Oxygen binding functions of blood and hemoglobin from the Chinese pangolin, Manis pentadactyla: possible implications of burrowing and low body temperature

Temminck pangolins relax the precision of body temperature regulation when resources are scarce in a semi-arid environment

Climate change is impacting mammals both directly (for example, through increased heat) and indirectly (for example, through altered food resources). Understanding the physiological and behavioural responses of mammals in already hot and dry environments to fluctuations in the climate and food availability allows for a better understanding of how they will cope with a rapidly changing climate. We measured the body temperature of seven Temminck's pangolins (Smutsia temminckii) in the semi-arid Kalahari for periods of between 4 months and 2 years. Pangolins regulated body temperature within a narrow range (34-36°C) over the 24-h cycle when food (and hence water, obtained from their prey) was abundant. When food resources were scarce, body temperature was regulated less precisely, 24-h minimum body temperatures were lower and the pangolins became more diurnally active, particularly during winter when prey was least available. The shift toward diurnal activity exposed pangolins to higher environmental heat loads, resulting in higher 24-h maximum body temperatures. Biologging of body temperature to detect heterothermy, or estimating food abundance (using pitfall trapping to monitor ant and termite availability), therefore provide tools to assess the welfare of this elusive but threatened mammal. Although the physiological and behavioural responses of pangolins buffered them against food scarcity during our study, whether this flexibility will be sufficient to allow them to cope with further reductions in food availability likely with climate change is unknown.

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.

Functional or Vestigial? The Genomics of the Pineal Gland in Xenarthra

Vestigial organs are historical echoes of past phenotypes. Determining whether a specific organ constitutes a functional or vestigial structure can be a challenging task, given that distinct levels of atrophy may arise between and within lineages. The mammalian pineal gland, an endocrine organ involved in melatonin biorhythmicity, represents a classic example, often yielding contradicting anatomical observations. In Xenarthra (sloths, anteaters, and armadillos), a peculiar mammalian order, the presence of a distinct pineal organ was clearly observed in some species (i.e., Linnaeus's two-toed sloth), but undetected in other closely related species (i.e., brown-throated sloth). In the nine-banded armadillo, contradicting evidence supports either functional or vestigial scenarios. Thus, to untangle the physiological status of the pineal gland in Xenarthra, we used a genomic approach to investigate the evolution of the gene hub responsible for melatonin synthesis and signaling. We show that both synthesis and signaling compartments are eroded and were probably lost independently among Xenarthra orders. Additionally, by expanding our analysis to 157 mammal genomes, we offer a comprehensive view showing that species with very distinctive habitats and lifestyles have convergently evolved a similar phenotype: Cetacea, Pholidota, Dermoptera, Sirenia, and Xenarthra. Our findings suggest that the recurrent inactivation of melatonin genes correlates with pineal atrophy and endorses the use of genomic analyses to ascertain the physiological status of suspected vestigial structures.

Emergence of a Chimeric Globin Pseudogene and Increased Hemoglobin Oxygen Affinity Underlie the Evolution of Aquatic Specializations in Sirenia

As limits on O₂ availability during submergence impose severe constraints on aerobic respiration, the oxygen binding globin proteins of marine mammals are expected to have evolved under strong evolutionary pressures during their land-to-sea transition. Here, we address this question for the order Sirenia by retrieving, annotating, and performing detailed selection analyses on the globin repertoire of the extinct Steller’s sea cow (Hydrodamalis gigas), dugong (Dugong dugon), and Florida manatee (Trichechus manatus latirostris) in relation to their closest living terrestrial relatives (elephants and hyraxes). These analyses indicate most loci experienced elevated nucleotide substitution rates during their transition to a fully aquatic lifestyle. While most of these genes evolved under neutrality or strong purifying selection, the rate of nonsynonymous/synonymous replacements increased in two genes (Hbz-T1 and Hba-T1) that encode the α-type chains of hemoglobin (Hb) during each stage of life. Notably, the relaxed evolution of Hba-T1 is temporally coupled with the emergence of a chimeric pseudogene (Hba-T2/Hbq-ps) that contributed to the tandemly linked Hba-T1 of stem sirenians via interparalog gene conversion. Functional tests on recombinant Hb proteins from extant and ancestral sirenians further revealed that the molecular remodeling of Hba-T1 coincided with increased Hb–O₂ affinity in early sirenians. Available evidence suggests that this trait evolved to maximize O₂ extraction from finite lung stores and suppress tissue O₂ offloading, thereby facilitating the low metabolic intensities of extant sirenians. In contrast, the derived reduction in Hb–O₂ affinity in (sub)Arctic Steller’s sea cows is consistent with fueling increased thermogenesis by these once colossal marine herbivores.

Establishing the pangolin mitochondrial D-loop sequences from the confiscated scales

Pangolin scales are encountered in traditional East Asian medicines (TEAM) and the ever increasing demand for these scales has escalated the decline in the numbers of these mammals. The identification of protected pangolin species is necessary to enforce international and national legislation as well as assist with conservation measures. There is limited morphological feature on a pangolin scale thus requiring DNA analysis as a means of identification. We report on the isolation of DNA from pangolin scales and a strategy for obtaining the full length of the mitochondrial D-loop, being 1159 bp. Primer sets creating five overlapping amplicons were designed to amplify sections of this mitochondrial DNA locus. DNA from the blood stain of nineteen Formosan pangolins (Manis pentadactyla pentadactyla) along with 145 scale samples that were suspected to have come from pangolins, was amplified and sequenced; leading to a total of 91 D-loop sequences being obtained. The 19 Formosan pangolin sequences produced 5 haplotypes and 72 of the 145 seized scales provided useable sequence classified as a further 38 haplotypes. The D-loop sequences from those scales suspected to be from a pangolin had a higher similarity to any of the 19 samples taken from M. p. pentadactyla compared to a D-loop sequence from Manis tetradactyla (the only pangolin D-loop sequence in GenBank, NC_004027). These 43 haplotypes were used to establish a local database for the D-loop sequence of pangolins and add to the data of Manis sp. held on GenBank. The PCR amplification strategy development in this study could be used in forensic DNA identification of scales suspected to be from protected pangolin species.

Hemoglobin–oxygen-affinity and acid-base properties of blood from the fossorial mole-rat, Cryptomys hottentotus pretoriae

Oxygen affinity and other hematological parameters in strictly subterranean mole-rats, Cryptomys hottentotus (subspecies pretoriae) were measured immediately upon capture and after 14-21 days in captivity. The pH, hematocrit, hemoglobin (Hb) concentration, blood oxygen content, 2,3 bisphosphoglycerate (2,3 BPG) concentration and oxygen dissociation curves (ODC), as well as tonometric measurements, were determined using whole blood. Additionally ODCs were also determined for stripped hemolysates of individual animals. Compared to other mammals, blood of freshly caught animals had low pH (7.32+/-0.22), elevated hematocrits (48.4+/-3.8 %) and significantly lower P50 values for whole blood (21.1+/-1.6 mm Hg at pH 7.4) than those reported for other similar-sized fossorial and terrestrial mammals. Blood carbon dioxide content (22.4+/-3.9 mMol L(-1)), hemoglobin concentration (1.9+/-0.15 mMol L(-1)), oxygen content (164.8+/-26 mL L(-1)), bicarbonate concentrations (22.5+/-3.5 mMol L(-1)) were within the range of values reported for similar-sized mammals. We conclude that high blood-oxygen affinity, low body temperature and possibly also high hematocrit enable C. h. pretoriae to maintain an adequate oxygen supply to the tissues in a potentially hypoxic burrow atmospheres, but that the blood of this species shows no exceptional CO2 sensitivity or buffering capacity.

Haemoglobin function in vertebrates: evolutionary changes in cellular regulation in hypoxia

The evolution of erythrocytic hypoxia responses is reviewed by comparing the cellular control of haemoglobin-oxygen affinity in agnathans, teleost fish and terrestrial vertebrates. The most ancient response to hypoxic conditions appears to be an increase in cell volume, which increases the haemoglobin-oxygen affinity in lampreys. In teleost fish, an increase of cell volume in hypoxic conditions is also evident. The volume increase is coupled to an increase in erythrocyte pH. These changes are caused by an adrenergic activation of sodium/proton exchange across the erythrocyte membrane. The mechanism is important in acute hypoxia and is followed by a decrease in cellular adenosine triphosphate (ATP) and guanosine triphosphate (GTP) concentrations in continued hypoxia. In hypoxic bird embryos, the ATP levels are also reduced. The mechanisms by which hypoxia decreases cellular ATP and GTP concentrations remains unknown, although at least in bird embryos cAMP-dependent mechanisms have been implicated. In mammals, hypoxia responses appear to occur mainly via modulation of cellular organic phosphate concentrations. In moderate hypoxia, 2,3-diphosphoglycerate levels are increased as a result of alkalosis caused by increased ventilation.

Embryonic pig hemoglobins Gower I (zeta 2 epsilon 2), Gower II (alpha 2 epsilon 2), Heide I (zeta 2 theta 2) and Heide II (alpha 2 theta 2): oxygen-binding functions related to structure and embryonic oxygen supply

The common pig lacks a fetal hemoglobin but has four embryonic hemoglobins: Gower I (zeta 2 epsilon 2), Gower II (alpha 2 epsilon 2), Heide I (zeta 2 theta 2) and Heide II (alpha 2 theta 2) as well as adult Hb A (alpha 2 beta 2) and the amino acid sequence for each of the five constituent polypeptide chains has been established. The oxygenation characteristics of the five components, measured in relation to pH, temperature and the erythrocytic ligand 2,3-diphosphoglycerate (DPG), together with the changes in their relative concentrations during early embryonic life, are given. The findings indicate a progressive decrease in maternal-fetal oxygen affinity difference and thus in oxygen transfer efficacy at a given diffusion gradient that correlates with the development of the gas exchange structures. The functional properties of the individual hemoglobins are additionally discussed in relation to molecular structure.