Abstract
Photic niche shifts of mammals are associated with changing visual capabilities, primarily mediated by three visual pigments, two (SWS1 and M/LWS) of them for color vision and rhodopsin ...(RH1) for dim-light vision. To further elucidate molecular mechanisms of mammalian visual adaptations to different light environments, a systematic study incorporating evolutionary analyses across diverse groups and in vitro assays have been carried out. Here, we collected gene sequences for the three opsins from 220 species covering all major mammalian clades. After screening for cone opsin gene losses, we estimated selective pressures on each of the three genes and compared the levels of selection experienced by species living in bright- and dim-light environments. SWS1 pigment is shown to experience accelerated evolution in species living in bright-light environments as has RH1 in aquatic cetaceans, indicating potential shifts for ecological adaptations. To further elucidate the functional mechanisms for these two pigments, we then carried out site-directed mutagenesis in representative taxa. For SWS1, violet and ultraviolet sensitivities in the pika and mouse are mainly affected by substitutions at the critical sites 86 and 93, which have strong epistatic interaction. For RH1, the phenotypic difference between the sperm whale and bovine sequences is largely contributed by a substitution at site 195, which could be critical for dim-light sensation for deep-diving species. Different evolutionary patterns for the visual pigments have been identified in mammals, which correspond to photic niches, although additional phenotypic assays are still required to fully explain the functional mechanisms.
The major histocompatibility complex (MHC) is a highly polymorphic gene family that is crucial in immunity, and its diversity can be effectively used as a fitness marker for populations. Despite ...this, MHC remains poorly characterised in non‐model species (e.g., cetaceans: whales, dolphins and porpoises) as high gene copy number variation, especially in the fast‐evolving class I region, makes analyses of genomic sequences difficult. To date, only small sections of class I and IIa genes have been used to assess functional diversity in cetacean populations. Here, we undertook a systematic characterisation of the MHC class I and IIa regions in available cetacean genomes. We extracted full‐length gene sequences to design pan‐cetacean primers that amplified the complete exon 2 from MHC class I and IIa genes in one combined sequencing panel. We validated this panel in 19 cetacean species and described 354 alleles for both classes. Furthermore, we identified likely assembly artefacts for many MHC class I assemblies based on the presence of class I genes in the amplicon data compared to missing genes from genomes. Finally, we investigated MHC diversity using the panel in 25 humpback and 30 southern right whales, including four paternity trios for humpback whales. This revealed copy‐number variable class I haplotypes in humpback whales, which is likely a common phenomenon across cetaceans. These MHC alleles will form the basis for a cetacean branch of the Immuno‐Polymorphism Database (IPD‐MHC), a curated resource intended to aid in the systematic compilation of MHC alleles across several species, to support conservation initiatives.
The evolution of cetaceans, fromtheir early transition to an aquatic lifestyle to their subsequent diversification, has been the subject of numerous studies. However, although the higher-level ...relationships among cetacean families have been largely settled, several aspects of the systematics within these groups remain unresolved. Problematic clades include the oceanic dolphins (37 spp.), which have experienced a recent rapid radiation, and the beaked whales (22 spp.), which have not been investigated in detail using nuclear loci. The combined application of high-throughput sequencing with techniques that target specific genomic sequences provide a powerful means of rapidly generating large volumes of orthologous sequence data for use in phylogenomic studies. To elucidate the phylogenetic relationships within the Cetacea,we combined sequence capture with Illumina sequencing to generate data for ∼3200 protein-coding genes for 68 cetacean species and their close relatives including the pygmy hippopotamus. By combining data from >38,000 exons with existing sequences from 11 cetaceans and seven outgroup taxa, we produced the first comprehensive comparative genomic data set for cetaceans, spanning 6,527,596 aligned base pairs (bp) and 89 taxa. Phylogenetic trees reconstructed with maximum likelihood and Bayesian inference of concatenated loci, as well as with coalescence analyses of individual gene trees, produced mostly concordant and well-supported trees. Our results completely resolve the relationships among beaked whales as well as the contentious relationships among oceanic dolphins, especially the problematic subfamily Delphinidae. We carried out Bayesian estimation of species divergence times using MCMCTree andcompared ourcomplete data set to a subset of clocklike genes. Analyses using the complete data set consistently showed less variance in divergence times than the reduced data set. In addition, integration of new fossils (e.g., Mystacodon selenensis) indicates that the diversification of Crown Cetacea began before the Late Eocene and the divergence of Crown Delphinidae as early as theMiddle Miocene.
The Antarctic minke whale (Balaenoptera bonaerensis) (AMW) is one of the smallest species among baleen whales, occurring in the southern hemisphere from Antarctica to near the equator, and performing ...seasonal migrations from polar to tropical waters. Information about (AMW) occurrence in the winter breeding grounds is scarce, mostly coming from old records from whaling stations before the 1960's international moratorium, such as Costinha Station in Northeastern Brazil (6° S / 34° W) and some sightings from few dedicated visual surveys. Acoustic methods can provide important data on the occurrence and distribution of migratory species. This work describes the occurrence of the Antarctic minke whale through acoustic detections of their "Bioduck" vocalisations in the Santos Basin, South-Southeastern Brazil (22° and 28° S / 42° and 48° W). Data was recorded between November 12 and December 19, 2015. AMW calls were detected for 12 days. We detected and classified 9 different Bio-duck calls in Brazilian coastal waters, evidencing a highly diverse acoustic behavior for the minke whale breeding ground. This is the first attempt to describe the acoustic diversity of AMW vocalizations in lower latitudes, contributing important information for future conservation efforts and management of AMW populations and their habitat. Therefore, our study presents the foremost acoustic evidence of the Antarctic minke whale in Brazilian coastal waters.
Solution super(1)H NMR spectroscopy has been carried out to investigate the molecular and electronic structures of the active site in H64Q/V68F double mutant mouse neuroglobin in the cyanomet form. ...Two heme orientations resulting from a 180 degree rotation about the alpha - gamma -meso axis were observed with a population ratio about 1:1, and the clearly distinguished B isomer was used to perform the study. Based on the analysis of the dipolar shifts and paramagnetic relaxation constants, the distal Gln super(64)(E7) side chain is obtained to adopt an orientation that may produce hydrogen bond between the N sub( epsilon )H sub(1) and the Fe-bound cyanide. The side chain of Phe super(68)(E11) is oriented out of the heme pocket just like that in triple mutant of cyanide complex of sperm whale myoglobin. A 15 degree rotation of the imidazole ring in axial His super(96) is observed, which is close to the phi angle determined from the crystal structure of NgbCO. The quantitative determinations of the orientation and anisotropies of the paramagnetic susceptibility tensor reveal that cyanide is tilted by 8 degree from the heme normal which allows for contact to the Gln super(64)(E7) N sub( epsilon )H sub(1). The E7 and E11 residues appear to control the direction and the extent of tilt of the bound ligand. Furthermore, the tilt of the ligand has no obvious influence on the heme heterogeneity of cyanide ligation for isomer A/B of the wild type and mutant protein, indicating that factors other than steric effects, such as polarity of heme pocket, impacts on ligand binding affinity.
The macroevolutionary transition from terra firma to obligatory inhabitance of the marine hydrosphere has occurred twice in the history of Mammalia: Cetacea and Sirenia. In the case of Cetacea ...(whales, dolphins, and porpoises), molecular phylogenies provide unambiguous evidence that fully aquatic cetaceans and semiaquatic hippopotamids (hippos) are each other’s closest living relatives. Ancestral reconstructions suggest that some adaptations to the aquatic realm evolved in the common ancestor of Cetancodonta (Cetacea + Hippopotamidae). An alternative hypothesis is that these adaptations evolved independently in cetaceans and hippos. Here, we focus on the integumentary system and evaluate these hypotheses by integrating new histological data for cetaceans and hippos, the first genome-scale data for pygmy hippopotamus, and comprehensive genomic screens and molecular evolutionary analyses for protein-coding genes that have been inactivated in hippos and cetaceans. We identified eight skin-related genes that are inactivated in both cetaceans and hippos, including genes that are related to sebaceous glands, hair follicles, and epidermal differentiation. However, none of these genes exhibit inactivating mutations that are shared by cetaceans and hippos. Mean dates for the inactivation of skin genes in these two clades serve as proxies for phenotypic changes and suggest that hair reduction/loss, the loss of sebaceous glands, and changes to the keratinization program occurred ∼16 Ma earlier in cetaceans (∼46.5 Ma) than in hippos (∼30.5 Ma). These results, together with histological differences in the integument and prior analyses of oxygen isotopes from stem hippopotamids (“anthracotheres”), support the hypothesis that aquatic skin adaptations evolved independently in hippos and cetaceans.
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•Cetaceans and hippos have differences in the thickness and organization of the skin•Genomic screens identified 8 skin genes that are inactivated in hippos and cetaceans•None of these 8 genes share inactivating mutations in hippos and cetaceans•Aquatic skin adaptations evolved independently in hippos and cetaceans
Springer et al. perform genomic and anatomical comparisons to determine whether aquatic adaptations of the skin in hippos and cetaceans are shared derived or convergent features in these two clades. The results of these comparisons support the hypothesis that aquatic adaptations of the skin are convergent characters in hippos and cetaceans.
Body sizes of marine amniotes span six orders of magnitude, yet the factors that governed the evolution of this diversity are largely unknown. High primary production of modern oceans is considered a ...prerequisite for the emergence of cetacean giants, but that condition cannot explain gigantism in Triassic ichthyosaurs. We describe the new giant ichthyosaur
sp. nov. with a 2-meter-long skull from the Middle Triassic Fossil Hill Fauna of Nevada, USA, underscoring rapid size evolution despite the absence of many modern primary producers. Surprisingly, the Fossil Hill Fauna rivaled the composition of modern marine mammal faunas in terms of size range, and energy-flux models suggest that Middle Triassic marine food webs were able to support several large-bodied ichthyosaurs at high trophic levels, shortly after ichthyosaur origins.
Fresh water dolphins are present in geographically different areas of the world. Although, they are the descendents of the single ancestor yet they have some genetic variabilities. The present study ...was conducted to discuss the characteristics and to analyze genomic differences among different fresh water dolphins. Literature survey was done to find out major habitat zone of fresh water dolphins. The mitochondrial DNA sequence of dolphins was taken from GenBank. Mitochondrial nucleotide sequence aligmnent of dolphins was performed using bio-informatics tool Clustal W. Phylogenetic tree was constructed and percentage similarity was calculated among different species of fresh water dolphins. On the basis of habitat, fresh water dolphins are divided into five major zones. Indus Dolphin mitochondrial genome indicated 99% homology with Ganges dolphin and 83% homology with Baiji Dolphin, 81% homology with the Franciscana Dolphin and 82% homology with the Boto Dolphin. There are genetic variations at mitochondrial genome level between Indus dolphin and other fresh water dolphins.
This paper focuses upon a growing activity within New Zealand's ecotourism market: viewing swimming with dolphins. Three sets of data inform this research: (1) promotional, such as postcards, ...brochures, Internet websites, and advertising; (2) observation on dolphin swim tours; and (3) interviews with tour operators.
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