Majority Of Vertebrate Species Research Articles

Sexual Dichromatism Is Decoupled from Diversification over Deep Time in Fishes.

AbstractSexually selected traits have long been thought to drive diversification, but support for this hypothesis has been persistently controversial. In fishes, sexually dimorphic coloration is associated with assortative mating and speciation among closely related species, as shown in classic studies. However, it is unclear whether these results can generalize to explain diversity patterns across ray-finned fishes, which contain the majority of vertebrate species and 96% of fishes. Here, we use phylogenetic approaches to test for an association between sexual dichromatism and diversification rates (speciation minus extinction) in ray-finned fishes. We assembled dichromatism data for 10,898 species, a data set of unprecedented size. We found no difference in diversification rates between monochromatic and dichromatic species when including all ray-finned fishes. However, at lower phylogenetic scales (within orders and families), some intermediate-sized clades did show an effect of dichromatism on diversification. Surprisingly, dichromatism could significantly increase or decrease diversification rates. Moreover, we found no effect in many of the clades initially used to link dichromatism to speciation in fishes (e.g., cichlids) or an effect only at shallow scales (within subclades). Overall, we show how the effects of dichromatism on diversification are highly variable in direction and restricted to certain clades and phylogenetic scales.

Integrative Computational Approaches to Inform Relative Bioaccumulation Potential of Per- and Polyfluoroalkyl Substances Across Species.

Predictive toxicology is increasingly reliant on innovative computational methods to address pressing questions in chemicals assessment. Of importance is the evaluation of contaminant impact differences across species to inform ecosystem protection and identify appropriate model species for human toxicity studies. Here we evaluated 2 complementary tools to predict cross-species differences in binding affinity between per- and polyfluoroalkyl substances (PFAS) and the liver fatty acid-binding protein (LFABP): the Sequence Alignment to Predict Across Species Susceptibility (SeqAPASS) tool and molecular dynamics (MD). SeqAPASS determined that the structure of human LFABP, a key determinant of PFAS bioaccumulation, was conserved in the majority of vertebrate species, indicating these species would have similar PFAS bioaccumulation potentials. Level 3 SeqAPASS evaluation identified several potentially destabilizing amino acid differences across species, which were generally supported by DUET stability change predictions. Nine single-residue mutations and 7 whole species sequences were selected for MD evaluation. One mutation (F50V for PFNA) showed a statistically significant difference with stronger affinity than wild-type human LFABP. Predicted binding affinities for 9 different PFAS across 7 species showed human, rat, chicken, and rainbow trout had similar binding affinities to one another for each PFAS, whereas Japanese medaka and fathead minnow had significantly weaker LFABP-binding affinity for some PFAS. Based on these analyses, the combined use of SeqAPASS and MD provides rapid screening for potential species differences with deeper structural insight. This approach can be easily extended to other important biological receptors and potential ligands.

Adaptive selection in the evolution of programmed cell death-1 and its ligands in vertebrates.

Programmed cell death-1 (PD-1) and its ligands, particularly PD-L1 and PD-L2, are the most important proteins responsible for signaling T-cell inhibition and arbitrating immune homeostasis and tolerance mechanisms. However, the adaptive evolution of these genes is poorly understood. In this study, we aligned protein-coding genes from vertebrate species to evaluate positive selection constraints and evolution in the PD1, PD-L1 and PD-L2 genes conserved across up to 166 vertebrate species, with an average of 55 species per gene. We determined that although the positive selection was obvious, an average of 5.3% of codons underwent positive selection in the three genes across vertebrate lineages, and increased positive selection pressure was detected in both the Ig-like domains and transmembrane domains of the proteins. Moreover, the PD1, PD-L1 and PD-L2 genes were highly expressed in almost all tissues of the selected species indicating a distinct expression pattern in different tissues among most species. Our study reveals that adaptive selection plays a key role in the evolution of PD1 and its ligands in the majority of vertebrate species, which is in agreement with the contribution of these residues to the mechanisms of pathogen identification and coevolution in the complexity and novelties of vertebrate immune systems.

The retinal pigment epithelium of the eye regulates the development of scleral cartilage

The majority of vertebrate species have a layer of hyaline cartilage within the fibrous sclera giving an extra degree of support to the eyeball. In chicks, this is seen as a cuplike structure throughout the scleral layer. However, the mechanisms that control the development of scleral cartilage are largely unknown.Here we have studied the phases of scleral cartilage development and characterised expression profiles of genes activated during the cartilage differentiation programme. CART1 and SOX9, the earliest markers of pre-committed cartilage, are expressed in the mesenchyme surrounding the optic cup. Later AGGRECAN, a matrix protein expressed during chondrocyte differentiation, is also expressed. The expression of these genes is lost following early removal of the optic cup, suggesting a role for this tissue in inducing scleral cartilage. By grafting young retinal pigment epithelium (RPE) and retina into cranial mesenchyme in vivo, it was found that RPE alone has the ability to induce cartilage formation.There are some exceptions within the vertebrates where scleral cartilage is not present; one such example is the placental mammals. However, we found that the cartilage differentiation pathway is initiated in mice as seen by the expression of Cart1 and Sox9, but expression of the later cartilage marker Aggrecan is weak. Furthermore, cartilage forms in mouse peri-ocular mesenchyme micromass culture. This suggests that the process halts in vivo before full differentiation into cartilage, but that murine scleral mesenchyme has retained the potential to make cartilage in vitro.RA, Wnts and Bmps have been linked to the cartilage development process and are expressed within the developing RPE. We find that RA may have a role in early scleral cartilage development but is not likely to be the main factor involved.These data reveal the course of scleral cartilage formation and highlight the key role that the optic cup plays in this process. The driving element within the optic cup is almost certainly the retinal pigmented epithelium.

Melatonin rhythms in the Australian freshwater crocodile (Crocodylus johnstoni): a reptile lacking a pineal complex?

The vertebrate pineal gland is the primary source of melatonin, the rhythmic secretion of which is influenced by environmental light and temperature, thereby providing animals with information about seasonally changing photoperiod and thermoperiod. Although pineal glands are present in the majority of vertebrate species, a discrete organ is reported to be absent in the Crocodilia. However, if the melatonin rhythm is crucial to the survival of the organism, it would be expected that the rhythm would be present in crocodiles. In the present study, we measured blood plasma melatonin over a 30-h period in aestivating Australian freshwater crocodiles (Crocodylus johnstoni) in their natural habitat at the end of the dry season (November) and found no discernible melatonin rhythm. However, another group of captive-reared C. johnstoni, maintained under natural light and temperature cycles and sampled in the early dry season (June) showed a clear melatonin rhythm. These results suggest that there is either an extrapineal source of melatonin in this crocodile species or that there is melatonin producing tissue elsewhere which heretofore has not been discovered. Further studies are needed to determine why the melatonin rhythm is intermittently expressed and whether this may be related to seasonal changes in the expression of the rhythm linked to tropical environments.