Ancient convergent losses of Paraoxonase 1 yield potential risks for modern marine mammals

Organohalogen contaminants threaten the survival of indo-pacific humpback dolphin calves in their largest habitat

As long-lived apex predators, marine mammal adults often accumulate alarmingly levels of environmental contaminants. Nevertheless, the accumulation and risks of these contaminants in the critical calf stage of marine mammals remain largely unknown. Here, we investigated the exposure status and health risks of 74 organohalogen contaminants (OHCs) in Indo-Pacific humpback dolphin calves (Sousa chinensis) collected from the Pearl River Estuary (PRE), China, during 2005-2019. Our findings revealed moderate levels of polychlorinated biphenyls (PCBs), medium-high levels of dichlorodiphenyltrichloroethanes (DDTs) and hexachlorocyclohexanes (HCHs), and the highest levels of polybrominated diphenyl ethers (PBDEs) and alternative halogenated flame retardants (AHFRs) compared to those reported for cetaceans elsewhere. Traditional OHCs like DDTs, PCBs, and PBDEs did not exhibit significant decreasing trends in the dolphin calves despite global restrictions on these compounds, and AHFRs as emerging OHCs showed an increasing trend over the study period. Risk quotients of DDTs, HCHs, PBDEs, and PCBs in most of the dolphin samples were > 1, indicating that humpback dolphin calves may have suffered long-term threats from OHC exposure. The significant correlation observed between the traditional OHC levels and the stranding death number of the dolphin calves suggests these OHCs may impact the survival of this endangered species.

Assessment of persistent organic pollutants in killer whales (Orcinus orca) of the Canadian Arctic: Implications for subsistence consumption and conservation strategies

Killer whales (Orcinus orca) historically restricted to certain Arctic regions due to extensive sea ice have recently been documented farther north and for longer durations in the Canadian Arctic. These apex predators accumulate high levels of persistent organic pollutants (POPs). The objective of this study was to evaluate the concentrations and profiles of POPs in killer whales of the Canadian Arctic, thus determining potential risks for Inuit communities if consumed. Biopsies were collected from 33 killer whales across areas of the Canadian Arctic between 2009 and 2021. Significant variability in POP concentrations was observed among whales. The cumulative POP concentrations ranged from 12 to >2270 mg/kg lw, representing ∼200-fold increase from the least to the most contaminated individual. The rank order of concentrations of the top five contaminant classes was ∑DDT, ∑PCB, ∑CHL, ∑Toxaphene, and Dieldrin. Several emerging Arctic contaminants were detected, including chlorpyrifos, endosulfan, pentachloroanisole, and polychlorinated naphthalenes, although at relatively lower concentrations than legacy POPs. Considering the elevated blubber POP levels in killer whales, recommended daily consumption thresholds, established based on human tolerable daily intake (TDI) values, were notably restricted for ∑PCB (<0.14 g), ∑DDT (<6.9 g), ∑CHL (<13 g), dieldrin (<8 g) and heptachlor epoxide (<5 g). Killer whales in the Canadian Arctic exhibited higher POP concentrations than other commonly hunted species such as polar bears, ringed seals, and Arctic char. We acknowledge that a more holistic risk assessment of diet is required to assess the cumulative impacts of contaminant mixtures as well as nutritional quality of tissues commonly consumed by northern communities.

Neurotoxicity of Benzotriazole Ultraviolet Stabilizers in Teleost Fishes: A Review

Plastic additives that maintain integrity have been extensively studied for potential toxicity to fish; however, chemicals that protect polymers from (artificial) UV degradation are less studied. Benzotriazole UV stabilizers (BUVSs) are the most widely used UV stabilizers in plastics and are often used in sunscreens, cosmetics, paint, and food packaging. BUVSs can negatively affect aquatic wildlife when released into the environment via plastic degradation. In this review, we summarize the distribution of BUVSs globally and discuss neurotoxicological endpoints measured in fish to understand how these plastic additives can affect the neurological health of teleost fishes. BUVSs have been detected in aquatic environments at concentrations ranging from 0.05 up to 99,200 ng/L. Studies show that BUVSs affect behavioral responses and acetylcholinesterase activity, indicators of neurotoxicity. Our computational analysis using transcriptome data suggests certain pathways associated with neurodegeneration are responsive to exposure to BUVSs, like "Complement Activation in Alzheimer's Disease". Based on our review, we identify some research needs for future investigations: (1) molecular studies in the central nervous system to define precise mechanisms of neurotoxicity; (2) a wider range of tests for assessing aberrant behaviors given that BUVSs can affect the activity of larval zebrafish; and (3) histopathology of the nervous system to accompany biochemical analyses. These data are expected to enhance understanding of the neurotoxicity potential of benzotriazoles and other plastic additives.

Varying Diet Composition Causes Striking Differences in Legacy and Emerging Contaminant Concentrations in Killer Whales across the North Atlantic

Lipophilic persistent organic pollutants (POPs) tend to biomagnify in food chains, resulting in higher concentrations in species such as killer whales (Orcinus orca) feeding on marine mammals compared to those consuming fish. Advancements in dietary studies include the use of quantitative fatty acid signature analysis (QFASA) and differentiation of feeding habits within and between populations of North Atlantic (NA) killer whales. This comprehensive study assessed the concentrations of legacy and emerging POPs in 162 killer whales from across the NA. We report significantly higher mean levels of polychlorinated biphenyls (PCBs), organochlorine pesticides, and flame retardants in Western NA killer whales compared to those of Eastern NA conspecifics. Mean ∑PCBs ranged from ∼100 mg/kg lipid weight (lw) in the Western NA (Canadian Arctic, Eastern Canada) to ∼50 mg/kg lw in the mid-NA (Greenland, Iceland) to ∼10 mg/kg lw in the Eastern NA (Norway, Faroe Islands). The observed variations in contaminant levels were strongly correlated with diet composition across locations (inferred from QFASA), emphasizing that diet and not environmental variation in contaminant concentrations among locations is crucial in assessing contaminant-associated health risks in killer whales. These findings highlight the urgency for implementing enhanced measures to safely dispose of POP-contaminated waste, prevent further environmental contamination, and mitigate the release of newer and potentially harmful contaminants.

Genome annotation: From human genetics to biodiversity genomics

Within the next decade, the genomes of 1.8 million eukaryotic species will be sequenced. Identifying genes in these sequences is essential to understand the biology of the species. This is challenging due to the transcriptional complexity of eukaryotic genomes, which encode hundreds of thousands of transcripts of multiple types. Among these, a small set of protein-coding mRNAs play a disproportionately large role in defining phenotypes. Due to their sequence conservation, orthology can be established, making it possible to define the universal catalog of eukaryotic protein-coding genes. This catalog should substantially contribute to uncovering the genomic events underlying the emergence of eukaryotic phenotypes. This piece briefly reviews the basics of protein-coding gene prediction, discusses challenges in finalizing annotation of the human genome, and proposes strategies for producing annotations across the eukaryotic Tree of Life. This lays the groundwork for obtaining the catalog of all genes-the Earth's code of life.

Reduction of Paraoxonase Expression Followed by Inactivation across Independent Semiaquatic Mammals Suggests Stepwise Path to Pseudogenization

Convergent adaptation to the same environment by multiple lineages frequently involves rapid evolutionary change at the same genes, implicating these genes as important for environmental adaptation. Such adaptive molecular changes may yield either change or loss of protein function; loss of function can eliminate newly deleterious proteins or reduce energy necessary for protein production. We previously found a striking case of recurrent pseudogenization of the Paraoxonase 1 (Pon1) gene among aquatic mammal lineages-Pon1 became a pseudogene with genetic lesions, such as stop codons and frameshifts, at least four times independently in aquatic and semiaquatic mammals. Here, we assess the landscape and pace of pseudogenization by studying Pon1 sequences, expression levels, and enzymatic activity across four aquatic and semiaquatic mammal lineages: pinnipeds, cetaceans, otters, and beavers. We observe in beavers and pinnipeds an unexpected reduction in expression of Pon3, a paralog with similar expression patterns but different substrate preferences. Ultimately, in all lineages with aquatic/semiaquatic members, we find that preceding any coding-level pseudogenization events in Pon1, there is a drastic decrease in expression, followed by relaxed selection, thus allowing accumulation of disrupting mutations. The recurrent loss of Pon1 function in aquatic/semiaquatic lineages is consistent with a benefit to Pon1 functional loss in aquatic environments. Accordingly, we examine diving and dietary traits across pinniped species as potential driving forces of Pon1 functional loss. We find that loss is best associated with diving activity and likely results from changes in selective pressures associated with hypoxia and hypoxia-induced inflammation.

Molecular mechanisms of adaptive evolution in wild animals and plants

Wild animals and plants have developed a variety of adaptive traits driven by adaptive evolution, an important strategy for species survival and persistence. Uncovering the molecular mechanisms of adaptive evolution is the key to understanding species diversification, phenotypic convergence, and inter-species interaction. As the genome sequences of more and more non-model organisms are becoming available, the focus of studies on molecular mechanisms of adaptive evolution has shifted from the candidate gene method to genetic mapping based on genome-wide scanning. In this study, we reviewed the latest research advances in wild animals and plants, focusing on adaptive traits, convergent evolution, and coevolution. Firstly, we focused on the adaptive evolution of morphological, behavioral, and physiological traits. Secondly, we reviewed the phenotypic convergences of life history traits and responding to environmental pressures, and the underlying molecular convergence mechanisms. Thirdly, we summarized the advances of coevolution, including the four main types: mutualism, parasitism, predation and competition. Overall, these latest advances greatly increase our understanding of the underlying molecular mechanisms for diverse adaptive traits and species interaction, demonstrating that the development of evolutionary biology has been greatly accelerated by multi-omics technologies. Finally, we highlighted the emerging trends and future prospects around the above three aspects of adaptive evolution.

Highly Dynamic Gene Family Evolution Suggests Changing Roles for PON Genes Within Metazoa

Change in gene family size has been shown to facilitate adaptation to different selective pressures. This includes gene duplication to increase dosage or diversification of enzymatic substrates and gene deletion due to relaxed selection. We recently found that the PON1 gene, an enzyme with arylesterase and lactonase activity, was lost repeatedly in different aquatic mammalian lineages, suggesting that the PON gene family is responsive to environmental change. We further investigated if these fluctuations in gene family size were restricted to mammals and approximately when this gene family was expanded within mammals. Using 112 metazoan protein models, we explored the evolutionary history of the PON family to characterize the dynamic evolution of this gene family. We found that there have been multiple, independent expansion events in tardigrades, cephalochordates, and echinoderms. In addition, there have been partial gene loss events in monotremes and sea cucumbers and what appears to be complete loss in arthropods, urochordates, platyhelminths, ctenophores, and placozoans. In addition, we show the mammalian expansion to three PON paralogs occurred in the ancestor of all mammals after the divergence of sauropsida but before the divergence of monotremes from therians. We also provide evidence of a novel PON expansion within the brushtail possum. In the face of repeated expansions and deletions in the context of changing environments, we suggest a range of selective pressures, including pathogen infection and mitigation of oxidative damage, are likely influencing the diversification of this dynamic gene family across metazoa.

Interactome of Paraoxonase PON2 Reveals New Pathways for Tumor Growth Regulation

The interactome of paraoxonase-2 encoded by the PON2 gene was investigated. A cDNA library was screened using a yeast two-hybrid system to search for new proteins interacting with human PON2. Analysis of the identified candidates, along with previously published data on interactors obtained by other methods, indicates the presence of a significant number of indirect interactions between PON2 and EGFR and, consequently, possible regulation of tumor growth with mutant EGFR involving PON2.

The plasma phospholipidome of the bottlenose dolphin (Tursiops truncatus) is modulated by both sex and developmental stage

Lipidomics represent a valid complementary tool to the biochemical analysis of plasma in humans. However, in cetaceans, these tools have been unexplored. Here, we evaluated how the plasma lipid composition of Tursiops truncatus is modulated by developmental stage and sex, aiming at a potential use of lipidomics in integrated strategies to monitor cetacean health. We characterized the fatty acid profile and detected a total of 26 fatty acids in T. truncatus plasma. The most abundant fatty acids were palmitic acid (C16:0), stearic acid (C18:0) and oleic acid (C18:1n-9). Interestingly, there are consistent differences between the fatty acid profile of mature female and mature male specimens. Phospholipidome analysis identified 320 different lipid species belonging to phosphatidylcholine (PC, 105 lipid species), lysophosphatidylcholine (42), phosphatidylethanolamine (PE, 67), lysophosphatidylethanolamine (18), phosphatidylglycerol (14), lysophosphatidylglycerol (8), phosphatidylinositol (14), lysophosphatidylinositol (2), phosphatidylserine (3), sphingomyelin (45) and ceramides (2) classes. The statistical analysis of the phospholipidome showed that its composition allows discriminating mature animals between sexes and mature males from immature males. Notably, discrimination between sexes is mainly determined by the contents of PE plasmalogens and lysophospholipids (LPC and LPE), while the differences between mature and immature male animals were mainly determined by the levels of PC lipids. This is the first time that a correlation between developmental stage and sex and the lipid composition of the plasma has been established in cetaceans. Being able to discern between age and sex-related changes is an encouraging step towards using these tools to also detect differences related to disease/dysfunction processes.

Long-Term Monitoring of Polybrominated Diphenyl Ethers (PBDEs) in Indo-Pacific Humpback Dolphins (Sousa chinensis) from the Pearl River Estuary Reveals High Risks for Calves due to Maternal Exposure

Although many studies have documented the wide occurrence of polybrominated diphenyl ethers (PBDEs) in cetaceans, little evidence exists regarding the detrimental effects of PBDE exposure on calf death rates for free-ranging cetaceans. This study analyzed life-history-associated PBDE bioaccumulation patterns in 128 stranding Indo-Pacific humpback dolphin (Sousa chinensis) samples over an 18-year timespan from the Pearl River Estuary (PRE). In comparison to the records of PBDE levels in cetaceans worldwide, the median levels of PBDEs (median = 10600 ng g^-1 lw, range = 721-50900 ng g^-1 lw) in all samples were the highest to date. One-way analysis of variance (ANOVA) showed that adult males (median = 16100 ng g^-1 lw, range = 4070-50900 ng g^-1 lw) and calves (12000 ng g^-1 lw, range = 1250-35300 ng g^-1 lw) both had the highest levels of PBDEs compared to the rest of the age/sex groups (p < 0.05). Concentrations of PBDEs in noncalves significantly decreased over the studied period, while those in calves had a slightly increasing trend, which may be due to different exposure routes via fish or milk, respectively. A significant and positive relationship was found between annual calf stranding death rates and body-length-adjusted PBDE concentrations in calves (r = 0.62, p < 0.05), suggesting that maternal exposure of calves to elevated levels of PBDEs may have contributed to the high annual stranding death rates of calves in the last two decades.

Occurrences and potential lipid-disrupting effects of phthalate metabolites in humpback dolphins from the South China Sea

Phthalate esters (PAEs) are ubiquitous environmental contaminants, arising growing public concern. Nevertheless, information on the exposure and risks of PAEs in wildlife remains limited. Here, we conducted the first investigation of the occurrences, spatiotemporal trends, and potential risks of twelve metabolites of PAEs (mPAEs) in 74 humpback dolphins from the northern South China Sea during 2005-2020. All twelve mPAEs (∑₁₂mPAEs: 9.6-810.7 ng g^-1 wet weight) were detected in the dolphin liver, and seven major mPAEs showed increasing trends during the study period, indicating high PAE contamination in the coastal environment of South China. Monoethylhexyl phthalate accounted for over half of the ∑₁₂mPAE concentrations. The accumulation of mPAEs in the dolphins was neither age-dependent nor sex-specific. Compared to parent PAEs, mPAEs generally induced higher agonistic effects on the dolphin peroxisome proliferator-activated receptor alpha/gamma (PPARA/G) as master regulators of lipid homeostasis. Although short-term in vitro assays revealed no significant activation of dolphin PPARA/G by tissue-relevant doses of mPAEs, long-term in vivo evidence (i.e., correlations between hepatic mPAEs and blubber fatty acids) suggested that chronic exposure to mPAEs might have impacted lipid metabolism in the dolphin. This study highlighted the potential health risks of PAE exposure on marine mammals.

Paraoxonase 1 and atherosclerosis

Paraoxonase 1 (PON1), residing almost exclusively on HDL, was discovered because of its hydrolytic activity towards organophosphates. Subsequently, it was also found to hydrolyse a wide range of substrates, including lactones and lipid hydroperoxides. PON1 is critical for the capacity of HDL to protect LDL and outer cell membranes against harmful oxidative modification, but this activity depends on its location within the hydrophobic lipid domains of HDL. It does not prevent conjugated diene formation, but directs lipid peroxidation products derived from these to become harmless carboxylic acids rather than aldehydes which might adduct to apolipoprotein B. Serum PON1 is inversely related to the incidence of new atherosclerotic cardiovascular disease (ASCVD) events, particularly in diabetes and established ASCVD. Its serum activity is frequently discordant with that of HDL cholesterol. PON1 activity is diminished in dyslipidaemia, diabetes, and inflammatory disease. Polymorphisms, most notably Q192R, can affect activity towards some substrates, but not towards phenyl acetate. Gene ablation or over-expression of human PON1 in rodent models is associated with increased and decreased atherosclerosis susceptibility respectively. PON1 antioxidant activity is enhanced by apolipoprotein AI and lecithin:cholesterol acyl transferase and diminished by apolipoprotein AII, serum amyloid A, and myeloperoxidase. PON1 loses this activity when separated from its lipid environment. Information about its structure has been obtained from water soluble mutants created by directed evolution. Such recombinant PON1 may, however, lose the capacity to hydrolyse non-polar substrates. Whilst nutrition and pre-existing lipid modifying drugs can influence PON1 activity there is a cogent need for more specific PON1-raising medication to be developed.

Occurrence of emerging brominated flame retardants and organophosphate esters in marine wildlife from the Norwegian Arctic

To understand the exposure and potential sources of emerging brominated flame retardants (EBFR) and organophosphate esters (OPEs) in marine wildlife from the Norwegian Arctic, we investigated concentrations of EBFRs in 157 tissue samples from nine species of marine vertebrates and OPEs in 34 samples from three whale species. The samples, collected from a wide range of species with contrasting areal use and diets, included blubber of blue whales, fin whales, humpback whales, white whales, killer whales, walruses and ringed seals and adipose tissue and plasma from polar bears, as well as adipose tissue from glaucous gulls. Tris(2-ethylhexyl) phosphate (TEHP) and tris(2-chloroisopropyl) phosphate (TCIPP) ranged from <0.61 to 164 and < 0.8-41 ng/g lipid weight, respectively, in blue whales and fin whales. All other EBRFs and OPEs were below the detection limit or detected only at low concentration. In addition to the baseline information on the occurrence of EBFRs and OPEs in marine wildlife from the Arctic, we provide an in-depth discussion regarding potential sources of the detected compounds. This information is important for future monitoring and management of EBFRs and OPEs.

Organotins Remain a Serious Threat to the Indo-Pacific Humpback Dolphins in the Pearl River Estuary

Marine mammals often accumulate high levels of environmental contaminants, even those that are globally regulated regarding usage, raising concerns about their health status. Here, we conducted the first investigation of tissue distribution, spatiotemporal trends, and potential risks of six organotin compounds (OTs) in Indo-Pacific humpback dolphins (n = 101) from the northern South China Sea during 2003-2021. We detected the highest level of hepatic triphenyltin in these humpback dolphins compared with the results reported in cetaceans globally, and the liver accumulated the highest OT concentrations than other analyzed tissues. Despite the downward trend of butyltins in humpback dolphins after the global ban on the use of OTs as antifouling paints, levels of phenyltins have continued to increase over the past 20 years, suggesting that the other applications of phenyltins in South China remain prevalent. In vitro and in vivo analyses revealed that tissue-relevant doses of OTs could induce agonistic effects on the dolphin peroxisome proliferator-activated receptor γ as a master regulator of lipid homeostasis and altered the dolphin fatty acid profiles. Our results highlight the lipid-disrupting effects of current OT exposure in humpback dolphins and emphasize the need for further efforts to eliminate OT contamination in South China.

Temporal Trends of Alternative Halogenated Flame Retardants in Humpback Dolphins from the South China Sea

Increasing human activities are altering marine ecosystems, which may have ramifications for predator feeding ecology and, thus, the degree of contaminant exposure. We conducted the first investigation of spatiotemporal trends for nine alternative halogenated flame retardants (AHFRs) and their relations with dietary variations in 128 humpback dolphins that were stranded along the northern South China Sea during 2003-2020. We detected the highest levels of seven major AHFRs in humpback dolphins compared with the results reported in cetaceans globally, indicating high AHFR contamination in coastal regions of South China. Dolphins that were stranded near urban regions generally contained higher AHFR concentrations than those that were stranded near rural areas, mirroring the environmental trends of AHFRs occurring in this area. Model-generated diet estimates suggested that humpback dolphins have reduced their consumption of high trophic-level prey in recent years, likely attributable to overfishing-induced prey decline in this region. After adjusting AHFR concentrations due to diet changes, the temporal trends of AHFR contamination in humpback dolphins were only slightly altered. Our results suggest that increasing discharges of AHFRs into the South China Sea during the 2000s and 2010s may have had a greater influence on AHFR trends in humpback dolphins than dietary shifts.

Gene losses may contribute to subterranean adaptations in naked mole-rat and blind mole-rat

Background

Naked mole-rats (Heterocephalus glaber, NMRs) and blind mole-rats (Spalax galili, BMRs) are representative subterranean rodents that have evolved many extraordinary traits, including hypoxia tolerance, longevity, and cancer resistance. Although multiple candidate loci responsible for these traits have been uncovered by genomic studies, many of them are limited to functional changes to amino acid sequence and little is known about the contributions of other genetic events. To address this issue, we focused on gene losses (unitary pseudogenes) and systematically analyzed gene losses in NMRs and BMRs, aiming to elucidate the potential roles of pseudogenes in their adaptation to subterranean lifestyle.

Results

We obtained the pseudogene repertoires in NMRs and BMRs, as well as their respective aboveground relatives, guinea pigs and rats, on a genome-wide scale. As a result, 167, 139, 341, and 112 pseudogenes were identified in NMRs, BMRs, guinea pigs, and rats, respectively. Functional enrichment analysis identified 4 shared and 2 species-specific enriched functional groups (EFGs) in subterranean lineages. Notably, the pseudogenes in these EFGs might be associated with either regressive (e.g., visual system) or adaptive (e.g., altered DNA damage response) traits. In addition, several pseudogenes including TNNI3K and PDE5A might be associated with specific cardiac features observed in subterranean lineages. Interestingly, we observed 20 convergent gene losses in NMRs and BMRs. Given that the functional investigations of these genes are generally scarce, we provided functional evidence that independent loss of TRIM17 in NMRs and BMRs might be beneficial for neuronal survival under hypoxia, supporting the positive role of eliminating TRIM17 function in hypoxia adaptation. Our results also suggested that pseudogenes, together with positively selected genes, reinforced subterranean adaptations cooperatively.

Conclusions

Our study provides new insights into the molecular underpinnings of subterranean adaptations and highlights the importance of gene losses in mammalian evolution.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12915-022-01243-0.

Convergent Loss of Chemoreceptors across Independent Origins of Slave-Making in Ants

The evolution of an obligate parasitic lifestyle often leads to the reduction of morphological and physiological traits, which may be accompanied by loss of genes and functions. Slave-making ants are social parasites that exploit the work force of closely related ant species for social behaviors such as brood care and foraging. Recent divergence between these social parasites and their hosts enables comparative studies of gene family evolution. We sequenced the genomes of eight ant species, representing three independent origins of ant slavery. During the evolution of eusociality, chemoreceptor genes multiplied due to the importance of chemical communication in insect societies. We investigated the evolutionary fate of these chemoreceptors and found that slave-making ant genomes harbored only half as many gustatory receptors as their hosts', potentially mirroring the outsourcing of foraging tasks to host workers. In addition, parasites had fewer odorant receptors and their loss shows striking patterns of convergence across independent origins of parasitism, in particular in orthologs often implicated in sociality like the 9-exon odorant receptors. These convergent losses represent a rare case of convergent molecular evolution at the level of individual genes. Thus, evolution can operate in a way that is both repeatable and reversible when independent ant lineages lose important social traits during the transition to a parasitic lifestyle.

Complementary evolution of coding and noncoding sequence underlies mammalian hairlessness

Body hair is a defining mammalian characteristic, but several mammals, such as whales, naked mole-rats, and humans, have notably less hair. To find the genetic basis of reduced hair quantity, we used our evolutionary-rates-based method, RERconverge, to identify coding and noncoding sequences that evolve at significantly different rates in so-called hairless mammals compared to hairy mammals. Using RERconverge, we performed a genome-wide scan over 62 mammal species using 19,149 genes and 343,598 conserved noncoding regions. In addition to detecting known and potential novel hair-related genes, we also discovered hundreds of putative hair-related regulatory elements. Computational investigation revealed that genes and their associated noncoding regions show different evolutionary patterns and influence different aspects of hair growth and development. Many genes under accelerated evolution are associated with the structure of the hair shaft itself, while evolutionary rate shifts in noncoding regions also included the dermal papilla and matrix regions of the hair follicle that contribute to hair growth and cycling. Genes that were top ranked for coding sequence acceleration included known hair and skin genes KRT2, KRT35, PKP1, and PTPRM that surprisingly showed no signals of evolutionary rate shifts in nearby noncoding regions. Conversely, accelerated noncoding regions are most strongly enriched near regulatory hair-related genes and microRNAs, such as mir205, ELF3, and FOXC1, that themselves do not show rate shifts in their protein-coding sequences. Such dichotomy highlights the interplay between the evolution of protein sequence and regulatory sequence to contribute to the emergence of a convergent phenotype.

Historic changes of polychlorinated biphenyls (PCBs) in juvenile and adult cetaceans from the Pearl River estuary from 2003 to 2020

Polychlorinated biphenyls (PCBs), as a type of legacy persistent organic pollutants, pose significant health threats to wildlife. However, long-term residue changes and profiles of PCBs in cetaceans have not been extensively studied in the Pearl River Estuary (PRE), an important marine mammal area in China. Here, the body burdens, spatiotemporal trends, and health risks of 21 chlorobiphenyl congeners (∑21CBs) were analyzed in blubber samples collected from twelve cetacean species (n = 172) in the PRE from 2003 to 2020. Our results revealed medium levels of PCBs (316-96,233 ng g^-1 lipid) compared to those reported for cetaceans elsewhere (70-370,000 ng g^-1 lipid). Clear differences in PCB distribution patterns between inshore and offshore cetaceans and between odontocetes and mysticetes were also found. Both the coastal Indo-Pacific humpback dolphins (Sousa chinensis) and Indo-Pacific finless porpoises (Neophocaena phocaenoides) displayed similarly fine-scale spatial distribution patterns of PCBs, suggesting that the two cetaceans could serve as bioindicators of PCB pollution in the PRE. Additionally, both cetaceans exhibited decreasing trends in their blubber PCB concentrations over the past 20 years, likely reflecting the effective regulation of PCBs in the PRE Delta. Nevertheless, the relatively high and stable PCB-toxic equivalent (TEQ) levels detected in calf humpback dolphins during the sampling period suggested that the calves are still under the stresses of high PCB-related health risks. Our results highlight the need for more efforts to eliminate PCB contamination to prevent these cetaceans from continuous population decline and further extinction.

Ontogeny of Carbon Monoxide-Related Gene Expression in a Deep-Diving Marine Mammal

Marine mammals such as northern elephant seals (NES) routinely experience hypoxemia and ischemia-reperfusion events to many tissues during deep dives with no apparent adverse effects. Adaptations to diving include increased antioxidants and elevated oxygen storage capacity associated with high hemoprotein content in blood and muscle. The natural turnover of heme by heme oxygenase enzymes (encoded by HMOX1 and HMOX2) produces endogenous carbon monoxide (CO), which is present at high levels in NES blood and has been shown to have cytoprotective effects in laboratory systems exposed to hypoxia. To understand how pathways associated with endogenous CO production and signaling change across ontogeny in diving mammals, we measured muscle CO and baseline expression of 17 CO-related genes in skeletal muscle and whole blood of three age classes of NES. Muscle CO levels approached those of animals exposed to high exogenous CO, increased with age, and were significantly correlated with gene expression levels. Muscle expression of genes associated with CO production and antioxidant defenses (HMOX1, BVR, GPX3, PRDX1) increased with age and was highest in adult females, while that of genes associated with protection from lipid peroxidation (GPX4, PRDX6, PRDX1, SIRT1) was highest in adult males. In contrast, muscle expression of mitochondrial biogenesis regulators (PGC1A, ESRRA, ESRRG) was highest in pups, while genes associated with inflammation (HMOX2, NRF2, IL1B) did not vary with age or sex. Blood expression of genes involved in regulation of inflammation (IL1B, NRF2, BVR, IL10) was highest in pups, while HMOX1, HMOX2 and pro-inflammatory markers (TLR4, CCL4, PRDX1, TNFA) did not vary with age. We propose that ontogenetic upregulation of baseline HMOX1 expression in skeletal muscle of NES may, in part, underlie increases in CO levels and expression of genes encoding antioxidant enzymes. HMOX2, in turn, may play a role in regulating inflammation related to ischemia and reperfusion in muscle and circulating immune cells. Our data suggest putative ontogenetic mechanisms that may enable phocid pups to transition to a deep-diving lifestyle, including high baseline expression of genes associated with mitochondrial biogenesis and immune system activation during postnatal development and increased expression of genes associated with protection from lipid peroxidation in adulthood.

Long-Range Transport, Trophic Transfer, and Ecological Risks of Organophosphate Esters in Remote Areas

Organophosphate esters (OPEs) have been a focus in the field of environmental science due to their large volume production, wide range of applications, ubiquitous occurrence, potential bioaccumulation, and worrisome ecological and health risks. Varied physicochemical properties among OPE analogues represent an outstanding scientific challenge in studying the environmental fate of OPEs in recent years. There is an increasing number of studies focusing on the long-range transport, trophic transfer, and ecological risks of OPEs. Therefore, it is necessary to conclude the OPE pollution status on a global scale, especially in the remote areas with vulnerable and fragile ecosystems. The present review links together the source, fate, and environmental behavior of OPEs in remote areas, integrates the occurrence and profile data, summarizes their bioaccumulation, trophic transfer, and ecological risks, and finally points out the predominant pollution burden of OPEs among organic pollutants in remote areas. Given the relatively high contamination level and bioaccumulation/biomagnification behavior of OPEs, in combination with the sensitivity of endemic species in remote areas, more attention should be paid to the potential ecological risks of OPEs.

Chronic exposure to glyphosate in Florida manatee

Florida manatees depend on freshwater environments as a source of drinking water and as warm-water refuges. These freshwater environments are in direct contact with human activities where glyphosate-based herbicides are being used. Glyphosate is the most used herbicide worldwide and it is intensively used in Florida as a sugarcane ripener and to control invasive aquatic plants. The objective of the present study was to determine the concentration of glyphosate and its breakdown product, aminomethylphosphonic acid (AMPA), in Florida manatee plasma and assess their exposure to manatees seeking a warm-water refuge in Crystal River (west central Florida), and in South Florida. We analyzed glyphosate's and AMPA's concentrations in Florida manatee plasma (n = 105) collected during 2009-2019 using HPLC-MS/MS. We sampled eight Florida water bodies between 2019 and 2020, three times a year: before, during and after the sugarcane harvest using grab samples and molecular imprinted passive Polar Organic Chemical Integrative Samplers (MIP-POCIS). Glyphosate was present in 55.8% of the sampled Florida manatees' plasma. The concentration of glyphosate has significantly increased in Florida manatee samples from 2009 until 2019. Glyphosate and AMPA were ubiquitous in water bodies. The concentration of glyphosate and AMPA was higher in South Florida than in Crystal River, particularly before and during the sugarcane harvest when Florida manatees depend on warm water refuges. Based on our results, Florida manatees were chronically exposed to glyphosate and AMPA, during and beyond the glyphosate applications to sugarcane, possibly associated with multiple uses of glyphosate-based herbicides for other crops or to control aquatic weeds. This chronic exposure in Florida water bodies may have consequences for Florida manatees' immune and renal systems which may further be compounded by other environmental exposures such as red tide or cold stress.

A drastic shift in the energetic landscape of toothed whale sperm cells

Mammalian spermatozoa are a notable example of metabolic compartmentalization.¹ Energy in the form of ATP production, vital for motility, capacitation, and fertilization, is subcellularly separated in sperm cells. While glycolysis provides a local, rapid, and low-yielding input of ATP along the flagellum fibrous sheath, oxidative phosphorylation (OXPHOS), far more efficient over a longer time frame, is concentrated in the midpiece mitochondria.² The relative weight of glycolysis and OXPHOS pathways in sperm function is variable among species and sensitive to oxygen and substrate availability.^3-5 Besides partitioning energy production, sperm cell energetics display an additional singularity: the occurrence of sperm-specific gene duplicates and alternative spliced variants, with conserved function but structurally bound to the flagellar fibrous sheath.^6,7 The wider selective forces driving the compartmentalization and adaptability of this energy system in mammalian species remain largely unknown, much like the impact of ecosystem resource availability (e.g., carbohydrates, fatty acids, and proteins) and dietary adaptations in reproductive physiology traits.⁸ Here, we investigated the Cetacea, an iconic group of fully aquatic and carnivorous marine mammals, evolutionarily related to extant terrestrial herbivores.⁹ In this lineage, episodes of profound trait remodeling have been accompanied by clear genomic signatures.^10-14 We show that toothed whales exhibit impaired sperm glycolysis, due to gene and exon erosion, and demonstrate that dolphin spermatozoa motility depends on endogenous fatty acid β-oxidation, but not carbohydrates. Such unique energetic rewiring substantiates the observation of large mitochondria in toothed whale spermatozoa and emphasizes the radical physiological reorganization imposed by the transition to a carbohydrate-depleted marine environment.

Recapitulating Evolutionary Divergence in a Single Cis-Regulatory Element Is Sufficient to Cause Expression Changes of the Lens Gene Tdrd7

Mutations in cis-regulatory elements play important roles for phenotypic changes during evolution. Eye degeneration in the blind mole rat (BMR; Nannospalax galili) and other subterranean mammals is significantly associated with widespread divergence of eye regulatory elements, but the effect of these regulatory mutations on eye development and function has not been explored. Here, we investigate the effect of mutations observed in the BMR sequence of a conserved noncoding element upstream of Tdrd7, a pleiotropic gene required for lens development and spermatogenesis. We first show that this conserved element is a transcriptional repressor in lens cells and that the BMR sequence partially lost repressor activity. Next, we recapitulated evolutionary changes in this element by precisely replacing the endogenous regulatory element in a mouse line by the orthologous BMR sequence with CRISPR-Cas9. Strikingly, this repressor replacement caused a more than 2-fold upregulation of Tdrd7 in the developing lens; however, increased mRNA level does not result in a corresponding increase in TDRD7 protein nor an obvious lens phenotype, possibly explained by buffering at the posttranscriptional level. Our results are consistent with eye degeneration in subterranean mammals having a polygenic basis where many small-effect mutations in different eye-regulatory elements collectively contribute to phenotypic differences.

Genomic and anatomical comparisons of skin support independent adaptation to life in water by cetaceans and hippos

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.

Analysis of narwhal tusks reveals lifelong feeding ecology and mercury exposure

The ability of animals to respond to changes in their environment is critical to their persistence. In the Arctic, climate change and mercury exposure are two of the most important environmental threats for top predators.^1-3 Rapid warming is causing precipitous sea-ice loss, with consequences on the distribution, composition, and dietary ecology of species^4-7 and, thus, exposure to food-borne mercury.⁸ Current understanding of global change and pollution impacts on Arctic wildlife relies on single-time-point individual data representing a snapshot in time. These data often lack comprehensive temporal resolution and overlook the cumulative lifelong nature of stressors as well as individual variation. To overcome these challenges, we explore the unique capacity of narwhal tusks to characterize chronological lifetime biogeochemical profiles, allowing for investigations of climate-induced dietary changes and contaminant trends. Using temporal patterns of stable isotopes (δ¹³C and δ¹⁵N) and mercury concentrations in annually deposited dentine growth layer groups in 10 tusks from Northwest Greenland (1962-2010), we show surprising plasticity in narwhal feeding ecology likely resulting from climate-induced changes in sea-ice cover, biological communities, and narwhal migration. Dietary changes consequently impacted mercury exposure primarily through trophic magnification effects. Mercury increased log-linearly over the study period, albeit with an unexpected rise in recent years, likely caused by increased emissions and/or greater bioavailability in a warmer, ice-free Arctic. Our findings are consistent with an emerging pattern in the Arctic of reduced sea-ice leading to changes in the migration, habitat use, food web, and contaminant exposure in Arctic top predators.

Phylogenetic Permulations: A Statistically Rigorous Approach to Measure Confidence in Associations in a Phylogenetic Context

Many evolutionary comparative methods seek to identify associations between phenotypic traits or between traits and genotypes, often with the goal of inferring potential functional relationships between them. Comparative genomics methods aimed at this goal measure the association between evolutionary changes at the genetic level with traits evolving convergently across phylogenetic lineages. However, these methods have complex statistical behaviors that are influenced by nontrivial and oftentimes unknown confounding factors. Consequently, using standard statistical analyses in interpreting the outputs of these methods leads to potentially inaccurate conclusions. Here, we introduce phylogenetic permulations, a novel statistical strategy that combines phylogenetic simulations and permutations to calculate accurate, unbiased P values from phylogenetic methods. Permulations construct the null expectation for P values from a given phylogenetic method by empirically generating null phenotypes. Subsequently, empirical P values that capture the true statistical confidence given the correlation structure in the data are directly calculated based on the empirical null expectation. We examine the performance of permulation methods by analyzing both binary and continuous phenotypes, including marine, subterranean, and long-lived large-bodied mammal phenotypes. Our results reveal that permulations improve the statistical power of phylogenetic analyses and correctly calibrate statements of confidence in rejecting complex null distributions while maintaining or improving the enrichment of known functions related to the phenotype. We also find that permulations refine pathway enrichment analyses by correcting for nonindependence in gene ranks. Our results demonstrate that permulations are a powerful tool for improving statistical confidence in the conclusions of phylogenetic analysis when the parametric null is unknown.

Independent evolution toward larger body size in the distinctive Faroe Island mice

Most phenotypic traits in nature involve the collective action of many genes. Traits that evolve repeatedly are particularly useful for understanding how selection may act on changing trait values. In mice, large body size has evolved repeatedly on islands and under artificial selection in the laboratory. Identifying the loci and genes involved in this process may shed light on the evolution of complex, polygenic traits. Here, we have mapped the genetic basis of body size variation by making a genetic cross between mice from the Faroe Islands, which are among the largest and most distinctive natural populations of mice in the world, and a laboratory mouse strain selected for small body size, SM/J. Using this F2 intercross of 841 animals, we have identified 111 loci controlling various aspects of body size, weight and growth hormone levels. By comparing against other studies, including the use of a joint meta-analysis, we found that the loci involved in the evolution of large size in the Faroese mice were largely independent from those of a different island population or other laboratory strains. We hypothesize that colonization bottleneck, historical hybridization, or the redundancy between multiple loci have resulted in the Faroese mice achieving an outwardly similar phenotype through a distinct evolutionary path.

Effects of pyriproxyfen on zebrafish brain mitochondria and acetylcholinesterase

Pyriproxyfen is an insecticide used worldwide that acts as a biomimetic of juvenile hormone. This study investigated metabolic and synaptic impairments triggered by pyriproxyfen using zebrafish acetylcholinesterase (zbAChE) and mitochondria as markers. A brain zbAChE assay was performed in vitro and in vivo covering a range of pyriproxyfen concentrations (0.001-10 μmol/L) to assess inhibition kinetics. Docking simulations were performed to characterize inhibitory interactions. Zebrafish male adults were acutely exposed to 0.001, 0.01 and 0.1 μg/mL pyriproxyfen for 16 h. Mitochondrial respiration of brain tissues was assessed. ROS generation was estimated using H₂DCF-DA and MitoSOX. Calcium transport was monitored by Calcium Green™ 5 N. NO synthesis activity was estimated using DAF-FM-DA. Brain acetylcholinesterase showed an in vivo IC₂₀ of 0.30 μmol/L pyriproxyfen, and an IC₅₀ of 92.5 μmol/L. The inhibitory effect on zbAChE activity was competitive-like. Respiratory control of Complex I/II decreased significantly after insecticide exposure. The MitoSOX test showed that O₂^- generation had a pyriproxyfen dose-dependent effect. Brain tissue lost 50% of Ca²⁺ uptake capacity at 0.1 μg/mL pyriproxyfen. Ca²⁺ release showed a clear mitochondrial impairment at lower pyriproxyfen exposures. Thus, Ca²⁺ transport imbalance caused by pyriproxyfen may be a novel deleterious mechanism of action. Overall, the results showed that pyriproxyfen can compromise multiple and interconnected pathways: (1) zbAChE impairment and (2) the functioning of the electron transport chain, ROS generation and calcium homeostasis in zebrafish brain mitochondria. Considering the many similarities between zebrafish and human, more caution is needed when pyriproxyfen is used in both urban and agricultural pest control.

Environmental management of two of the world's most endangered marine and terrestrial predators: Vaquita and cheetah

Two of the world most endangered marine and terrestrial species are at the brink of extinction. The vaquita (Phocoena sinus) is the smallest existing cetacean and the population has declined to barely 22 individuals now remaining in Mexico's Gulf of California. With the ongoing decline, it is likely to go extinct within few years. The primary threat to this species has been mortality as a result of by-catch from gillnet fishing as well as environmental toxic chemicals and disturbance. This has called for the need to establish a National Park within the Gulf of California to expand essential habitat and provide the critical ecosystem protection for vaquita to thrive and multiply, given that proper conservation enforcement and management of the park are accomplished. In the terrestrial environment, the cheetah (Acinonyx jubatus) is reduced to a low number worldwide with the Iran subpopulation currently listed as Critically Endangered and the Indian subpopulation already extinct. There is a need for conservation efforts due to habitat loss, but also an indication of the conspicuous threat of illegal trade and trafficking from Africa and Arab countries in the Middle East. Funds have also been set up to provide refuges for the cheetah by working directly with farmers and landowners, which is a critical movement in adaptive management. These are the potential options for the preservation and possibly the expansion of the overall vaquita and cheetah populations.

Diet Shifts Explain Temporal Trends of Pollutant Levels in Indo-Pacific Humpback Dolphins (Sousa chinensis) from the Pearl River Estuary, China

We examined spatiotemporal trends of diet compositions and their relationship with pollutant accumulation levels in 46 weaning Indo-Pacific humpback dolphins (n = 46) from 2004 to 2017 in the Pearl River Estuary (PRE) based on blubber fatty acid signatures using quantitative fatty acid signature analysis in R (QFASAR). Fifty-one potential prey species were tested, among which 13 had a mean relative proportion greater than 1% in dolphin diets. Bombay duck was the predominant prey species, followed by Dussumier's thryssa and mullet, whereas other prey species were present at considerably reduced proportions in diets. The proportion of larger fishes (Bombay duck and mullet) in the diet has exhibited a significant decreasing trend in recent years, whereas the smaller fish (Dussumier's thryssa) steadily increased over the whole period, possibly due to the severe impacts of climate change and other human stressors on large fishes in estuarine waters. The proportions of Bombay duck in the diet were significantly and positively correlated with hepatic Cr levels in dolphins, whereas the temporal change in Bombay duck consumption mirrored that in the hepatic levels of several per- and polyfluoroalkyl substances, because Bombay duck was the most contaminated species among all the prey fishes.

A fully-automated method discovers loss of mouse-lethal and human-monogenic disease genes in 58 mammals

Gene losses provide an insightful route for studying the morphological and physiological adaptations of species, but their discovery is challenging. Existing genome annotation tools focus on annotating intact genes and do not attempt to distinguish nonfunctional genes from genes missing annotation due to sequencing and assembly artifacts. Previous attempts to annotate gene losses have required significant manual curation, which hampers their scalability for the ever-increasing deluge of newly sequenced genomes. Using extreme sequence erosion (amino acid deletions and substitutions) and sister species support as an unambiguous signature of loss, we developed an automated approach for detecting high-confidence gene loss events across a species tree. Our approach relies solely on gene annotation in a single reference genome, raw assemblies for the remaining species to analyze, and the associated phylogenetic tree for all organisms involved. Using human as reference, we discovered over 400 unique human ortholog erosion events across 58 mammals. This includes dozens of clade-specific losses of genes that result in early mouse lethality or are associated with severe human congenital diseases. Our discoveries yield intriguing potential for translational medical genetics and evolutionary biology, and our approach is readily applicable to large-scale genome sequencing efforts across the tree of life.

Functional Studies with Primary Cells Provide a System for Genome-to-Phenome Investigations in Marine Mammals

Marine mammals exhibit some of the most dramatic physiological adaptations in their clade and offer unparalleled insights into the mechanisms driving convergent evolution on relatively short time scales. Some of these adaptations, such as extreme tolerance to hypoxia and prolonged food deprivation, are uncommon among most terrestrial mammals and challenge established metabolic principles of supply and demand balance. Non-targeted omics studies are starting to uncover the genetic foundations of such adaptations, but tools for testing functional significance in these animals are currently lacking. Cellular modeling with primary cells represents a powerful approach for elucidating the molecular etiology of physiological adaptation, a critical step in accelerating genome-to-phenome studies in organisms in which transgenesis is impossible (e.g., large-bodied, long-lived, fully aquatic, federally protected species). Gene perturbation studies in primary cells can directly evaluate whether specific mutations, gene loss, or duplication confer functional advantages such as hypoxia or stress tolerance in marine mammals. Here, we summarize how genetic and pharmacological manipulation approaches in primary cells have advanced mechanistic investigations in other non-traditional mammalian species, and highlight the need for such investigations in marine mammals. We also provide key considerations for isolating, culturing, and conducting experiments with marine mammal cells under conditions that mimic in vivo states. We propose that primary cell culture is a critical tool for conducting functional mechanistic studies (e.g., gene knockdown, over-expression, or editing) that can provide the missing link between genome- and organismal-level understanding of physiological adaptations in marine mammals.

Molecular adaptation and convergent evolution of frugivory in Old World and neotropical fruit bats

Although cases of independent adaptation to the same dietary niche have been documented in mammalian ecology, the molecular correlates of such shifts are seldom known. Here, we used genomewide analyses of molecular evolution to examine two lineages of bats that, from an insectivorous ancestor, have both independently evolved obligate frugivory: the Old World family Pteropodidae and the neotropical subfamily Stenodermatinae. New genome assemblies from two neotropical fruit bats (Artibeus jamaicensis and Sturnira hondurensis) provide a framework for comparisons with Old World fruit bats. Comparative genomics of 10 bat species encompassing dietary diversity across the phylogeny revealed convergent molecular signatures of frugivory in both multigene family evolution and single-copy genes. Evidence for convergent molecular adaptations associated with frugivorous diets includes the composition of three subfamilies of olfactory receptor genes, losses of three bitter taste receptor genes, losses of two digestive enzyme genes and convergent amino acid substitutions in several metabolic genes. By identifying suites of adaptations associated with the convergent evolution of frugivory, our analyses both reveal the extent of molecular mechanisms under selection in dietary shifts and will facilitate future studies of molecular ecology in mammals.

PseudoChecker: an integrated online platform for gene inactivation inference

The rapid expansion of high-quality genome assemblies, exemplified by ongoing initiatives such as the Genome-10K and i5k, demands novel automated methods to approach comparative genomics. Of these, the study of inactivating mutations in the coding region of genes, or pseudogenization, as a source of evolutionary novelty is mostly overlooked. Thus, to address such evolutionary/genomic events, a systematic, accurate and computationally automated approach is required. Here, we present PseudoChecker, the first integrated online platform for gene inactivation inference. Unlike the few existing methods, our comparative genomics-based approach displays full automation, a built-in graphical user interface and a novel index, PseudoIndex, for an empirical evaluation of the gene coding status. As a multi-platform online service, PseudoChecker simplifies access and usability, allowing a fast identification of disruptive mutations. An analysis of 30 genes previously reported to be eroded in mammals, and 30 viable genes from the same lineages, demonstrated that PseudoChecker was able to correctly infer 97% of loss events and 95% of functional genes, confirming its reliability. PseudoChecker is freely available, without login required, at http://pseudochecker.ciimar.up.pt.

RERconverge: an R package for associating evolutionary rates with convergent traits

MOTIVATION

When different lineages of organisms independently adapt to similar environments, selection often acts repeatedly upon the same genes, leading to signatures of convergent evolutionary rate shifts at these genes. With the increasing availability of genome sequences for organisms displaying a variety of convergent traits, the ability to identify genes with such convergent rate signatures would enable new insights into the molecular basis of these traits.

RESULTS

Here we present the R package RERconverge, which tests for association between relative evolutionary rates of genes and the evolution of traits across a phylogeny. RERconverge can perform associations with binary and continuous traits, and it contains tools for visualization and enrichment analyses of association results.

AVAILABILITY AND IMPLEMENTATION

RERconverge source code, documentation and a detailed usage walk-through are freely available at https://github.com/nclark-lab/RERconverge. Datasets for mammals, Drosophila and yeast are available at https://bit.ly/2J2QBnj.

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

MCM8IP activates the MCM8-9 helicase to promote DNA synthesis and homologous recombination upon DNA damage

Homologous recombination (HR) mediates the error-free repair of DNA double-strand breaks to maintain genomic stability. Here we characterize C17orf53/MCM8IP, an OB-fold containing protein that binds ssDNA, as a DNA repair factor involved in HR. MCM8IP-deficient cells exhibit HR defects, especially in long-tract gene conversion, occurring downstream of RAD51 loading, consistent with a role for MCM8IP in HR-dependent DNA synthesis. Moreover, loss of MCM8IP confers cellular sensitivity to crosslinking agents and PARP inhibition. Importantly, we report that MCM8IP directly associates with MCM8-9, a helicase complex mutated in primary ovarian insufficiency, and RPA1. We additionally show that the interactions of MCM8IP with MCM8-9 and RPA facilitate HR and promote replication fork progression and cellular viability in response to treatment with crosslinking agents. Mechanistically, MCM8IP stimulates the helicase activity of MCM8-9. Collectively, our work identifies MCM8IP as a key regulator of MCM8-9-dependent DNA synthesis during DNA recombination and replication.

Diving deep: understanding the genetic components of hypoxia tolerance in marine mammals

Marine mammals have highly specialized physiology, exhibited in many species by extreme breath-holding capabilities that allow deep dives and extended submergence. Cardiovascular control and cell-level hypoxia tolerance are key features of this phenotype. Identifying genomic signatures tied to physiology will be valuable in understanding these natural model species, which may generate translational opportunities to human diseases arising from hypoxic stress or tissue injury. Genomic analyses have now been conducted in dolphins, river dolphins, minke whales, bowhead whales, and polar bears, with multispecies studies exploring evolutionary signals across marine mammal lineages, encompassing extinct and extant divers. Single-species genome studies for sirenians do not yet exist. Extant marine mammals arose in three lineages from separate aquatic recolonizations. Their physiological specializations, along with these independent origins create an interesting case to examine convergent evolution. Although molecular mechanisms of hypoxia tolerance are not universally apparent across marine mammal genomic studies, altered evolutionary rates have been identified for genes linked to oxygen binding and transport (e.g., MB, HBA, and HBB), blood pressure control (e.g., endothelin pathway genes), and cell protection in multiple species. Despite convergent phenotypes across clades, instances of identical molecular convergence have been uncommon. Given the inherent logistical and regulatory difficulties associated with functional genetic experiments in marine mammals, several avenues of further investigation are suggested to enable validation of candidate genes for hypoxia tolerance: leveraging phylogeny to better understand convergent phenotypes; ontogenic studies to identify regulation of key genes underlying the elite, adult, hypoxia-tolerant physiology; and cell culture manipulations to understand gene function.

Paraoxonase 3 functions as a chaperone to decrease functional expression of the epithelial sodium channel

The paraoxonase (PON) family comprises three highly conserved members: PON1, PON2, and PON3. They are orthologs of Caenorhabditis elegans MEC-6, an endoplasmic reticulum-resident chaperone that has a critical role in proper assembly and surface expression of the touch-sensing degenerin channel in nematodes. We have shown recently that MEC-6 and PON2 negatively regulate functional expression of the epithelial Na⁺ channel (ENaC), suggesting that the chaperone function is conserved within this family. We hypothesized that other PON family members also modulate ion channel expression. Pon3 is specifically expressed in the aldosterone-sensitive distal tubules in the mouse kidney. We found here that knocking down endogenous Pon3 in mouse cortical collecting duct cells enhanced Na⁺ transport, which was associated with increased γENaC abundance. We further examined Pon3 regulation of ENaC in two heterologous expression systems, Fisher rat thyroid cells and Xenopus oocytes. Pon3 coimmunoprecipitated with each of the three ENaC subunits in Fisher rat thyroid cells. As a result of this interaction, the whole-cell and surface abundance of ENaC α and γ subunits was reduced by Pon3. When expressed in oocytes, Pon3 inhibited ENaC-mediated amiloride-sensitive Na⁺ currents, in part by reducing the surface expression of ENaC. In contrast, Pon3 did not alter the response of ENaC to chymotrypsin-mediated proteolytic activation or [2-(trimethylammonium)ethyl]methanethiosulfonate-induced activation of αβ_S518Cγ, suggesting that Pon3 does not affect channel open probability. Together, our results suggest that PON3 regulates ENaC expression by inhibiting its biogenesis and/or trafficking.

Pan-mammalian analysis of molecular constraints underlying extended lifespan

Although lifespan in mammals varies over 100-fold, the precise evolutionary mechanisms underlying variation in longevity remain unknown. Species-specific genetic changes have been observed in long-lived species including the naked mole-rat, bats, and the bowhead whale, but these adaptations do not generalize to other mammals. We present a novel method to identify associations between rates of protein evolution and continuous phenotypes across the entire mammalian phylogeny. Unlike previous analyses that focused on individual species, we treat absolute and relative longevity as quantitative traits and demonstrate that these lifespan traits affect the evolutionary constraint on hundreds of genes. Specifically, we find that genes related to cell cycle, DNA repair, cell death, the IGF1 pathway, and immunity are under increased evolutionary constraint in large and long-lived mammals. For mammals exceptionally long-lived for their body size, we find increased constraint in inflammation, DNA repair, and NFKB-related pathways. Strikingly, these pathways have considerable overlap with those that have been previously reported to have potentially adaptive changes in single-species studies, and thus would be expected to show decreased constraint in our analysis. This unexpected finding of increased constraint in many longevity-associated pathways underscores the power of our quantitative approach to detect patterns that generalize across the mammalian phylogeny.

Robust Method for Detecting Convergent Shifts in Evolutionary Rates

Identifying genomic elements underlying phenotypic adaptations is an important problem in evolutionary biology. Comparative analyses learning from convergent evolution of traits are gaining momentum in accurately detecting such elements. We previously developed a method for predicting phenotypic associations of genetic elements by contrasting patterns of sequence evolution in species showing a phenotype with those that do not. Using this method, we successfully demonstrated convergent evolutionary rate shifts in genetic elements associated with two phenotypic adaptations, namely the independent subterranean and marine transitions of terrestrial mammalian lineages. Our original method calculates gene-specific rates of evolution on branches of phylogenetic trees using linear regression. These rates represent the extent of sequence divergence on a branch after removing the expected divergence on the branch due to background factors. The rates calculated using this regression analysis exhibit an important statistical limitation, namely heteroscedasticity. We observe that the rates on branches that are longer on average show higher variance, and describe how this problem adversely affects the confidence with which we can make inferences about rate shifts. Using a combination of data transformation and weighted regression, we have developed an updated method that corrects this heteroscedasticity in the rates. We additionally illustrate the improved performance offered by the updated method at robust detection of convergent rate shifts in phylogenetic trees of protein-coding genes across mammals, as well as using simulated tree data sets. Overall, we present an important extension to our evolutionary-rates-based method that performs more robustly and consistently at detecting convergent shifts in evolutionary rates.

Are vitamins A and E associated with persistent organic pollutants and fatty acids in the blubber of highly contaminated killer whales (Orcinus orca) from Greenland?

We quantified blubber concentrations of vitamins A (retinol) and E (α-tocopherol) and evaluated associations with persistent organic pollutants (ΣPOPs) in 14 highly-contaminated killer whales (Orcinus orca) sampled in Greenland from 2012 to 2014. We considered the influence of blubber depth, sex/age class and diet (based on biomass % of major fatty acids) in these relationships. Blubber concentrations of vitamin A averaged 34.1 ± 4.7 μg g^-1 wet weight (ww) and vitamin E averaged 35.6 ± 4.4 μg g^-1 ww. Although overall vitamin A concentrations did not vary between inner (closer to the muscle) and outer (closer to the skin) blubber layer or between sub-adults and adult females, concentrations in the outer layer of sub-adults were lower compared to the outer layer of adult females (p = 0.03). Outer layer may therefore reflect age accumulation of vitamin A, while in the more active inner layer, age effects might be masked by metabolic needs such as lactation. Neither diet nor ΣPOPs affected vitamin A variation, suggesting this vitamin is highly regulated in the body. Given the high exposures in these killer whales, vitamin A might not be a sensitive biomarker for POPs adverse effects. Vitamin E concentrations were significantly higher in inner compared to outer layer (p < 0.001), likely associated with blubber composition, suggesting that biopsies may not fully represent vitamin E concentrations in blubber. Age-accumulation of vitamin E also occurred with higher concentrations in adult females compared to sub-adults, independent of blubber depth (p < 0.01). Diet, ΣPOPs, and an interaction between these two variables significantly affected vitamin E variation in inner blubber, explaining 91% of this variation. The negative relationship between ΣPOPs (especially Σdichlorodiphenyltrichloroethane (DDT) and Σchlordanes in outer layers) and vitamin E was observed only in killer whales with a diet poorer in polyunsaturated fatty acids, suggested that killer whales feeding more consistently on marine mammals in Arctic environments over a fish-based diet, may be at higher risk of POP-induced disruption in vitamin E homeostasis. Considering diet is therefore important to understand the potential effects of elevated contaminant exposures on levels of certain essential nutrients, i.e., vitamin E, in killer whales.

Natural Tolerance to Ischemia and Hypoxemia in Diving Mammals: A Review

Reperfusion injury follows ischemia/reperfusion events occurring during myocardial infarction, stroke, embolism, and other peripheral vascular diseases. Decreased blood flow and reduced oxygen tension during ischemic episodes activate cellular pathways that upregulate pro-inflammatory signaling and promote oxidant generation. Reperfusion after ischemia recruits inflammatory cells to the vascular wall, further exacerbating oxidant production and ultimately resulting in cell death, tissue injury, and organ dysfunction. Diving mammals tolerate repetitive episodes of peripheral ischemia/reperfusion as part of the cardiovascular adjustments supporting long duration dives. These adjustments allow marine mammals to optimize the use of their body oxygen stores while diving but can result in selectively reduced perfusion to peripheral tissues. Remarkably, diving mammals show no apparent detrimental effects associated with these ischemia/reperfusion events. Here, we review the current knowledge regarding the strategies marine mammals use to suppress inflammation and cope with oxidant generation potentially derived from diving-induced ischemia/reperfusion.

Adaptive substitutions underlying cardiac glycoside insensitivity in insects exhibit epistasis in vivo

Predicting how species will respond to selection pressures requires understanding the factors that constrain their evolution. We use genome engineering of Drosophila to investigate constraints on the repeated evolution of unrelated herbivorous insects to toxic cardiac glycosides, which primarily occurs via a small subset of possible functionally-relevant substitutions to Na⁺,K⁺-ATPase. Surprisingly, we find that frequently observed adaptive substitutions at two sites, 111 and 122, are lethal when homozygous and adult heterozygotes exhibit dominant neural dysfunction. We identify a phylogenetically correlated substitution, A119S, that partially ameliorates the deleterious effects of substitutions at 111 and 122. Despite contributing little to cardiac glycoside-insensitivity in vitro, A119S, like substitutions at 111 and 122, substantially increases adult survivorship upon cardiac glycoside exposure. Our results demonstrate the importance of epistasis in constraining adaptive paths. Moreover, by revealing distinct effects of substitutions in vitro and in vivo, our results underscore the importance of evaluating the fitness of adaptive substitutions and their interactions in whole organisms.

Contraction of the ROS Scavenging Enzyme Glutathione S-Transferase Gene Family in Cetaceans

Cetaceans are a group of marine mammals whose ancestors were adaptated for life on land. Life in an aquatic environment poses many challenges for air-breathing mammals. Diving marine mammals have adapted to rapid reoxygenation and reactive oxygen species (ROS)-mediated reperfusion injury. Here, we considered the evolution of the glutathione transferase (GST) gene family which has important roles in the detoxification of endogenously-derived ROS and environmental pollutants. We characterized the cytosolic GST gene family in 21 mammalian species; cetaceans, sirenians, pinnipeds, and their terrestrial relatives. All seven GST classes were identified, showing that GSTs are ubiquitous in mammals. Some GST genes are the product of lineage-specific duplications and losses, in line with a birth-and-death evolutionary model. We detected sites with signatures of positive selection that possibly influence GST structure and function, suggesting that adaptive evolution of GST genes is important for defending mammals from various types of noxious environmental compounds. We also found evidence for loss of alpha and mu GST subclass genes in cetacean lineages. Notably, cetaceans have retained a homolog of at least one of the genes GSTA1, GSTA4, and GSTM1; GSTs that are present in both the cytosol and mitochondria. The observed variation in number and selection pressure on GST genes suggest that the gene family structure is dynamic within cetaceans.

The Genome of the Steller Sea Lion (Eumetopias jubatus)

The Steller sea lion is the largest member of the Otariidae family and is found in the coastal waters of the northern Pacific Rim. Here, we present the Steller sea lion genome, determined through DNA sequencing approaches that utilized microfluidic partitioning library construction, as well as nanopore technologies. These methods constructed a highly contiguous assembly with a scaffold N50 length of over 14 megabases, a contig N50 length of over 242 kilobases and a total length of 2.404 gigabases. As a measure of completeness, 95.1% of 4104 highly conserved mammalian genes were found to be complete within the assembly. Further annotation identified 19,668 protein coding genes. The assembled genome sequence and underlying sequence data can be found at the National Center for Biotechnology Information (NCBI) under the BioProject accession number PRJNA475770.

Acute Phase Proteins in Marine Mammals: State of Art, Perspectives and Challenges

The term “acute phase response” (APR) is referred to a nonspecific and complex reaction of an organism that occurs shortly after any tissue damage, such as infection, trauma, neoplasia, inflammation, and stress. The APR can be identified and monitored with some laboratory tests, such as the concentration of several plasma proteins, the acute phase proteins (APPs). The APPs are components of the non-specific innate immune response, and their plasma concentration is proportional to the severity and/or the extent of tissue damage. The evaluation of health status of marine mammals is difficult because the classical clinical signs of illness used for human and domestic animals are difficult to recognize and understand. For this reason, in the past years, several efforts were done to identify laboratory markers of disease in these animals. The APPs have demonstrated their role as early markers of inflammation in veterinary medicine, thus several APPs were tested in marine mammals, such as C-reactive protein (CRP), serum amyloid-A (SAA), and Haptoglobin (Hp). However, the difficulty to extrapolate the knowledge about APPs in one species to another, the lack of specie-specific reagents, the absence of data about negative APPs have hampered their extent use in marine mammals. Herein, the state of art of APPs in marine mammals is reviewed, with particular attention to pre-analytical and analytical factors that should be taken into account in validation and interpretation of APPs assays. Moreover, the current application, potential utility and the future developments of APPs in marine mammals is highlighted and discussed.

Convergent regulatory evolution and loss of flight in paleognathous birds

A core question in evolutionary biology is whether convergent phenotypic evolution is driven by convergent molecular changes in proteins or regulatory regions. We combined phylogenomic, developmental, and epigenomic analysis of 11 new genomes of paleognathous birds, including an extinct moa, to show that convergent evolution of regulatory regions, more so than protein-coding genes, is prevalent among developmental pathways associated with independent losses of flight. A Bayesian analysis of 284,001 conserved noncoding elements, 60,665 of which are corroborated as enhancers by open chromatin states during development, identified 2355 independent accelerations along lineages of flightless paleognaths, with functional consequences for driving gene expression in the developing forelimb. Our results suggest that the genomic landscape associated with morphological convergence in ratites has a substantial shared regulatory component.