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opencc-zeroJun 2020View details →

Data from: Host-induced genome instability rapidly generates phenotypic variation across Candida albicans strains and ploidy states

Candida albicans is an opportunistic fungal pathogen of humans that is typically diploid yet has a highly labile genome tolerant of large-scale perturbations including chromosomal aneuploidy and loss-of-heterozygosity events. The ability to rapidly generate genetic variation is crucial for C. albicans to adapt to changing or stressful environments, like those encountered in the host. Genetic variation occurs via stress-induced mutagenesis or can be generated through its parasexual cycle, in which tetraploids arise via diploid mating or stress-induced mitotic defects and undergo nonmeiotic ploidy reduction. However, it remains largely unknown how genetic background contributes to C. albicans genome instability in vitro or in the host environment. Here, we tested how genetic background, ploidy, and the host environment impacts C. albicans genome stability. We found that host association induced both loss-of-heterozygosity events and genome size changes, regardless of genetic background or ploidy. However, the magnitude and types of genome changes varied across C. albicans strain background and ploidy state. We then assessed if host-induced genomic changes resulted in fitness consequences on growth rate and nonlethal virulence phenotypes and found that many host-derived isolates significantly changed relative to their parental strain. Interestingly, diploid host-associated C. albicans predominantly decreased host reproductive fitness, whereas tetraploid host-associated C. albicans increased host reproductive fitness. Together, these results are important for understanding how host-induced genomic changes in C. albicans alter its relationship with the host. IMPORTANCE Candida albicans is an opportunistic fungal pathogen of humans. The ability to generate genetic variation is essential for adaptation and is a strategy that C. albicans and other fungal pathogens use to change their genome size. Stressful environments, including the host, induce C. albicans genome instability. Here, we investigated how C. albicans genetic background and ploidy state impact genome instability, both in vitro and in a host environment. We show that the host environment induces genome instability, but the magnitude depends on C. albicans genetic background. Furthermore, we show that tetraploid C. albicans is highly unstable in host environments and rapidly reduces in genome size. These reductions in genome size often resulted in reduced virulence. In contrast, diploid C. albicans displayed modest host-induced genome size changes, yet these frequently resulted in increased virulence. Such studies are essential for understanding how opportunistic pathogens respond and potentially adapt to the host environment.

opencc-zeroJun 2020View details →

Data from: Phenotypic, ecological and genomic variation in common bully (Gobiomorphus cotidianus) populations along depth gradients in New Zealand's Southern Great Lakes

Depth gradients in lakes are often key drivers of population divergence and speciation in fishes. New Zealand has many deep lakes but no known profundal specialist fishes or cases of intralacustrine speciation. We sampled a native benthic fish, the common bully, from 5–90 m depth in four South Island lakes, to test for morphological, ecological, or genetic differentiation associated with depth. Deeper fish consistently had narrower bodies, while other morphological traits showed variable relationships with depth. Carbon and nitrogen stable isotope values of fish increased with depth, largely tracking isotopic trends with depth of benthic invertebrate prey. Genotyping-by-sequencing showed some genome-wide differentiation between two of the lakes, but no evidence for within-lake genetic structuring along depth gradients. These results indicate that individual bullies associate with shallower or deeper habitats within their lifetimes, but we found no evidence of progress toward genetic divergence within lakes. The apparent lack of intralacustrine genetic divergence in New Zealand's fishes may be explained by a combination of environmental factors and constraints intrinsic to its marine-derived freshwater fish fauna.

opencc-zeroDec 2020View details →

Cis-regulatory variation in the shavenbaby gene underlies intraspecific phenotypic variation, mirroring interspecific divergence in the same trait

Despite considerable progress in recent decades in dissecting the genetic causes of natural morphological variation, there is limited understanding of how variation within species ultimately contributes to species differences. We have studied patterning of the non-sensory hairs, commonly known as "trichomes," on the dorsal cuticle of first-instar larvae of Drosophila. Most Drosophila species produce a dense lawn of trichomes, but a subset of dorsal trichomes were lost in D. sechellia and D. ezoana due entirely to regulatory evolution of the shavenbaby (svb) gene. Here we describe intraspecific variation in dorsal trichome patterns of first-instar larvae of D. virilis that is similar to the trichome pattern variation identified previously between species. We found that 67% of this difference is explained by a QTL that contains svb and that svb expression correlates with trichome variation within D. virilis . Despite using an experimental design with reasonable power to detect a second locus accounting for the remainder of the variance in trichome number, only a single QTL could be mapped, suggesting that multiple other loci each make a small contribution to trichome patterning. Thus, the genetic architecture of intraspecific variation and interspecific differences exhibit similarities and differences that may reflect differences between short-term and long-term evolutionary processes.

opencc-zeroJan 2021View details →

Diet variation driven by color vision phenotype in wild capuchin monkeys

The polymorphic color vision of platyrrhine monkeys is a fascinating example of balancing selection acting on multiple genetic and phenotypic morphs. Yet, the mechanism of natural selection maintaining this variation remains elusive. Past research has demonstrated task-specific foraging advantages to dichromatic (two-opsin vision, red-green colorblind) and trichromatic (three-opsin vision, human "normal") monkeys, raising the potential for dietary niche differentiation. We ask whether color vision type influences diet variation in a population of wild, white-faced capuchins (Cebus imitator) in Costa Rica. To assess this, we record food intake during simultaneous focal follows of adult female dichromats and trichromats, and classify the conspicuity of diet items in capuchin visual space. We assess the degree of dietary and nutritional niche overlap during periods of high and low fruit abundance using nutritional geometry and Pianka's index. We find that in months of high fruit abundance, trichromats have higher intake of conspicuously-colored fruits, while dichromats have higher intake of camouflaged invertebrates, resulting in lower niche overlap. These differences disappear in months of low habitat-wide fruit abundance, a time when overall dietary breadth collapses. Our results support the hypothesis that niche differentiation in diet contributes to maintaining color vision variation without compromising species-specific nutritional intake.

Data from: Mimicry refinement: Phenotypic variations tracking the local optimum

1. Müllerian mimicry between chemically defended preys is a textbook example of natural selection favouring phenotypic convergence onto a shared warning signal. Studies of mimicry have concentrated on deciphering the ecological and genetic underpinnings of dramatic switches in mimicry association, producing a well-known mosaic distribution of mimicry patterns across geography. However, little is known about the accuracy of resemblance between natural co-mimics when the local phenotypic optimum varies. 2. In this study, using analyses of wing shape, pattern and hue, we quantify multimodal phenotypic similarity between butterfly co-mimics sharing the so-called postman pattern in different localities with varying species composition. 3. We show that subtle but consistent variation between populations of the localised species, Heliconius timareta thelxinoe, enhance resemblance to the abundant co-mimics which drive the mimicry in each locality. 4. Those results suggest that rarer co-mimics track the changes in the phenotypic optimum caused by gradual changes in the composition of the mimicry community, providing insights into the process by which intra-specific diversity of mimetic pattern may arise. Furthermore, our results suggest a multimodal evolution of similarity, with coordinated convergence in different features of the phenotype such as wing outline, pattern and hue. 5. Finally, multilocus genotyping allows estimating local hybridization rates between H. timareta and co-mimic H. melpomene in different populations, raising the hypothesis that mimicry refinement between closely-related co-mimics may be enhanced by adaptive introgression at loci modifying the accuracy of resemblance.

opencc-zeroDec 2011View details →

Data from: Consistency and variation in phenotypic selection exerted by a community of seed predators

Phenotypic selection that is sustained over time underlies both anagenesis and cladogenesis, but the conditions that lead to such selection and what causes variation in selection are not well known. We measured the selection exerted by three species of predispersal seed predators of lodgepole pine (Pinus contorta latifolia) in the South Hills, Idaho and found that net selection on different cone and seed traits exerted by red crossbills (Loxia curvirostra) and cone borer moths (Eucosma recissoriana) over 10 years of seed crops was similar to that measured in another mountain range. We also found that the strength of selection increased as seed predation increased, which provides a mechanism for the correlation between the escalation of seed defenses and the density of seed predators. Red crossbills consume the most seeds and selection they exert accounts for much of the selection experienced by lodgepole pine, providing additional support for a coevolutionary arms race between crossbills and lodgepole pine in the South Hills. The third seed predator, hairy woodpeckers (Picoides villosus), consumed less than one-sixth as many seeds as crossbills. Across the northern Rocky Mountains, woodpecker abundance and therefore selective impact appears limited by the elevated seed defenses of lodgepole pine.

opencc-zeroDec 2016View details →

Data from: Linking innate immunogenetic variation with phenotypic traits in a wild population of tree swallows, Tachycineta bicolor

Unravelling the genetic basis of phenotypic variation among individuals is an important step in our understanding of evolution. Recent studies of innate immune genes, such as β -defensins, revealed that these genes had high levels of polymorphism. However, researchers have yet to quantify the effects of such variability on immune responses and fitness-related traits in wild populations. In this study, we assessed how the variability at six avian β -defensin (AvBD) genes was linked to an immune function and reproductive success in adult tree swallows (Tachycineta bicolor). We investigated the links between genetic variations using single nucleotide polymorphisms at AvBD genes, immune function as the bacterial killing ability (BKA) and fledging success. We assessed how female immunogenetics were linked to the presence of eggshell bacteria in their clutches and hatching success. We found weak associations between the presence of AvBD genes, BKA and eggshell bacteria. Our results suggested that homozygosity at some loci may be advantageous for defence against bacteria. Variability at β -defensin genes was not related to either hatching or fledging success. BKA of parents was positively linked with fledging success. More studies are needed to assess whether or not β -defensin genes are significantly affecting fitness-related traits in wild populations.

opencc-zeroDec 2014View details →

Data from: The alignment between phenotypic plasticity, the major axis of genetic variation and the response to selection

Phenotypic plasticity is the ability of a genotype to produce more than one phenotype in order to match the environment. Recent theory proposes that the major axis of genetic variation in a phenotypically plastic population can align with the direction of selection. Therefore, theory predicts that plasticity directly aids adaptation by increasing genetic variation in the direction favoured by selection and reflected in plasticity. We evaluated this theory in the freshwater crustacean Daphnia pulex, facing predation risk from two contrasting size-selective predators. We estimated plasticity in several life-history traits, the G matrix of these traits, the selection gradients on reproduction and survival, and the predicted responses to selection. Using these data, we tested whether the genetic lines of least resistance and the predicted response to selection aligned with plasticity. We found predator environment-specific G matrices, but shared genetic architecture across environments resulted in more constraint in the G matrix than in the plasticity of the traits, sometimes preventing alignment of the two. However, as the importance of survival selection increased, the difference between environments in their predicted response to selection increased and resulted in closer alignment between the plasticity and the predicted selection response. Therefore, plasticity may indeed aid adaptation to new environments.

Data from: Striking phenotypic variation yet low genetic differentiation in sympatric lake trout (Salvelinus namaycush)

The study of population differentiation in the context of ecological speciation is commonly assessed using populations with obvious discreteness. Fewer studies have examined diversifying populations with occasional adaptive variation and minor reproductive isolation, so factors impeding or facilitating the progress of early stage differentiation are less understood. We detected non-random genetic structuring in lake trout (Salvelinus namaycush) inhabiting a large, pristine, postglacial lake (Mistassini Lake, Canada), with up to five discernible genetic clusters having distinctions in body shape, size, colouration and head shape. However, genetic differentiation was low (FST = 0.017) and genetic clustering was largely incongruent between several population- and individual-based clustering approaches. Genotype- and phenotype-environment associations with spatial habitat, depth and fish community structure (competitors and prey) were either inconsistent or weak. Striking morphological variation was often more continuous within than among defined genetic clusters. Low genetic differentiation was a consequence of relatively high contemporary gene flow despite large effective population sizes, not migration-drift disequilibrium. Our results suggest a highly plastic propensity for occupying multiple habitat niches in lake trout and a low cost of morphological plasticity, which may constrain the speed and extent of adaptive divergence. We discuss how factors relating to niche conservatism in this species may also influence how plasticity affects adaptive divergence, even where ample ecological opportunity apparently exists.

opencc-zeroApr 2020View details →

Intraspecific variation of Phragmites australis: Clinal adaption of functional traits and phenotypic plasticity vary with latitude of origin

1. Widespread plant species generally have high intraspecific variation in functional traits, which is reflected in their great variety of phenotypes. This variety can result from both genetic differences due to local adaptation and phenotypic plasticity. With high intraspecific variation and nearly global distribution, the common reed Phragmites australis is a suitable model species for studying the underlying mechanisms of intraspecific trait variation. 2. In this study, 71 genotypes of P. australis from seven phylogeographic groups were transplanted into two replicate common gardens located in very different climates: northern Europe and mid-east Asia. We measured seven functional traits of all these genotypes over the growing season, including shoot height, maximum biomass per shoot, shoot density, node number per stem, leaf lifespan, flowering occurrence and flowering date. Our aim was to assess the relative effects of genetic (phylogeographic origin) and environmental (common garden) status, and interactions between them, on intraspecific variation in functional traits of P. australis. 3. We found common garden having the strongest influence on most functional traits studied. All traits except flowering occurrence varied significantly across gardens, revealing the important role of phenotypic plasticity on trait variation of P. australis. We also found significant differences in trait variation among the different phylogeographic groups of P. australis and, thus, evidence for genetically determined intraspecific variation in the morphological and life-history traits addressed in this study. All functional traits showed significant (p≤0.0054), albeit minor to moderately explained (R2 ≤0.57), latitudinal patterns in both gardens. Covariation of multiple traits was similar in the two gardens. Phenotypic plasticity was trait-specific, and the plasticity of shoot height and maximum biomass per shoot increased towards higher latitude of genotypic origin. Our results indicate that the latitude of origin affects the evolution of functional traits, as well as their phenotypic plasticity. 4. Since phenotypic plasticity is a crucial mechanism for acclimation and evolution, our findings support the role of gene-based adaptive phenotypic plasticity in plant evolution. The intraspecific spatial variation of functional traits and their phenotypic plasticity can help predict species distribution, persistence and invasion under global climate change.

opencc-zeroDec 2018View details →

Data from: When one phenotype is not enough - divergent evolutionary trajectories govern venom variation in a widespread rattlesnake species

Understanding the origin and maintenance of phenotypic variation, particularly across a continuous spatial distribution, represents a key challenge in evolutionary biology. For this, animal venoms represent ideal study systems: they are complex, variable, yet easily quantifiable molecular phenotypes with a clear function. Rattlesnakes display tremendous variation in their venom composition, mostly through strongly dichotomous venom strategies, which may even coexist within single species. Here, through dense, widespread population-level sampling of the Mojave rattlesnake, Crotalus scutulatus, we show that genomic structural variation at multiple loci underlies extreme geographic variation in venom composition, which is maintained despite extensive gene flow. Unexpectedly, neither diet composition nor neutral population structure explain venom variation. Instead, venom divergence is strongly correlated with environmental conditions. Individual toxin genes correlate with distinct environmental factors, suggesting that different selective pressures can act on individual loci independently of their co-expression patterns or genomic proximity. Our results challenge common assumptions about diet composition as the key selective driver of snake venom evolution and emphasise how the interplay between genomic architecture and local-scale spatial heterogeneity in selective pressures may facilitate the retention of adaptive functional polymorphisms across a continuous space.

Data from: Genetic variation in variability: phenotypic variability of fledging weight and its evolution in a songbird population

Variation in traits is essential for natural selection to operate and genetic and environmental effects can contribute to this phenotypic variation. From domesticated populations, we know that families can differ in their level of within-family variance, which leads to the intriguing situation that within-family variance can be heritable. For offspring traits, such as birth weight, this implies that within-family variance in traits can vary among families and can thus be shaped by natural selection. Empirical evidence for this in wild populations is however lacking. We investigated whether within-family variance in fledging weight is heritable in a wild great tit (Parus major) population and whether these differences are associated with fitness. We found significant evidence for genetic variance in within-family variance. The genetic coefficient of variation (GCV) was 0.18 and 0.25, when considering fledging weight a parental or offspring trait, respectively. We found a significant quadratic relationship between within-family variance and fitness: families with low or high within-family variance had lower fitness than families with intermediate within-family variance. Our results show that within-family variance can respond to selection and provides evidence for stabilizing selection on within-family variance.

Data from: Egg rejection and clutch phenotype variation in the plain prinia (Prinia inornata)

Avian hosts of brood parasites can evolve anti-parasitic defenses to recognize and reject foreign eggs from their nests. Theory predicts that higher inter-clutch and lower intra-clutch variation in egg appearance facilitates hosts to detect parasitic eggs as egg-rejection mainly depends on the appearance of the egg. Therefore, we predict that egg patterns and rejection rates will differ when hosts face different intensity of cuckoo parasitism. We tested this prediction in two populations of the plain prinia (Prinia inornata): Guangxi in mainland China with high diversity and density of cuckoo species, and Taiwan where there is only one breeding cuckoo species, the Oriental cuckoo (Cuculus optatus). As expected, egg patterns were similar within clutches but different among clutches (polymorphic eggs) in the mainland population, while the island population produced more uniform egg morphs. Furthermore, the mainland population showed a high rate of egg rejection, while the island population exhibited dramatically reduced egg grasp-rejection ability in the absence of parasitism by the common cuckoo (Cuculus canorus). Our study suggests that prinias show lower intra-clutch consistency in egg colour and lose egg-rejecting ability under relaxed selection pressure from brood parasitism.

opencc-zeroDec 2017View details →

Data from: Adaptive phenotypic variation among clonal ant workers

Phenotypic variations are observed in most organisms, but their significance is not always known. The phenotypic variations observed in social insects are exceptions. Genetically based response threshold variances have been identified among workers and are thought to play several important adaptive roles in social life, e.g. allocating tasks among workers according to demand, promoting the sustainability of the colony and forming the basis of rationality in collective decision-making. Several parthenogenetic ants produce clonal workers and new queens by asexual reproduction. It is not clearly known whether such genetically equivalent workers show phenotypic variations. Here, we demonstrate that clonal workers of the parthenogenetic ant Strumigenys membranifera show large threshold variances among clonal workers. A multi-locus genetic marker confirmed that colony members are genetic clones, but they showed variations in their sucrose response thresholds. We examined the changing pattern of the thresholds over time generating hypotheses regarding the mechanism underlying the observed phenotypic variations. The results support the hypothesis that epigenetic modifications that occur after eclosion into the adult form are the cause of the phenotypic variations in this asexual species.

FIGURE 3 in Phenotypic variation and vocal divergence reveals a species complex in White-eared Ground-sparrows (Cabanis) (Aves: Passerellidae)

FIGURE 3. Plot of the first two discriminant functions for morphometric measurements, plumage patterns, and vocalizations showing separation between the three subspecies of Melozone leucotis (black circles: M. l. leucotis, gray circles: M. l. nigrior, addition sign: M. l. occipitalis) based on the best model for each comparison (see text for details on percentage of classification and variables included in each model).

FIGURE 2 in Phenotypic variation and vocal divergence reveals a species complex in White-eared Ground-sparrows (Cabanis) (Aves: Passerellidae)

FIGURE 2. Photographs of museum specimens reveal plumage color and pattern differences between the three subspecies of Melozone leucotis. Photographs were taken under the same light conditions at the Field Museum of Natural History, Chicago. The top row compares the ventral surfaces, the middle row shows lateral surfaces, and the bottom row shows dorsal surfaces.

FIGURE 1 in Phenotypic variation and vocal divergence reveals a species complex in White-eared Ground-sparrows (Cabanis) (Aves: Passerellidae)

FIGURE 1. Map of the distribution of the Melozone leucotis subspecies from southern Mexico to Costa Rica, based on data from Stiles & Skutch (1989), Howell & Webb (1995), and Rising (2011). Melozone l. occipitalis is separated from M. l. nigrior by at least 370 km, and M. l. nigrior is separated from M. l. leucotis by at least 250 km.

FIGURE 5 in Phenotypic variation and vocal divergence reveals a species complex in White-eared Ground-sparrows (Cabanis) (Aves: Passerellidae)

FIGURE 5. Sound spectrograms of two call types, male solo songs, and duets of the three subspecies of Melozone leucotis.