Creationism in Crisis - Evolution of Rock Doves & Domestic Pigeons

Rock dove, Colmba livia neglecta (Iran)

Picture: Γεωργός via Wikimedia (CC BY-SA 4.0)

Rock dove, Columba livia.
The wild ancestor of the domestic or town pigeon

Redefining the Evolutionary History of the Rock Dove, Columba livia, Using Whole Genome Sequences | Molecular Biology and Evolution | Oxford Academic

A great deal is understood about how the many different varieties of domestic pigeon were produced ever since Charles Darwin used them to illustrate the role of selection in evolution. In this case, selection is human selection rather than natural selection, although the difference is a matter of semantics if you regard human selective breeders as part of the domestic pigeon's environment.

Incidentally, creationists should note that Darwin never claimed evolution always resulted in new species. As he showed with his selective breeding examples, it produced new varieties too. Some of these have become so far removed from their wild ancestors that they rank as subspecies, like the domestic pigeon, Columba livia domestica

Although the radiation of domestic varieties is now well understood, the wild ancestors, the rock doves, have received far less attention until now. Now a paper by a team led by Germán Hernández-Alonso of the Center for Evolutionary Hologenomics, The Globe Institute, University of Copenhagen, Copenhagen, Denmark, redresses that discrepancy by analysing the entire genomes of 65 historical rock doves that represent all currently recognized subspecies and span the species’ original geographic distribution. 3 of these specimens were from Charles Darwin's collection.

This works shows that rock doves have diversified into a number of subspecies across their range, stemming from a subspecies now restricted to a small coastal strip of Northwest Africa, C. livia gymnocyclus. One of these subspecies received a substantial ingression of genes from a related species, C. rupestris after it split from the West African population but before it became domesticated. The result is that C. livia gymnocyclus should now probably rank as a species in its own right, C. gymnocyclus.

First a little about the evolution of domestic pigeons:

Domestic pigeons are known to have evolved from at least one domestication event in the Levant, of what is now thought to be the subspecies C. livia gaddi which hybridized with C. rupestris. The domestic and wild forms regularly interbreed where their ranges overlap, and this complicates efforts to trace the genomic relationship between the different regional subspecies.

The difference between the rock dove and the domestic pigeon is that rock doves are shy birds inhabiting remote rocky places like sea cliffs whereas domestic pigeons have adapted to living in an urban environment alongside humans where ledges on buildings have been substituted for rock ledges and their diet is composed mostly of human food waste rather than the seeds and leaves of their wild ancestors. Several varieties of domestic pigeon are still used for ornamentation, racing and food.

In the British Isles, rock doves are now restricted to the northwest coast of England and Scotland and to the west coast of Ireland. The only time I have seen them in the wild was in Oman, on the coast south of Muscat, where the local subspecies is C. livia palaestinae

What information do you have on the evidence for the evolution of feral or town pigeons from wild rock doves? The evolution of feral or town pigeons (Columba livia domestica) from wild rock doves (Columba livia) is an interesting aspect of avian evolution. Feral pigeons are domestic pigeons that have returned to the wild or semi-wild state. Here are some key points regarding the evidence for their evolution:

1. Domestication History:
   • Rock doves were likely first domesticated by humans over 5,000 years ago in the Middle East.
   • The process of domestication involved selecting birds with specific traits, such as docility, coloration, and homing ability.
2. Feral Pigeons as Descendants:
   • Feral pigeons found in urban environments are descendants of domesticated pigeons that have either escaped or been released into the wild.
   • Over generations, these feral pigeons have adapted to urban environments, developing traits that help them survive in cities.
3. Genetic Studies:
   • Genetic studies have been conducted to trace the relationship between wild rock doves and feral pigeons.
   • These studies often involve analyzing mitochondrial DNA and microsatellite markers to determine the genetic relatedness between different pigeon populations.
4. Adaptations to Urban Life:
   • Feral pigeons exhibit adaptations to urban life, such as changes in behavior, diet, and plumage color.
   • They have become well-adapted to feeding on human-derived food sources, such as discarded food in urban areas.
5. Observational Studies:
   • Observational studies have documented the behavior and ecology of feral pigeons in both urban and rural settings.
   • These studies help understand how feral pigeons have adjusted their behavior and lifestyle compared to their wild ancestors.
6. Morphological Changes:
   • Feral pigeons may show morphological differences from their wild counterparts, including variations in size, coloration, and markings.
   • These changes can result from natural selection acting on traits that confer advantages in the urban environment.
7. Homing Ability:
   • Some feral pigeons may retain the homing ability of their domestic ancestors, and this trait can influence their movement patterns and dispersal.

It's important to note that the evolution of feral pigeons from wild rock doves is a dynamic and ongoing process influenced by various factors, including natural selection, genetic variation, and environmental pressures. Studying the evidence for this evolution provides insights into the ways in which animals can adapt to and thrive in human-altered environments.

The research team’s findings are published open access in the journal Molecular Biology and Evolution. Using detailed genomic analysis, they have shown that the evolution of the different subspecies of Rock dove, Columba livia, was in response to climate changes that allowed migration across North Africa during period when the Sahara was green, then isolation in refugia when the Sahara dried up, in classical allopatric evolution. One of the subspecies then hybridized with the related species C rupestris in the Middle East, and it is from that hybrid that the domestic pigeon, C. l. domestica has descended.

They outline their findings in the Abstract and explain how they went about the study in the introduction:

Abstract

The domestic pigeon's exceptional phenotypic diversity was key in developing Darwin's Theory of Evolution and establishing the concept of artificial selection. However, unlike its domestic counterpart, its wild progenitor, the rock dove Columba livia has received considerably less attention. Therefore, questions regarding its domestication, evolution, taxonomy, and conservation status remain unresolved. We generated whole-genome sequencing data from 65 historical rock doves that represent all currently recognized subspecies and span the species’ original geographic distribution. Our dataset includes 3 specimens from Darwin's collection, and the type specimens of 5 different taxa. We characterized their population structure, genomic diversity, and gene-flow patterns. Our results show the West African subspecies C. l. gymnocyclus is basal to rock doves and domestic pigeons, and suggests gene-flow between the rock dove's sister species C. rupestris, and the ancestor of rock doves after its split from West African populations. These genomes allowed us to propose a model for the evolution of the rock dove in light of the refugia theory. We propose that rock dove genetic diversity and introgression patterns derive from a history of allopatric cycles and dispersion waves during the Quaternary glacial and interglacial periods. To explore the rock dove domestication history, we combined our new dataset with available genomes from domestic pigeons. Our results point to at least 1 domestication event in the Levant that gave rise to all domestic breeds analysed in this study. Finally, we propose a species-level taxonomic arrangement to reflect the evolutionary history of the West African rock dove populations.

Introduction

The pigeon (Columba livia) is one the most well-known birds worldwide due to the near ubiquitous distribution of its feral populations, and the extended breeding practices of its domestic form. The domestic pigeon, which on occasion has been bred to extreme exuberance, has been an important model organism for the study of evolution, behavior, and genotype expression, among other research areas (Helms and Brugmann 2007). In contrast to the domestic pigeon, its parental species, the rock dove, has received relatively little attention and consequently, several unresolved questions remain. For instance, the intraspecific taxonomic classification of the rock dove is characterized by significant ambiguity, with several inconclusive or invalidated subspecies. The genetic diversity of the rock dove remains largely unexplored, including its evolutionary history, ongoing evolutionary dynamics, and the extent of its admixture with feral pigeons (free-living birds mainly descended from domestics). Consequently, it is difficult to determine their conservation status, as feral pigeons may have replaced wild rock dove populations in several locations. Furthermore, the number of rock dove domestication events and their geographic locations remain uncertain.

Archaeological evidence suggests that the rock dove was first domesticated between 3,000 to 10,000 yr ago in either the Mediterranean Basin (Johnston 1992; Johnston and Janiga 1995; Stringham et al. 2012) or in the Fertile Crescent alongside the Neolithic Revolution (Driscoll et al. 2009). It has been argued that rock doves were probably domesticated several times and in different places spanning their natural distribution range, possibly over a period of thousands of years (Johnston 1992; Johnston and Janiga 1995; Shapiro and Domyan 2013). After an early domestication phase, humans spread domestic pigeons throughout Eurasia and North Africa where they diversified (Pacheco et al. 2020). Today, there are over 350 recognized domestic breeds, the majority of which are believed to have originated in the Middle East and South Asia. However, extensive admixture among domestic breeds and between domestic and wild populations make it difficult to study the rock dove domestication history (Shapiro et al. 2013.1).

The historical native range of rock doves covered extensive areas of Europe, North Africa, the Middle East, and South Asia, as well as the seacoasts from the Faroe Islands and Britain, to Madeira, the Canaries, and the Cape Verde islands, associated to nesting sites on rock faces and cliffs (Cramp 1985; Johnston 1992; Johnston and Janiga 1995; Gibbs et al. 2001; Shapiro and Domyan 2013; Urban et al. 2014). However, this long domestication history and the challenges distinguishing wild from feral populations make it difficult to accurately estimate their present and past distributions. For example, in some regions, such as most of Continental Europe, the extirpation of natural populations, or their complete absorption by the expanding feral birds, hinders the identification of the wild rock dove geographic range (Cramp 1985; Johnston and Janiga 1995; Gibbs et al. 2001). Furthermore, it has even been suggested that true wild rock dove populations only remain in locations that are outside of the range of feral populations (Johnston et al. 1988; Johnston and Janiga 1995). This is in line with a recent genomic study showing that rock doves from 1 of the regions believed to harbor wild populations in the British Isles had genetic admixture from feral and/or domestic pigeons (Smith et al. 2022).

Phenotypic variability such as the size and coloration of the rock dove is geographically structured (Cramp 1985), and has been used to categorize their populations into subspecies (Johnston 1992). At present, most authors recognize 9 subspecies: C. l. livia, C. l. gaddi, C. l. palaestinae, C. l. schimperi, C. l. targia, C. l. dakhale, C. l. gymnocyclus, C. l. neglecta, and C. l. intermedia (Goodwin 1977). Additionally, at least 3 more inconclusive subspecies have been proposed: C. l. canariensis from Canaries Islands, C. l. atlantis from Azores Islands, Madeira and Cape Verde, and C. l. nigricans from Mongolia and Northwest China (Cramp 1985; Gibbs et al. 2001; Urban et al. 2014). However, it has been debated whether these inconclusive subspecies have feral origins (Dickinson and Remsen 2013.2), or if they are simply morphological variants of the C. l. livia subspecies, as it is the case of the Subtropical Atlantic Islands rock doves (Murton and Clarke 1968; Cramp 1985; Gibbs et al. 2001).

Nevertheless, given that the morphological characteristics used to describe rock dove subspecies are clinally distributed, it is challenging to define the range limits of the subspecies, sometimes morphologically indistinguishable between adjacent populations (Goodwin 1977). Thus, there is little consensus about the subspecies distribution ranges (Johnston 1992). Taking this into consideration, as well as the contiguously continental distribution of rock doves, the currently recognized subspecies could be questioned in terms of their evolutionary relevance (Mayr 1982).

Regarding their current conservation status, the IUCN Red List of Threatened Species lists the rock dove in the “Least Concern” status with decreasing populations (2022) due to its extremely large range and population size. However, it has been argued that it is difficult to accurately evaluate the rock dove's conservation status, due to the high degree of admixture with feral populations (Johnston and Janiga 1995; Baptista et al. 1997). Furthermore, it has been suggested that the main threat to rock doves is the dissolution of their genetic pool, derived from genetic introgression from feral pigeons, which could lead to their imminent extinction within this century (Johnston et al. 1988; Johnston 1992; Johnston and Janiga 1995).

To explore the diversity and evolutionary history of the rock dove, we generated whole-genome sequencing data from 65 historical rock doves collected between 1865 and 1986, at localities spanning the species’ original distribution range. These samples represent all currently recognized subspecies. Our dataset includes 3 specimens from Darwin's collection (collected in Madeira, Sierra Leone, and the Shetland Islands), and the type specimens of 5 different taxa: C. l. atlantis Bannerman, 1931, C. l. canariensis Bannerman, 1914, C. l. butleri Meinertzhagen, 1921 (currently merged with C. l. shimperi), C. l. dakhlae Meinertzhagen, 1928, and C. l. lividor Bates, 1932 (currently merged with C. l. gymnocyclus). We used these genomes to study the diversity of rock dove populations, taking advantage of the extensive available collections, and under the expectation of finding lower levels of admixture with feral pigeons in historical (as opposed to modern) specimens, particularly in populations that distributed far from significant human influence at the time of collection. Simultaneously, in combination with previously published genomes from domestic pigeons, we used our new dataset to re-investigate the origin of the domestic pigeon lineages. Moreover, we used our results to propose a model for the evolution of rock doves and their domestication. Finally, our results allowed us to confirm the feral origin of the subspecies C. l. atlantis and C. l. canariensis, identify the possible feral origin of C. l. dakhlae subspecies, and propose that C. l. gymnocyclus should be considered a full species, Columba gymnocyclus Gray, 1856.

Geographic distribution of rock dove subspecies, and location of the specimens sequenced in this study. The geographic distribution of currently recognized and not recognized subspecies of the rock dove (C. l. atlantis, C. l. canariensis, C. l. lividor, C. l. nigricans, and C. l. butleri) is shown in the map. The differently colored areas represent the estimated ranges of each subspecies, as described by Peters in 1931. The map displays the approximate locations of the specimens labeled as wild rock doves and feral pigeons according to the information from museum descriptions. Darwin's collection specimens (D) and the type specimens (T) are shown in bold font. To enhance clarity, the size of the Tropical Atlantic Islands has been increased.

Phylogenetic relationships among wild and domesticated pigeons. a) NJ tree based on genomic pairwise-distances. Branch length was disregarded in the tree representation (see also supplementary fig. S5, Supplementary Material online). Bootstrap values are shown next to each internal node. Different colors indicate the main geographical regions. The domestic pigeon breeds are shown as a collapsed clade. b and c) D-statistic analyses testing the possibility of hybridization in the West African rock doves that could explain its basal placement in the tree. b) D-statistic test in the form D (C. palumbus, C. guinea; West African rock doves, X), where C. palumbus has been used as an outgroup, all West African rock doves are grouped in a single population, and X represents all other rock doves and domestic pigeons in the dataset. c) D-statistic of the form D (C. palumbus, C. rupestris; West African rock doves, X) testing for hybridization between rock doves and its sister species C. rupestris. Horizontal bars show 3 standard errors estimated through a block jackknife approach. Tests with a resulting |Z-score|>3 were considered statistically significant.

Schematic representation of the proposed model of the rock dove evolutionary history under the refugia theory. a) Representation of the approximate geographic distribution of the rock dove previous to the LGM. b) An allopatric distribution or rock doves during the LGM. Two main populations survived in West Africa and in Central Asia, giving rise to the 2 differentiated clusters we observe in our data. Other populations may have also survived in other Pleistocene refugia, as exemplified by the question marks. During this time, we hypothesize that admixture occurred between C. rupestris and the rock dove population from Central Asia over the range where the 2 species cohabit, as indicated by the D-statistic results. c) Re-expansion of rock doves after the LGM. Due to isolation, West African rock doves diverged genetically, and possibly expanded to Central Sahara. Admixed rock doves from Central Asia expanded quickly throughout Eurasia and North Africa producing a secondary contact with the West African rock dove population, as also suggested by the D-statistic results (supplementary fig. S8, Supplementary Material online). Other rock dove populations may have become extinct or were replaced by the expansion of the admixed rock doves. d) Approximate modern rock dove geographic distribution (see Fig. 1 for the geographic distribution based on Peters 1931). West African rock dove populations are isolated from the rest of rock dove populations due to the current dry Sahara period.

Germán Hernández-Alonso, Jazmín Ramos-Madrigal, Hein van Grouw, Marta Maria Ciucani, Emily Louisa Cavill, Mikkel-Holger S Sinding, Shyam Gopalakrishnan, George Pacheco, M Thomas P Gilbert
Redefining the Evolutionary History of the Rock Dove, Columba livia, Using Whole Genome Sequences
Molecular Biology and Evolution, Volume 40, Issue 11, November 2023, msad243, https://doi.org/10.1093/molbev/msad243

Copyright: © 2023 The authors.
Published by Published by Oxford University Press on behalf of Society for Molecular Biology and Evolution. Open access.
Reprinted under a Creative Commons Attribution 4.0 International license (CC BY 4.0)

A couple of things for creationists to pretend not to understand here:

1. Darwin's work is no less relevant today than it was in the 19th century in respect of how varieties and subspecies evolve in response to human and natural selection.
2. The evolution of the different subspecies of rock dove and of domestic pigeons follows the classical allopatric speciation process where isolated populations diverge. It also includes a hybridization event with a related species which gave rise to the ancestral domestic pigeon.
3. The authors show no doubt that the genetic evidence can be explained by reference to the Theory of Evolution by natural selection, with no place in the explanation for magic or supernatural intervention.
4. As usual, all this happened in that prolonged period of 'pre-Creation Week' history.

I wonder if the authors of the Bible story ever guessed that the dove the legendary Noah released from his Ark was the result of millions of years of evolution from a stem species from West Africa, hybridized with a related Species somewhere in the Middle East, and then subjected to thousands of years of selective breeding. Probably not, since they had no more idea of how species arise than they had of how stars and planets are formed.

---

Advertisement

What Makes You So Special? From The Big Bang To You

How did you come to be here, now? This books takes you from the Big Bang to the evolution of modern humans and the history of human cultures, showing that science is an adventure of discovery and a source of limitless wonder, giving us richer and more rewarding appreciation of the phenomenal privilege of merely being alive and able to begin to understand it all.

Available in Hardcover, Paperback or ebook for Kindle

Advertisement

Ten Reasons To Lose Faith: And Why You Are Better Off Without It

This book explains why faith is a fallacy and serves no useful purpose other than providing an excuse for pretending to know things that are unknown. It also explains how losing faith liberates former sufferers from fear, delusion and the control of others, freeing them to see the world in a different light, to recognise the injustices that religions cause and to accept people for who they are, not which group they happened to be born in. A society based on atheist, Humanist principles would be a less divided, more inclusive, more peaceful society and one more appreciative of the one opportunity that life gives us to enjoy and wonder at the world we live in.

Available in Hardcover, Paperback or ebook for Kindle

Advertisement

Thank you for sharing!

Tweet Link