Introgression and the fate of domesticated genes in a wild mammal population

When domesticated species are not reproductively isolated from their wild relatives, the opportunity arises for artificially selected variants to be re‐introduced into the wild. However, the evolutionary consequences of introgression of domesticated genes back into the wild are poorly understood. By combining high‐throughput genotyping with 25 years of long‐term ecological field data, we describe the occurrence and consequences of admixture between a primitive sheep breed, the free‐living Soay sheep of St Kilda, and more modern breeds. Utilizing data from a 50 K ovine SNP chip, together with forward simulations of demographic scenarios, we show that admixture occurred between Soay sheep and a more modern breed, consistent with historical accounts, approximately 150 years ago. Haplotype‐sharing analyses with other breeds revealed that polymorphisms in coat colour and pattern in Soay sheep arose as a result of introgression of genetic variants favoured by artificial selection. Because the haplotypes carrying the causative mutations are known to be under natural selection in free‐living Soay sheep, the admixture event created an opportunity to observe the outcome of a ‘natural laboratory’ experiment where ancestral and domesticated genes competed with each other. The haplotype carrying the domesticated light coat colour allele was favoured by natural selection, while the haplotype associated with the domesticated self coat pattern allele was associated with decreased survival. Therefore, we demonstrate that introgression of domesticated alleles into wild populations can provide a novel source of variation capable of generating rapid evolutionary changes.     

The brown coat colour of Coppernecked goats is associated with a non‐synonymous variant at the TYRP1 locus on chromosome 8

The recent development of a goat SNP genotyping microarray enables genome‐wide association studies in this important livestock species. We investigated the genetic basis of the black and brown coat colour in Valais Blacknecked and Coppernecked goats. A genome‐wide association analysis using goat SNP50 BeadChip genotypes of 22 cases and 23 controls allowed us to map the locus for the brown coat colour to goat chromosome 8. The TYRP1 gene is located within the associated chromosomal region, and TYRP1 variants cause similar coat colour phenotypes in different species. We thus considered TYRP1 as a strong positional and functional candidate. We resequenced the caprine TYRP1 gene by Sanger and Illumina sequencing and identified two non‐synonymous variants, p.Ile478Thr and p.Gly496Asp, that might have a functional impact on the TYRP1 protein. However, based on the obtained pedigree and genotype data, the brown coat colour in these goats is not due to a single recessive loss‐of‐function allele. Surprisingly, the genotype distribution and the pedigree data suggest that the ⁴⁹⁶Asp allele might possibly act in a dominant manner. The ⁴⁹⁶Asp allele was present in 77 of 81 investigated Coppernecked goats and did not occur in black goats. This strongly suggests heterogeneity underlying the brown coat colour in Coppernecked goats. Functional experiments or targeted matings will be required to verify the unexpected preliminary findings.     

The colour of paternity: extra‐pair paternity in the wild Gouldian finch does not appear to be driven by genetic incompatibility between morphs

In socially monogamous species, individuals can use extra‐pair paternity and offspring sex allocation as adaptive strategies to ameliorate costs of genetic incompatibility with their partner. Previous studies on domesticated Gouldian finches (Erythrura gouldiae) demonstrated a genetic incompatibility between head colour morphs, the effects of which are more severe in female offspring. Domesticated females use differential sex allocation, and extra‐pair paternity with males of compatible head colour, to reduce fitness costs associated with incompatibility in mixed‐morph pairings. However, laboratory studies are an oversimplification of the complex ecological factors experienced in the wild and may only reflect the biology of a domesticated species. This study aimed to examine the patterns of parentage and sex ratio bias with respect to colour pairing combinations in a wild population of the Gouldian finch. We utilized a novel PCR assay that allowed us to genotype the morph of offspring before the morph phenotype develops and to explore bias in morph paternity and selection at the nest. Contrary to previous findings in the laboratory, we found no effect of pairing combinations on patterns of extra‐pair paternity, offspring sex ratio or selection on morphs in nestlings. In the wild, the effect of morph incompatibility is likely much smaller, or absent, than was observed in the domesticated birds. Furthermore, the previously studied domesticated population is genetically differentiated from the wild population, consistent with the effects of domestication. It is possible that the domestication process fostered the emergence (or enhancement) of incompatibility between colour morphs previously demonstrated in the laboratory.     

Candidate genes underlying heritable differences in reproductive seasonality between wild and domestic rabbits

Reproductive seasonality is a trait that often differs between domestic animals and their wild ancestors, with domestic animals showing prolonged or even continuous breeding seasons. However, the genetic basis underlying this trait is still poorly understood for most species, and because environmental factors and resource availability are known to play an important role in determining breeding seasons, it is also not clear in most cases to what extent this phenotypic shift is determined by the more lenient captive conditions or by genetic factors. Here, using animals resulting from an initial cross between wild and domestic rabbits followed by two consecutive backcrosses (BC1 and BC2) to wild rabbits, we evaluated the yearly distribution of births for the different generations. Similar to domestic rabbits, F1 animals could be bred all year round but BC1 and BC2 animals showed a progressive and significant reduction in the span of the breeding season, providing experimental evidence that reduced seasonal breeding in domestic rabbits has a clear genetic component and is not a simple by‐product of rearing conditions. We then took advantage of a recently published genome‐wide scan of selection in the domesticated lineage and searched for candidate genes potentially associated with this phenotypic shift. Candidate genes located within regions targeted by selection include well‐known examples of genes controlling clock functions (CRY1 and NR3C1) and reproduction (PRLR).     

Melanin‐based colour polymorphism responding to climate change

Climate warming leads to a decrease in biodiversity. Organisms can deal with the new prevailing environmental conditions by one of two main routes, namely evolving new genetic adaptations or through phenotypic plasticity to modify behaviour and physiology. Melanin‐based colouration has important functions in animals including a role in camouflage and thermoregulation, protection against UV‐radiation and pathogens and, furthermore, genes involved in melanogenesis can pleiotropically regulate behaviour and physiology. In this article, I review the current evidence that differently coloured individuals are differentially sensitive to climate change. Predicting which of dark or pale colour variants (or morphs) will be more penalized by climate change will depend on the adaptive function of melanism in each species as well as how the degree of colouration covaries with behaviour and physiology. For instance, because climate change leads to a rise in temperature and UV‐radiation and dark colouration plays a role in UV‐protection, dark individuals may be less affected from global warming, if this phenomenon implies more solar radiation particularly in habitats of pale individuals. In contrast, as desertification increases, pale colouration may expand in those regions, whereas dark colourations may expand in regions where humidity is predicted to increase. Dark colouration may be also indirectly selected by climate warming because genes involved in the production of melanin pigments confer resistance to a number of stressful factors including those associated with climate warming. Furthermore, darker melanic individuals are commonly more aggressive than paler conspecifics, and hence they may better cope with competitive interactions due to invading species that expand their range in northern latitudes and at higher altitudes. To conclude, melanin may be a major component involved in adaptation to climate warming, and hence in animal populations melanin‐based colouration is likely to change as an evolutionary or plastic response to climate warming.     

Colouration in Atlantic puffins and blacklegged kittiwakes: monochromatism and links to body condition in both sexes

Sexual dimorphism is widely used as an indirect measure of the intensity of sexual selection. It is also a way to evaluate whether different selective pressures act on males and females. Dichromatism, defined as a difference in colouration between males and females, may for instance result from selection for crypsis in females and selection for conspicuousness in males. Here, we conducted a study to investigate whether differential sexual selective pressures might act on the colour traits of two colonial seabird species, the Atlantic puffin Fratercula artica and the black‐legged kittiwake Rissa tricactyla. First, we used spectrophotometry and visual modelling to determine whether these presumed monomorphic birds are really monochromatic from an avian perspective (birds and humans have a different vision). Second, we estimated whether some of their colourations have the potential to be sexually or socially selected by determining whether these colourations were related to body condition in males and females, and whether the yellow, orange and red colourations may contain carotenoid pigments. Our results indicated that both species were fully monochromatic from an avian perspective. Moreover, our preliminary analyses suggested that the yellow, orange and red colours of these birds contained carotenoids. Lastly, some indices of colouration were positively linked to estimates of condition. Birds in better condition had redder gape (both species) and bill (puffins). In puffins, the relation between condition and gape colouration was significantly stronger in females than males. By contrast, the size of the gape rosette was larger in males than females. The positive links we found between colour indices and condition, together with the absence of sexual dichromatism, suggest that mutual sexual selection may act in these two species.     

Signatures of de‐domestication in autochthonous pig breeds and of domestication in wild boar populations from MC1R and NR6A1 allele distribution

Autochthonous pig breeds are usually reared in extensive or semi‐extensive production systems that might facilitate contact with wild boars and, thus, reciprocal genetic exchanges. In this study, we analysed variants in the melanocortin 1 receptor (MC1R) gene (which cause different coat colour phenotypes) and in the nuclear receptor subfamily 6 group A member 1 (NR6A1) gene (associated with increased vertebral number) in 712 pigs of 12 local pig breeds raised in Italy (Apulo‐Calabrese, Casertana, Cinta Senese, Mora Romagnola, Nero Siciliano and Sarda) and south‐eastern European countries (Kr?kopolje from Slovenia, Black Slavonian and Turopolje from Croatia, Mangalitsa and Moravka from Serbia and East Balkan Swine from Bulgaria) and compared the data with the genetic variability at these loci investigated in 229 wild boars from populations spread in the same macro‐geographic areas. None of the autochthonous pig breeds or wild boar populations were fixed for one allele at both loci. Domestic and wild‐type alleles at these two genes were present in both domestic and wild populations. Findings of the distribution of MC1R alleles might be useful for tracing back the complex genetic history of autochthonous breeds. Altogether, these results indirectly demonstrate that bidirectional introgression of wild and domestic alleles is derived and affected by the human and naturally driven evolutionary forces that are shaping the Sus scrofa genome: autochthonous breeds are experiencing a sort of ‘de‐domestication’ process, and wild resources are challenged by a ‘domestication’ drift. Both need to be further investigated and managed.     

Melanism and coat colour polymorphism in the Egyptian Wolf Canis lupaster Hemprich & Ehrenberg (Carnivora: Canidae) from Egypt

The Egyptian Wolf Canis lupaster was recently rediscovered as a distinct species on the basis of both morphologic and molecular genetic evidence. Phenotypical variability, including coat colour of this species across its vast, ecologically diverse range is yet to be investigated. In this paper, we present the first record of melanistic individuals of this species and compare their morphological characters and mitochondrial cytochrome b DNA sequences with those of typically coloured Canis lupaster and other closely related canids to verify their identity. We also study pelage polymorphism in a population of this species in the Egyptian Nile Valley and the Nile Delta and define its different colour variants. The typical colour, as well as the rare, very light and reddish coat colours are described. We discuss the possibility that the observed coat colour polymorphism is the result of hybridisation with the domestic dog and their potential adaptive significance.     

Malaysian weedy rice shows its true stripes: wild Oryza and elite rice cultivars shape agricultural weed evolution in Southeast Asia

Weedy rice is a close relative of domesticated rice (Oryza sativa) that competes aggressively with the crop and limits rice productivity worldwide. Most genetic studies of weedy rice have focused on populations in regions where no reproductively compatible wild Oryza species occur (North America, Europe and northern Asia). Here, we examined the population genetics of weedy rice in Malaysia, where wild rice (O. rufipogon) can be found growing in close proximity to cultivated and weedy rice. Using 375 accessions and a combined analysis of 24 neutral SSR loci and two rice domestication genes (sh4, controlling seed shattering, and Bh4, controlling hull colour), we addressed the following questions: (i) What is the relationship of Malaysian weedy rice to domesticated and wild rice, and to weedy rice strains in the USA? (ii) To what extent does the presence of O. rufipogon influence the genetic and phenotypic diversity of Malaysian weeds? (iii) What do the distributions of sh4 and Bh4 alleles and associated phenotypes reveal about the origin and contemporary evolution of Malaysian weedy rice? Our results reveal the following: independent evolutionary origins for Malaysian weeds and US strains, despite their very close phenotypic resemblance; wild‐to‐weed gene flow in Malaysian weed populations, including apparent adaptive introgression of seed‐shattering alleles; and a prominent role for modern Malaysian cultivars in the origin and recent proliferation of Malaysian weeds. These findings suggest that the genetic complexity and adaptability of weedy crop relatives can be profoundly influenced by proximity to reproductively compatible wild and domesticated populations.     

The genomics of wild yeast populations sheds light on the domestication of man's best (micro) friend

The domestication of plants, animals and microbes by humans are the longest artificial evolution experiments ever performed. The study of these long‐term experiments can teach us about the genomics of adaptation through the identification of the genetic bases underlying the traits favoured by humans. In laboratory evolution, the characterization of the molecular changes that evolved specifically in some lineages is straightforward because the ancestors are readily available, for instance in the freezer. However, in the case of domesticated species, the ancestor is often missing, which leads to the necessity of going back to nature in order to infer the most likely ancestral state. Significant and relatively recent examples of this approach include wolves as the closest wild relative to domestic dogs (Axelsson et al. 2013) and teosinte as the closest relative to maize (reviewed in Hake & Ross‐Ibarra 2015). In both cases, the joint analysis of domesticated lineages and their wild cousins has been key in reconstructing the molecular history of their domestication. While the identification of closest wild relatives has been done for many plants and animals, these comparisons represent challenges for micro‐organisms. This has been the case for the budding yeast Saccharomyces cerevisiae, whose natural ecological niche is particularly challenging to define. For centuries, this unicellular fungus has been the cellular factory for wine, beer and bread crafting, and currently for bioethanol and drug production. While the recent development of genomics has lead to the identification of many genetic elements associated with important wine characteristics, the historical origin of some of the domesticated wine strains has remained elusive due to the lack of knowledge of their close wild relatives. In this issue of Molecular Ecology, Almeida et al. (2015) identified what is to date the closest known wild population of the wine yeast. This population is found associated with oak trees in Europe, presumably its natural host. Using population genomics analyses, Almeida and colleagues discovered that the initial divergence between natural and domesticated wine yeasts in the Mediterranean region took place around the early days of wine production. Surprisingly, genomic regions that are key to wine production today appeared not to be derived from these natural populations but from genes gained from other yeast species.     

A test of the relationship between cuticular melanism and immune function in wild‐caught Mormon crickets

Cuticular melanism and innate immune parameters can share common physiological pathways in insects, and this functional connection may contribute to the maintenance of insect colour polymorphisms. However, evidence linking colouration and immune function has been equivocal, particularly when tested in wild populations. The present study investigates phenotypic links between colouration and immune function in migratory Mormon crickets (Anabrus simplex, Haldeman), in which juveniles occur in conspicuous colour variants but mature to become uniformly melanic adults. Wild‐caught insects are used to evaluate the relationship between juvenile colouration and three immune parameters: encapsulation ability, lysozyme‐like activity and phenoloxidase activity. As nymphs, brown crickets are better able to encapsulate an inert implant introduced into the haemocoel than green crickets, although the difference is slight and ceases after they all become darkly‐coloured adults. By contrast, adults that develop from brown nymphs have a higher basal phenoloxidase activity than those that develop from green nymphs, regardless of the fact that all adults are brown. Intrinsic factors other than colouration exert larger effects on immunity: males show stronger encapsulation responses but lower phenoloxidase activity than females, suggesting a sex‐specific trade‐off between these two immune parameters, and adults exhibit higher immune function than nymphs. In summary, modest support is found for a correlation between cuticular melanism and increased immune function in wild Mormon crickets. Additional intrinsic factors such as developmental stage and sex appear to interact with colouration and have a more substantial connection to immune function in the wild.     

Genetic structure in Red Junglefowl (Gallus gallus) populations: Strong spatial patterns in the wild ancestors of domestic chickens in a core distribution range

Red Junglefowl (Gallus gallus) are among the few remaining ancestors of an extant domesticated livestock species, the domestic chicken, that still occur in the wild. Little is known about genetic diversity, population structure, and demography of wild Red Junglefowl in their natural habitats. Extinction threats from habitat loss or genetic alteration from domestic introgression exacerbate further the conservation status of this progenitor species. In a previous study, we reported extraordinary adaptive genetic variation in the MHC B‐locus in wild Red Junglefowl and no evidence of allelic introgression between wild and domestic chickens was observed. In this study, we characterized spatial genetic variation and population structure in naturally occurring populations of Red Junglefowl in their core distribution range in South Central Vietnam. A sample of 212 Red Junglefowl was obtained from geographically and ecologically diverse habitats across an area of 250 × 350 km. We used amplified fragment‐length polymorphism markers obtained from 431 loci to determine whether genetic diversity and population structure varies. We found that Red Junglefowl are widely distributed but form small and isolated populations. Strong spatial genetic patterns occur at both local and regional scales. At local scale, population stratification can be identified to approximately 5 km. At regional scale, we identified distinct populations of Red Junglefowl in the southern lowlands, northern highlands, and eastern coastal portions of the study area. Both local and long‐distance genetic patterns observed in wild Red Junglefowl may reflect the species’ ground‐dwelling and territorial characteristics, including dispersal barriers imposed by the Annamite Mountain Range. Spatially explicit analyses with neutral genetic markers can be highly informative and here elevates the conservation profile of the wild ancestors of domesticated chickens.     

Characterisation of flower colouration in 30 Rhododendron species via anthocyanin and flavonol identification and quantitative traits

• Floral colour is a key reproductive character, often associated with environmental adaptation, and subject to human intervention. A large number of Rhododendron species differ widely in flower colour, providing a good model for flower colouration. The chromatic features and anthocyanin compositions of 30 species from seven subgenera were systematically analysed.
• The Royal Horticultural Society Colour Chart and CIE L*a*b* system were employed to describe and investigate flower colours. The UPLC‐PDA/ESI‐MSⁿ system was used to identify and quantify anthocyanins in petal extracts.
• The flower colours of 30 Rhododendron species were categorised into four groups – red, purplish pink, purple and white. Seven anthocyanins were identified and quantified in petals: delphinidin, cyanidin and malvidin 3‐O‐arabinoside‐5‐O‐glucosides, cyanidin 3,5‐di‐O‐glucoside, 3‐O‐galactoside and 3‐O‐arabinoside, and delphinidin 3‐O‐glucoside. The red‐flowered species mainly contained cyanidin monoglycosides and had much higher total anthocyanin content than purplish pink‐ and purple‐flowered species. Purplish pink‐ and purple‐flowered species had similar anthocyanin types and content. The chromatic differences were significant among groups, except the purplish pink and purple groups. Statistical analysis showed that Cy3Gal and Cy3Arb are characteristic for red‐flowered species, and Mv3Arb5G and Dp3Arb5G play important roles in purple colouration; their contents were major components that greatly affected the chromatic parameters. In total, 21 flavonol derivates were identified. However, total flavonol content and co‐pigmentation index showed no significant difference or correlation among/with colour groups, suggesting that flavonols might not play a major role in colouration.
• These results enhance our knowledge of the biochemical basis of flower colouration in Rhododendron species, and provide a foundation for genetic variation studies and aid in breeding cultivars with novel flower colours.

     

The complex history of the domestication of rice

BACKGROUND: Rice has been found in archaeological sites dating to 8000 bc, although the date of rice domestication is a matter of continuing debate. Two species of domesticated rice, Oryza sativa (Asian) and Oryza glaberrima (African) are grown globally. Numerous traits separate wild and domesticated rices including changes in: pericarp colour, dormancy, shattering, panicle architecture, tiller number, mating type and number and size of seeds. SCOPE: Genetic studies using diverse methodologies have uncovered a deep population structure within domesticated rice. Two main groups, the indica and japonica subspecies, have been identified with several subpopulations existing within each group. The antiquity of the divide has been estimated at more than 100 000 years ago. This date far precedes domestication, supporting independent domestications of indica and japonica from pre-differentiated pools of the wild ancestor. Crosses between subspecies display sterility and segregate for domestication traits, indicating that different populations are fixed for different networks of alleles conditioning these traits. Numerous domestication QTLs have been identified in crosses between the subspecies and in crosses between wild and domesticated accessions of rice. Many of the QTLs cluster in the same genomic regions, suggesting that a single gene with pleiotropic effects or that closely linked clusters of genes underlie these QTL. Recently, several domestication loci have been cloned from rice, including the gene controlling pericarp colour and two loci for shattering. The distribution and evolutionary history of these genes gives insight into the domestication process and the relationship between the subspecies. CONCLUSIONS: The evolutionary history of rice is complex, but recent work has shed light on the genetics of the transition from wild (O. rufipogon and O. nivara) to domesticated (O. sativa) rice. The types of genes involved and the geographic and genetic distribution of alleles will allow scientists to better understand our ancestors and breed better rice for our descendents.     

The highly divergent Jekyll genes,required for sexual reproduction,are lineage specific for the related grass tribes Triticeae and Bromeae

Phylogenetically related groups of species contain lineage‐specific genes that exhibit no sequence similarity to any genes outside the lineage. We describe here that the Jekyll gene, required for sexual reproduction, exists in two much diverged allelic variants, Jek1 and Jek3. Despite low similarity, the Jek1 and Jek3 proteins share identical signal peptides, conserved cysteine positions and direct repeats. The Jek1/Jek3 sequences are located at the same chromosomal locus and inherited in a monogenic Mendelian fashion. Jek3 has a similar expression as Jek1 and complements the Jek1 function in Jek1‐deficient plants. Jek1 and Jek3 allelic variants were almost equally distributed in a collection of 485 wild and domesticated barley accessions. All domesticated barleys harboring the Jek1 allele belong to single haplotype J1‐H1 indicating a genetic bottleneck during domestication. Domesticated barleys harboring the Jek3 allele consisted of three haplotypes. Jekyll‐like sequences were found only in species of the closely related tribes Bromeae and Triticeae but not in other Poaceae. Non‐invasive magnetic resonance imaging revealed intrinsic grain structure in Triticeae and Bromeae, associated with the Jekyll function. The emergence of Jekyll suggests its role in the separation of the Bromeae and Triticeae lineages within the Poaceae and identifies the Jekyll genes as lineage‐specific.     

On the heritability of blue‐green eggshell coloration

Abstract Avian blue‐green eggshell coloration has been proposed as a female signal of genetic or phenotypic quality to males. However, little is known about the relative importance of additive genetic and environmental effects as sources of eggshell colour variation in natural populations. Using 5 years of data and animal models, we explored these effects in a free‐living population of pied flycatchers. Permanent environmental and year effects were negligible, although year environmental variance (V_Year) was significant for all but one of the traits. However, we found high–moderate narrow‐sense heritabilities for some colour parameters. Within‐clutch colour variability showed the highest coefficient of additive genetic variation (i.e. evolvability). Previous evidence suggests that eggshell colour is sexually selected in this species, males enhancing parental effort in clutches with higher colour variability and peak values. Eggshell colour could be driven by good‐genes selection in pied flycatchers although further genetic studies should confirm this possibility.     

Red and blond Mangalitza pigs display a signature of divergent directional selection in the SLC45A2 gene

The Mangalitza lard‐type pig breed is well known for its fat appearance and curly hair, and it is mainly distributed in Eastern Europe. Four main lines were created in the nineteenth century by artificial selection: Blond Mangalitza, Black Mangalitza, Swallow‐Belly Mangalitza and Red Mangalitza. The Swallow‐Belly line has a black coat combined with yellow‐blond throat and underbelly. In the current work, we aimed to investigate if the colourations of Mangalitza pigs are genetically determined by one or a few loci whose frequencies have been modified by artificial selection. The results of selection scans, with Hap FLK and BayeScan , and of a GWAS for coat colour highlighted the existence of one region on SSC16 (18–20 Mb) with potential effects on hair pigmentation (Red vs. Blond contrast). The analysis of the gene content of this region allowed us to detect the solute carrier family 45 member 2 (SLC45A2) locus as a candidate gene for this trait. The polymorphism of the SLC45A2 locus has been associated with reduced levels or the absence of melanin in several mammalian species. The genotyping of four missense polymorphisms evidenced that rs341599992:G > A and rs693695020:G > A SNPs are strongly but not fully associated with the red and blond coat colours of Mangalitza pigs, a result that was confirmed by performing a haplotype association test. The near fixation of alternative SLC45A2 genotypes in Red and Blond Mangalitza pigs provides a compelling example of the consequences of a divergent directional selection for coat colour in a domestic species.     

Ephemeral Sexual Dichromatism in Zebrafish (Danio rerio)

Secondary sexual displays may be overlooked in many species, especially when they are ephemerally expressed or imperceptible to human senses. Zebrafish (Danio rerio), like many schooling fish, do not appear sexually dichromatic, but previous anecdotal observations indicate that sexual colouration is expressed briefly during courtship (ephemeral nuptial colouration). Our goals were to compare colour estimates of male vs. female zebrafish using digital photography in situ, computer software and human observations. We found that both sexes changed their colour estimates during spawning (dark and light stripes) and that some sex differences (light stripes) were larger or only became apparent during this time. We also found that individual males that appeared more colourful and conspicuous to the human eye engaged in courtship more often than less conspicuous males. We detected differences in the colour estimates between wild‐derived vs. a laboratory strain of zebrafish and reduced individual variation in the laboratory strain. This is the first study to systematically and objectively quantify body colour in zebrafish by utilizing colour estimates, although further studies are needed to determine the underlying mechanisms and signalling functions of this sexual dichromatism.     

The Mendelian inheritance of rare flesh and shell colour variants in the black‐lipped pearl oyster (Pinctada margaritifera)

Pinctada margaritifera is French Polynesia's most economically important aquaculture species. This pearl oyster has the specific ability to produce cultured pearls with a very wide range of colours, depending on the colour phenotypes of donor oysters used. Its aquaculture is still based on natural spat collection from wild stocks. We investigated three rare colour variants of P. margaritifera – orange flesh, and red and white shell colour phenotypes – in comparison with the wild‐type black flesh and shell commonly found in this species. The study aimed to assess the geographic distribution and genetic basis of these colour variants. Colour frequencies were evaluated during transfer and graft processes of pearl oyster seed captured at collector stations. Among the collection locations studied, Mangareva Island showed the highest rate of the orange flesh phenotype, whereas Takaroa and Takume atolls had relatively high rates of red and white shell phenotypes respectively. Broodstocks were made of these rare colour variants, and crosses were performed to produce first‐ and second‐generation progenies to investigate segregation. The results were consistent with Mendelian ratios and suggest a distinct model with no co‐dominance: (i) a two‐allele model for flesh trait, whereby the orange allele is recessive to the black fleshed type, and (ii) a three‐allele model for shell trait, whereby the black wild‐type allele is dominant to the red coloration, which is dominant to the white shell. Furthermore, the proposed model provides the basis for producing selected donor pearl oyster lines through hatchery propagation.     

Extreme‐phenotype genome‐wide association study (XP‐GWAS): a method for identifying trait‐associated variants by sequencing pools of individuals selected from a diversity panel

Although approaches for performing genome‐wide association studies (GWAS) are well developed, conventional GWAS requires high‐density genotyping of large numbers of individuals from a diversity panel. Here we report a method for performing GWAS that does not require genotyping of large numbers of individuals. Instead XP‐GWAS (extreme‐phenotype GWAS) relies on genotyping pools of individuals from a diversity panel that have extreme phenotypes. This analysis measures allele frequencies in the extreme pools, enabling discovery of associations between genetic variants and traits of interest. This method was evaluated in maize (Zea mays) using the well‐characterized kernel row number trait, which was selected to enable comparisons between the results of XP‐GWAS and conventional GWAS. An exome‐sequencing strategy was used to focus sequencing resources on genes and their flanking regions. A total of 0.94 million variants were identified and served as evaluation markers; comparisons among pools showed that 145 of these variants were statistically associated with the kernel row number phenotype. These trait‐associated variants were significantly enriched in regions identified by conventional GWAS. XP‐GWAS was able to resolve several linked QTL and detect trait‐associated variants within a single gene under a QTL peak. XP‐GWAS is expected to be particularly valuable for detecting genes or alleles responsible for quantitative variation in species for which extensive genotyping resources are not available, such as wild progenitors of crops, orphan crops, and other poorly characterized species such as those of ecological interest.