Complex genetic architecture of three-dimensional craniofacial shape variation in domestic pigeons

AbstractDeciphering the genetic basis of vertebrate craniofacial variation is a longstanding biological problem with broad implications in evolution, development, and human pathology. One of the most stunning examples of craniofacial diversification is the adaptive radiation of birds, in which the beak serves essential roles in virtually every aspect of their life histories. The domestic pigeon (Columba livia) provides an exceptional opportunity to study the genetic underpinnings of craniofacial variation because of its unique balance of experimental accessibility and extraordinary phenotypic diversity within a single species. We used traditional and geometric morphometrics to quantify craniofacial variation in an F2 laboratory cross derived from the straight-beaked Pomeranian Pouter and curved-beak Scandaroon pigeon breeds. Using a combination of genome-wide quantitative trait locus scans and multi-locus modeling, we identified a set of genetic loci associated with complex shape variation in the craniofacial skeleton, including beak curvature, braincase shape, and mandible shape. Some of these loci control coordinated changes between different structures, while others explain variation in the size and shape of specific skull and jaw regions. We find that in domestic pigeons, a complex blend of both independent and coupled genetic effects underlie three-dimensional craniofacial morphology.

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ShapeRotator: an R tool for standardised rigid rotations of articulated Three-Dimensional structures with application for geometric morphometrics

10.1101/159392 ◽

2017 ◽

Cited By ~ 2

Author(s):

Marta Vidal-García ◽

Lashi Bandara ◽

J. Scott Keogh

Keyword(s):

Geometric Morphometrics ◽

Phenotypic Diversity ◽

Three Dimensional ◽

R Package ◽

Morphological Data ◽

List Type ◽

Shape Variation ◽

Data Set ◽

Articulated Structures ◽

Shape And Size

SummaryThe quantification of complex morphological patterns typically involves comprehensive shape and size analyses, usually obtained by gathering morphological data from all the structures that capture the phenotypic diversity of an organism or object. Articulated structures are a critical component of overall phenotypic diversity, but data gathered from these structures are difficult to incorporate in to modern analyses because of the complexities associated with jointly quantifying 3D shape in multiple structures.While there are existing methods for analysing shape variation in articulated structures in Two-Dimensional (2D) space, these methods do not work in 3D, a rapidly growing area of capability and research.Here we describe a simple geometric rigid rotation approach that removes the effect of random translation and rotation, enabling the morphological analysis of 3D articulated structures. Our method is based on Cartesian coordinates in 3D space so it can be applied to any morphometric problem that also uses 3D coordinates (e.g. spherical harmonics). We demonstrate the method by applying it to a landmark-based data set for analysing shape variation using geometric morphometrics.We have developed an R tool (ShapeRotator) so that the method can be easily implemented in the commonly used R package geomorph and MorphoJ software. This method will be a valuable tool for 3D morphological analyses in articulated structures by allowing an exhaustive examination of shape and size diversity.

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Two Genomic Loci Control Three Eye Colors in the Domestic Pigeon (Columba livia)

10.1101/2021.03.11.434326 ◽

2021 ◽

Author(s):

Emily T. Maclary ◽

Bridget Phillips ◽

Ryan Wauer ◽

Elena F. Boer ◽

Rebecca Bruders ◽

...

Keyword(s):

Genetic Basis ◽

Single Species ◽

Columba Livia ◽

Color Pattern ◽

Color Variation ◽

Domestic Pigeon ◽

Eye Color ◽

Solute Carrier ◽

Neural Crest Migration ◽

Domestic Pigeons

ABSTRACTThe iris of the eye shows striking color variation across vertebrate species, and may play important roles in crypsis and communication. The domestic pigeon (Columba livia) has three common iris colors, orange, pearl (white), and bull (dark brown), segregating in a single species, thereby providing a unique opportunity to identify the genetic basis of iris coloration. We used comparative genomics and genetic mapping in laboratory crosses to identify two candidate genes that control variation in iris color in domestic pigeons. We identified a nonsense mutation in the solute carrier SLC2A11B that is shared among all pigeons with pearl eye color, and a locus associated with bull eye color that includes EDNRB2, a gene involved in neural crest migration and pigment development. However, bull eye is likely controlled by a heterogeneous collection of alleles across pigeon breeds. We also found that the EDNRB2 region is associated with regionalized plumage depigmentation (piebalding). Our results establish a genetic link between iris and plumage color, two traits that were long known by pigeon breeders to co-occur, and demonstrate the importance of gene duplicates in establishing possibilities and constraints in the evolution of color and color pattern among vertebrates.

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Two Genomic Loci Control Three Eye Colors in the Domestic Pigeon (Columba livia)

Molecular Biology and Evolution ◽

10.1093/molbev/msab260 ◽

2021 ◽

Author(s):

Emily T Maclary ◽

Bridget Phillips ◽

Ryan Wauer ◽

Elena F Boer ◽

Rebecca Bruders ◽

...

Keyword(s):

Candidate Genes ◽

Single Species ◽

Columba Livia ◽

Color Variation ◽

Domestic Pigeon ◽

Eye Color ◽

Evolution Of Birds ◽

Solute Carrier ◽

Neural Crest Migration ◽

Domestic Pigeons

Abstract The iris of the eye shows striking color variation across vertebrate species, and may play important roles in crypsis and communication. The domestic pigeon (Columba livia) has three common iris colors, orange, pearl (white), and bull (dark brown), segregating in a single species, thereby providing a unique opportunity to identify the genetic basis of iris coloration. We used comparative genomics and genetic mapping in laboratory crosses to identify two candidate genes that control variation in iris color in domestic pigeons. We identified a nonsense mutation in the solute carrier SLC2A11B that is shared among all pigeons with pearl eye color, and a locus associated with bull eye color that includes EDNRB2, a gene involved in neural crest migration and pigment development. However, bull eye is likely controlled by a heterogeneous collection of alleles across pigeon breeds. We also found that the EDNRB2 region is associated with regionalized plumage depigmentation (piebalding). Our study identifies two candidate genes for eye colors variation, and establishes a genetic link between iris and plumage color, two traits that vary widely in the evolution of birds and other vertebrates.

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A ROR2 coding variant is associated with craniofacial variation in domestic pigeons

10.1101/2021.03.15.435542 ◽

2021 ◽

Cited By ~ 1

Author(s):

Elena F. Boer ◽

Hannah F. Van Hollebeke ◽

Carson Holt ◽

Mark Yandell ◽

Michael D. Shapiro

Keyword(s):

Columba Livia ◽

Craniofacial Morphology ◽

Z Chromosome ◽

Comparative Genomic ◽

Facial Skeleton ◽

Beak Length ◽

Canonical Wnt ◽

Short Beak ◽

Craniofacial Variation ◽

Craniofacial Morphogenesis

SummaryVertebrate craniofacial morphogenesis is a highly orchestrated process that is directed by evolutionarily conserved developmental pathways 1,2. Within species, canalized developmental programs typically produce only modest morphological variation. However, as a result of millennia of artificial selection, the domestic pigeon (Columba livia) displays radical variation in craniofacial morphology within a single species. One of the most striking cases of pigeon craniofacial variation is the short beak phenotype, which has been selected in numerous breeds. Classical genetic experiments suggest that pigeon beak length is regulated by a small number of genetic factors, one of which is sex-linked (Ku2 locus) 3–5. However, the molecular genetic underpinnings of pigeon craniofacial variation remain unknown. To determine the genetic basis of the short beak phenotype, we used geometric morphometrics and quantitative trait loci (QTL) mapping on an F2 intercross between a short-beaked Old German Owl (OGO) and a medium-beaked Racing Homer (RH). We identified a single locus on the Z-chromosome that explains a majority of the variation in beak morphology in the RH x OGO F2 population. In complementary comparative genomic analyses, we found that the same locus is also strongly differentiated between breeds with short and medium beaks. Within the differentiated Ku2 locus, we identified an amino acid substitution in the non-canonical Wnt receptor ROR2 as a putative regulator of pigeon beak length. The non-canonical Wnt (planar cell polarity) pathway serves critical roles in vertebrate neural crest cell migration and craniofacial morphogenesis 6,7. In humans, homozygous ROR2 mutations cause autosomal recessive Robinow syndrome, a rare congenital disorder characterized by skeletal abnormalities, including a widened and shortened facial skeleton 8,9. Our results illustrate how the extraordinary craniofacial variation among pigeons can reveal genetic regulators of vertebrate craniofacial diversity.

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Complex genetic architecture of three‐dimensional craniofacial shape variation in domestic pigeons

Evolution & Development ◽

10.1111/ede.12395 ◽

2021 ◽

Author(s):

Elena F. Boer ◽

Emily T. Maclary ◽

Michael D. Shapiro

Keyword(s):

Genetic Architecture ◽

Three Dimensional ◽

Shape Variation ◽

Domestic Pigeons

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MICROSCOPIC AND MOLECULAR DIAGNOSIS OF Ascaridia spp. IN DOMESTIC PIGEONS(Columba livia domestica) IN BAGHDAD CITY,IRAQ

IRAQI JOURNAL OF AGRICULTURAL SCIENCES ◽

10.36103/ijas.v51i4.1101 ◽

2020 ◽

Vol 51 (4) ◽

pp. 1220-1225

Author(s):

Faraj & Al- Amery

Keyword(s):

Molecular Diagnosis ◽

Columba Livia ◽

Ascaridia Galli ◽

Molecular Assay ◽

Infection Rates ◽

Conventional Pcr ◽

Significant Difference ◽

Pcr Products ◽

Males And Females ◽

Domestic Pigeons

Ascaridiosis is a very important parasitic disease of birds, it is caused by Ascaridia. This study was conducted to identify the Ascaridia species by microscopic and molecular assay in Baghdad city. One hundred and sixty fecal samples were collected from domestic pigeons during the period from 1/1/ 2019 to 31/3/ 2019. Results showed that the rate of infection for Ascaridia spp. 15.62% by microscopic examination. Significant difference was observed in infection rates between males and females pigeons. Fifty samples randomly selected and subjected to molecular diagnosis of Ascaridia spp.. Molecular examination results, the total infection rate showed 16%(8/50). The eight positive PCR products were sequenced and deposited in Gene bank data base, phylogenic analysis demonstrated that 4 sequences belongs to Ascaridia galli ( MK918635.1, MK918636.1, MK918847.1, MK919081.1), while 2 (MK919199.1, MK919200.1) belong to Ascaridia nymphii and 2 (MK919207.1, MK919264.1) belong to Ascaridia numidae. It is the first study in Iraq to diagnosis of Ascaridia nymphii and Ascaridia numidae in domesticed pigeons by using conventional PCR.

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Impact of Subclinical Haemoproteus columbae Infection on Farmed Domestic Pigeons from Central Java (Yogyakarta), Indonesia, with Special Reference to Changes in the Hemogram

Pathogens ◽

10.3390/pathogens10040440 ◽

2021 ◽

Vol 10 (4) ◽

pp. 440

Author(s):

Imron Rosyadi ◽

Siti Isrina Oktavia Salasia ◽

Bayanzul Argamjav ◽

Hiroshi Sato

Keyword(s):

Chronic Phase ◽

Hypochromic Anemia ◽

Hemoglobin Concentration ◽

Columba Livia ◽

Nucleotide Sequencing ◽

Mean Corpuscular Hemoglobin ◽

Haemoproteus Columbae ◽

Central Java ◽

Mitochondrial Cytochrome B ◽

Domestic Pigeons

Pigeon haemoproteosis caused by Haemoproteus columbae (Apicomplexa: Haemosporida: Haemoproteidae) is globally prevalent in rock doves (Columba livia), although little is known regarding this disease in pigeons and doves in Indonesia. Blood samples of 35 farmed domestic pigeons (C. livia f. domestica) from four localities in Yogyakarta Special Region, Central Java, Indonesia, were collected from March to June, 2016, subjected to a hemogram, and analyzed for the presence of hemoprotozoan infections. Microscopic examination of blood smears revealed a prevalence of 62.5–100% of H. columbae at the four localities (n = 8–10 for each locality), and geometric means of 3.0–5.6% of erythrocytes were parasitized by young and mature gametocytes, suggesting that all infected pigeons were in the chronic phase of infection with repeated recurrences and/or reinfections. Nucleotide sequencing of mitochondrial cytochrome b gene (cytb) for haemosporidian species demonstrated the distribution of four major cytb lineages of H. columbae (mainly HAECOL1, accompanied by COLIV03, COQUI05, and CXNEA02 according to the MalAvi database). Hemogram analysis, involving the estimation of packed cell volume, erythrocyte counts, mean corpuscular volume, mean corpuscular hemoglobin concentration, and plasma protein and fibrinogen levels of 20 parasitized pigeons and five non-infected pigeons demonstrated significant macrocytic hypochromic anemia with hypoproteinemia and hyperfibrinogenemia in the infected pigeons. This study shows the profound impact of long-lasting subclinical pigeon haemoproteosis caused by H. columbae on the health of farmed domestic pigeons.

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Geometric morphometric investigation of craniofacial morphological change in domesticated silver foxes

Scientific Reports ◽

10.1038/s41598-021-82111-9 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Timothy M. Kistner ◽

Katherine D. Zink ◽

Steven Worthington ◽

Daniel E. Lieberman

Keyword(s):

Three Dimensional ◽

Cranial Base ◽

Craniofacial Morphology ◽

Wild Populations ◽

Linear Measurements ◽

Skeletal Morphology ◽

Geometric Morphometric ◽

Domestication Syndrome ◽

Morphometric Investigation ◽

Unselected Population

AbstractTo test the effects of domestication on craniofacial skeletal morphology, we used three-dimensional geometric morphometrics (GM) along with linear and endocranial measurements to compare selected (domesticated) and unselected foxes from the Russian Farm-Fox Experiment to wild foxes from the progenitor population from which the farmed foxes are derived. Contrary to previous findings, we find that domesticated and unselected foxes show minimal differences in craniofacial shape and size compared to the more substantial differences between the wild foxes and both populations of farmed foxes. GM analyses and linear measurements demonstrate that wild foxes differ from farmed foxes largely in terms of less cranial base flexion, relatively expanded cranial vaults, and increased endocranial volumes. These results challenge the assumption that the unselected population of foxes kept as part of the Russian Farm-Fox experiment are an appropriate proxy for ‘wild’ foxes in terms of craniofacial morphology and highlight the need to include wild populations in further studies of domestication syndrome to disentangle the phenotypic effects of multiple selection pressures. These findings also suggest that marked increases in docility cannot be reliably diagnosed from shape differences in craniofacial skeletal morphology.

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A developmentally descriptive method for quantifying shape in gastropod shells

Journal of The Royal Society Interface ◽

10.1098/rsif.2019.0721 ◽

2020 ◽

Vol 17 (163) ◽

pp. 20190721

Author(s):

J. Larsson ◽

A. M. Westram ◽

S. Bengmark ◽

T. Lundh ◽

R. K. Butlin

Keyword(s):

Empirical Studies ◽

Three Dimensional ◽

Shell Shape ◽

Large Set ◽

Littorina Saxatilis ◽

Shape Variation ◽

Gastropod Shell ◽

Geometric Morphometric ◽

Wide Range ◽

Descriptive Method

The growth of snail shells can be described by simple mathematical rules. Variation in a few parameters can explain much of the diversity of shell shapes seen in nature. However, empirical studies of gastropod shell shape variation typically use geometric morphometric approaches, which do not capture this growth pattern. We have developed a way to infer a set of developmentally descriptive shape parameters based on three-dimensional logarithmic helicospiral growth and using landmarks from two-dimensional shell images as input. We demonstrate the utility of this approach, and compare it to the geometric morphometric approach, using a large set of Littorina saxatilis shells in which locally adapted populations differ in shape. Our method can be modified easily to make it applicable to a wide range of shell forms, which would allow for investigations of the similarities and differences between and within many different species of gastropods.

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