Closely related species may produce hybrids, and these hybrids often display intermediate traits that can influence fitness and reproductive isolation. In this study, we examine Ambystoma barbouri and Ambystoma texanum, two sister salamander species that breed in contrasting aquatic habitats with differing levels of ultraviolet radiation (UVR) exposure. Although these species can hybridize, it remains unclear whether hybrid pigmentation responses to UVR confer an advantage, a disadvantage, or are simply intermediate between parental forms. Pigmentation in salamanders is regulated by chromatophores, melanophores, and xanthophores, which help mitigate UVR-induced damage. Given previous knowledge on the species, habitats, and behaviors, we hypothesized that: (1) A. barbouri would show stronger UVR-induced pigmentation (i.e., greater darkening) than A. texanum, due to its exposure to clearer, shallower streams; (2) hybrids would exhibit intermediate responses; and (3) xanthophore coverage would remain stable or decrease under UVR as melanophores expand. To test these hypotheses, we conducted a fully factorial breeding experiment using pure and reciprocal hybrid crosses, exposing larvae to four UVR durations (0, 1, 4, and 12 h). We quantified skin darkness and chromatophore-specific pigmentation using standardized digital image analysis, Bayesian beta regression, and Bayesian compositional regression. Our results supported all three hypotheses. A. barbouri showed greater darkening under UVR exposure than A. texanum, and hybrids exhibited intermediate responses, but with a greater similarity toward their maternal phenotype. Xanthophore coverage remained stable or declined with increasing UVR exposure, evidencing that their main purpose is different from UVR protection. These findings raise the possibility that hybrids could experience reduced performance if intermediate pigmentation is suboptimal, but that maternal effects may offset some of these disadvantages.

The opposing forces of gene flow and isolation are two major processes shaping genetic diversity. Understanding how these vary across space and time is necessary to identify the environmental features that promote diversification. The detection of considerable geographic structure in taxa from the arid Nearctic has prompted research into the drivers of isolation in the region. Several geographic features have been proposed as barriers to gene flow, including the Colorado River, Western Continental Divide (WCD), and a hypothetical Mid-Peninsular Seaway in Baja California. However, recent studies suggest that the role of barriers in genetic differentiation may have been overestimated when compared to other mechanisms of divergence. In this study, we infer historical and spatial patterns of connectivity and isolation in Desert Spiny Lizards (Sceloporus magister) and Baja Spiny Lizards (Sceloporus zosteromus), which together form a species complex composed of parapatric lineages with wide distributions in arid western North America. Our analyses incorporate mitochondrial sequences, genomic-scale data, and past and present climatic data to evaluate the nature and strength of barriers to gene flow in the region. Our approach relies on estimates of migration under the multispecies coalescent to understand the history of lineage divergence in the face of gene flow. Results show that the S. magister complex is geographically structured, but we also detect instances of gene flow. The WCD is a strong barrier to gene flow, while the Colorado River is more permeable. Analyses yield conflicting results for the catalyst of differentiation of peninsular lineages in S. zosteromus. Our study shows how large-scale genomic data for thoroughly sampled species can shed new light on biogeography. Furthermore, our approach highlights the need for the combined analysis of multiple sources of evidence to adequately characterize the drivers of divergence.

Ecological niche differentiation is a process that accompanies lineage diversification and community assembly. Traditionally, the degree of niche differentiation is estimated by contrasting niche hypervolumes of two taxa, reconstructed using ecologically relevant variables. These methods disregard the fact that niches can shift in different ways and directions. Without means of discriminating between different types of niche differentiation, important evolutionary and ecological patterns may go unrecognized. Herein, we introduce a new conceptual and methodological framework that allows quantification and classification of niche differentiation and divergence between taxa along single niche axis. This new method, the Niche Divergence Plane, is based on species' responses to an underlying environmental gradient, from which we derive a two-dimensional plane defined by two indices, niche exclusivity and niche dissimilarity. These two indices identify the proportion of the environmental gradient that is unique to each species, that is, how much of the environmental gradient species do not share (niche breadth exclusivity) and how different the species' responses are along the environmental gradient (niche dissimilarity). Thus, the latter can also be seen as a measure of the differences in niche preference or importance, even when there is significant overlap in niche breadth (i.e., low niche exclusivity). Based on the position of the two indices on the divergence plane, we can distinguish niche conservatism from four other general types of niche divergence: hard, soft, weighted, and nested. We demonstrate that the Niche Divergence Plane complements traditional measures of niche similarity (e.g., Schoener's D or Hellinger's I). Additionally, we show an empirical comparison using the Niche Divergence Plane framework on two Ambystoma salamanders. Overall, we demonstrate that the Niche Divergence Plane is a versatile tool that can be used to complement and expand previous methods of ecological niche comparisons and the study of ecological niche divergence.

Understanding the dynamics of coral recruitment and post-settlement is fundamental to a better comprehension of coral reef dynamics and recovery. We studied the abundance and survivorship of coral recruits and juveniles together with benthic dynamics at a scale of months and centimeters in Playa Mero reef, a disturbed reef in Morrocoy National Park. For this, we used photogrammetry to monitor eight permanent 50x50 cm quadrats haphazardly deployed every 3–4 months over 18 months. Juveniles and recruits of Agaricia spp. were at least four times more abundant than reef builders such as Orbicella spp. A distance-based linear model showed that rugosity, macroalgae, coral cover, and sand were the most important benthic variables and predicted up to 46% of the spatial and temporal variation of recruit and juvenile corals. The mortality of juvenile corals was higher than net recruitment rates, and only a limited number of genera such as Agariciids, Colpophyllia, Porites, and Scolymia were observed as recruits. Using a logit model, we also found a positive relationship between the mean growth rate and survivorship of juvenile corals (Nagelkerke R2= 0.67). We concluded the lack of recruitment of large reef builders, and the rapid mortality of a limited number of juvenile species, might be a sign of a coral community's failure to increase coral cover.

The chemical composition and stoichiometry of vertebrate bodies changes greatly during ontogeny as phosphorus-rich bones form, but we know little about variation among species during early development. Such variation is important because element ratios in animal bodies influence which element limits growth, and how animals contribute to nutrient cycling. We quantified ontogenetic variation from embryos through 2-3 months of age in 10 species of fish in 6 different families, ranging in adult size from 73 to 720 mm length. We measured whole-body concentrations (percentage of dry mass) and ratios of carbon (C), nitrogen (N) and phosphorus (P) as fish developed. We also quantified whole-body concentrations of calcium (Ca), because Ca should reflect bone development, and RNA which can be a major pool of body P. To account for interspecific differences in adult size, we also examined how trends changed with relative size, defined as body length divided by adult length. Ontogenetic changes in body composition and ratios were relatively similar among species, and were more similar when expressed as a function of relative size, compared to age. Body P increased rapidly in all species (likely because of bone development) from embryos until individuals were ~5-8% of adult size. Body N also increased, while body C, C:N, C:P and N:P all decreased over this period. Body Ca increased with development, but was more variable among species. Body RNA was low in embryos, increased rapidly in young larvae, then decreased as fish reached 5-8% of adult size. After fish were about 5-8% of adult size, changes in body composition were relatively slight for all elements and ratios. These results reveal a consistency in the dynamics of body stoichiometry during early ontogeny, presumably because of similar constraints on the allocation of elements to bones and other body pools. Because most changes occur when individuals are <1 month old (<10% of adult size for that species), early ontogenetic variation in body stoichiometry may be especially important for growth limitation of individuals and ecosystem-level nutrient cycling. This article is protected by copyright. All rights reserved.

Hybridization facilitates recombination between divergent genetic lineages and can be shaped by both neutral and selective processes. Upon hybridization, loci with no net fitness effects introgress randomly from parental species into the genomes of hybrid individuals. Conversely, alleles from one parental species at some loci may provide a selective advantage to hybrids, resulting in patterns of introgression that do not conform to random expectations. We investigated genomic patterns of differential introgression in natural hybrids of two species of Caribbean anoles, Anolis pulchellus and A. krugi in Puerto Rico. Hybrids exhibit A. pulchellus phenotypes but possess A. krugi mitochondrial DNA, originated from multiple, independent hybridization events, and appear to have replaced pure A. pulchellus across a large area in western Puerto Rico. Combining genome-wide SNP datasets with bioinformatic methods to identify signals of differential introgression in hybrids, we demonstrate that the genomes of hybrids are dominated by pulchellus-derived alleles and show only 10%-20% A. krugi ancestry. The majority of A. krugi loci in hybrids exhibit a signal of non-random differential introgression and include loci linked to genes involved in development and immune function. Three of these genes (delta like canonical notch ligand 1, jagged1 and notch receptor 1) affect cell differentiation and growth and interact with mitochondrial function. Our results suggest that differential non-random introgression for a subset of loci may be driven by selection favouring the inheritance of compatible mitochondrial and nuclear-encoded genes in hybrids.

Hybridization can have a profound negative effect on population fitness when species exhibit divergence in adaptive traits. The Streamside salamander, Ambystoma barbouri, and the Smallmouth salamander, A. texanum, are closely related species differentiated primarily by breeding habitat and reproduction-related traits, but previous work suggests patterns of hybridization and introgression between them. Here we investigate whether 1) hybridization occurs between the two species in laboratory settings, 2) their divergent reproduction-related traits are retained under a common treatment, and 3) hybrid offspring exhibit similar fitness as their non-hybrid counterparts. We bred conspecific and heterospecific pairs of A. barbouri and A. texanum and raised hybrid and non-hybrid offspring to metamorphosis. Reproduction-related traits such as oviposition location and clutch size remained well differentiated between the two species. Heterospecific pairs hybridized readily, at similar rates to conspecific pairs. The hybrid larvae generally exhibited a maternal effect and, less frequently, intermediate phenotypes with respect to measured traits. Hybrid larvae did not exhibit reduced fitness as measured by survival to metamorphosis. Our results suggest that traits differentiating A. barbouri and A. texanum are likely genetically determined despite the lack of reproductive isolation between them. This suggests that the generally parapatric distribution of the two species, often paired with abrupt transition in traits, might be driven by selection on these traits in local habitats. Further, the maternal effect and consequent lack of intermediate phenotypes observed for several traits likely reduces the negative effect of hybridization in locally adapted populations.

BACKGROUND:The increasing number of chromosome-level genome assemblies has advanced our knowledge and understanding of macroevolutionary processes. Here, we introduce the genome of the desert horned lizard, Phrynosoma platyrhinos, an iguanid lizard occupying extreme desert conditions of the American southwest. We conduct analysis of the chromosomal structure and composition of this species and compare these features across genomes of 12 other reptiles (5 species of lizards, 3 snakes, 3 turtles, and 1 bird). FINDINGS:The desert horned lizard genome was sequenced using Illumina paired-end reads and assembled and scaffolded using Dovetail Genomics Hi-C and Chicago long-range contact data. The resulting genome assembly has a total length of 1,901.85 Mb, scaffold N50 length of 273.213 Mb, and includes 5,294 scaffolds. The chromosome-level assembly is composed of 6 macrochromosomes and 11 microchromosomes. A total of 20,764 genes were annotated in the assembly. GC content and gene density are higher for microchromosomes than macrochromosomes, while repeat element distributions show the opposite trend. Pathway analyses provide preliminary evidence that microchromosome and macrochromosome gene content are functionally distinct. Synteny analysis indicates that large microchromosome blocks are conserved among closely related species, whereas macrochromosomes show evidence of frequent fusion and fission events among reptiles, even between closely related species. CONCLUSIONS:Our results demonstrate dynamic karyotypic evolution across Reptilia, with frequent inferred splits, fusions, and rearrangements that have resulted in shuffling of chromosomal blocks between macrochromosomes and microchromosomes. Our analyses also provide new evidence for distinct gene content and chromosomal structure between microchromosomes and macrochromosomes within reptiles.

This dataset contains 2850 photographs of the seafloor in coral communities from Venezuela that were taken during 2017 and 2018. We used a hierarchical experimental design with four random factors representing four different spatial scales: (1) region (hundreds of kilometers), (2) localities (tens of kilometers), (2) reef sites (hundreds of meters) and (3) transects (a couple meters) across the Venezuelan coast. At each site, four 30-m transects were deployed parallel to the coastline, and 15 pictures were taken every other meter at each transect, containing an area of at least 80 × 90cm with enough resolution to identify benthic groups. This dataset covers spatial scales from a few meters to hundreds of kilometers; marine protected areas, and non-protected areas; coastal zones, continental and oceanic islands. These images have the potential to be further used for training researchers in benthic organisms identification, and training artificial intelligence classification algorithms. Also, they represent and updated baseline to perform spatial and temporal comparisons in Venezuela or further studies involving multiple spatial scales in the region.

The characteristics of coral reef sampling and monitoring are highly variable, with numbers of units and sampling effort varying from one study to another.Numerous works have been carried out to determine an appropriate effect size through statistical power, however, always from a univariate perspective.In this work, we aimed to assess the multivariate standard error of a series of reefs in Venezuela, sampled between 2017 and 2018, and also, to evaluate the consequences of using different combinations of points, quadrats, and transects over this error.For this, the multivariate standard error of 36 sites previously sampled was estimated, using four 30m-transects with 15 photo-quadrats each and 25 random points per quadrat.We obtained that the multivariate standard error was highly variable between sites and is not correlated with the univariate standard error nor with the richness of species.Then, a subset of sites were re-annotated using 100 uniformly distributed points, which allowed the simulation of different numbers of transects per site, quadrats per transect and points per quadrat using resampling techniques.The magnitude of the multivariate standard error stabilized by adding more transects, however, adding more quadrats or points does not improve the estimate.For this case study, when comparing between sampling with 10 transects, 10 quadrats per transect and 25 points per quadrat; and the original data for Venezuela, we find that the error is reduced by half.We recommend the use of multivariate standard error in reef monitoring programs, in particular when conducting pilot surveys to optimize the estimation of the community structure.

ABSTRACT The characteristics of coral reef sampling and monitoring are highly variable, with numbers of units and sampling effort varying from one study to another. Numerous works have been carried out to determine an appropriate effect size through statistical power, however, always from a univariate perspective. In this work, we used the pseudo multivariate dissimilarity-based standard error (MultSE) approach to assess the precision of sampling scleractinian coral assemblages in reefs of Venezuela between 2017 and 2018 when using different combinations of number of transects, quadrats and points. For this, the MultSE of 36 sites previously sampled was estimated, using four 30m-transects with 15 photo-quadrats each and 25 random points per quadrat. We obtained that the MultSE was highly variable between sites and is not correlated with the univariate standard error nor with the richness of species. Then, a subset of sites was re-annotated using 100 uniformly distributed points, which allowed the simulation of different numbers of transects per site, quadrats per transect and points per quadrat using resampling techniques. The magnitude of the MultSE stabilized by adding more transects, however, adding more quadrats or points does not improve the estimate. For this case study, the error was reduced by half when using 10 transects, 10 quadrats per transect and 25 points per quadrat. We recommend the use of MultSE in reef monitoring programs, in particular when conducting pilot surveys to optimize the estimation of the community structure.

Estimating variability across spatial scales has been a major issue in ecology because describing patterns in space is extremely valuable to propose specific hypotheses aim to unveil key processes behind these patterns.This paper aims to estimate the variability of the coral assemblage structure at different spatial scales in order to determine which scales explain the greatest variability onβ-diversity.For this, a fully-nested design including a series of hierarchical-random factors encompassing three spatial scales:(1) regions, (2) localities and (3) reefs sites across the Venezuelan territory.The variability among spatial scales were tested with a permutation analysis of variance (Permanova) based on Bray-Curtis index.Dispersion in species presence/absence across scales (i.e., βdiversity) was tested with a PermDisp analysis based on Jaccard's index.We found the highest variability in the coral assemblage structure between sites within locality (Pseudo-F = 5.34; p-value = 0.001, CV = 35.10%),We also found that longitude (Canonical corr = 0.867, p = 0.001) is a better predictor of the coral assemblage structure in Venezuela, rather than latitude (Canonical corr = 0.552, p = 0.021).Largest changes inβ-diversity of corals occurred within sites (F = 2.764, df1= 35, df2 = 107, p = 0.045) and within localities (F = 4.438, df1= 6, df2 = 29, p = 0.026).Our results suggest that processes operating at spatial scales of hundreds of meters and hundreds of kilometers might both be critical to shape coral assemblage structure in Venezuela, whereas smaller scales (i.e., hundreds of meters) showed to be highly-important for the species turnover component of β-diversity.This result highlights the importance of creating scale-adapted management actions in Venezuela and likely across the Caribbean region.

The characteristics of coral reef sampling and monitoring are highly variable, with numbers of units and sampling effort varying from one study to another. Numerous works have been carried out to determine an appropriate effect size through statistical power; however, these were always from a univariate perspective. In this work, we used the pseudo multivariate dissimilarity-based standard error (MultSE) approach to assess the precision of sampling scleractinian coral assemblages in reefs of Venezuela between 2017 and 2018 when using different combinations of number of transects, quadrats and points. For this, the MultSE of 36 sites previously sampled was estimated, using four 30m-transects with 15 photo-quadrats each and 25 random points per quadrat. We obtained that the MultSE was highly variable between sites and is not correlated with the univariate standard error nor with the richness of species. Then, a subset of sites was re-annotated using 100 uniformly distributed points, which allowed the simulation of different numbers of transects per site, quadrats per transect and points per quadrat using resampling techniques. The magnitude of the MultSE stabilized by adding more transects, however, adding more quadrats or points does not improve the estimate. For this case study, the error was reduced by half when using 10 transects, 10 quadrats per transect and 25 points per quadrat. We recommend the use of MultSE in reef monitoring programs, in particular when conducting pilot surveys to optimize the estimation of the community structure.

This repository contains the data and code for our paper: Montilla et al. (2020). *Transects, quadrats, or points? What is the best combination to get a precise estimation of a coral community?* PeerJ. https://doi.org/10.7717/peerj.8429

Estimating variability across spatial scales has been a major issue in ecology because the description of patterns in space is extremely valuable to propose specific hypotheses to unveil key processes behind these patterns. This paper aims to estimate the variability of the coral assemblage structure at different spatial scales in order to determine which scales explain the largest variability on β-diversity. For this, a fully-nested design including a series of hierarchical-random factors encompassing three spatial scales: (1) regions, (2) localities and (3) reefs sites across the Venezuelan territory. The variability among spatial scales was tested with a permutation-based analysis of variance (Permanova) based on Bray-Curtis index. Dispersion in species presence/absence across scales (i.e., β-diversity) was tested with a PermDisp analysis based on Jaccard’s index. We found the highest variability in the coral assemblage structure between sites within localities (Pseudo-F = 5.34; p-value = 0.001, CV = 35.10%). We also found that longitude (Canonical corr = 0.867, p = 0.001) is a better predictor of the coral assemblage structure in Venezuela, than latitude (Canonical corr = 0.552, p = 0.021). Largest changes in β-diversity of corals occurred within sites (F = 2.764, df1= 35, df2 = 107, p = 0.045) and within localities (F = 4.438, df1= 6, df2 = 29, p = 0.026). Our results suggest that processes operating at spatial scales of hundreds of meters and hundreds of kilometers might both be critical to shape coral assemblage structure in Venezuela, whereas smaller scales (i.e., hundreds of meters) showed to be highly- important for the species turnover component of β-diversity. This result highlights the importance of creating scale-adapted management actions in Venezuela and likely across the Caribbean region.

Coral disease research encompasses five decades of undeniable progress. Since the first descriptions of anomalous signs, we have come to understand multiple processes and environmental drivers that interact with coral pathologies. In order to gain a better insight into the knowledge we already have, we explored how key topics in coral disease research have been related to each other using network analysis. We reviewed 719 papers and conference proceedings published from 1965 to 2017. From each study, four elements determined our network nodes: (1) studied disease(s); (2) host genus; (3) marine ecoregion(s) associated with the study site; and (4) research objectives. Basic properties of this network confirmed that there is a set of specific topics comprising the majority of research. The top five diseases, genera, and ecoregions studied accounted for over 48% of the research effort in all cases. The community structure analysis identified 15 clusters of topics with different degrees of overlap among them. These clusters represent the typical sets of elements that appear together for a given study. Our results show that while some coral diseases have been studied considering multiple aspects, the overall trend is for most diseases to be understood under a limited range of approaches, e.g., bacterial assemblages have been considerably studied in Yellow and Black band diseases while immune response has been better examined for the aspergillosis-Gorgonia system. Thus, our challenge in the near future is to identify and resolve potential gaps in order to achieve a more comprehensive progress on coral disease research.