Viability, behaviour, and colour expression in the offspring of matings between common wall lizard Podarcis muralis colour morphs

Abstract Colour polymorphisms are widely studied to identify the mechanisms responsible for the origin and maintenance of phenotypic variability in nature. Two of the mechanisms of balancing selection currently thought to explain the long-term persistence of polymorphisms are the evolution of alternative phenotypic optima through correlational selection on suites of traits including colour, and heterosis. Both of these mechanisms can generate differences in offspring viability and fitness arising from different morph combinations. Here, we examined the effect of parental morph combination on fertilisation success, embryonic viability, newborn quality, antipredator and foraging behaviour, as well as inter-annual survival by conducting controlled matings in a polymorphic lacertid Podarcis muralis, where colour morphs are frequently assumed to reflect alternative phenotypic optima (e.g. alternative reproductive strategies). Juveniles were kept in outdoor tubs for a year in order to study inter-annual growth, survival, and morph inheritance. In agreement with a previous genome-wide association analysis, morph frequencies in the year-old juveniles matched the frequencies expected if orange and yellow expression depended on recessive homozygosity at two separate loci. Our findings also agree with previous literature reporting higher reproductive output of heavy females and the higher overall viability of heavy newborn lizards, but we found no evidence for the existence of alternative breeding investment strategies in female morphs, or morph-combination effects on offspring viability and behaviour. We conclude that inter-morph breeding remains entirely viable and genetic incompatibilities are of little significance for the maintenance of discrete colour morphs in P. muralis from the Pyrenees.

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Population genetics of the coral Acropora millepora: Towards a genomic predictor of bleaching

10.1101/867754 ◽

2019 ◽

Cited By ~ 7

Author(s):

Zachary L. Fuller ◽

Veronique J.L. Mocellin ◽

Luke Morris ◽

Neal Cantin ◽

Jihanne Shepherd ◽

...

Keyword(s):

Genome Wide Association Study ◽

Balancing Selection ◽

Genome Wide Association ◽

Conservation Strategies ◽

Genome Sequences ◽

Acropora Millepora ◽

Genome Wide ◽

A Genome ◽

In The Wild

AbstractAlthough reef-building corals are rapidly declining worldwide, responses to bleaching vary both within and among species. Because these inter-individual differences are partly heritable, they should in principle be predictable from genomic data. Towards that goal, we generated a chromosome-scale genome assembly for the coral Acropora millepora. We then obtained whole genome sequences for 237 phenotyped samples collected at 12 reefs distributed along the Great Barrier Reef, among which we inferred very little population structure. Scanning the genome for evidence of local adaptation, we detected signatures of long-term balancing selection in the heat-shock co-chaperone sacsin. We further used 213 of the samples to conduct a genome-wide association study of visual bleaching score, incorporating the polygenic score derived from it into a predictive model for bleaching in the wild. These results set the stage for the use of genomics-based approaches in conservation strategies.

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Morph-specific immunity in male Podarcis muralis

Amphibia-Reptilia ◽

10.1163/156853807781374700 ◽

2007 ◽

Vol 28 (3) ◽

pp. 408-412 ◽

Cited By ~ 33

Author(s):

Stefano Scali ◽

Diego Rubolini ◽

Mauro Fasola ◽

Edoardo Razzetti ◽

Roberto Sacchi ◽

...

Keyword(s):

Immune Response ◽

Colour Polymorphism ◽

Immune Responsiveness ◽

Podarcis Muralis ◽

Environmental Pressures ◽

White Males ◽

Complex Interactions ◽

Common Wall ◽

Cell Mediated Immune Response ◽

Colour Morphs

AbstractPermanent colour polymorphism in lizards is maintained by complex interactions between environmental pressures and physiological traits (such as immune responsiveness) that differ among morphs. In this study we investigated whether T-cell mediated immune response vary among male colour morphs in the trimorphic (white, yellow and red) common wall lizard, Podarcis muralis. We found that yellow males showed a lower immune response compared to both red and white males, whose responses were similar. Thus, immune responsiveness is morph-specific in male common wall lizards, suggesting that this physiological trait could play an important role in maintaining colour polymorphism in this species. Moreover, immune responsiveness significantly increased with increasing male size, irrespective of colour morph, indicating that it could be regarded as a condition-dependent trait.

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Evidence for widespread selection in shaping the genomic landscape during speciation of Populus

10.1101/819219 ◽

2019 ◽

Cited By ~ 1

Author(s):

Jing Wang ◽

Nathaniel R. Street ◽

Eung-Jun Park ◽

Jianquan Liu ◽

Pär K. Ingvarsson

Keyword(s):

Recurrent Selection ◽

Balancing Selection ◽

Forest Tree ◽

Species Variation ◽

Recombination Rates ◽

Genome Wide ◽

Genomic Landscape ◽

Speciation Continuum ◽

Whole Genome Resequencing

AbstractIncreasing our understanding of how various evolutionary processes drive the genomic landscape of variation is fundamental to a better understanding of the genomic consequences of speciation. However, the genome-wide patterns of within- and between-species variation have not been fully investigated in most forest tree species despite their global ecological and economic importance. Here, we use whole-genome resequencing data from four Populus species spanning the speciation continuum to reconstruct their demographic histories, investigate patterns of diversity and divergence, infer their genealogical relationships and estimate the extent of ancient introgression across the genome. Our results show substantial variation in these patterns along the genomes although this variation is not randomly distributed but is strongly predicted by the local recombination rates and the density of functional elements. This implies that the interaction between recurrent selection and intrinsic genomic features has dramatically sculpted the genomic landscape over long periods of time. In addition, our findings provide evidence that, apart from background selection, recent positive selection and long-term balancing selection are also crucial components in shaping patterns of genome-wide variation during the speciation process.

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Population genetics of the coral Acropora millepora: Toward genomic prediction of bleaching

Science ◽

10.1126/science.aba4674 ◽

2020 ◽

Vol 369 (6501) ◽

pp. eaba4674 ◽

Cited By ~ 14

Author(s):

Zachary L. Fuller ◽

Veronique J. L. Mocellin ◽

Luke A. Morris ◽

Neal Cantin ◽

Jihanne Shepherd ◽

...

Keyword(s):

Genome Wide Association Study ◽

Balancing Selection ◽

Conservation Strategies ◽

Genome Sequences ◽

Acropora Millepora ◽

Genome Wide ◽

A Genome ◽

Bleaching Response ◽

In The Wild

Although reef-building corals are declining worldwide, responses to bleaching vary within and across species and are partly heritable. Toward predicting bleaching response from genomic data, we generated a chromosome-scale genome assembly for the coral Acropora millepora. We obtained whole-genome sequences for 237 phenotyped samples collected at 12 reefs along the Great Barrier Reef, among which we inferred little population structure. Scanning the genome for evidence of local adaptation, we detected signatures of long-term balancing selection in the heat-shock co-chaperone sacsin. We conducted a genome-wide association study of visual bleaching score for 213 samples, incorporating the polygenic score derived from it into a predictive model for bleaching in the wild. These results set the stage for genomics-based approaches in conservation strategies.

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Genetic differentiation predicts body size divergence between island and mainland populations of common wall lizards (Podarcis muralis)

Biological Journal of the Linnean Society ◽

10.1093/biolinnean/blz052 ◽

2019 ◽

Vol 127 (4) ◽

pp. 771-786

Author(s):

Tobias Uller ◽

Hanna Laakkonen ◽

Sozos Michaelides ◽

Geoffrey M While ◽

Aurélie Coulon ◽

...

Keyword(s):

Gene Flow ◽

Body Size ◽

Ecological Factors ◽

Western Coast ◽

Island Size ◽

Podarcis Muralis ◽

Island Populations ◽

Common Wall ◽

Size Evolution ◽

Colour Morphs

Abstract Small-bodied vertebrates sometimes evolve gigantism on islands, but there is a lack of consistent association with ecological factors or island characteristics. One possible reason is that, even if the ecological conditions are right, body size might fail to diverge on islands that were isolated recently or if there is gene flow between islands and the mainland. We studied body size, ventral colour polymorphism and genetic structure across nine islands and adjacent mainland populations of common wall lizards (Podarcis muralis) off the western coast of France. Population genetic data suggested that island populations might have maintained gene flow after their geographical isolation from the mainland. Island lizards were larger and heavier than mainland lizards on average, but the extent of gigantism varied substantially between islands. Island size and distance from the mainland were poor predictors of body size, but lizards from populations that were highly genetically differentiated from the mainland were larger than lizards from less differentiated populations. Colour morphs that were rare on the mainland tended to be more common on islands. We propose that genetic isolation or bottlenecks promote body size evolution in island lizards, which makes it challenging to identify ecological causes of island gigantism without complementary genetic information.

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Signatures of long-term balancing selection in human genomes

10.1101/119529 ◽

2017 ◽

Cited By ~ 2

Author(s):

Bárbara Domingues Bitarello ◽

Cesare de Filippo ◽

João Carlos Teixeira ◽

Joshua M. Schmidt ◽

Philip Kleinert ◽

...

Keyword(s):

Balancing Selection ◽

Theoretical Perspective ◽

Human Populations ◽

Protein Coding ◽

Human Genomes ◽

Genome Wide ◽

Higher Power ◽

Genome Wide Data ◽

Immune Related Genes

AbstractBalancing selection maintains advantageous diversity in populations through various mechanisms. While extensively explored from a theoretical perspective, an empirical understanding of its prevalence and targets lags behind our knowledge of positive selection. Here we describe the Non-Central Deviation (NCD), a simple yet powerful statistic to detect long-term balancing selection (LTBS) that quantifies how close frequencies are to expectations under LTBS, and provides the basis for a neutrality test. NCD can be applied to a single locus or genomic data, and can be implemented considering only polymorphisms (NCD1) or also considering fixed differences with respect to an outgroup (NCD2) species. Incorporating fixed differences improves power, and NCD2 has higher power to detect LTBS in humans under different frequencies of the balanced allele(s) than other available methods. Applied to genome-wide data from African and European human populations, in both cases using chimpanzee as an outgroup, NCD2 shows that, albeit not prevalent, LTBS affects a sizable portion of the genome: about 0.6% of analyzed genomic windows and 0.8% of analyzed positions. Significant windows (p < 0.0001) contain 1.6% of SNPs in the genome, which disproportionally fall within exons and change protein sequence, but are not enriched in putatively regulatory sites. These windows overlap about 8% of the protein-coding genes, and these have larger number of transcripts than expected by chance even after controlling for gene length. Our catalog includes known targets of LTBS but a majority of them (90%) are novel. As expected, immune-related genes are among those with the strongest signatures, although most candidates are involved in other biological functions, suggesting that LTBS potentially influences diverse human phenotypes.

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A non-coding region near Follistatin controls head colour polymorphism in the Gouldian finch

Proceedings of The Royal Society B Biological Sciences ◽

10.1098/rspb.2018.1788 ◽

2018 ◽

Vol 285 (1888) ◽

pp. 20181788 ◽

Cited By ~ 16

Author(s):

Matthew B. Toomey ◽

Cristiana I. Marques ◽

Pedro Andrade ◽

Pedro M. Araújo ◽

Stephen Sabatino ◽

...

Keyword(s):

Phenotypic Variability ◽

Z Chromosome ◽

Coding Region ◽

Candidate Locus ◽

Black Head ◽

Nucleotide Divergence ◽

Gouldian Finch ◽

Polymorphic System ◽

Colour Morphs

Discrete colour morphs coexisting within a single population are common in nature. In a broad range of organisms, sympatric colour morphs often display major differences in other traits, including morphology, physiology or behaviour. Despite the repeated occurrence of this phenomenon, our understanding of the genetics that underlie multi-trait differences and the factors that promote the long-term maintenance of phenotypic variability within a freely interbreeding population are incomplete. Here, we investigated the genetic basis of red and black head colour in the Gouldian finch ( Erythrura gouldiae ), a classic polymorphic system in which naturally occurring colour morphs also display differences in aggressivity and reproductive success. We show that the candidate locus is a small (approx. 70 kb) non-coding region mapping to the Z chromosome near the Follistatin ( FST ) gene. Unlike recent findings in other systems where phenotypic morphs are explained by large inversions containing hundreds of genes (so-called supergenes), we did not identify any structural rearrangements between the two haplotypes using linked-read sequencing technology. Nucleotide divergence between the red and black alleles was high when compared to the remainder of the Z chromosome, consistent with their maintenance as balanced polymorphisms over several million years. Our results illustrate how pleiotropic phenotypes can arise from simple genetic variation, probably regulatory in nature.

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