scholarly journals Evolutionary Dynamics of Structural Variation at a Key Locus for Color Pattern Diversification in Cichlid Fishes

2019 ◽  
Vol 11 (12) ◽  
pp. 3452-3465 ◽  
Author(s):  
Claudius F Kratochwil ◽  
Yipeng Liang ◽  
Sabine Urban ◽  
Julián Torres-Dowdall ◽  
Axel Meyer
Keyword(s):  
Evolutionary Dynamics ◽  
Lake Victoria ◽  
Functional Divergence ◽  
Color Pattern ◽  
Color Variation ◽  
Comparative Genomic ◽  
Color Patterns ◽  
East African ◽  
Cichlid Fishes ◽  
Adaptive Radiations

Abstract Color patterns in African cichlid fishes vary spectacularly. Although phylogenetic analysis showed already 30 years ago that many color patterns evolved repeatedly in these adaptive radiations, only recently have we begun to understand the genomic basis of color variation. Horizontal stripe patterns evolved and were lost several times independently across the adaptive radiations of Lake Victoria, Malawi, and Tanganyika and regulatory evolution of agouti-related peptide 2 (agrp2/asip2b) has been linked to this phenotypically labile trait. Here, we asked whether the agrp2 locus exhibits particular characteristics that facilitate divergence in color patterns. Based on comparative genomic analyses, we discovered several recent duplications, insertions, and deletions. Interestingly, one of these events resulted in a tandem duplication of the last exon of agrp2. The duplication likely precedes the East African radiations that started 8–12 Ma, is not fixed within any of the radiations, and is found to vary even within some species. Moreover, we also observed variation in copy number (two to five copies) and secondary loss of the duplication, illustrating a surprising dynamic at this locus that possibly promoted functional divergence of agrp2. Our work suggests that such instances of exon duplications are a neglected mechanism potentially involved in the repeated evolution and diversification that deserves more attention.

scholarly journals Back to Tanganyika: a case of recent trans-species-flock dispersal in East African haplochromine cichlid fishes

2015 ◽  
Vol 2 (3) ◽  
pp. 140498 ◽  
Author(s):  
Britta S. Meyer ◽  
Adrian Indermaur ◽  
Xenia Ehrensperger ◽  
Bernd Egger ◽  
Gaspard Banyankimbona ◽  
...  
Keyword(s):  
Lake Tanganyika ◽  
Lake Victoria ◽  
Species Flock ◽  
East African ◽  
Cichlid Species ◽  
African Great Lakes ◽  
Cichlid Fishes ◽  
Haplochromine Cichlid ◽  
Lake Victoria Region ◽  
Adaptive Radiations

The species flocks of cichlid fishes in the East African Great Lakes are the largest vertebrate adaptive radiations in the world and illustrious textbook examples of convergent evolution between independent species assemblages. Although recent studies suggest some degrees of genetic exchange between riverine taxa and the lake faunas, not a single cichlid species is known from Lakes Tanganyika, Malawi and Victoria that is derived from the radiation associated with another of these lakes. Here, we report the discovery of a haplochromine cichlid species in Lake Tanganyika, which belongs genetically to the species flock of haplochromines of the Lake Victoria region. The new species colonized Lake Tanganyika only recently, suggesting that faunal exchange across watersheds and, hence, between isolated ichthyofaunas, is more common than previously thought.

scholarly journals Colormesh: A novel method for quantifying variation in complex color patterns

2020 ◽  
Author(s):  
Jennifer J. Valvo ◽  
F. Helen Rodd ◽  
David Houle ◽  
J. David Aponte ◽  
Mitchel J. Daniel ◽  
...  
Keyword(s):  
Spatial Information ◽  
Color Pattern ◽  
Color Variation ◽  
Sampling Location ◽  
Continuous Measure ◽  
Color Patterns ◽  
Color Categories ◽  
Wide Range ◽  
Novel Method ◽  
Pattern Quantification

AbstractColor variation is one of the most obvious examples of variation in nature. Objective quantification and interpretation of variation in color and complex patterns is challenging. Assessment of variation in color patterns is limited by the reduction of color into categorical measures and lack of spatial information. We present Colormesh as a novel method for analyzing complex color patterns that offers unique capabilities. Compared to other methods, Colormesh maintains the continuous measure of color at individual sampling points throughout the pattern. This is particularly useful for analyses of variation in color patterns, whether interest is in specific locations or the pattern as a whole. In our approach, the use of Delaunay triangulation to determine sampling location eliminates the need for color patterns to have clearly defined pattern elements, and users are not required to identify discrete color categories. This method is complementary to several other methods available for color pattern quantification, and can be usefully deployed to address a wide range of questions about color pattern variation.

scholarly journals Molecular investigation of genetic assimilation during the rapid adaptive radiations of East African cichlid fishes

2017 ◽  
Vol 26 (23) ◽  
pp. 6634-6653 ◽  
Author(s):  
Helen M. Gunter ◽  
Ralf F. Schneider ◽  
Immanuel Karner ◽  
Christian Sturmbauer ◽  
Axel Meyer
Keyword(s):  
Genetic Assimilation ◽  
East African ◽  
Cichlid Fishes ◽  
African Cichlid ◽  
Molecular Investigation ◽  
Adaptive Radiations

scholarly journals Dog color patterns explained by modular promoters of ancient canid origin

2020 ◽  
Author(s):  
Danika L. Bannasch ◽  
Christopher B. Kaelin ◽  
Anna Letko ◽  
Robert Loechel ◽  
Petra Hug ◽  
...  
Keyword(s):  
Color Pattern ◽  
Color Variation ◽  
Hair Cycle ◽  
Color Patterns ◽  
Temporal And Spatial Distribution ◽  
Multiple Alleles ◽  
Haplotype Combination ◽  
Regulatory Modules ◽  
Regulatory Module ◽  
Temporal And Spatial

Distinctive color patterns in dogs are an integral component of canine diversity. Color pattern differences are thought to have arisen from mutation and artificial selection during and after domestication from wolves 1,2 but important gaps remain in understanding how these patterns evolved and are genetically controlled 3,4. In other mammals, variation at the ASIP gene controls both the temporal and spatial distribution of yellow and black pigments 3,5-7. Here we identify independent regulatory modules for ventral and hair cycle ASIP expression, and we characterize their action and evolutionary origin. Structural variants define multiple alleles for each regulatory module and are combined in different ways to explain five distinctive dog color patterns. Phylogenetic analysis reveals that the haplotype combination for one of these patterns is shared with arctic white wolves and that its hair cycle-specific module likely originated from an extinct canid that diverged from grey wolves more than 2 million years before present. Natural selection for a lighter coat during the Pleistocene provided the genetic framework for widespread color variation in dogs and wolves.

scholarly journals Batch-Mask: An automated Mask R-CNN workflow to isolate non-standard biological specimens for color pattern analysis

2021 ◽  
Author(s):  
John David Curlis ◽  
Timothy J Renney ◽  
Alison R Davis Rabosky ◽  
Talia Y Moore
Keyword(s):  
Neural Network ◽  
Large Scale ◽  
Visual Analysis ◽  
Source Region ◽  
Color Pattern ◽  
Color Variation ◽  
Data Sets ◽  
Color Patterns ◽  
Color Analysis ◽  
Data Set

Efficient comparisons of biological color patterns are critical for understanding the mechanisms by which organisms evolve in ecosystems, including sexual selection, predator-prey interactions, and thermoregulation. However, elongate or spiral-shaped organisms do not conform to the standard orientation and photographic techniques required for automated analysis. Currently, large-scale color analysis of elongate animals requires time-consuming manual landmarking, which reduces their representation in coloration research despite their ecological importance. We present Batch-Mask: an automated and customizable workflow to facilitate the analysis of large photographic data sets of non-standard biological subjects. First, we present a user guide to run an open-source region-based convolutional neural network with fine-tuned weights for identifying and isolating a biological subject from a background (masking). Then, we demonstrate how to combine masking with existing manual visual analysis tools into a single streamlined, automated workflow for comparing color patterns across images. Batch-Mask was 60x faster than manual landmarking, produced masks that correctly identified 96% of all snake pixels, and produced pattern energy results that were not significantly different from the manually landmarked data set. The fine-tuned weights for the masking neural network, user guide, and automated workflow substantially decrease the amount of time and attention required to quantitatively analyze non-standard biological subjects. By using these tools, biologists will be able to compare color, pattern, and shape differences in large data sets that include significant morphological variation in elongate body forms. This advance will be especially valuable for comparative analyses of natural history collections, and through automation can greatly expand the scale of space, time, or taxonomic breadth across which color variation can be quantitatively examined.

scholarly journals A Hybrid Genetic Linkage Map of Two Ecologically and Morphologically Divergent Midas Cichlid Fishes (Amphilophus spp.) Obtained by Massively Parallel DNA Sequencing (ddRADSeq)

2013 ◽  
Vol 3 (1) ◽  
pp. 65-74 ◽  
Author(s):  
Hans Recknagel ◽  
Kathryn R Elmer ◽  
Axel Meyer
Keyword(s):  
Dna Sequencing ◽  
Linkage Map ◽  
Phenotypic Diversity ◽  
Interspecific Cross ◽  
Comparative Genomic ◽  
Linkage Groups ◽  
Cichlid Species ◽  
Cichlid Fishes ◽  
A Genome ◽  
Adaptive Radiations

Abstract Cichlid fishes are an excellent model system for studying speciation and the formation of adaptive radiations because of their tremendous species richness and astonishing phenotypic diversity. Most research has focused on African rift lake fishes, although Neotropical cichlid species display much variability as well. Almost one dozen species of the Midas cichlid species complex (Amphilophus spp.) have been described so far and have formed repeated adaptive radiations in several Nicaraguan crater lakes. Here we apply double-digest restriction-site associated DNA sequencing to obtain a high-density linkage map of an interspecific cross between the benthic Amphilophus astorquii and the limnetic Amphilophus zaliosus, which are sympatric species endemic to Crater Lake Apoyo, Nicaragua. A total of 755 RAD markers were genotyped in 343 F2 hybrids. The map resolved 25 linkage groups and spans a total distance of 1427 cM with an average marker spacing distance of 1.95 cM, almost matching the total number of chromosomes (n = 24) in these species. Regions of segregation distortion were identified in five linkage groups. Based on the pedigree of parents to F2 offspring, we calculated a genome-wide mutation rate of 6.6 × 10−8 mutations per nucleotide per generation. This genetic map will facilitate the mapping of ecomorphologically relevant adaptive traits in the repeated phenotypes that evolved within the Midas cichlid lineage and, as the first linkage map of a Neotropical cichlid, facilitate comparative genomic analyses between African cichlids, Neotropical cichlids and other teleost fishes.

scholarly journals Identification of a novel sex determining chromosome in cichlid fishes that acts as XY or ZW in different lineages

Hydrobiologia ◽  
2021 ◽  
Author(s):  
Anna F. Feller ◽  
Vera Ogi ◽  
Ole Seehausen ◽  
Joana I. Meier
Keyword(s):  
Sex Determination ◽  
Sex Chromosome ◽  
Lake Victoria ◽  
Interspecific Crosses ◽  
Turnover Rates ◽  
Cichlid Fishes ◽  
Haplochromine Cichlid ◽  
Adaptive Radiations ◽  
Heterogametic Sex

AbstractSex determination systems are highly conserved among most vertebrates with genetic sex determination, but can be variable and evolve rapidly in some. Here, we study sex determination in a clade with exceptionally high sex chromosome turnover rates. We identify the sex determining chromosomes in three interspecific crosses of haplochromine cichlid fishes from Lakes Victoria and Malawi. We find evidence for different sex determiners in each cross. In the Malawi cross and one Victoria cross the same chromosome is sex-linked but while females are the heterogametic sex in the Malawi species, males are the heterogametic sex in the Victoria species. This chromosome has not previously been reported to be sex determining in cichlids, increasing the number of different chromosomes shown to be sex determining in cichlids to 12. All Lake Victoria species of our crosses are less than 15,000 years divergent, and we identified different sex determiners among them. Our study provides further evidence for the diversity and evolutionary flexibility of sex determination in cichlids, factors which might contribute to their rapid adaptive radiations.

Functional significance of preserved color patterns of mollusks from the Gosport Sand (Eocene) of Alabama

1988 ◽  
Vol 62 (01) ◽  
pp. 83-87 ◽  
Author(s):  
Patricia H. Kelley ◽  
Charles T. Swann
Keyword(s):  
Functional Morphology ◽  
Functional Significance ◽  
Intraspecific Variability ◽  
Color Pattern ◽  
Color Patterns ◽  
Historical Factors ◽  
Life Mode ◽  
Molluscan Fauna ◽  
Excellent Preservation ◽  
Architectural Constraints

The excellent preservation of the molluscan fauna from the Gosport Sand (Eocene) at Little Stave Creek, Alabama, has made it possible to describe the preserved color patterns of 15 species. In this study the functional significance of these color patterns is tested in the context of the current adaptationist controversy. The pigment of the color pattern is thought to be a result of metabolic waste disposal. Therefore, the presence of the pigment is functional, although the patterns formed by the pigment may or may not have been adaptive. In this investigation the criteria proposed by Seilacher (1972) for testing the functionality of color patterns were applied to the Gosport fauna and the results compared with life mode as interpreted from knowledge of extant relatives and functional morphology. Using Seilacher's criteria of little ontogenetic and intraspecific variability, the color patterns appear to have been functional. However, the functional morphology studies indicate an infaunal life mode which would preclude functional color patterns. Particular color patterns are instead interpreted to be the result of historical factors, such as multiple adaptive peaks or random fixation of alleles, or of architectural constraints including possibly pleiotropy or allometry. The low variability of color patterns, which was noted within species and genera, suggests that color patterns may also serve a useful taxonomic purpose.

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