Matthew J. Powers

Hypoxia-induced regulatory changes are well understood across aquatic and terrestrial systems. These changes are normally initiated by elements belonging to hypoxia-inducible factor (HIF) pathway. These elements generate responses that help organisms survive hypoxia, such as protein stabilization, antioxidant activity, or the switch from aerobic to anaerobic metabolism. The HIF pathway is initiated by the transcription factor HIF-α via deactivation of its repressor EGLN. However, recent work revealed that many aquatic invertebrates do not possess HIF-α or EGLN. Among these is the intertidal copepod Tigriopus californicus. Although this copepod experiences daily bouts of hypoxia, T. californicus tolerates even extended anoxia with minimal mortality. Because T. californicus lacks HIF-α, it is unclear how the transcriptional response proceeds on a fine timescale in this species and which physiological strategies they use to cope with severe hypoxia. In this study, we captured gene expression over a species-typical course of hypoxia including normoxia, mild hypoxia (∼3.5 mg O2 L−1), at critical oxygen tension (Pcrit; ∼0.5 mg O2 L−1), anoxia (0 mg O2 L−1), and recovery. We identified and clustered genes affected by this hypoxia course and tested for enrichment of Gene Ontology and transcription factor binding site motifs. We identified genes with known responses to hypoxia, including genes with interactions with HIF-α in other systems. We also identified genes related to functions unique to T. californicus, including exoskeletal modifications that could represent a specialized response allowing T. californicus to persist in extreme hypoxic environments despite lacking HIF-α.

In a hybrid zone between two tropical lekking birds, yellow male plumage of one species has introgressed asymmetrically replacing white plumage of another via sexual selection. Here, we present a detailed analysis of the plumage trait to uncover its physical and genetic bases and trace its evolutionary history. We determine that the carotenoid lutein underlies the yellow phenotype and describe microstructural feather features likely to enhance color appearance. These same features reduce predicted water shedding capacity of feathers, a potential liability in the tropics. Through genome-scale DNA sequencing of hybrids and each species in the genus, we identify BCO2 as the major gene responsible for the color polymorphism. The BCO2 gene tree and genome-wide allele frequency patterns suggest that carotenoid-pigmented collars initially arose in a third species and reached the hybrid zone through historical gene flow. Complex interplay between sexual selection and hybridization has thus shaped phenotypes of these species, where conspicuous sexual traits are key to male reproductive success.

Carotenoid pigmentation produces the yellow and red coloration of birds and other vertebrates, but our understanding of the genetic architecture of carotenoid ornamentation is largely limited to studies of novel color variants observed in captively bred populations. The complexity of carotenoid-based color evolution in nature remains poorly characterized. Here, we examine the long-tailed finch Poephila acuticauda , an Australian songbird with two hybridizing subspecies that differ in bill coloration: yellow in western subspecies acuticauda and red in eastern subspecies hecki . We characterize the carotenoid composition of each subspecies and find that yellow bills can be explained by the loss of C(4)-oxidation, thus blocking yellow dietary pigments from being metabolized to red. Combining linked-read genomic sequencing and reflectance spectrophotometry measurements of bill color collected from wild-sampled finches and laboratory crosses, we identify four loci that together explain 53% of variance in this trait. The two loci of largest effect contain the genes CYP2J19 , an essential enzyme for the ketolation via C(4)-oxidation of dietary carotenoids, and TTC39B , an enhancer of ketocarotenoid production. Evolutionary genealogy reconstruction indicates that the red-billed phenotype is ancestral and yellow alleles at both CYP2J19 and TTC39B arose and fixed in acuticauda approximately 100 kya. Yellow alleles then introgressed into hecki less than 5 kya. Across all four loci, acuticauda derived variants show evidence of selective sweeps, implying that yellow bill coloration has been favored by natural selection. Our study suggests that the frequent adaptive evolutionary transitions between red and yellow ornamentation in nature can have a simple genetic basis. Significance: We studied variation in carotenoid ornamentation of an Australian songbird with two hybridizing subspecies that differ in bill color: one yellow and the other red. We identified a single metabolic process, C(4)-oxidation, underlying the distinct carotenoid composition of these two bill colors. Genetic association mapping revealed four major effect loci that explained most of the observed variation the trait, including the oxidative ketolation enzyme CYP2J19 and the carotenoid ketolation enhancer gene TTC39B . Evolutionary reconstruction indicates that yellow alleles are derived, ancient (~100 kya), and under positive selection. This has driven their recent (<5 kya) adaptive introgression across the hybrid zone. These findings have important implications for understanding the role of natural selection in phenotypic evolution in natural systems.

The shared-pathway hypothesis offers a cellular explanation for the connection between ketocarotenoid pigmentation and individual quality. Under this hypothesis, ketocarotenoid metabolism shares cellular pathways with mitochondrial oxidative phosphorylation such that red carotenoid-based coloration is inextricably linked mitochondrial function. To test this hypothesis, we exposed Tigriopus californicus copepods to a mitochondrially targeted protonophore, 2,4-dinitrophenol (DNP), to induce proton leak in the inner mitochondrial membranes. We then measured whole-animal metabolic rate and ketocarotenoid accumulation. As observed in prior studies of vertebrates, we observed that DNP treatment of copepods significantly increased respiration and that DNP-treated copepods accumulated more ketocarotenoid than control animals. Moreover, we observed a relationship between ketocarotenoid concentration and metabolic rate, and this association was strongest in DNP-treated copepods. These data support the hypothesis that ketocarotenoid and mitochondrial metabolism are biochemically intertwined. Moreover, these results corroborate observations in vertebrates, perhaps suggesting a fundamental connection between ketocarotenoid pigmentation and mitochondrial function that should be explored further.

The marine copepod, Tigriopus californicus, produces the red carotenoid pigment astaxanthin from yellow dietary precursors. This ‘bioconversion’ of yellow carotenoids to red is hypothesized to be linked to individual condition, possibly through shared metabolic pathways with mitochondrial oxidative phosphorylation. Experimental inter-population crosses of lab-reared T. californicus typically produces low-fitness hybrids is due in large part to the disruption of coadapted sets nuclear and mitochondrial genes within the parental populations. These hybrid incompatibilities can increase variability in life history traits and energy production among hybrid lines. Here, we tested if production of astaxanthin was compromised in hybrid copepods and if it was linked to mitochondrial metabolism and offspring development. We observed no clear mitonuclear dysfunction in hybrids fed a limited, carotenoid-deficient diet of nutritional yeast. However, when yellow carotenoids were restored to their diet, hybrid lines produced less astaxanthin than parental lines. We observed that lines fed a yeast diet produced less ATP and had slower offspring development compared to lines fed a more complete diet of algae, suggesting the yeast-only diet may have obscured effects of mitonuclear dysfunction. Astaxanthin production was not significantly associated with development among lines fed a yeast diet but was negatively related to development in early generation hybrids fed an algal diet. In lines fed yeast, astaxanthin was negatively related to ATP synthesis, but in lines fed algae, the relationship was reversed. Although the effects of the yeast diet may have obscured evidence of hybrid dysfunction, these results suggest that astaxanthin bioconversion may still be related to mitochondrial performance and reproductive success.

Synopsis: For decades, scientists have noted connections between individual condition and carotenoid-based coloration in terrestrial and aquatic animals. Organisms that produce more vibrant carotenoid-based coloration tend to have better physiological performance and behavioral displays compared with less colorful members of the same species. Traditional explanations for this association between ornamental coloration and performance invoked the need for color displays to be costly, but evidence for such hypothesized costs is equivocal. An alternative explanation for the condition-dependence of carotenoid-based coloration, the Shared-Pathway Hypothesis (SPH), was developed in response. This hypothesis proposes that red ketocarotenoid-based coloration is tied to core cellular processes involving a shared pathway with mitochondrial energy metabolism, making the concentration of carotenoids an index of mitochondrial function. Since the presentation of this hypothesis, empirical tests of the mechanisms proposed therein have been conducted in several species. In this manuscript, we review the SPH and the growing number of studies that have investigated a connection between carotenoid-based coloration and mitochondrial function. We also discuss future strategies for assessing the SPH to more effectively disentangle evidence that may simultaneously support evidence of carotenoid-resource tradeoffs.

To produce viable offspring, organisms may assess mates via criteria that include traits, such as sex, species, age, reproductive status, population identity and individual quality. Copepods are small, ubiquitous crustaceans that live in freshwater and marine systems around the world whose patterns of mate choice have been long studied in numerous species. Herein, we synthesized decades of experiments describing sexual selection in copepods to assess the importance of mating criteria. We used formal, meta-analytical techniques and mixed modeling to quantify the likelihood of non-random mating associated with mating criteria. In our synthesis of the scientific literature, we found that copepods use several criteria when assessing mates and that these criteria are associated with different likelihood estimates. We report the strongest likelihood of non-random mating when copepods assess the reproductive status of females or when copepods select between conspecific vs. heterospecific mates. We found weak likelihood of non-random mating in studies that provide mates from different populations or that manipulate operational sex ratio. Studies that directly test assessment of individual quality are sparse in copepods when compared to equivalent studies in vertebrates, and we encourage future researchers to explore whether copepods use individual characteristics as key mating criteria.

Colorful ornaments are hypothesized to have evolved in response to sexual selection for honest signals of individual quality that provide information about potential mates. Red carotenoid coloration is common in diverse groups, and in some vertebrate taxa, red coloration is a sexually selected trait whereby mates with the reddest ornaments are preferred. Despite being widespread among invertebrates, whether red carotenoid coloration is assessed during mate choice in these taxa is unclear. The marine copepod Tigriopus californicus displays red coloration from the accumulation of the carotenoid astaxanthin. Previous research on copepods has shown that astaxanthin provides protection from UV radiation and xenobiotic exposure and that carotenoid production is sensitive to external stressors. Because of the condition dependency of the red coloration, we hypothesized that Tigriopus would use it as a criterion during mate choice. To test this hypothesis, we conducted trials in which males chose between females that were wild‐type red (carotenoid‐rich algae diet) or white (carotenoid‐deficient yeast diet). To control for dietary differences and to isolate the effect of carotenoid coloration, we also presented males with restored‐red females fed a carotenoid‐supplemented yeast diet. We found that wild‐type red females were weakly preferred over white females. After controlling for diet, however, we found that restored‐red females were avoided. Our observations do not support the hypothesis that male copepods prefer the carotenoid coloration of females during mate choice. We hypothesize that algal‐derived compounds other than carotenoids play a role in mate choice. Red coloration in copepods appears to be a condition‐dependent trait that is not assessed during mating.