Ecomorphological disparity in an adaptive radiation: opercular bone shape and stable isotopes in Antarctic icefishes

Morphology and diet are decoupled in nearshore notothenoids from King George Island, West Antarctica

Antarctic notothenioid fishes show wide adaptive morphological radiation, linked to habitat preferences and food composition. However, direct comparisons of phenotypic variability and feeding habits are still lacking, particularly in stages inhabiting nearshore areas. To assess these relationships, we collected juveniles and adults of the most common benthic species inhabiting shallow waters off the South Shetland Islands within a similar size range, the plunderfish Harpagifer antarcticus, the black rockcod Notothenia coriiceps, and the marbled rockcod Notothenia rossii. Individual size ranges varied from 44.0 to 98.9 mm standard length (LS) (H. antarcticus), from 95.8 to 109.3 mm LS (N. coriiceps), and from 63.0 to 113.0 mm LS (N. rossii). Notothenioid fish showed different morphospace variability, being larger for H. antarcticus than the other Notothenia species and associated with the position of the posterior end of the operculum, along with the location and relative size of the eye. The evolutionary allometry was low, but the static allometry was much higher, especially for H. antarcticus and N. rossii. The diet was mainly carnivorous, consisting of amphipods and euphausiids. Macroalgae were scarce or totally absent in the gut contents of all species. Only H. antarcticus showed an increase in the prey number and ingested prey volume with fish size. Finally, there was a significant covariation between shape changes and LS in all species (allometric effects), however, not with prey composition, probably due to the small size range or ontogenetic stage and the relative similarity (or lack of contrast) in the benthic environment that they utilized.

The transcriptional state and chromatin landscape of cichlid jaw shape variation across species and environments

Adaptive phenotypes are shaped by a combination of genetic and environmental forces, but how they interact remains poorly understood. Here, we utilize the cichlid oral jaw apparatus to better understand these gene-by-environment effects. First, we employed RNA-seq in bony and ligamentous tissues important for jaw opening to identify differentially expressed genes between species and across foraging environments. We used two Lake Malawi species adapted to different foraging habitats along the pelagic-benthic ecomorphological axis. Our foraging treatments were designed to force animals to employ either suction or biting/scraping, which broadly mimic pelagic or benthic modes of feeding. We found a large number of differentially expressed genes between species, and while we identified relatively few differences between environments, species differences were far more pronounced when they were challenged with a pelagic versus benthic foraging mode. Expression data carried the signature of genetic assimilation, and implicated cell cycle regulation in shaping the jaw across species and environments. Next, we repeated the foraging experiment and performed ATAC-seq procedures on nuclei harvested from the same tissues. Cross-referencing results from both analyses revealed subsets of genes that were both differentially expressed and differentially accessible. This reduced dataset implicated notable candidate genes including the Hedgehog effector, KIAA0586 and the ETS transcription factor, etv4, which connects environmental stress and craniofacial morphogenesis. Taken together, these data provide novel insights into the epigenetic, genetic and cellular bases of species- and environment-specific bone shapes.

A latitudinal gradient of deep-sea invasions for marine fishes

Although the tropics harbor the greatest species richness globally, recent work has demonstrated that, for many taxa, speciation rates are faster at higher latitudes. Here, we explore lability in oceanic depth as a potential mechanism for this pattern in the most biodiverse vertebrates - fishes. We demonstrate that clades with the highest speciation rates also diversify more rapidly along the depth gradient, drawing a fundamental link between evolutionary and ecological processes on a global scale. Crucially, these same clades also inhabit higher latitudes, creating a prevailing latitudinal gradient of deep-sea invasions concentrated in poleward regions. We interpret these findings in the light of classic ecological theory, unifying the latitudinal variation of oceanic features and the physiological tolerances of the species living there. This work advances the understanding of how niche lability sculpts global patterns of species distributions and underscores the vulnerability of polar ecosystems to changing environmental conditions.

Distributions of extinction times from fossil ages and tree topologies: the example of mid-Permian synapsid extinctions

Given a phylogenetic tree that includes only extinct, or a mix of extinct and extant taxa, where at least some fossil data are available, we present a method to compute the distribution of the extinction time of a given set of taxa under the Fossilized-Birth-Death model. Our approach differs from the previous ones in that it takes into account (i) the possibility that the taxa or the clade considered may diversify before going extinct and (ii) the whole phylogenetic tree to estimate extinction times, whilst previous methods do not consider the diversification process and deal with each branch independently. Because of this, our method can estimate extinction times of lineages represented by a single fossil, provided that they belong to a clade that includes other fossil occurrences. We assess and compare our new approach with a standard previous one using simulated data. Results show that our method provides more accurate confidence intervals. This new approach is applied to the study of the extinction time of three Permo-Carboniferous synapsid taxa (Ophiacodontidae, Edaphosauridae, and Sphenacodontidae) that are thought to have disappeared toward the end of the Cisuralian (early Permian), or possibly shortly thereafter. The timing of extinctions of these three taxa and of their component lineages supports the idea that the biological crisis in the late Kungurian/early Roadian consisted of a progressive decline in biodiversity throughout the Kungurian.

Sexual dimorphism in an adaptive radiation: Does intersexual niche differentiation result in ecological character displacement?

Evolutionary radiations are one plausible explanation for the rich biodiversity on Earth. Adaptive radiations are the most studied form of evolutionary radiations, and ecological opportunity has been identified as one factor permitting them. Competition among individuals is supposedly highest in populations of conspecifics. Divergent modes of resource use might minimize trophic overlap, and thus intersexual competition, resulting in ecological character displacement between sexes. However, the role of intersexual differentiation in speciation processes is insufficiently studied. The few studies available suggest that intersexual niche differentiation exists in adaptive radiations, but their role within the radiation, and the extent of differentiation within the organism itself, remains largely unexplored. Here, we test the hypothesis that multiple morphological structures are affected by intersexual niche differentiation in "roundfin" Telmatherina, the first case where intersexual niche differentiation was demonstrated in an adaptive fish radiation. We show that sexes of two of the three morphospecies differ in several structural components of the head, all of these are likely adaptive. Sexual dimorphism is linked to the respective morphospecies-specific ecology and affects several axes of variation. Trait variation translates into different feeding modes, processing types, and habitat usages that add to interspecific variation in all three morphospecies. Intrasexual selection, that is, male-male competition, may contribute to variation in some of the traits, but appears unlikely in internal structures, which are invisible to other individuals. We conclude that intersexual variation adds to the adaptive diversity of roundfins and might play a key role in minimizing intersexual competition in emerging radiations.

Developmental tuning of mineralization drives morphological diversity of gill cover bones in sculpins and their relatives

The role of osteoblast placement in skeletal morphological variation is relatively well understood, but alternative developmental mechanisms affecting bone shape remain largely unknown. Specifically, very little attention has been paid to variation in later mineralization stages of intramembranous ossification as a driver of morphological diversity. We discover the occurrence of specific, sometimes large, regions of nonmineralized osteoid within bones that also contain mineralized tissue. We show through a variety of histological, molecular, and tomographic tests that this “extended” osteoid material is most likely nonmineralized bone matrix. This tissue type is a significant determinant of gill cover bone shape in the teleostean suborder Cottoidei. We demonstrate repeated evolution of extended osteoid in Cottoidei through ancestral state reconstruction and test for an association between extended osteoid variation and habitat differences among species. Through measurement of extended osteoid at various stages of gill cover development in species across the phylogeny, we gain insight into possible evolutionary developmental origins of the trait. We conclude that this fine‐tuned developmental regulation of bone matrix mineralization reflects heterochrony at multiple biological levels and is a novel mechanism for the evolution of diversity in skeletal morphology. This research lays the groundwork for a new model in which to study bone mineralization and evolutionary developmental processes, particularly as they may relate to adaptation during a prominent evolutionary radiation of fishes.

Evolution of opercle bone shape along a macrohabitat gradient: species identification using mtDNA and geometric morphometric analyses in neotropical sea catfishes (Ariidae)

Transitions between the marine and freshwater macrohabitat have occurred repeatedly in the evolution of teleost fishes. For example, ariid catfishes have moved from freshwater to marine environments, and vice versa. Opercles, a skeletal feature that has been shown to change during such transitions, were subjected to 2D geometric morphometric analyses in order to investigate evolutionary shape changes during habitat transition in ariid catfishes and to test the influence of habitat on shape changes. A mtDNA marker, which proved useful in previous studies, was used to verify species identities. It greatly improved the assignment of specimens to a species, which are difficult to assign by morphology alone. The application of a mtDNA marker confirmed the occurrence of Notarius biffi in Central America, South of El Salvador. Molecular identification together with principal component analysis (PCA) and further morphological inspection of neurocrania indicated the existence of a cryptic species within Bagre pinnimaculatus. Principal component (PC) scores of individual specimens clustered in morphospace by genus rather than by habitat. Strong phylogenetic structure was detected using a permutation test of PC scores of species means on a phylogenetic tree. Calculation of Pagel's λ suggested that opercle shape evolved according to a Brownian model of evolution. Yet canonical variate analysis (CVA) conducted on the habitat groups showed significant differences in opercle shapes among freshwater and marine species. Overall, opercle shape in tropical American Ariidae appears to be phylogenetically constrained. This verifies the application of opercle shape as a taxonomic tool for species identification in fossil ariid catfishes. At the same time, adaptation to freshwater habitats shows characteristic opercle shape trajectories in ariid catfishes, which might be used to detect habitat preferences in fossils.

Evolution of opercle shape in cichlid fishes from Lake Tanganyika - adaptive trait interactions in extant and extinct species flocks

Phenotype-environment correlations and the evolution of trait interactions in adaptive radiations have been widely studied to gain insight into the dynamics underpinning rapid species diversification. In this study we explore the phenotype-environment correlation and evolution of operculum shape in cichlid fishes using an outline-based geometric morphometric approach combined with stable isotope indicators of macrohabitat and trophic niche. We then apply our method to a sample of extinct saurichthyid fishes, a highly diverse and near globally distributed group of actinopterygians occurring throughout the Triassic, to assess the utility of extant data to inform our understanding of ecomorphological evolution in extinct species flocks. A series of comparative methods were used to analyze shape data for 54 extant species of cichlids (N = 416), and 6 extinct species of saurichthyids (N = 44). Results provide evidence for a relationship between operculum shape and feeding ecology, a concentration in shape evolution towards present along with evidence for convergence in form, and significant correlation between the major axes of shape change and measures of gut length and body elongation. The operculum is one of few features that can be compared in extant and extinct groups, enabling reconstruction of phenotype-environment interactions and modes of evolutionary diversification in deep time.

Diversity and disparity through time in the adaptive radiation of Antarctic notothenioid fishes

According to theory, adaptive radiation is triggered by ecological opportunity that can arise through the colonization of new habitats, the extinction of antagonists or the origin of key innovations. In the course of an adaptive radiation, diversification and morphological evolution are expected to slow down after an initial phase of rapid adaptation to vacant ecological niches, followed by speciation. Such 'early bursts' of diversification are thought to occur because niche space becomes increasingly filled over time. The diversification of Antarctic notothenioid fishes into over 120 species has become one of the prime examples of adaptive radiation in the marine realm and has likely been triggered by an evolutionary key innovation in the form of the emergence of antifreeze glycoproteins. Here, we test, using a novel time-calibrated phylogeny of 49 species and five traits that characterize notothenioid body size and shape as well as buoyancy adaptations and habitat preferences, whether the notothenioid adaptive radiation is compatible with an early burst scenario. Extensive Bayesian model comparison shows that phylogenetic age estimates are highly dependent on model choice and that models with unlinked gene trees are generally better supported and result in younger age estimates. We find strong evidence for elevated diversification rates in Antarctic notothenioids compared to outgroups, yet no sign of rate heterogeneity in the course of the radiation, except that the notothenioid family Artedidraconidae appears to show secondarily elevated diversification rates. We further observe an early burst in trophic morphology, suggesting that the notothenioid radiation proceeds in stages similar to other prominent examples of adaptive radiation.

Divergence in skeletal mass and bone morphology in antarctic notothenioid fishes

Although notothenioid fishes lack swim bladders, some species live temporarily or permanently in the water column. Given its relatively high density, skeletal mass is a key determinant of buoyancy. Notothenioids have reduced skeletal ossification, but there is little quantitative data on the phylogenetic distribution of this trait. We obtained dry skeletal masses for 54 specimens representing 20 species from six notothenioid families. Although comparative data are sparse, notothenioid skeletons comprise a smaller percentage of body mass, <3.5%, than those of three non-notothenioid perciforms. With relatively high skeletal mass, the non-Antarctic Bovichtus diacanthus is similar in skeletal mass to some non-notothenioids. Eleginops maclovinus, the non-Antarctic sister group of the Antarctic clade, has a relatively light skeleton (<2% of body mass) similar to many species in the Antarctic clade. Low skeletal mass is therefore a synapomorphy shared by Eleginops plus the Antarctic clade. We provide gross, histological, and micro-CT documentation of the structure and location of bone and cartilage in skulls, pectoral girdles, and vertebrae, with emphasis on the bovichtid B. diacanthus, the eleginopsid E. maclovinus, and the channichthyid Chaenodraco wilsoni. In Eleginops and the Antarctic clade, most bone is spongy and most species have persisting cartilage in the skull and appendicular skeleton. We also measured the relative size of the notochordal canal in adult vertebral centra of 38 species representing all eight families. There is considerable interspecific variation in this pedomorphic trait and all species show an ontogenetic reduction in the relative size of the canal. However, large persisting canals are present in adults of the Antarctic clade, especially in the nototheniids Pleuragramma and Aethotaxis and in a number of bathydraconid and channichthyid genera.