europe and Singapore
(Southeast Asia) through the inventory of phenotypic frequencies and the estimation of allele frequencies for the Pattern,
Grizzle, Background colour, Spread, Crest, Recessive white and Feathered feet loci. The Hardy–Weinberg equilibrium was
evaluated based on the Pattern and Grizzle loci. The results showed a higher genetic diversity in populations from
northern South America with respect to the one from Western Europe, although the differentiation among cities
was low (GST = 0.0759). Several populations were not in the Hardy–Weinberg equilibrium for the evaluated loci, and a
significant correlation between genetic and geographic distances was not found. The relatively small home range of the
pigeons and the dispersion carried out by humans are discussed as possible explanations for the current genetic profiles.

Keywords
Allele frequencies, Columba livia, population equilibrium, structure, transcontinental analysis

Introduction lifestyles, being responsible for the great variety of col-

The pigeon Columba livia is common in the Middle East,
North Africa and Europe.1 Most likely, the species is native
to the Middle East and was dispersed to other territories by
civilizations such as the Babylonians, Sumerians, Egyptians
and Greeks, who have records of their proximity to the spe-
cies, and included them in religious stories.1 From the time
of the Romans until the late 19th century, pigeons have
been bred for human consumption or as an effective inter-
mediary in communication. Generally, the current urban
populations of C. livia are the descendants of escaped
domestic birds and erratic specimens of homing pigeons.2
The largest numbers of feral C. livia live in urban
areas. Two circumstances can explain this phenomenon:
(1) the similarity between their natural environment
(rocky cliffs) and the structure of the city (where build-
ings and monuments rise vertically above the ground)
and (2) the food supply provided by food waste of diverse
origin (marketplaces, stores, etc.) and the voluntary baits
provided by some citizens.2 Studies on pigeon density
have been conducted in some European cities, conclud-
ing that the largest concentrations usually appear in the
centre,3 coinciding with the historic district. Pigeons
preferably colonize these ancient neighbourhoods. It is
probable that group size and the number of groups vary
depending on the food supply at the locations, the nesting
places and the deficient dispersion of nestlings.2 It is evi-
dent that human proximity has moulded the pigeon’s
ours and plumage patterns present in modern cities.
C. livia have probably the greatest variation of plumage
compared to all other birds.4 It is worth remembering that
urban pigeon populations that live out of the ancestral range
of the species have originated from domestic pigeons.4–6
The colour variety and patterns displayed by urban pigeons
can be the result of interactions between common muta-
tions in escaped domestic pigeons and selection pressure.7
The variations of the plumage polymorphism of urban
pigeons come from their domestic ancestors.1,4,8 Generally,
pigeons of large cities show more melanic plumages and
less blue-barred plumages (wild) than pigeon from small
towns, farms and ranches.1 However, the pattern and colour
range of wild pigeons are considered reduced compared to
those of domestic pigeons.9 Recent genomic analysis
showed that urban pigeons clustered with homing pigeons,10
1Departamento de Biología, Facultad de Ciencias Naturales y Exactas,
Universidad del Valle, Cali, Colombia
2Grupo de Investigación en Microbiología y Genética. Escuela de
Biología, Universidad Industrial de Santander, Bucaramanga - Colombia.
Apartado Aéreo 687 Bucaramanga (Santander).
Corresponding author:
Mauricio Peñuela, Posgrado en Ciencias-Biología, Facultad de Ciencias
Naturales y Exactas, Universidad del Valle, Apartado Aéreo 25157 Cali,
Colombia.
Email: mauricio.penuela@hotmail.com
Peñuela et al. 153
supporting the idea that escaped breeding individuals are
likely the greatest contributors to urban populations.11
In general, C. livia have a blue-grey body with two black
bars at the end of the wings and a structural bright green-
purple colouration around the neck and chest,12 which are
important during the mating display.13 Nevertheless, this
species shows mutations that affect the wild phenotype by
modifying the plumage colouration and common patterns.
These mutations present Mendelian and non-Mendelian
inheritance, and some of them are sex linked.14 Studies in
Europe and America have performed phenotypic invento-
ries for several cities.4,14–17
Although inheritance of plumage characters for this
species was determined during the early 20th century,18–25
subsequent population inventories that were published
were limited to describing ratios of colour morphs and to
hypothesizing on why the frequencies changed. Only
Dunmore26 and Cole7 estimated gene frequencies through
the Hardy–Weinberg equilibrium for their studied popula-
tions. Papers published on C. livia have been presented
from an ecological and behavioural point of view.
Nevertheless, they have underused valuable information
by ignoring genetic population concepts, and just few
recent studies are beginning to use this information to
make genetic descriptions of populations.27–30
In this study, we used the phenotypic information, apply-
ing concepts of population genetics to extract allele fre-
quencies and learn about factors such as random mating
and relationships among pigeon populations. To learn how
humans have interfered with feral pigeon populations, we
sampled cities from two continents: Western Europe
because it is the ancient distribution range of the species
and northern South America because it was a colonization
territory of Western Europe ever since its discovery. We
also included the pigeon population of Singapore from
Southeast Asia to learn how allele frequencies vary in iso-
lated populations with an independent colonization history.
We used phenotypic data to extract allele frequencies from
the populations, and through classical analytical methods in
population genetics, we tried to answer three big questions:
(1) Are the inventoried populations in Hardy–Weinberg
equilibrium? (2) How do allele frequencies vary across
populations? (3) How are the continents being structured?
Through this process, we provide an innovative methodol-
ogy to estimate the allele frequencies of two of the seven
loci with evident phenotypic expression in C. livia popula-
tions. We also evaluate the grade of diversity and the
genetic structure of studied populations at several levels,
including the relationship among geographic and genetic
distances.
Materials and methods
Marketplaces, parks and community spaces of Western
Europe, northern South America and Singapore visited by
the researchers between 2012 and 2013 were chosen for
photographic sampling. One square of 9 m2 by site was
marked on the floor with chalk, and bread was spread inside
to attract pigeon groups for taking several pictures. The pic-
ture with more individuals and better quality was chosen
for the analysis. For the cities with more of one group of
pigeons, the distance between groups was around 800 m,
and the pictures were taken the same day. Phenotypic mark-
ers of plumage consisted of colour modifications, pigment
distribution and coat characteristics as shown in Table 1.
Population equilibrium analysis
The Hardy–Weinberg equilibrium was estimated for the
autosomal loci Grizzle and Pattern, using the exact test for
randomness of mating of Haldane31 for the Grizzle locus
and a hierarchical dominance method for Pattern. This lat-
ter estimate was done with C+, C and CT alleles due to the
absence of the c allele in all samples. We developed an
algebraic method to extract expected allele frequencies in
Hardy–Weinberg equilibrium and evaluate the population
equilibrium for the Pattern locus (Supplemental S1).
Estimation of allelic frequencies
Allele frequencies were calculated using the phenotypic
frequencies of recessive alleles for Mendelian loci with
two alleles: q = √q2 and p = 1 − q. The counting method
for Grizzle where the heterozygous alleles are visible.
And the method previously described for the Pattern
locus. Finally to estimate the allele frequencies for the
Background colour locus, we developed an algebraic
approximation (Supplemental S2).
Structure analysis
To measure the structure at a continental level, fixing indi-
ces of Wright32 were estimated based on the loci:
Background colour, Pattern, Spread and Grizzle because
these were the most polymorphic loci. The following
parameters were calculated: (HS) the average heterozygo-
sity expected within subpopulations and (HT) the expected
heterozygosity in the total population. For these calcula-
tions, ‘subpopulations’ in the first analysis refers to the cit-
ies within each continent, and in the second analysis,
‘subpopulations’ refers to continents with respect to the
total populations (Table 2). Singapore was excluded from
this analysis because it was an isolated population. A prin-
cipal component analysis (PCA) was implemented to deter-
mine the relationships among loci. For this test, only the
recessive allele frequencies (B+, C+, s+, g+, zwt, cr and f+)
were used. In addition, pairwise FST between localities was
estimated and presented in a dendrogram for each continent
using the unweighted pair group method with arithmetic
mean (UPGMA) algorithm. Finally, a Mantel test with
9999 repetitions was implemented to determine whether
the genetic and geographic distances were correlated.
Results
A total of 3261 individuals were sampled in 22 popula-
tions: 2004 individuals in 13 cities from northern South
America, 1082 individuals in eight cities from Western
Europe and 175 individuals from Singapore (Southeast
Asia). Twenty-nine groups (flocks) were sampled within
154 Avian Biology Research 12(4)

Table 1.  Description of loci and alleles that alter the plumage in C. livia pigeons.

Locus Alleles Description

Background colour
(sex-linked gene, Z
chromosome)
Pattern (autosomal
gene)
Spread (autosomal
gene)
Grizzle (autosomal
gene)
White recessive (auto-
somal gene)
Crest (autosomal gene)
Feathered foot (autoso-
mal gene)
b Mutant, brown colour, recessive to the rest
B+ Wild, black colour, dominant for b and recessive for BA
BA Mutant, red colour, dominant to the rest
c Mutant, without bars, recessive to the rest
C+ Wild, with bars, dominant for c, recessive to the rest
C Mutant, checkered, dominant for c and C+, recessive to CT
CT Mutant, T-pattern, dominant to the rest
s+ Wild, without colour spread, recessive to S
S Mutant, colour spread, all coat pigmented, dominant
g+ Wild, without white spots on plumage, recessive
G Mutant, white spots on plumage, incomplete dominant, heterozygous can be seen
zwt Mutant, (white colour) depigmented individual, epistatic for all other colours, recessive to Z+
Z+ Wild, normal colour, dominant
cr Mutant, with crest, recessive to CR+
CR+ Wild, without crest, dominant
f+ Wild, without feathers on feet, recessive to F
F Mutant, with feathers on feet, dominant (grouse type)

Table 2.  Model of hierarchical analysis of population genetic structure.

Continents
(N cities) Genetic structure for each continent Genetic structure for both continents

Within cities Among cities within conti- Within continents Among continents (GST)
within continents nents
North-  
ern South  n1   n1 
HSS. Ame   HT S. Ame − HSS. Ame  
America (n1) N N
HT total HT S. Ame
 
( HSS. Ame + HSW .Euro ) 2 HT total − ( HSS. Ame + HSW .Euro ) / 2
HT total HT total

Western  
Europe (n2)  n2   n2 
HSW .Euro   HT W .Euro − HSW .Euro  
N N
HT total HT W .Euro

HS is the average heterozygosity expected within subpopulations and HT is the expected heterozygosity in the total population.

cities. The distribution was as follows: northern South
America (Bogota (2), Cali (2), Manizales (2), Medellin
(2) and Quito (2)), Western Europe (Barcelona (2),
Florence (4), Madrid (3), Paris (2), Rome (3) and Venice
(3)) and Southeast Asia (Singapore (2)). The respective
phenotypic inventory was conducted according to the
sample size by the locus and population. The allele fre-
quencies, expected heterozygosity, equilibrium analysis
and respective sample size per locus, population and
groups inside populations are shown in Figures 1 and 2,
as well as in the Supplemental material (S3–S12).
The structure analysis showed that European cities were
more uniform within individual cities and more structured
among the cities at a continental level in comparison with
the South American ones (Table 3), being the differentia-
tion index GST among continents of 7.59%. The PCA
showed high correlations between some loci and made evi-
dent how populations respond spatially to their respective
allele composition (Figure 3). Pairwise FST evaluated by
continent did not show specific clusters among the South
American populations; however, two clusters were evident
in European cities (Figure 4). Correlations between genetic
and geographic distances were not found in the Mantel
tests performed for each continent.
Discussion
Are the inventoried populations in Hardy–
Weinberg equilibrium?
Most of the inventoried populations in this study were
not in equilibrium for the Pattern and Grizzle loci
Peñuela et al. 155

Figure 1.  Allele frequencies of the loci (a) Pattern, (b) Grizzle and (c) Background colour of C. livia for populations in northern
South America and Western Europe. In the Western Europe graph, we included the Singapore population from Southeast Asia
for comparison purposes. For the Pattern and Grizzle loci, the colours of the population name indicates the population status. For
these same loci, the small circles on the left side of each frequency pie represent groups within each city. Green: Hardy–Weinberg
equilibrium; red: absence of Hardy–Weinberg equilibrium; and blue: absence of the alleles (the tests cannot be performed).
San. Quil. = Santander de Quilichao.

(Figure 1a and 1b; Supplemental S9–S12). If the allele
frequencies estimated deviate from equilibrium, it
means that any of the conditions of random mating and
absence of selection, mutation or migration are being
violated and are probably responsible for the population
imbalance.33 It is difficult to know for each population
and locus which condition is being violated; neverthe-
less, in populations that are in equilibrium, these condi-
tions are met. For both loci, some groups inside cities
were in equilibrium; however, in several cities and
groups, it was not possible to test for equilibrium due to
the absence of individuals with CT_ and G_ phenotypes.
The substructuring present in some cities that had more
than one group sampled is due to the differentiation of
allele frequencies among groups. However, these groups
behave independently, and some of them are actually in
equilibrium. A static behaviour of feral pigeon popula-
tions has been reported in rural and urban environments,
showing little miscegenation among them.26 This popula-
tion structure could be a product of the pigeon’s ability to
156 Avian Biology Research 12(4)

Figure 2.  Allele frequencies of the loci (a) Spread, (b) Crest, (c) Recessive white and (d) Feathered foot of C. livia for populations in
northern South America and Western Europe. In the Western Europe graph, we included the Singapore population from Southeast
Asia for comparison purposes. San. Quil. = Santander de Quilichao.

respond adaptively to dramatic changes in environmental For the Pattern locus, all populations and groups that were
conditions, such as the amount and accessibility of food not in equilibrium presented an excess of observed CT_ indi-
and nesting places,34 which can easily divide populations viduals. Although this was the tendency, the reasons for why
into several groups inside a city. this excess is present is not clear. For the Grizzle locus, we
Peñuela et al. 157
Table 3.  Hierarchical analysis of genetic population structure of C. livia in northern South America and Western Europe, from the
allelic frequencies of B+, C+, s+ and g+.
Continent (number of cities) Genetic structure for each continent
Within cities Among cities in
within continents continents
Northern South America (13) 0.5943 0.4057
Western Europe (8) 0.3699 0.6301
Figure 3.  Principal component analysis (PCA) performed with
the recessive allele frequencies of loci that affect the plumage
in C. livia. Green: Populations of northern South America;
violet: populations from Western Europe; and red: Singapore
(Southeast Asia). Populations are represented by the first
letters of the name, except for Cartago = Cgo.
could observe both the homozygous and heterozygous indi-
viduals, which allowed us to review in detail each test and
hypothesize about each of the genetic profiles. For example,
in Bogota, the equilibrium evaluated for the Grizzle locus at
the city level was present in one of the two groups, where two
grizzle individuals were registered; the second group did not
present any G alleles. These same individuals allowed ascer-
tainment of the equilibrium at the city level. In Madrid, equi-
librium was present in two of the three groups evaluated,
presenting heterozygous individuals for G. When these data
were evaluated at the city level, equilibrium was maintained;
thus, we can say that for the assessment under this locus, the
groups in Bogota and Madrid behaved in panmixia at the city
level. In groups such as Barcelona-b, Medellin-a and
Medellin-b, grizzle individuals were mostly homozygous. In
the subpopulation of Cali-a, the amounts of heterozygous and
homozygous individuals for G were very similar, which evi-
dently moves away from population equilibrium. Two
hypotheses can explain this: a recent fusion of groups, where
one had higher frequencies of G, and the sampling of two
colonies in the same place being evaluated as the same group.
The opposite occurred in Cali-b, where many heterozygous
individuals were observed, indicating the expansion process
of the G allele in this group by random mating.
Although the Grizzle locus can be more informative
about why the population imbalance is occurring, its fre-
quencies in global populations are low, and this could be a
Genetic structure for both continents
Within continents Among continents (GST)
0.9241 0.0759
disadvantage for performing the tests. The Pattern and
Grizzle loci were concordant in many results; nevertheless,
the Pattern locus seems to be a better candidate to perform
an effective equilibrium test, as the frequencies of CT, C
and C+ were more constant in almost all cities and the
groups within them, thereby indicating that these alleles are
more ancient and stable in feral pigeon populations than the
G allele. However, if possible, we recommend carrying out
the tests for both loci.
How do allelic frequencies vary across
populations?
In regard to the phenotype morphs, two mutations are
known for the Background colour locus in the Z chromo-
some. Mutations affect the distribution, amount and
brown-black pigment ratio of eumelanin and the yellow-
red ratio of pheomelanin.35 The BA mutant (dominant red
or ash red) changes the grey-blue parts and the iridescent
areas of plumage to ashen or a faint grey and the thick
areas of spread to a brown-red colour.14 The second
mutant, b (brown), results in a brown colour on the bars of
the wings and the tail.35 No individual showing the brown
phenotype was inventoried in this study. This could be
because it is an uncommon mutation and that it is the most
recessive of them all.
In northern South America, the highest allelic frequen-
cies for BA were registered in Santander de Quilichao, Buga
and Quito. One hypothesis to explain the high frequencies
of the allele in Santander de Quilichao and Buga can be the
small size of these populations. It is probable that in small
populations, one dominant allele can rise randomly and
generate relatively high frequencies. However, in Quito,
the population size is almost double, and the BA frequencies
remain high (Supplemental S3). These allelic frequencies
of a mutant allele in a large group of individuals can likely
be due to past stochastic events, such as a founder effect.
The rest of the populations in northern of South America
showed low frequencies of this allele. In Western Europe,
the BA frequencies were really low, and in populations of
cities such as Lisbon, Paris and Venice, individuals with the
red phenotype were not registered (Figure 1c). This sup-
ports the previous hypothesis that more stable populations,
in this case, more ancient ones, preserve their allelic fre-
quencies and resist the introgression of foreign alleles. It is
worth noting that Western Europe is the natural distribution
of C. livia.1 These results agree with those obtained by
Obukhova6 who reported that in the Iberian Peninsula, the
colour ratio is different from the rest of Europe, with the
blue pigeons being 60% more frequent.
158 Avian Biology Research 12(4)
Figure 4.  Dendrograms of pairwise FST based on loci that affect the plumage in C. livia. Top: Populations from northern South
America and bottom: populations from Western Europe.
For the Pattern locus, the highest frequencies of C
(checkered) in northern South America were found in
Medellin, Palmira and Popayan. This allele was always
present in South American populations and was distrib-
uted throughout the continent. In Western Europe, the
highest frequencies were found in Paris, Florence and
Venice and the lowest in Lisbon, Madrid and Barcelona,
which suggest a continental structuring based on this
allele between the Iberian Peninsula and the east popula-
tions (Figure 1a). The CT allele (T-pattern) presented the
highest frequencies in Bogota, Buga, Cartagena, Cartago,
Popayan and Loja. The CT allele, as with C, was present
in all populations from the northern South America.
Nevertheless, in Western Europe, there was the same
zonal variation for CT that was reported for C, as Venice,
Florence and Paris had the highest frequencies of CT,
contrasting with Lisbon, Madrid, Zaragoza and Barcelona.
In Venice between 2000 and 2001, pigeon groups con-
sisted of 60% of melanic individuals and less than 10% of
blue-barred ones.6 Mayr36 noted that in Venice during the
years 1941 and 1951, there was a drastic increase in the
ratios of dark-winged pattern mutants (both checkered
and T-patterned). This was apparently a transitory case of
polymorphism, with a mutant allele tending to replace the
wild-type allele. The real causes that gave rise to the par-
ticular genetic profile of the Venetian pigeons are
unknown. However, it is probable that a genetic bottle-
neck had occurred.
The S allele from the Spread locus generates a full
pigmentation over the entire individual in all its feath-
ers.9 S is epistatic for every allele from the Pattern locus
due to the pigment spread (brown, black or red) around
the coat. In northern South America, the S frequencies
were low, with the greatest values in Medellin, Cartagena
Peñuela et al. 159
and Buga. However, the distribution continued to be uni-
form in the continent. In Western Europe, Lisbon, Paris
and Venice had the highest frequencies of the S allele,
and Madrid, Zaragoza, Barcelona and Rome, the lowest
ones. The S allele is another structuring factor at the con-
tinental level (Figure 2a). Individuals with the pheno-
type spread S_ and T-pattern CT_ are commonly referred
to as melanics as these are darker birds than the blue-
barred pigeons.9
The Spread and Pattern loci are found on the same
chromosome. Nevertheless, their distance is large
enough to allow for frequent recombination.23 Recently,
using whole-genome scans, Vickrey et al.37 identified
NDP as a candidate gene for Pattern variation. The
Grizzle morphotype is a product of pigment absence on
the feathers of some body parts. In these pigeons, their
colour looks greyish white, and it spreads with points
and spots.6 For northern South America, the highest fre-
quencies of the G allele were present in Santander de
Quilichao, Cartago and Buga, and these frequencies for
the G allele were far higher in South American cities
than in any European city. In Western Europe, the great-
est frequencies were in Madrid, Paris and Florence.
Thus, the frequency of this allele shows the genetic
structuring in each continent (Figure 1b). Pigeons with
white spots are rare in European populations. Many white-
spotted pigeons appear in dovecotes of non-professional
pigeon breeders due to random crosses between races.6
This might reinforce the idea that the pigeons of northern
South America are a heterogeneous mix of different
races that formed feral populations. Other evidence that
supports this idea is that cr (with crest), zwt(white pheno-
type) and F (feathered foot, grouse type) alleles were not
registered in the European cities inventoried (Figure
2b–d). It is necessary to clarify that feathered foot phe-
notype can be originated by two different genes;38 for
this study, only individuals with grouse phenotype were
inventoried.
Selective advantages and distribution gradients have
been conferred upon melanic individuals (Spread,
Checkered and T-patterned phenotypes). Johnston and
Janiga1 concluded that a high frequency of blue-barred
pigeons was correlated with low distributions and natural
lifestyles, while melanic birds were associated with high
latitudes and city lifestyles. Apparently, these authors
suggested an advantage for melanic individuals at lower
temperatures, which are common for higher latitudes.
Colouration can be a key trait for thermoregulation,39 and
because it is known that melanins affect the solar absorp-
tion efficiency, non-melanic morphs can show a major
reflectance.40,41 However, there is doubt as to whether
latitude is influencing the ratio of melanic individuals.
Another reasonable explanation can be that these higher
latitude populations are not in the original distribution
range of the species, as these are recent populations in
comparison with those located in cities at lower latitudes.
Thus, the influence of melanic ratios may be reasonably
higher due to the possible foundation of these popula-
tions by escaped breeding individuals, who tend to be
more polymorphic, as discussed above. For example, in
the European part of Russia (where melanic frequencies
are high), the first feral pigeons probably appeared in the
second half of the 16th century. This was related to the
spread of pigeon breeding that flourished in Yaroslavl,
Novgorod and Moscow.42
How are continents being structured?
The heterozygosities expected for all loci were higher for
populations from northern South America than for Western
Europe, indicating that South American populations are
genetically more diverse, probably due to the establish-
ment of these populations by various races (Supplemental
S5). The hierarchical structure analysis made with the
most polymorphic loci (Table 3) confirms that popula-
tions from northern South America are more heterogene-
ous inside individual cities than Western European
populations. The South American continent, by being
more heterogeneous, hides the differentiation between cit-
ies, and the European by being more homogeneous shows
the differentiation between cities better. Protein analysis
has shown that feral populations from North America and
Italy have greater heterozygosity in comparison with wild
pigeons populations from natural territories of the spe-
cies.5 The value of GST = 0.0759 matches the genetic dif-
ferentiation values reported for 16 bird species (0.0760).43
This is attributed to the geographic interchange that occurs
in birds due to flight.44
The correlations obtained for the recessive frequen-
cies of every inventoried loci in all populations showed
that three groups of loci were correlated. More specifi-
cally, zwt was correlated with cr, s+ with C+ and f+ with
B+ and g+ (Figure 3). It is very important to know the
correlation level among variables as it can determine
which variables provide the greatest differentiation
among the populations studied, as shown by PCA (Table
4). A biplot of the PCA from the two first principal com-
ponents shows that the European populations are concen-
trated in a small space on the first factor, while the South
American populations are spread out, indicating that
South American populations are more heterogeneous in
regard to their allele frequencies.
Note that the Singapore population from Southeast
Asia is associated with the European cities of Lisbon and
Paris. This association with European cities could be
explained by the occupation of this territory by
Englishmen in 1819, as local headquarters of the British
East Indian Company.45 This allows us to hypothesize
that C. livia would have come with the English. This
study did not include London. Nonetheless, it is histori-
cally known that England and Portugal have had the old-
est military and commercial alliance in Europe since
1386,46 so they probably share similar profiles in their
pigeon populations. In addition, Obukhova6 presents the
profile of morphotypes for London, which is very similar
to that of Paris. These facts reinforce our hypothesis as to
why the Singapore profile is closer to Lisbon and Paris in
the PCA biplot.
The genetic differentiation indices (FST) of Wright32 and
the genetic distance (D) of Nei47 are not correlated with the
160 Avian Biology Research 12(4)
Table 4.  Eigenvalues, percentage of contribution and their accumulated values for the PCA performed with the alleles B+, C+, s+,
g+, zwt, cr and f+.
Allele Eigenvalue % Contribution
B+ 3.75 53.62
C+ 1.36 19.50
s+ 0.71 10.26
g+ 0.57  8.23
zwt 0.33  4.76
Cr 0.14  2.01
f+ 0.11  1.59
PCA: principal component analysis.
geographic distance matrices developed for each continent,
suggesting that populations have not followed a coloniza-
tion route. Dendrograms of FST do not suggest large differ-
ences between South American populations, but they
clearly show structure for two groups in Europe (Madrid,
Zaragoza, Lisbon and Rome in comparison with Paris,
Florence and Venice) (Figure 4). This subdivision is pro-
duced by differential allelic frequencies of the Pattern
locus, which shows more melanic morphs CT_ in the cities
of Paris, Florence and Venice. A similar structure was
observed between populations from the Iberian Peninsula
and the rest of Europe by Obukhova.6
Conclusion
Compared to others studies investigating colour morphs in
pigeons, this study showed how it is possible to determine
the genetic diversity of pigeon populations by applying
genetic models based on colour morphs and patterns.
Separately, the study of allelic frequencies allowed us to
obtain a detailed interpretation of how relationships are
spatially set up, showing that natural migration was not the
main dispersing force of the feral pigeon allelic frequen-
cies. The most likely explanation for the current genetic
profiles is the influence of human interference.
Several populations and groups within them were not
in the Hardy–Weinberg equilibrium for the Pattern and
Grizzle loci. On the Grizzle locus, it is possible to recog-
nize homozygous and heterozygous individuals, which
can help to discover why the equilibrium is not present;
nevertheless, the G allele was infrequent in many popula-
tions and groups, which is why the tests could not be per-
formed. Thus, the Pattern locus is the candidate to be
chosen in an equilibrium test due to its higher allele fre-
quencies in global populations.
Colour morphs allow us to detect how populations have
been structured at continental levels and which allele fre-
quencies are contributing to the structuring. In general,
populations from northern South America were more het-
erogeneous inside the individual cities sampled but more
homogeneous when evaluated at a continental scale. A dif-
ferent situation occurred in Western Europe, where popu-
lations were homogeneous inside the sampled cities but
showed a marked structure when the comparison was
made on a continental level. The melanic morphs of
T-pattern, Checker and Spread were the ones responsible
Accumulated eigenvalues % Accumulated contributions
3.75  53.62
5.11  73.12
5.83  83.39
6.41  91.62
6.74  96.39
6.88  98.40
7.00 100.00
for the difference among populations from Western
Europe. The human interference hypothesis for pigeon
colour morphs can explain the high heterogeneity present
in South American populations and the similarity of pigeons
from Singapore with some European populations.
For future studies, we recommend maintaining photo-
graphic sampling to minimize the sampling error in deter-
mining individual phenotypes, and we also recommend
creating inventories focussing on the loci Background col-
our, Pattern, Spread and Grizzle as these are the most poly-
morphic loci and are present in most of the populations.
The detailed inventory of global population profiles will
help hypothesize possible allele migration routes and help
understand how the process of genetic structuring of the
species has been carried out. Finally, we propose using C.
livia as a model organism for the study of population genet-
ics, and we promote the inventory of genetic profiles of its
populations around the world.
Acknowledgements
Special thanks to Luz Clemencia Aristizábal, who financed most
of this research and provided support. Thanks to Anderson
Arenas for sampling in Loja and to Carolina Peñuela for sam-
pling in Arequipa. Acknowledgments to the pigeon breeder
Oscar Jaramillo for his teachings on colour morphs and patterns
of the plumage. Finally, thanks to Enrique Pardo, Yherson
Molina, Jenny Gallo, Ronald Viáfara and Daniel Poveda for
their valuable comments on this paper. This work is dedicated to
the memory of Carlos Alberto Duque Castaño, who always
showed his admiration for the project.
Declaration of conflicting interests
The author(s) declared no potential conflicts of interest with respect
to the research, authorship and/or publication of this article
Funding
The author(s) received no financial support for the research,
authorship and/or publication of this article.
ORCID iD
Mauricio Peñuela https://orcid.org/0000-0003-3417-8950
Statement on the welfare of animals
This article did not carry out experiments with animals; all of the
analyses were performed with photographic samplings.
Peñuela et al. 161
Supplemental material
Supplemental material for this article is available online.
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