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Figure 6 in Phylogenetics of modern shorebirds (Charadriiformes) based on phenotypic evidence: analysis and discussion

Figure 6. Prior phylogenetic analyses of Charadriiformes: A, Baker et al. (2007); B, Fain & Houde (2007).

Figure 8 in Phylogenetics of modern shorebirds (Charadriiformes) based on phenotypic evidence: analysis and discussion

Figure 8. Higher-order groups of Charadriiformes in the present study. Majority rule consensus (MRC) tree for subordinal and family-group nodes. All nodes shown are conserved at 100% in an MRC tree. Dashes indicate nodes that are either monotypic or analysed as familial exemplars; bootstrap percentages (O, <50%; •, 100%); decay (Bremer) indices are given below selected branches.

Figure 3 in Phylogenetics of modern shorebirds (Charadriiformes) based on phenotypic evidence: analysis and discussion

Figure 3. Prior phylogenetic analyses of Charadriiformes: A, Paton et al. (2003); B, Fain & Houde (2004).

Figure 1 in Phylogenetics of modern shorebirds (Charadriiformes) based on phenotypic evidence: analysis and discussion

Figure 1. Prior phylogenetic analyses of Charadriiformes: A, Strauch (1978); B, Sibley & Ahlquist (1990) fide Harshman (1994).

Phenotypic assortment by morphology in social partners of the forked fungus beetle Bolitotherus cornutus

Social interactions with conspecifics can dramatically affect an individual's fitness. The positive or negative consequences of interacting with social partners typically depend on the value of traits that they express. These pathways of social selection connect the traits and genes expressed in some individuals to the fitness realized by others, thereby altering the total phenotypic selection on and evolutionary response of traits across the multivariate phenotype. The downstream effects of social selection are mediated by the patterns of phenotypic assortment between focal individuals and their social partners (the interactant covariance, Cij , or the multivariate form, CI). Depending on the sign and magnitude of the interactant covariance, the direction of social selection can be reinforced, reversed, or erased. We report estimates of Cij from a variety of studies of forked fungus beetles to address the largely unexplored questions of consistency and plasticity of phenotypic assortment in natural populations. We found that phenotypic assortment of male beetles based on body size or horn length was highly variable among subpopulations, but that those differences also were broadly consistent from year to year. At the same time, the strength and direction of Cij changed quickly in response to experimental changes in resource distribution and social properties of populations. Generally, interactant covariances were more negative in contexts in which the number of social interactions was greater in both field and experimental situations. These results suggest that patterns of phenotypic assortment could be important contributors to variability in multilevel selection through their mediation of social selection gradients.

Phenotypic rates of change evolutionary and ecological dataset (PROCEED) version 5.0

Wild populations must continuously respond to environmental changes or they risk extinction. Those responses can be measured as phenotypic rates of change which can allow us to predict contemporary adaptive responses, some of which are evolutionary. About two decades ago, a database of phenotypic rates of change in wild populations was compiled. Since then, researchers have used (and expanded) this database to examine phenotypic responses to specific types of human disturbance. Here, we updatedthe database adding 5675 new estimates of phenotypic changes. Using this newer version of the database, now containing 7338 estimates of phenotypic change, we revisit the conclusions of four published articles. We then synthesize the expanded dataset to compare rates of change across different types of human disturbance. Analyses of this expanded database suggests that: I. a small absolute difference in rates of change exists between human disturbed and natural populations, II. harvesting by humans results in higher rates of change than other types of disturbances, III. introduced populations have increased rates of change, and IV. body size does not increase through time. Thus, findings from earlier analyses have largely held-up in analyses of our new database that encompass a much larger breadth of species, traits, and human disturbances. Lastly, we use new analyses to explore how various types of human disturbances affect rates of phenotypic change, and we call for this database to serve as a stepping stone for further analyses to understand patterns of contemporary phenotypic change.

Phenotypic plasticity and genetic diversity elucidate rarity and vulnerability of an endangered riparian plant

Anthropogenic environmental change threatens many species and can be especially challenging for rare species given their potentially limited capacity for migration and adaptation relative to more common species. The ability to acclimate via phenotypic plasticity could provide an important path to persistence, especially for rare species. We investigated the responses of an endangered plant species endemic to a highly dynamic riparian habitat in southeastern Tennessee, USA, and its most widespread congener to environmental change to elucidate their current statuses and future vulnerability. Specifically, we compared the population- and species-level plasticity of rare Pityopsis ruthii and common P. graminifolia to contrasting light, temperature, and water conditions in a growth chamber experiment to evaluate their potential to acclimate to environmental change. Contrary to our expectations, P. ruthii had greater phenotypic plasticity than its common congener in response to both altered light and water availability. But this plasticity was not associated with increased fitness, suggesting that it was not adaptive. Concurrently, we genotyped these individuals at nine putatively neutral microsatellite loci to contrast genetic diversity across the range of each species. As expected, P. ruthii exhibited reduced genetic diversity relative to its more common congener. Overall, our findings accord with the narrow range and current habitat specificity of P. ruthii, especially its tolerance of highly variable water, and highlight its potential vulnerability to future environmental change.

Genomic data from: Are you ready for the heat? Phenotypic plasticity vs adaptation of heat tolerance in three-spined stickleback

Heat waves constitute a challenge for aquatic ectotherms. However, the thermal tolerance of animals and their individual phenotypic plasticity to respond to heat waves may be influenced by thermal history. We tested these hypotheses by comparing the upper thermal tolerance and the individual capacities of three-spined sticklebacks from populations with different thermal histories to respond to heat waves. Two populations originated from thermally polluted nuclear power plant (NPP) habitats, while four locations represented geographically adjacent control areas. To disentangle the genetic adaptation from the phenotypic plastic response, we measured the individual upper thermal tolerance and the responses at molecular level in common garden conditions before and after a laboratory-mimicked heat wave. We found that the sticklebacks exhibit considerable phenotypic plasticity in thermal tolerance since the heat wave increased fish upper thermal tolerance significantly. The individual plasticity to respond to the heat wave was also negatively correlated to initial thermal tolerance. On the other hand, neither the thermal tolerance nor the plastic responses differed between NPP and control sites despite detection of significant but low genome-wide divergence in 10 out of 15 pairwise comparisons. Our results suggest that five decades of nuclear power plant activity with warmer water has not resulted in a detectable evolutionary change in either the upper thermal tolerance or its plasticity in three-spined sticklebacks potentially rendering them sensitive to frequent heat waves.

Context dependent variation in corticosterone and phenotypic divergence of Rana arvalis populations along an acidification gradient

Background Physiological processes, as immediate responses to the environment, are important mechanisms of phenotypic plasticity and can influence evolution at ecological time scales. In stressful environments, physiological stress responses of individuals are initiated and integrated via the release of hormones, such as corticosterone (CORT). In vertebrates, CORT influences energy metabolism and resource allocation to multiple fitness traits (e.g. growth and morphology) and can be an important mediator of rapid adaptation to environmental stress, such as acidification. The moor frog, Rana arvalis, shows adaptive divergence in larval life-histories and predator defense traits along an acidification gradient in Sweden. Here we take a first step to understanding the role of CORT in this adaptive divergence. We conducted a fully factorial laboratory experiment and reared tadpoles from three populations (one acidic, one neutral and one intermediate pH origin) in two pH treatments (Acid versus Neutral pH) from hatching to metamorphosis. We tested how the populations differ in tadpole CORT profiles and how CORT is associated with tadpole life-history and morphological traits. Results We found clear differences among the populations in CORT profiles across the developmental stages, but only weak effects of pH treatment on CORT. Tadpoles from the acid origin population had, on average, lower CORT levels than tadpoles from the neutral origin population, and the intermediate pH origin population had intermediate CORT levels. Overall, tadpoles with higher CORT levels developed faster and had shorter and shallower tails as well as shallower tail muscles. Conclusions Our common garden results indicate among population divergence in CORT levels, likely reflecting acidification mediated divergent selection on tadpole physiology, concomitant to selection on larval life-histories and morphology. However, CORT levels were highly environmental context dependent. Jointly these results indicate a potential role for CORT as a mediator of multi-trait divergence along environmental stress gradients in natural populations. At the same time, the population level differences and high context dependency in CORT levels suggest that snapshot assessment of CORT in nature may not be reliable bioindicators of stress.

FIGURE 2 in Integrating voice and phenotype in a revision of the brush cuckoo Cacomantis variolosus (Aves: Cuculidae) complex

FIGURE 2. The seven element shapes found in the Cacomantis variolosus complex. Taxon names given represent the following geographic song types (see Results): sepulcralis—Sundaland and Philippines, virescens—Sulawesi and Sula, aeruginosus—resident Moluccas, variolosus—Australasia, blandus—Admiralty Islands, addendus—Solomon Islands.

FIGURE 4 in Integrating voice and phenotype in a revision of the brush cuckoo Cacomantis variolosus (Aves: Cuculidae) complex

FIGURE 4. Boxplots of vocal measurements. Explanation of variables: pacing—elements per second; element duration in seconds; changes in center frequency in Hertz. For further explanation of vocal parameters, see Methods.

FIGURE 3 in Integrating voice and phenotype in a revision of the brush cuckoo Cacomantis variolosus (Aves: Cuculidae) complex

FIGURE 3. Principal component analysis plot based on the four vocal parameters measured. The first principal component (PC1) chiefly differentiates addendus and virescens, while the second PC splits the sepulcralis group and variolosus group. The inferred Australian migrant variolosus individual (ML 168559) found on Flores, Nusa Tenggara, Indonesia, is denoted by an arrow.

FIGURE 1 in Integrating voice and phenotype in a revision of the brush cuckoo Cacomantis variolosus (Aves: Cuculidae) complex

FIGURE 1. Distribution of the Cacomantis variolosus complex across the Indo-Pacific region: (a) showing the ranges of taxa listed in Table 1; (b) showing all species and subspecies recognized as a result of this study, with species encircled.

Phenotypic variation and genome-wide association studies of main culm panicle node number, maximum node production rate, and degree-days to heading in rice

To understand the genetic basis of main culm panicle node number, maximum node production rate, and degree-days to heading in rice (Oryza sativa), we conducted genome-wide association studies using a diversity panel of 220 rice accessions and 854,832 SNP markers generated using genotyping-by-sequencing (GBS), with 1X coverage. The raw genotype data was filtered, selecting single nucleotide polymorphisms (SNPs) having less than 50% missing data and minimum allele frequency (MAF) >5%. After initial filtering, imputation was conducted using BEAGLE V4.0 in 1,075,302 SNP markers. After imputation, the dataset was filtered a second time by removing SNPs with less than 5% MAF and more than 5% missing data. A total of 854,832 SNPs were used in the genome-wide association analyses. The dataset representing the genotype data of 854,832 SNP markers by 220 rice accessions is presented here.

opencc-by-4.0Jan 2022View details →

Data for manuscript on objective phenotyping of alfalfa roots

These are images for the manuscript, "Objective phenotyping of root system architecture using image augmentation and machine learning in alfalfa." Alfalfa_root_ML_segmented.zip contains the root images segmented from the background using RootPainter and that were used as input for RhizoVision Explorer. Alfalfa_root_ML_color_photographs.zip contains the original color photographs of the roots, except that the circular scale and ID tag have been cropped out and filled with black to aid image analysis.

opencc-zeroJan 2022View details →

Host genetics, phenotype and geography structure the microbiome of a foundational seaweed

Interactions between hosts and their microbiota are critical to the functioning and resilience of eukaryotic macro-organisms. Critically, for hosts that play foundational roles in communities, understanding what drives these interactions is essential for informing restoration and conservation of entire ecosystems. Here, we investigated the relative influence of host traits and the surrounding environment on microbial communities associated with the foundational seaweed Phyllospora comosa. We collected data on 16 morphological and functional phenotypic traits, host genetics (using 354 Single Nucleotide Polymorphisms) and surface-associated microbial communities (using 16S rRNA gene amplicon sequencing) from 160 individuals sampled from eight sites spanning Phyllospora's entire latitudinal distribution (1300 km). Combined, these factors explained 54% of the overall variation in Phyllospora's associated microbial community structure, much of which was related to the local environment (~32%). We found that putative "core" microbial taxa (i.e. present on all Phyllospora individuals sampled) exhibited slightly higher association with host traits when compared to "variable" taxa (not present on all individuals). We identified several key genetic loci and phenotypic traits in Phyllospora that were strongly related to multiple microbial amplicon sequence variants, including taxa with known associations to seaweed defense, disease and tissue degradation. This information on how host-associated microbial communities vary with host traits and the environment enhances our current understanding of holobionts and how they are structured. Such understanding can be used to inform management strategies of these important and vulnerable habitats.

opencc-zeroJan 2022View details →

Phenotypic data for M. edulis responses to warming and ocean acidification

1. In mosaic marine habitats, such as intertidal zones, ocean acidification (OA) is exacerbated by high variability of pH, temperature, and biological CO2 production. The non-linear interactions among these drivers can be context-specific and their effect on organisms in these habitats remains largely unknown, warranting further investigation. 2. We were particularly interested in Mytilus edulis (the blue mussel) from intertidal zones of the Gulf of Maine (GOM), USA for this study. GOM is a hot spot of global climate change (average Sea Surface Temperature (SST) increasing by > 0.2 °C y−1 ) with > 60% decline in mussel population over the past 40 years. 3. Here, we utilize bioenergetic underpinnings to identify limits of stress tolerance in M. edulis from GOM exposed to warming and OA. We have measured whole-organism oxygen consumption rates and metabolic biomarkers in mussels exposed to control and elevated temperatures (10 vs. 15 °C, respectively) and current and moderately elevated PCO2 levels (~ 400 vs. 800 µatm, respectively). 4. Our study demonstrates that adult M. edulis from GOM are metabolically resilient to the moderate OA scenario but responsive to warming as seen in changes in metabolic rate, energy reserves (total lipids), metabolite profiles (glucose and osmolyte dimethyl amine) and enzyme activities (carbonic anhydrase and calcium-ATPase). 5. Our results are in agreement with recent literature that OA scenarios for the next 100-300 years do not affect this species, possibly as a consequence of maintaining its in vivo acid−base balance.

opencc-zeroFeb 2022View details →

Multiple modes of selection can influence the role of phenotypic plasticity in species' invasions: Evidence from a manipulative field experiment

In exploring the roles of phenotypic plasticity in the establishment and early evolution of invading species, little empirical attention has been given to the importance of correlational selection acting upon suites of functionally related plastic traits in nature. We illustrate how this lack of attention has limited our ability to evaluate plasticity's role during invasion and also, the costs and benefits of plasticity. We addressed these issues by transplanting clones of European-derived Plantago lanceolata L. genotypes into two temporally variable habitats in the species' introduced range in North America. Phenotypic selection analyses were performed for each habitat to estimate linear, quadratic, and correlational selection on phenotypic trait values and plasticities in the reproductive traits: flowering onset, spike and scape lengths. Also, we measured pairwise genetic correlations for our "colonists". Results showed that 1) correlational selection acted on trait plasticity after transplantation, 2) selection favored certain combinations of genetically correlated and uncorrelated trait values and plasticities, 3) Using signed, instead of absolute, values of plasticity in analyses facilitated the detection of correlational selection on trait value-plasticity combinations and their adaptive value. Based on our results, we urge future studies on species invasions to: 1) measure correlational selection and 2) retain signed values of plasticity in order to better discriminate between adaptive and maladaptive plasticity.

opencc-zeroFeb 2022View details →

Data from: Rich resource environment of fish farms facilitates phenotypic variation and virulence in an opportunistic fish pathogen

Phenotypic variation is suggested to facilitate the persistence of environmentally growing pathogens under environmental change. Here we hypothesized that the intensive farming environment induces higher phenotypic variation in microbial pathogens than natural environment, because of high stochasticity for growth and stronger survival selection compared to the natural environment. We tested the hypothesis with an opportunistic fish pathogen Flavobacterium columnare isolated either from fish farms or from natural waters. We measured growth parameters of two morphotypes from all isolates in different resource concentrations and two temperatures relevant for the occurrence of disease epidemics at farms and tested their virulence using a zebrafish (Danio rerio) infection model. According to our hypothesis, isolates originating from the fish farms had higher phenotypic variation in growth between the morphotypes than the isolates from natural waters. The difference was more pronounced in higher resource concentrations and the higher temperature, suggesting that phenotypic variation is driven by the exploitation of increased outside-host resources at farms. Phenotypic variation of virulence was not observed based on isolate origin but only based on morphotype. However, when in contact with the larger fish, the less virulent morphotype of some of the isolates also had high virulence. As the less virulent morphotype also had higher growth rate in outside-host resources, the results suggest that both morphotypes can contribute to F. columnare epidemics at fish farms, especially with current prospects of warming temperatures. Our results suggest that higher phenotypic variation per se does not lead to higher virulence, but that environmental conditions at fish farms could select isolates with high phenotypic variation in bacterial population and hence affect evolution in F. columnare at fish farms. Our results highlight the multifaceted effects of human-induced environmental alterations in shaping epidemiology and evolution in microbial pathogens.