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•A current and comprehensive maximum-likelihood phylogeny of Zoanthidea is proposed.•Inference based upon concatenated multi-gene, multi-genomic staggered alignment.•Staggered ...alignment is phylogeny-informed and retains all nucleotides in the analysis.•Complete-data tree is more robust and defensible than the hypervariable-excluded tree.
The recent rapid proliferation of novel taxon identification in the Zoanthidea has been accompanied by a parallel propagation of gene trees as a tool of species discovery, but not a corresponding increase in our understanding of phylogeny. This disparity is caused by the trade-off between the capabilities of automated DNA sequence alignment and data content of genes applied to phylogenetic inference in this group. Conserved genes or segments are easily aligned across the order, but produce poorly resolved trees; hypervariable genes or segments contain the evolutionary signal necessary for resolution and robust support, but sequence alignment is daunting. Staggered alignments are a form of phylogeny-informed sequence alignment composed of a mosaic of local and universal regions that allow phylogenetic inference to be applied to all nucleotides from both hypervariable and conserved gene segments. Comparisons between species tree phylogenies inferred from all data (staggered alignment) and hypervariable-excluded data (standard alignment) demonstrate improved confidence and greater topological agreement with other sources of data for the complete-data tree. This novel phylogeny is the most comprehensive to date (in terms of taxa and data) and can serve as an expandable tool for evolutionary hypothesis testing in the Zoanthidea. Spanish language abstract available in Text S1. Translation by L. O. Swain, DePaul University, Chicago, Illinois, 60604, USA.
Calcium carbonate skeletons of scleractinian corals amplify light availability to their algal symbionts by diffuse scattering, optimizing photosynthetic energy acquisition. However, the mechanism of ...scattering and its role in coral evolution and dissolution of algal symbioses during "bleaching" events are largely unknown. Here we show that differences in skeletal fractal architecture at nano/micro-lengthscales within 96 coral taxa result in an 8-fold variation in light-scattering and considerably alter the algal light environment. We identified a continuum of properties that fall between two extremes: (1) corals with low skeletal fractality that are efficient at transporting and redistributing light throughout the colony with low scatter but are at higher risk of bleaching and (2) corals with high skeletal fractality that are inefficient at transporting and redistributing light with high scatter and are at lower risk of bleaching. While levels of excess light derived from the coral skeleton is similar in both groups, the low-scatter corals have a higher rate of light-amplification increase when symbiont concentration is reduced during bleaching, thus creating a positive feedback-loop between symbiont concentration and light-amplification that exposes the remaining symbionts to increasingly higher light intensities. By placing our findings in an evolutionary framework, in conjunction with a novel empirical index of coral bleaching susceptibility, we find significant correlations between bleaching susceptibility and light-scattering despite rich homoplasy in both characters; suggesting that the cost of enhancing light-amplification to the algae is revealed in decreased resilience of the partnership to stress.
Summary
Corals may reduce the effects of heat‐induced bleaching through associations with thermotolerant algal symbionts (Symbiodinium). Although hundreds of Symbiodinium genetic types (phylotypes) ...are known, thermotolerance has been systematically evaluated for small subsamples within individual reports, making consensus a challenging task.
Data on 110 phylotypes were aggregated from 35 reports, each assessing 2–24 phylotypes (median 4). One‐third of reports include ties (phylotypes with indistinguishable thermotolerance). Between reports, most phylotypes are unique (74% assessed once), most pairwise comparisons are unknown (relative thermotolerance for 15% of the possible 5995 phylotype pairs are evaluated) and many rankings are inconsistent (52% of 58 phylotype pairs assessed in more than one report are discordantly ranked).
Ranking of Symbiodinium phylotypes resulted in 64 thermotolerance cohorts (47 are single phylotypes, 17 contain 2–10 phylotypes with a median of 3 phylotypes) and indicates diverse thermotolerance capabilities within clades and among closely related phylotypes.
The iterative partial‐rank aggregation method (with error estimation) introduced here is broadly applicable to any quantitative consensus rank building problem where qualitative input ranks are not fully comprehensive nor resolved.
Reconstructions based on simulated data (mirroring the empirical data set) indicate robust predictive capabilities for resolving rankings (1·28 approximation of the true solution) and inferring unknown pairwise comparisons (83% correctly predicted pair rankings from only 16% known a priori).
Application to Symbiodinium phylotypes represents an additional tool to generate testable hypotheses on the role of symbiont thermotolerance in an ecosystem that is collapsing in the face of climate change and provides the first quantitative index of Symbiodinium thermotolerance and its associated uncertainty.
A Lay Summary is available for this article.
Lay Summary
Adjuvant trastuzumab reduces invasive breast cancer (IBC) recurrence and risk for death in patients with HER2-amplified or overexpressing IBC. A subset of patients in the landmark trastuzumab ...adjuvant trials who originally tested HER2-positive but were HER2-negative by central HER2 testing appeared to possibly benefit from trastuzumab. The objective for the NSABP B-47 trial was to determine whether the addition of trastuzumab to adjuvant chemotherapy (CRx) would improve invasive disease-free survival (IDFS) in patients with HER2-negative breast cancer.
A total of 3,270 women with high-risk primary IBC were randomly assigned to CRx with or without 1 year of trastuzumab. Eligibility criteria included immunohistochemistry (IHC) score 1+ or 2+ with fluorescence in situ hybridization ratio (FISH) < 2.0 or, if ratio was not performed, HER2 gene copy number < 4.0. CRx was either docetaxel plus cyclophosphamide or doxorubicin and cyclophosphamide followed by weekly paclitaxel for 12 weeks.
At a median follow-up of 46 months, the addition of trastuzumab to CRx did not improve IDFS (5-year IDFS: 89.8% with CRx plus trastuzumab CRxT
89.2% with CRx alone; hazard ratio HR, 0.98; 95% CI, 0.76 to 1.25;
= .85). These findings did not differ by level of HER2 IHC expression, lymph node involvement, or hormone-receptor status. For distant recurrence-free interval, 5-year estimates were 92.7% with CRxT compared with 93.6% for CRx alone (HR, 1.10; 95% CI, 0.81 to 1.50;
= .55) and for overall survival (OS) were 94.8% with CRxT and 96.3% in CRx alone (HR, 1.33; 95% CI, 0.90 to 1.95;
= .15). There were no unexpected toxicities from the addition of trastuzumab to CRx.
The addition of trastuzumab to CRx did not improve IDFS, distant recurrence-free interval, or OS in women with non-HER2-overexpressing IBC. Trastuzumab does not benefit women without IHC 3+ or FISH ratio-amplified breast cancer.
Biodiversity and productivity of coral-reef ecosystems depend upon reef-building corals and their associations with endosymbiotic Symbiodiniaceae, which offer diverse functional capabilities to their ...hosts. The number of unique symbiotic partners (richness) and relative abundances (evenness) have been hypothesized to affect host response to climate change induced thermal stress. Symbiodiniaceae assemblages with many unique phylotypes may provide greater physiological flexibility or form less stable symbioses; assemblages with low abundance phylotypes may allow corals to retain thermotolerant symbionts or represent associations with less-suitable symbionts.
Here we demonstrate that true richness of Symbiodiniaceae phylotype assemblages is generally not discoverable from direct enumeration of unique phylotypes in association records and that cross host-species comparisons are biased by sampling and evolutionary patterns among species. These biases can be minimized through rarefaction of richness (rarefied-richness) and evenness (Probability of Interspecific Encounter, PIE), and analyses that account for phylogenetic patterns. These standardized metrics were calculated for individual Symbiodiniaceae assemblages composed of 377 unique ITS2 phylotypes associated with 123 coral species. Rarefied-richness minimized correlations with sampling effort, while maintaining important underlying characteristics across host bathymetry and geography. Phylogenetic comparative methods reveal significant increases in coral bleaching and mortality associated with increasing Symbiodiniaceae assemblage richness and evenness at the level of host species.
These results indicate that the potential flexibility afforded by assemblages characterized by many phylotypes present at similar relative abundances does not result in decreased bleaching risk and point to the need to characterize the overall functional and genetic diversity of Symbiodiniaceae assemblages to quantify their effect on host fitness under climate change.
Two fundamental symbiosis‐based trophic types are recognized among Zoanthidea (Cnidaria, Anthozoa): fixed carbon is either obtained directly from zooxanthellae photosymbionts or from environmental ...sources through feeding with the assistance of host‐invertebrate behaviour and structure. Each trophic type is characteristic of the suborders of Zoanthidea and is associated with substantial distributional asymmetries: suborder Macrocnemina are symbionts of invertebrates and have global geographic and bathymetric distributions and suborder Brachycnemina are hosts of endosymbiotic zooxanthellae and are restricted to tropical photic zones. While exposure to solar radiation could explain the bathymetric asymmetry it does not explain the geographic asymmetry, nor is it clear why evolutionary transitions to the zooxanthellae‐free state have apparently occurred within Macrocnemina but not within Brachycnemina. To better understand the transitions between symbiosis‐based trophic types of Zoanthidea, a concatenated data set of nuclear and mitochondrial nucleotide sequences were used to test hypotheses of monophyly for groups defined by morphology and symbiosis, and to reconstruct the evolutionary transitions of morphological and symbiotic characters. The results indicate that the morphological characters that define Macrocnemina are plesiomorphic and the characters that define its subordinate taxa are homoplasious. Symbioses with invertebrates have ancient and recent transitions with a general pattern of stability in host associations through evolutionary time. The reduction in distribution of Zoanthidea is independent of the evolution of zooxanthellae symbiosis and consistent with hypotheses of the benefits of invertebrate symbioses, indicating that the ability to persist in most habitats may have been lost with the termination of symbioses with invertebrates.
In order to reconcile existing data and hypotheses on the relationship outcomes of Caribbean Zoanthidea-Demospongiae symbioses, the context-dependent survival and growth (metrics of host sponge ...condition) were monitored for 8–12 months, with and without Zoanthidean symbionts, in native (coral reef) and novel (mangrove) habitats. Experiments repeated over space and time revealed significant positive effects of Zoanthidea colonization on metrics of host condition and indicated that the outcome of these symbioses can shift from mutualism to parasitism when transplanted to novel habitats. Although the precise mechanisms of the symbioses remain obscured and most of the species associations have not been examined, these experiments demonstrate an example where relationship outcomes are more conserved across their evolutionary history than host associations.
Retraction is among the most important basic behaviors of anthozoan Cnidaria polyps and is achieved through the coordinated contraction of at least six different muscle groups. Across the Anthozoa, ...these muscles range from unrecognizable atrophies to massive hypertrophies, producing a wide diversity of retraction abilities and functional morphologies. The marginal musculature is often the single largest component of the retraction mechanism and is composed of a diversity of muscular, attachment, and structural features. Although the arrangements of these features have defined the higher taxonomy of Zoanthidea for more than 100 years, a decade of inferring phylogenies from nucleotide sequences has demonstrated fundamental misconceptions of their evolution.
Here we expand the diversity of known marginal muscle forms from two to at least ten basic states and reconstruct the evolution of its functional morphology across the most comprehensive molecular phylogeny available. We demonstrate that the evolution of these forms follows a series of transitions that are much more complex than previously hypothesized and converge on similar forms multiple times. Evolution of the marginal musculature and its attachment and support structures are partially scaled according to variation in polyp and muscle size, but also vary through evolutionary allometry.
Although the retraction mechanisms are diverse and their evolutionary histories complex, their morphologies are largely reflective of the evolutionary relationships among Zoanthidea higher taxa and may offer a key feature for integrative systematics. The convergence on similar forms across multiple linages of Zoanthidea mirrors the evolution of the marginal musculature in another anthozoan order (Actiniaria). The marginal musculature varies through evolutionary allometry of functional morphologies in response to requirements for additional force and resistance, and the specific ecological and symbiotic functions of individual taxa.
As coral bleaching events become more frequent and intense, our ability to predict and mitigate future events depends upon our capacity to interpret patterns within previous episodes. Responses to ...thermal stress vary among coral species; however the diversity of coral assemblages, environmental conditions, assessment protocols, and severity criteria applied in the global effort to document bleaching patterns creates challenges for the development of a systemic metric of taxon‐specific response. Here, we describe and validate a novel framework to standardize bleaching response records and estimate their measurement uncertainties. Taxon‐specific bleaching and mortality records (2036) of 374 coral taxa (during 1982–2006) at 316 sites were standardized to average percent tissue area affected and a taxon‐specific bleaching response index (taxon‐BRI) was calculated by averaging taxon‐specific response over all sites where a taxon was present. Differential bleaching among corals was widely variable (mean taxon‐BRI = 25.06 ± 18.44%, ±SE). Coral response may differ because holobionts are biologically different (intrinsic factors), they were exposed to different environmental conditions (extrinsic factors), or inconsistencies in reporting (measurement uncertainty). We found that both extrinsic and intrinsic factors have comparable influence within a given site and event (60% and 40% of bleaching response variance of all records explained, respectively). However, when responses of individual taxa are averaged across sites to obtain taxon‐BRI, differential response was primarily driven by intrinsic differences among taxa (65% of taxon‐BRI variance explained), not conditions across sites (6% explained), nor measurement uncertainty (29% explained). Thus, taxon‐BRI is a robust metric of intrinsic susceptibility of coral taxa. Taxon‐BRI provides a broadly applicable framework for standardization and error estimation for disparate historical records and collection of novel data, allowing for unprecedented accuracy in parameterization of mechanistic and predictive models and conservation plans.
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