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The "horse series" icon of evolution was one of the most commonly cited "proofs" of evolution for over 150 years (Janis, 2008, p. 251). Due to new research and newer discoveries, the popular horse series diagram used in many science textbooks to document straight-line (orthogenetic) horse evolution is now widely acknowledged as inaccurate. It is now recognized that the fossil record documents only that an enormous amount of morphological variety exists in horses, not their gradual evolution from a common ancestor (see Figure 1). Although gradual Darwinian evolution has been rejected, horse evolution has been revised in an attempt to document a scenario more similar to Gould's Punctuated Equilibrium theory and/or Mayr's saltation theory. [ABSTRACT FROM AUTHOR]

Transcriptional enhancers orchestrate cell type- and time point-specific gene expression programs. Genetic variation within enhancer sequences is an important contributor to phenotypic variation including evolutionary adaptations and human disease. Certain genes and pathways may be more prone to regulatory evolution than others, with different patterns across diverse organisms, but whether such patterns exist has not been investigated at a sufficient scale. To address this question, we identified signatures of accelerated sequence evolution in conserved enhancer elements throughout the mammalian phylogeny at an unprecedented scale. While different genes and pathways were enriched for regulatory evolution in different parts of the tree, we found a striking overall pattern of pleiotropic genes involved in gene regulatory and developmental processes being enriched for accelerated enhancer evolution. These genes were connected to more enhancers than other genes, which was the basis for having an increased amount of sequence acceleration over all their enhancers combined. We provide evidence that sequence acceleration is associated with turnover of regulatory function. Detailed study of one acceleration event in an enhancer of HES1 revealed that sequence evolution led to a new activity domain in the developing limb that emerged concurrently with the evolution of digit reduction in hoofed mammals. Our results provide evidence that enhancer evolution has been a frequent contributor to regulatory innovation at conserved developmental signaling genes in mammals. [ABSTRACT FROM AUTHOR]

ABSTRACT Aim Location Time Period Major Taxa Studied Methods Results Main Conclusions To describe worldwide distribution of mammalian cradles and museums using the rates of phylogenetic lineage turnover as a surrogate. Additionally, we investigated the influences of current water–energy dynamics, climate instability, past climate changes and elevational ranges on the distribution of these evolutionary zones.Global.Current.Terrestrial mammals.We developed a new methodology that consists of calculating the spatial phylogenetic turnover for non‐overlapping temporal segments of phylogenetic trees. By calculating the relative turnover in each tree segment, we quantified the rate of accumulation of phylogenetic turnover through time. We depicted cold and hotspots of rates of lineage turnover using bivariate maps and examined the effects of environmental factors using a path model.The distributions of cradles and museums of biodiversity are primarily driven by water–energy dynamics. Environments with higher water availability than energetic demand predominantly act as cradles, as seen in tropical rainforests, while xeric‐like environments predominantly serve as museums. Conversely, regions undergoing higher historical climate changes become cradles, such as in higher northern latitudes, while climatically stable areas function as museums. Mountains play a dual role, acting as both cradles and museums by generating new lineages along their elevation bands while simultaneously providing climate refuges for ancient mammal lineages.Our findings demonstrate that cradles and museums are not merely a dichotomy but exist along an evolutionary continuum. Furthermore, they reveal how spatial patterns of mammalian cradles and museums are intricately shaped by biogeographical processes governed by environmental forces. Uncovering these hidden effects provides insights into the ecological mechanisms by which ongoing climate changes continually shape evolutionary assemblages over time. [ABSTRACT FROM AUTHOR]

Chromosome number is a fundamental genomic trait that is often the first recorded characteristic of a genome. Across large clades, a common pattern emerges: many or even most lineages exhibit relative stasis, while a handful of lineages or species exhibit striking variation. Despite recent developments in comparative methods, most of this heterogeneity is still poorly understood. It is essential to understand why some lineages have rapid rates of chromosome number evolution, as it can impact a variety of other traits. Previous research suggests that biased female meiotic drive may shape rates of karyotype evolution in some mammals. However, Carnivora exhibits variation that this female meiotic drive model cannot explain. We hypothesize that variation in effective population size may underlie rate variation in Carnivora. To test this hypothesis, we estimated rates of fusions and fissions while accounting for range size, which we use as a proxy for effective population size. We reason fusions and fissions are deleterious or underdominant and that only in lineages with small range sizes will these changes be able to fix due to genetic drift. In this study, we find that the rates of fusions and fissions are elevated in taxa with small range sizes relative to those with large range sizes. Based on these findings, we conclude that 1) naturally occurring structural mutations that change chromosome number are underdominant or mildly deleterious, and 2) when population sizes are small, structural rearrangements may play an important role in speciation and reduction in gene flow among populations. [ABSTRACT FROM AUTHOR]

Different aspects of foraging strategies in bats have been studied to understand the evolution of flight in mammals. General descriptors of wing morphology associated with flight performance, such as aspect ratio and wing loading, allowed us to describe ecomorphs determined by the dietary preferences of bat species. However, the role of wing shape divergence in the evolution of bat foraging strategies remains little explored. We adopted a two-dimensional geometric morphometric approach to quantify the wing shape and size variation explained by phylogenetic relatedness (families) and to evaluate the covariance between foraging guilds and flight descriptors based on phylogenetic comparative methods in 69 Neotropical bat species. We tested whether wing morphology represents a reliable marker of the foraging guild, and we explored the rate of shape evolution among foraging guilds to describe divergent trends that could explain the morphological and ecological diversification. Our results suggest that the earliest bat ancestor was an aerial forager occupying the edge space, which is congruent with the observed evolution of wing shape from an edge space wing morphology. The relationship between wing shape and foraging space defines wing ecomorphs, which probably evolved early in bat ancestors; a process other than convergence could explain this association. [ABSTRACT FROM AUTHOR]

In mammals, sexual size dimorphism often reflects the intensity of sexual selection, yet its connection to genomic evolution remains unexplored. Gene family size evolution can reflect shifts in the relative importance of different molecular functions. Here, we investigate the associate between brain development gene repertoire to sexual size dimorphism using 124 mammalian species. We reveal significant changes in gene family size associations with sexual size dimorphism. High levels of dimorphism correlate with an expansion of gene families enriched in olfactory sensory perception and a contraction of gene families associated with brain development functions, many of which exhibited particularly high expression in the human adult brain. These findings suggest a relationship between intense sexual selection and alterations in gene family size. These insights illustrate the complex interplay between sexual dimorphism, gene family size evolution, and their roles in mammalian brain development and function, offering a valuable understanding of mammalian genome evolution. Sexual size dimorphism in mammals, often linked to sexual selection, can impacts genome evolution. This study finds sexual dimorphism in body size is associated with expanded gene families for olfactory functions and contracted gene families for brain development. [ABSTRACT FROM AUTHOR]

At the 3' end of the C2 gene in the mammalian TRB locus, a distinct reverse TRBV30 gene (named TRBV31 in mice) has been conserved throughout evolution. In the fully annotated TRB locus of 14 mammals (including six orders), we observed noteworthy variations in the localization and quality of the reverse V30 genes and Recombination Signal Sequences (RSSs) in the gene trees of 13 mammals. Conversely, the forward V29 genes and RSSs were generally consistent with the species tree of their corresponding species. This finding suggested that the evolution of the reverse V30 gene was not synchronous and likely played a crucial role in regulating adaptive immune responses. To further investigate this possibility, we utilized single-cell TCR sequencing (scTCR-seq) and high-throughput sequencing (HTS) to analyze TCRβ CDR3 repertoires from both central and peripheral tissues of Primates (Homo sapiens and Macaca mulatta), Rodentia (Mus musculus: BALB/c, C57BL/6, and Kunming mice), Artiodactyla (Bos taurus and Bubalus bubalis), and Chiroptera (Rhinolophus affinis and Hipposideros armige). Our investigation revealed several novel observations: (1) The reverse V30 gene exhibits classical rearrangement patterns adhering to the '12/23 rule' and the 'D-J rearrangement preceding the V-(D-J) rearrangement'. This results in the formation of rearranged V30-D2J2, V30-D1J1, and V30-D1J2. However, we also identified 'special rearrangement patterns' wherein V30-D rearrangement preceding D-J rearrangement, giving rise to rearranged V30-D2-J1 and forward Vx-D2-J. (2) Compared to the 'deletional rearrangement' (looping out) of forward V1-V29 genes, the reverse V30 gene exhibits preferential utilization with 'inversional rearrangement'. This may be attributed to the shorter distance between the V30 gene and D gene and the 'inversional rearrangement' modes. In summary, in the mammalian TRB locus, the reverse V30 gene has been uniquely preserved throughout evolution and preferentially utilized in V(D)J recombination, potentially serving a significant role in adaptive immunity. These results will pave the way for novel and specialized research into the mechanisms, efficiency, and function of V(D)J recombination in mammals. [ABSTRACT FROM AUTHOR]

Unravelling the functional steps that underlie major transitions in the fossil record is a significant challenge for biologists owing to the difficulties of interpreting functional capabilities of extinct organisms. New computational modelling approaches provide exciting avenues for testing function in the fossil record. Here, we conduct digital bending experiments to reconstruct vertebral function in non-mammalian synapsids, the extinct forerunners of mammals, to provide insights into the functional underpinnings of the synapsid–mammal transition. We estimate range of motion and stiffness of intervertebral joints in eight non-mammalian synapsid species alongside a comparative sample of extant tetrapods, including salamanders, reptiles and mammals. We show that several key aspects of mammalian vertebral function evolved outside crown Mammalia. Compared to early diverging non-mammalian synapsids, cynodonts stabilized the posterior trunk against lateroflexion, while evolving axial rotation in the anterior trunk. This was later accompanied by posterior sagittal bending in crown mammals, and perhaps even therians specifically. Our data also support the prior hypothesis that functional diversification of the mammalian trunk occurred via co-option of existing morphological regions in response to changing selective demands. Thus, multiple functional and evolutionary steps underlie the origin of remarkable complexity in the mammalian backbone. [ABSTRACT FROM AUTHOR]

Cancer is a disease that many multicellular organisms have faced for millions of years, and species have evolved various tumour suppression mechanisms to control oncogenesis. Although cancer occurs across the tree of life, cancer related mortality risks vary across mammalian orders, with Carnivorans particularly affected. Evolutionary theory predicts different selection pressures on genes associated with cancer progression and suppression, including oncogenes, tumour suppressor genes and immune genes. Therefore, we investigated the evolutionary history of cancer associated gene sequences across 384 mammalian taxa, to detect signatures of selection across categories of oncogenes (GRB2, FGL2 and CDC42), tumour suppressors (LITAF, Casp8 and BRCA2) and immune genes (IL2, CD274 and B2M). This approach allowed us to conduct a fine scale analysis of gene wide and site-specific signatures of selection across mammalian lineages under the lens of cancer susceptibility. Phylogenetic analyses revealed that for most species the evolution of cancer associated genes follows the species' evolution. The gene wide selection analyses revealed oncogenes being the most conserved, tumour suppressor and immune genes having similar amounts of episodic diversifying selection. Despite BRCA2's status as a key caretaker gene, episodic diversifying selection was detected across mammals. The site-specific selection analyses revealed that the two apoptosis associated domains of the Casp8 gene of bats (Chiroptera) are under opposing forces of selection (positive and negative respectively), highlighting the importance of site-specific selection analyses to understand the evolution of highly complex gene families. Our results highlighted the need to critically assess different types of selection pressure on cancer associated genes when investigating evolutionary adaptations to cancer across the tree of life. This study provides an extensive assessment of cancer associated genes in mammals with highly representative, and substantially large sample size for a comparative genomic analysis in the field and identifies various avenues for future research into the mechanisms of cancer resistance and susceptibility in mammals. [ABSTRACT FROM AUTHOR]

To cope with the damage from oxidative stress caused by hypoxia, mammals have evolved a series of physiological and biochemical traits, including antioxidant ability. Although numerous research studies about the mechanisms of hypoxia evolution have been reported, the molecular mechanisms of antioxidase-related genes in mammals living in different environments are yet to be completely understood. In this study, we constructed a dataset comprising 7 antioxidase-related genes (CAT, SOD1, SOD2, SOD3, GPX1, GPX2, and GPX3) from 43 mammalian species to implement evolutionary analysis. The results showed that six genes (CAT, SOD1, SOD2, SOD3, GPX1, and GPX3) have undergone divergent evolution based on the free-ratio (M1) model. Furthermore, multi-ratio model analyses uncovered the divergent evolution between hypoxic and non-hypoxic lineages, as well as various hypoxic lineages. In addition, the branch-site model identified 9 positively selected branches in 6 genes (CAT, SOD1, SOD2, SOD3, GPX2, and GPX3) that contained 35 positively selected sites, among which 31 positively selected sites were identified in hypoxia-tolerant branches, accounting for 89% of the total number of positively selected sites. Interestingly, 65 parallel/convergent sites were identified in the 7 genes. In summary, antioxidase-related genes are subjected to different selective pressures among hypoxia-tolerant species living in different habitats. This study provides a valuable insight into the molecular evolution of antioxidase-related genes in hypoxia evolution in mammals. [ABSTRACT FROM AUTHOR]

Studies of vertebrate bone biomechanics often focus on skeletal adaptations at upper extremes of body mass, disregarding the importance of skeletal adaptations at lower extremes. Yet mammals are ancestrally small and most modern species have masses under 5 kg, so the evolution of morphology and function at small size should be prioritized for understanding how mammals subsist. We examined allometric scaling of lumbar vertebrae in the small-bodied Philippine endemic rodents known as cloud rats, which vary in mass across two orders of magnitude (15.5 g–2700 g). External vertebral dimensions scale with isometry or positive allometry, likely relating to body size and nuances in quadrupedal posture. In contrast to most mammalian trabecular bone studies, bone volume fraction and trabecular thickness scale with positive allometry and isometry, respectively. It is physiologically impossible for these trends to continue to the upper extremes of mammalian body size, and we demonstrate a fundamental difference in trabecular bone allometry between large- and small-bodied mammals. These findings have important implications for the biomechanical capabilities of mammalian bone at small body size; for the selective pressures that govern skeletal evolution in small mammals; and for the way we define 'small' and 'large' in the context of vertebrate skeletons. [ABSTRACT FROM AUTHOR]

Although gene/genome duplications in the early stage of vertebrates have been thought to provide major resources of raw genetic materials for evolutionary innovations, it is unclear whether they continuously contribute to the evolution of morphological complexity during the course of vertebrate evolution, such as the evolution from two heart chambers (fishes) to four heart chambers (mammals and birds). We addressed this issue by our heart RNA‐Seq experiments combined with published data, using 13 vertebrates and one invertebrate (sea squirt, as an outgroup). Our evolutionary transcriptome analysis showed that number of ancient paralogous genes expressed in heart tends to increase with the increase of heart chamber number along the vertebrate phylogeny, in spite that most of them were duplicated at the time near to the origin of vertebrates or even more ancient. Moreover, those paralogs expressed in heart exert considerably different functions from heart‐expressed singletons: the former are functionally enriched in cardiac muscle and muscle contraction‐related categories, whereas the latter play more basic functions of energy generation like aerobic respiration. These findings together support the notion that recruiting anciently paralogous genes that are expressed in heart is associated with the increase of chamber number in vertebrate evolution. Research Highlights: Correlation between the expression of paralogous genes and heart chamber complexity.Paralogs expressed in heart exert considerably different functions from heart‐expressed singletons.Paralogous genes expressed in heart is associated with the increase of chamber number in evolution. [ABSTRACT FROM AUTHOR]

The Corpus Callosum (CC) is a bundle of axons connecting the cerebral hemispheres. It is the most recent structure to have appeared during evolution of placental mammals. Its development is controlled by a very complex interplay of many molecules. In humans it contains almost 80% of all commissural axons in the brain. The formation of the CC can be divided into four main stages, each controlled by numerous intracellular and extracellular molecular factors. First, a newborn neuron has to specify an axon, leave proliferative compartments, the Ventricular Zone (VZ) and Subventricular Zone (SVZ), migrate through the Intermediate Zone (IZ), and then settle at the Cortical Plate (CP). During the second stage, callosal axons navigate toward the midline within a compact bundle. Next stage is the midline crossing into contralateral hemisphere. The last step is targeting a defined area and synapse formation. This review provides an insight into these four phases of callosal axons development, as well as a description of the main molecular players involved. [ABSTRACT FROM AUTHOR]

Egg-laying mammals (monotremes) are considered "primitive" due to traits such as oviparity, cloaca, and incomplete homeothermy, all of which they share with reptiles. Two groups of monotremes, the terrestrial echidna (Tachyglossidae) and semiaquatic platypus (Ornithorhynchidae), have evolved highly divergent characters since their emergence in the Cenozoic era. These evolutionary differences, notably including distinct electrosensory and chemosensory systems, result from adaptations to species-specific habitat conditions. To date, very few studies have examined the visual adaptation of echidna and platypus. In the present study, we show that echidna and platypus have different light absorption spectra in their dichromatic visual sensory systems at the molecular level. We analyzed absorption spectra of monotreme color opsins, long-wavelength sensitive opsin (LWS) and short-wavelength sensitive opsin 2 (SWS2). The wavelength of maximum absorbance (λmax) in LWS was 570.2 in short-beaked echidna (Tachyglossus aculeatus) and 560.6 nm in platypus (Ornithorhynchus anatinus); in SWS2, λmax was 451.7 and 442.6 nm, respectively. Thus, the spectral range in echidna color vision is ~ 10 nm longer overall than in platypus. Natural selection analysis showed that the molecular evolution of monotreme color opsins is generally functionally conserved, suggesting that these taxa rely on species-specific color vision. In order to understand the usage of color vision in monotremes, we made 24-h behavioral observations of captive echidnas at warm temperatures and analyzed the resultant ethograms. Echidnas showed cathemeral activity and various behavioral repertoires such as feeding, traveling, digging, and self-grooming without light/dark environment selectivity. Halting (careful) behavior is more frequent in dark conditions, which suggests that echidnas may be more dependent on vision during the day and olfaction at night. Color vision functions have contributed to dynamic adaptations and dramatic ecological changes during the ~ 60 million years of divergent monotreme evolution. The ethogram of various day and night behaviors in captive echidnas also contributes information relevant to habitat conservation and animal welfare in this iconic species, which is locally endangered. [ABSTRACT FROM AUTHOR]

Chromosome reshuffling events are often a foundational mechanism by which speciation can occur, giving rise to highly derivative karyotypes even amongst closely related species. Yet, the features that distinguish lineages prone to such rapid chromosome evolution from those that maintain stable karyotypes across evolutionary time are still to be defined. In this review, we summarize lineages prone to rapid karyotypic evolution in the context of Simpson's rates of evolution—tachytelic, horotelic, and bradytelic—and outline the mechanisms proposed to contribute to chromosome rearrangements, their fixation, and their potential impact on speciation events. Furthermore, we discuss relevant genomic features that underpin chromosome variation, including patterns of fusions/fissions, centromere positioning, and epigenetic marks such as DNA methylation. Finally, in the era of telomere-to-telomere genomics, we discuss the value of gapless genome resources to the future of research focused on the plasticity of highly rearranged karyotypes. [ABSTRACT FROM AUTHOR]

The escape of DNA from mitochondria into the nuclear genome (nuclear mitochondrial DNA, NUMT) is an ongoing process. Although pervasively observed in eukaryotic genomes, their evolutionary trajectories in a mammal-wide context are poorly understood. The main challenge lies in the orthology assignment of NUMTs across species due to their fast evolution and chromosomal rearrangements over the past 200 million years. To address this issue, we systematically investigated the characteristics of NUMT insertions in 45 mammalian genomes and established a novel, synteny-based method to accurately predict orthologous NUMTs and ascertain their evolution across mammals. With a series of comparative analyses across taxa, we revealed that NUMTs may originate from nonrandom regions in mtDNA, are likely found in transposon-rich and intergenic regions, and unlikely code for functional proteins. Using our synteny-based approach, we leveraged 630 pairwise comparisons of genome-wide microsynteny and predicted the NUMT orthology relationships across 36 mammals. With the phylogenetic patterns of NUMT presence-and-absence across taxa, we constructed the ancestral state of NUMTs given the mammal tree using a coalescent method. We found support on the ancestral node of Fereuungulata within Laurasiatheria, whose subordinal relationships are still controversial. This study broadens our knowledge on NUMT insertion and evolution in mammalian genomes and highlights the merit of NUMTs as alternative genetic markers in phylogenetic inference. [ABSTRACT FROM AUTHOR]

Forkhead box E1 (FoxE1) protein is a transcriptional regulator known to play a major role in the development of the thyroid gland. By performing sequence alignments, we detected a deletion in FoxE1, which occurred in the evolution of mammals, near the point of divergence of placental mammals. This deletion led to the loss of the majority of the Eh1 motif, which was important for interactions with transcriptional corepressors. To investigate a potential mechanism for this deletion, we analyzed replication through the deletion area in mammalian cells with two-dimensional gel electrophoresis, and in vitro, using a primer extension reaction. We demonstrated that the area of the deletion presented an obstacle for replication in both assays. The exact position of polymerization arrest in primer extension indicated that it was most likely caused by a quadruplex DNA structure. The quadruplex structure hypothesis is also consistent with the exact borders of the deletion. The exact roles of these evolutionary changes in FoxE1 family proteins are still to be determined. [ABSTRACT FROM AUTHOR]

Modern views on the origin and early evolution of mammals are presented. The material accumulated by the author on the morphology of modern and fossil monotremes, marsupials, and placentals are used. Data on Mesozoic mammals, including those obtained in recent years, are summarized. A model of the mechanism of morphogenetic transformations during the evolutionary development of Mammalia is proposed. An overview of the main directions of the formation of mammals from the Late Triassic to the Cenozoic is given. [ABSTRACT FROM AUTHOR]

Instantaneous head posture (IHP) can extensively alter resting hyoid position in humans, yet postural effects on resting hyoid position remain poorly documented among mammals in general. Clarifying this relationship is essential for evaluating interspecific variation in hyoid posture across evolution, and understanding its implications for hyolingual soft tissue function and swallowing motor control. Using Didelphis virginiana as a model, we conducted static manipulation experiments to show that head flexion shifts hyoid position rostrally relative to the cranium across different gapes. IHP-induced shifts in hyoid position along the anteroposterior axis are comparable to in vivo hyoid protraction distance during swallowing. IHP also has opposite effects on passive genio- and stylohyoid muscle lengths. High-speed biplanar videoradiography suggests Didelphis consistently swallows at neutral to flexed posture, with stereotyped hyoid kinematics across different head postures. IHP change can affect suprahyoid muscle force production by shifting their positions on the length-tension curve, and redirecting lines of action and the resultant force from supra- and infrahyoid muscles. We hypothesize that demands on muscle performance may constrain the range of swallowing head postures in mammals. This article is part of the theme issue 'Food processing and nutritional assimilation in animals'. [ABSTRACT FROM AUTHOR]

The genetic basis underlying adaptive physiological mechanisms has been extensively explored in mammals after colonizing the seas. However, independent lineages of aquatic mammals exhibit complex patterns of secondary colonization in freshwater environments. This change in habitat represents new osmotic challenges, and additional changes in key systems, such as the osmoregulatory system, are expected. Here, we studied the selective regime on coding and regulatory regions of 20 genes related to the osmoregulation system in strict aquatic mammals from independent evolutionary lineages, cetaceans, and sirenians, with representatives in marine and freshwater aquatic environments. We identified positive selection signals in genes encoding the protein vasopressin (AVP) in mammalian lineages with secondary colonization in the fluvial environment and in aquaporins for lineages inhabiting the marine and fluvial environments. A greater number of sites with positive selection signals were found for the dolphin species compared to the Amazonian manatee. Only the AQP5 and AVP genes showed selection signals in more than one independent lineage of these mammals. Furthermore, the vasopressin gene tree indicates greater similarity in river dolphin sequences despite the independence of their lineages based on the species tree. Patterns of distribution and enrichment of Transcription Factors in the promoter regions of target genes were analyzed and appear to be phylogenetically conserved among sister species. We found accelerated evolution signs in genes ACE, AQP1, AQP5, AQP7, AVP, NPP4, and NPR1 for the fluvial mammals. Together, these results allow a greater understanding of the molecular bases of the evolution of genes responsible for osmotic control in aquatic mammals. [ABSTRACT FROM AUTHOR]

In the course of evolution, the most highly developed organ is likely the brain, which has become more complex over time and acquired diverse forms and functions in different species. In particular, mammals have developed complex and high-functioning brains, and it has been reported that several genes derived from retroviruses were involved in mammalian brain evolution, that is, generating the complexity of the nervous system. Especially, the sushi-ichi-related retrotransposon homolog (SIRH)/retrotransposon gag-like (RTL) genes have been suggested to play a role in the evolutionary processes shaping brain morphology and function in mammals. Genetic mutation and altered expression of genes are linked to neurological disorders, highlighting how the acquisition of virus-derived genes in mammals has both driven brain evolution and imposed a susceptibility to diseases. This review provides an overview of the functions, diversity, evolution and diseases associated with SIRH/RTL genes in the nervous system. The contribution of retroviruses to brain evolution is an important research topic in evolutionary biology and neuroscience, and further insights are expected to be gained through future studies. [ABSTRACT FROM AUTHOR]

Aims: Mechanochemical signalling drives organogenesis and is highly conserved in mammal evolution. Regaining recovery in myocardial jeopardy by inducing principles linking cardiovascular therapy and clinical outcome has been the dream of scientists for decades. Concepts involving embryonic pathways to regenerate adult failing hearts became popular in the early millennium. Since then, abundant data on stem cell research have been published, never reaching widespread application in heart failure therapy. Another conceptual access, using mechanotransduction in cardiac veins to limit myocardial decay, is pressure‐controlled intermittent coronary sinus occlusion (PICSO). Recently, we reported acute molecular signs and signals of PICSO activating regulatory miRNA and inducing cell proliferation mimicking cardiac development in adult failing hearts. According to a previously formulated hypothesis, 'embryonic recall', this study aimed to define molecular signals involved in endogenous heart repair during PICSO and study their relation to patient survival. Methods and results: We previously reported a study on the acute molecular effects of PICSO in an observational non‐randomized study. Eight out of the thirty‐two patients with advanced heart failure undergoing cardiac resynchronization therapy (CRT) were treated with PICSO. Survival was monitored over 10 years, and coronary sinus blood samples were collected during intervention before and after 20 min and tested for miRNA signalling and proliferation when co‐cultured with cardiomyocytes. A numerically lower death rate post‐CRT and PICSO as compared with control CRT only, and a non‐significant reduction in all‐cause mortality risk of 42% was observed (37.5% vs. 54.0%, relative risk = 0.58, 95% confidence interval: 0.17–2.05; P = 0.402). Four miRNAs involved in cell cycle, proliferation, morphogenesis, embryonic development, and apoptosis significantly increased concomitantly in survivors and PICSO compared with a decrease in non‐survivors (hsa‐miR Let7b, P < 0.01; hsa‐miR‐ 421, P < 0.006; hsa‐miR 363‐3p, P < 0.03 and hsa‐miR 19b‐3p P < 0.01). In contrast, three miRNAs involved in proliferation and survival, determining cell fate, and recycling endosomes decreased in survivors and PICSO (hsa miR 101‐3p, P < 0.03; hsa‐miR 25‐3p, P < 002; hsa‐miR 30d‐5p P < 0.04). In vitro cellular proliferation increased in survivors and lowered in non‐survivors showing a pattern distinction, discriminating longevity according to up to 10‐year survival in heart failure patients. Conclusions: This study proposes that generating regenerative signals observed during PICSO intervention relate to patient outcomes. Morphogenetic pathways induced by periods of flow reversal in cardiac veins in a domino‐like pattern transform embryonic into regenerative signals. Studies supporting the conversion of mechanochemical signals into regenerative molecules during PICSO are warranted to substantiate predictive power on patient longevity, opening new therapeutic avenues in otherwise untreatable heart failure. [ABSTRACT FROM AUTHOR]

Allotheria are an extinct group of mammaliaforms that originally comprised multituberculates, to which 'haramiyidans' and gondwanatherians were later added. Phylogenetic relationships of allotherians have remained controversial since the first reports of the allotherian fossils in the 1800s. Here we report a new euharamiyidan based on a skeletal specimen from the Jurassic Daohugou phase of the Yanliao Biota, China. The superb specimen preserves impressions of differentiated hairs. The pes with impressions of toe skin and claw sheath represents the first such evidence in Mesozoic mammaliamorphs. The remarkable tooth morphologies surpass in complexity any Mesozoic mammals previously known. Phylogenetic analyses place the new species within euharamiyidans from Eurasia and support euharamiyidans, multituberculates, and gondwanatherians as a tripartite monophyletic Allotheria within mammals. This clade is supported not only by their similar molar pattern, but also by many shared derived features of the dental system recognized from discoveries during the last two decades. Allotherians and therians represent the two most successful groups of mammals that are characterized by distinct dental systems. They originated at the latest in the Late Triassic and became diversified in the Middle Jurassic, representing two directions of ecomorphological adaptation during early evolution of mammals. [ABSTRACT FROM AUTHOR]

Background: Exploring evolution regularities of genome sequences and constructing more objective species evolution relationships at the genomic level are high-profile topics. Based on the evolution mechanism of genome sequences proposed in our previous research, we found that only the 8-mers containing CG or TA dinucleotides correlate directly with the evolution of genome sequences, and the relative frequency rather than the actual frequency of these 8-mers is more suitable to characterize the evolution of genome sequences. Result: Therefore, two types of feature sets were obtained, they are the relative frequency sets of CG1 + CG2 8-mers and TA1 + TA2 8-mers. The evolution relationships of mammals and reptiles were constructed by the relative frequency set of CG1 + CG2 8-mers, and two types of evolution relationships of insects were constructed by the relative frequency sets of CG1 + CG2 8-mers and TA1 + TA2 8-mers respectively. Through comparison and analysis, we found that evolution relationships are consistent with the known conclusions. According to the evolution mechanism, we considered that the evolution relationship constructed by CG1 + CG2 8-mers reflects the evolution state of genome sequences in current time, and the evolution relationship constructed by TA1 + TA2 8-mers reflects the evolution state in the early stage. Conclusion: Our study provides objective feature sets in constructing evolution relationships at the genomic level. [ABSTRACT FROM AUTHOR]

Background: The primary differentially methylated regions (DMRs) which are maternally hypermethylated serve as imprinting control regions (ICRs) that drive monoallelic gene expression, and these ICRs have been investigated due to their implications in mammalian development. Although a subset of genes has been identified as imprinted, in-depth comparative approach needs to be developed for identification of species-specific imprinted genes. Here, we examined DNA methylation status and allelic expression at the KBTBD6 locus across species and tissues and explored potential mechanisms of imprinting. Results: Using whole-genome bisulfite sequencing and RNA-sequencing on parthenogenetic and normal porcine embryos, we identified a maternally hypermethylated DMR between the embryos at the KBTBD6 promoter CpG island and paternal monoallelic expression of KBTBD6. Also, in analyzed domesticated mammals but not in humans, non-human primates and mice, the KBTBD6 promoter CpG islands were methylated in oocytes and/or allelically methylated in tissues, and monoallelic KBTBD6 expression was observed, indicating livestock-specific imprinting. Further analysis revealed that these CpG islands were embedded within transcripts in porcine and bovine oocytes which coexisted with an active transcription mark and DNA methylation, implying the presence of transcription-dependent imprinting. Conclusions: In this study, our comparative approach revealed an imprinted expression of the KBTBD6 gene in domesticated mammals, but not in humans, non-human primates, and mice which implicates species-specific evolution of genomic imprinting. [ABSTRACT FROM AUTHOR]

Same-sex sexual behaviour has attracted the attention of many scientists working in disparate areas, from sociology and psychology to behavioural and evolutionary biology. Since it does not contribute directly to reproduction, same-sex sexual behaviour is considered an evolutionary conundrum. Here, using phylogenetic analyses, we explore the evolution of same-sex sexual behaviour in mammals. According to currently available data, this behaviour is not randomly distributed across mammal lineages, but tends to be particularly prevalent in some clades, especially primates. Ancestral reconstruction suggests that same-sex sexual behaviour may have evolved multiple times, with its appearance being a recent phenomenon in most mammalian lineages. Our phylogenetically informed analyses testing for associations between same-sex sexual behaviour and other species characteristics suggest that it may play an adaptive role in maintaining social relationships and mitigating conflict. There is still no consensus on the factors favouring the evolution of same-sex sexual behaviour in mammals. This study presents evidence that it is a widespread behaviour that has evolved repeatedly in mammals, and that may play an adaptive role in bonding and conflict resolution. [ABSTRACT FROM AUTHOR]

The emergence of colorectal cancer cells is associated with the inactivation of the adenomatosis polyposis coli (APC) gene which increases the activity of ß-catenin, one of which is due to oncomiRNA (cancer-inducing microRNA). miR-135a/b-5p and miR-494-3p were thought to be involved in silencing the APC gene and increasing cell proliferation and could potentially be used as anti-miR targets. However, there is a need for an in-depth evaluation of the involvement of the oncomiR as a therapeutic target in preventing the formation of CRC. Therefore, this study aimed to predict the mechanism of inhibition of oncomiR hsa-miR-135a/b, and has-miR-494-3p against APC in the Wnt/ß-catenin signaling pathway. This research was conducted through in silico analysis using a web-based application to describe the stability of the secondary structure, binding position on mRNA, and conserved nucleotides that support biological activity. The data obtained were then used to develop miRNA interaction networks with APCs on the CRCassociated Wnt/ß-catenin signaling pathway. This study suggests that miR-135a-5p, and miR-135b-5p probably evolved earlier in the evolutionary evolution of the conserved oncomiR CRC in various vertebrate species, whereas miR-494-3p is more conserved and commonly found in mammals. The biological activity of miR-494-3p is likely to be more stable and patent to bind to APC gene mRNA and trigger CRC cell proliferation. Furthermore, miR-135a/b-5p and miR-494-3p have the potential to be developed as targets for anti-miR-based transcriptomic therapy as well as for early diagnosis of CRC development. Anti-miR therapy will likely need to involve more than 1 miRNA, as each gene has more than 1 miRNA binding site. [ABSTRACT FROM AUTHOR]

The hypothalamus regulates fundamental aspects of physiological homeostasis and behavior, including stress response, reproduction, growth, sleep, and feeding, several of which are affected in patients with Prader–Willi (PWS) and Schaaf–Yang syndrome (SYS). PWS is caused by paternal deletion, maternal uniparental disomy, or imprinting defects that lead to loss of expression of a maternally imprinted region of chromosome 15 encompassing non-coding RNAs and five protein-coding genes; SYS patients have a mutation in one of them, MAGEL2. Throughout life, PWS and SYS patients suffer from musculoskeletal deficiencies, intellectual disabilities, and hormonal abnormalities, which lead to compulsive behaviors like hyperphagia and temper outbursts. Management of PWS and SYS is mostly symptomatic and cures for these debilitating disorders do not exist, highlighting a clear, unmet medical need. Research over several decades into the molecular and cellular roles of PWS genes has uncovered that several impinge on the neuroendocrine system. In this review, we will discuss the expression and molecular functions of PWS genes, connecting them with hormonal imbalances in patients and animal models. Besides the observed hormonal imbalances, we will describe the recent findings about how the loss of individual genes, particularly MAGEL2, affects the molecular mechanisms of hormone secretion. These results suggest that MAGEL2 evolved as a mammalian-specific regulator of hypothalamic neuroendocrine function. [ABSTRACT FROM AUTHOR]

Although bats can serve as reservoirs for several viruses and bacteria, there is limited knowledge regarding the diversity of apicomplexan protozoan belonging to the Piroplasmida and Haemosporida orders within this group of mammals. The present study aimed to investigate the occurrence and phylogenetic assessment of piroplasmids and hemosporidians in spleen samples collected from 229 vampire bats (228 Desmodus rotundus and 1 Diaemus youngii) in the states of Pará, Roraima, Amapá, and Amazonas, northern Brazil. Out of 229 bat spleen samples, 43 (18.77%) tested positive in a nested PCR for piroplasmids based on the 18S rRNA gene. Thirteen sequences (ranging from 474 to 828 base pairs) of the partial 18S rRNA gene showed 91.04–100% identity to Theileria sp., Babesia sp., and Piroplasmida previously detected in deer, tapirs, opossums, and crab-eating raccoons. The phylogenetic analysis based on the near-complete 18S rRNA gene positioned the obtained sequences from three D. rotundus in distinct clades (Theileria sensu stricto, Tapirus terrestris, and "South America Marsupialia"). All bat spleen DNA samples tested negative in a nested PCR assay for hemosporidians based on the cytB gene. The present study reported, for the first time, the presence Babesia sp. and Theileria sp. DNA in D. rotundus. The distinct positioning of the 18S rRNA gene sequences within different clades demonstrates the occurrence of different piroplasmid species in vampire bats. [ABSTRACT FROM AUTHOR]

The genomes of mammals contain fingerprints of past infections by ancient retroviruses that invaded the germline of their ancestors. Most of these endogenous retroviruses (ERVs) contain only remnants of the original retrovirus; however, on rare occasions, ERV genes can be co-opted for a beneficial host function. While most studies of co-opted ERVs have focused on envelope genes, including the syncytins that function in placentation, there are examples of co-opted gag genes including one we recently discovered in simian primates. Here, we searched for other intact gag genes in nonprimate mammalian lineages. We began by examining the genomes of extant camel species, which represent a basal lineage in the order Artiodactyla. This identified a gagpol gene with a large open reading frame (ORF) (>3,500 bp) in the same orthologous location in Artiodactyla species but that is absent in other mammals. Thus, this ERV was fixed in the common ancestor of all Artiodactyla at least 64 million years ago. The amino acid sequence of this gene, termed ARTgagpol, contains recognizable matrix, capsid, nucleocapsid, and reverse transcriptase domains in ruminants, with an RNase H domain in camels and pigs. Phylogenetic analysis and structural prediction of its reverse transcriptase and RNase H domains groups ARTgagpol with gammaretroviruses. Transcriptomic analysis shows ARTgagpol expression in multiple tissues suggestive of a co-opted host function. These findings identify the oldest and largest ERV-derived gagpol gene with an intact ORF in mammals, an intriguing milestone in the co-evolution of mammals and retroviruses. IMPORTANCE: Retroviruses are unique among viruses that infect animals as they integrate their reverse-transcribed double-stranded DNA into host chromosomes. When this happens in a germline cell, such as sperm, egg, or their precursors, the integrated retroviral copies can be passed on to the next generation as endogenous retroviruses (ERVs). On rare occasions, the genes of these ERVs can be domesticated by the host. In this study we used computational similarity searches to identify an ancient ERV with an intact viral gagpol gene in the genomes of camels that is also found in the same genomic location in other even-toed ungulates suggesting that it is at least 64 million years old. Broad tissue expression and predicted preservation of the reverse transcriptase fold of this protein suggest that it may be domesticated for a host function. This is the oldest known intact gagpol gene of an ancient retrovirus in mammals. [ABSTRACT FROM AUTHOR]

Tooth classes are an innovation that has contributed to the evolutionary success of mammals. However, our understanding of the mechanisms by which tooth classes diversified remain limited. We use the evolutionary radiation of noctilionoid bats to show how the tooth developmental program evolved during the adaptation to new diet types. Combining morphological, developmental and mathematical modeling approaches, we demonstrate that tooth classes develop through independent developmental cascades that deviate from classical models. We show that the diversification of tooth number and size is driven by jaw growth rate modulation, explaining the rapid gain/loss of teeth in this clade. Finally, we mathematically model the successive appearance of tooth buds, supporting the hypothesis that growth acts as a key driver of the evolution of tooth number and size. Our work reveal how growth, by tinkering with reaction/diffusion processes, drives the diversification of tooth classes and other repeated structure during adaptive radiations. Despite their key role in the evolution of mammals, the origin and diversification of tooth classes (incisors, canines, premolars and molars) remain relatively obscure. Here the authors use integrative approaches to explain the independent evolution and rapid diversification of two tooth classes, premolar and molars, in noctilionoid bats. [ABSTRACT FROM AUTHOR]

Background: Lifespan extension has independently evolved several times during mammalian evolution, leading to the emergence of a group of long-lived animals. Though mammalian/mechanistic target of rapamycin (mTOR) signaling pathway is shown as a central regulator of lifespan and aging, the underlying influence of mTOR pathway on the evolution of lifespan in mammals is not well understood. Results: Here, we performed evolution analyses of 72 genes involved in the mTOR network across 48 mammals to explore the underlying mechanism of lifespan extension. We identified a total of 20 genes with significant evolution signals unique to long-lived species, including 12 positively selected genes, four convergent evolution genes, and five longevity associated genes whose evolution rate related to the maximum lifespan (MLS). Of these genes, four positively selected genes, two convergent evolution genes and one longevity-associated gene were involved in the autophagy response and aging-related diseases, while eight genes were known as cancer genes, indicating the long-lived species might have evolved effective regulation mechanisms of autophagy and cancer to extend lifespan. Conclusion: Our study revealed genes with significant evolutionary signals unique to long-lived species, which provided new insight into the lifespan extension of mammals and might bring new strategies to extend human lifespan. [ABSTRACT FROM AUTHOR]

Aquaporins (AQPs) are integral membrane proteins responsible for water transport across cellular membranes in both prokaryotes and eukaryotes. A subfamily of AQPs, known as aquaglyceroporins (AQGPs), facilitate the transport of small solutes such as glycerol, water, and other solutes across cellular membranes. These proteins are involved in a variety of physiological processes, such as organogenesis, wound healing, and hydration. Although AQPs have been studied extensively in different species, their conservation patterns, phylogenetic relationships, and evolution in mammals remain unexplored. In the present study, 119 AQGP coding sequences from 31 mammalian species were analysed to identify conserved residues, gene organisation, and most importantly, the nature of AQGP gene selection. Repertoire analysis revealed the absence of AQP7, 9, and 10 genes in certain species of Primates, Rodentia, and Diprotodontia, although not all three genes were absent in a single species. Two Asparagine-Proline-Alanine (NPA) motifs located at the N- and C-terminal ends, aspartic acid (D) residues, and the ar/R region were conserved in AQP3, 9, and 10. Six exons encoding the functional MIP domain of AQGP genes were found to be conserved across mammalian species. Evolutionary analysis indicated signatures of positive selection in AQP7, 9, and 10 amongst different mammalian lineages. Furthermore, substitutions of certain amino acids located close to critical residues may alter AQGP functionality, which is crucial for substrate selectivity, pore formation, and transport efficiency required for the maintenance of homeostasis in different mammalian species. [ABSTRACT FROM AUTHOR]

PLAC8 is a cysteine-rich protein that serves as a central mediator of tumor evolution in mammals. PLAC8 motif-containing proteins widely distribute in fungi, algae, higher plants and animals that have been described to be implicated in fruit size, cell number and the transport of heavy metals such as cadmium or zinc. In tomatoes, FW2.2 is a PLAC8 motif-containing gene that negatively controls fruit size by regulating cell division and expansion in the carpel ovary during fruit development. However, despite FW2.2, other FWL (FW2.2-Like) genes in tomatoes have not been investigated. In this study, we identified the 21 SlFWL genes, including FW2.2, examined their expression profiles under various abiotic adversity-related conditions. The SlFWL gene structures and motif compositions are conserved, indicating that tomato SlFWL genes may have similar roles. Cis-acting element analysis revealed that the SlFWL genes may participate in light and abiotic stress responses, and they also interacted with a variety of phytohormone-responsive proteins and plant development elements. Phylogenetic analyses were performed on five additional plant species, including Arabidopsis, pepper, soybean, rice and maize, these genes were classified into five subfamilies. Based on the results of collinearity analyses, the SlFWL genes have a tighter homologous evolutionary relationship with soybean, and these orthologous FWL gene pairs might have the common ancestor. Expression profiling of SlFWL genes show that they were all responsive to abiotic stresses, each subgroup of genes exhibited a different expression trend. Our findings provide a strong foundation for investigating the function and abiotic stress responses of the SlFWL family genes. [ABSTRACT FROM AUTHOR]

The evolutionary shift from a single-element ear, multi-element jaw to a multi-element ear, single-element jaw during the transition to crown mammals marks one of the most dramatic structural transformations in vertebrates. Research on this transformation has focused on mammalian middle-ear evolution, but a mandible comprising only the dentary is equally emblematic of this evolutionary radiation. Here, we show that the remarkably diverse jaw shapes of crown mammals are coupled with surprisingly stereotyped jaw stiffness. This strength-based morphofunctional regime has a genetic basis and allowed mammalian jaws to effectively resist deformation as they radiated into highly disparate forms with markedly distinct diets. The main functional consequences for the mandible of decoupling hearing and mastication were a trade-off between higher jaw stiffness versus decreased mechanical efficiency and speed compared with non-mammals. This fundamental and consequential shift in jaw form–function underpins the ecological and taxonomic diversification of crown mammals. This article is part of the theme issue 'The mammalian skull: development, structure and function'. [ABSTRACT FROM AUTHOR]

Mammals are diagnosed by more than 30 osteological characters (e.g. squamosal-dentary jaw joint, three inner ear ossicles, etc.) that are readily preserved in the fossil record. However, it is the suite of physiological, soft tissue and behavioural characters (e.g. endothermy, hair, lactation, isocortex and parental care), the evolutionary origins of which have eluded scholars for decades, that most prominently distinguishes living mammals from other amniotes. Here, we review recent works that illustrate how evolutionary changes concentrated in the cranial and dental morphology of mammalian ancestors, the Permian–Jurassic Cynodontia and Mammaliaformes, can potentially be used to document the origin of some of the most crucial defining features of mammals. We discuss how these soft tissue and behavioural traits are highly integrated, and how their evolution is intermingled with that of craniodental traits, thus enabling the tracing of their previously out-of-reach phylogenetic history. Most of these osteological and dental proxies, such as the maxillary canal, bony labyrinth and dental replacement only recently became more easily accessible—thanks, in large part, to the widespread use of X-ray microtomography scanning in palaeontology—because they are linked to internal cranial characters. This article is part of the theme issue 'The mammalian skull: development, structure and function'. [ABSTRACT FROM AUTHOR]

Simple Summary: The current study reassesses the systematic status of Suncus niger from its original geographical distribution in Southern India. Both morphology and mitochondrial genetic data clearly distinguish S. niger (endemic to India) from Suncus montanus (endemic to Sri Lanka) and substantiate the prior hypothesis of a distinct species. Furthermore, the present study adds new range extension, elevation records, and Pliocene colonization for this small mammal in the Western Ghats biodiversity hotspot. Given the matrilineal affinities between Indian and African lineages, and their recent transcontinental colonization, we believe that more in-depth genomic studies, including divergence time estimation, are crucial to clarify the global evolutionary trend of Soricomorphs. The Indian highland shrew, Suncus niger (Horsfield, 1851), is the least studied soricid species from its original range distribution in Southern India, with several systematics conundrums. Following its discovery in 1851, the species was synonymized with Suncus montanus (Kelaart, 1850) (endemic to Sri Lanka) and subsequently identified as a separate Indian population. However, the systematic status of S. niger from topotype specimens in Southern India has yet to be determined through an integrated approach. Both taxonomy and mitochondrial genetic data (Cytochrome b and 16S ribosomal RNA) were used to re-examine the systematics of S. niger. The mtCytb gene clearly distinguished topotypic S. niger from other Suncus species, with high genetic divergences varying from 8.49% to 26.29%. Further, the Bayesian and maximum likelihood topologies clearly segregated S. niger from other congeners and corroborated the sister relationship with S. stoliczkanus with expected divergence in the late Pliocene (2.62 MYA). The TimeTree analysis also exhibits a strong matrilineal affinity of S. dayi (endemic to India) toward the African species. The current study hypothesizes that the ancestor of the soricids evolved in Africa and that genetic lineages were subsequently shifted by plate tectonic events that subsequently colonized different continents as distinct species during the late Miocene (Tortonian) to the Holocene era. In addition to the new range expansion and elevation records of S. niger in the Central Western Ghats, we propose that additional sampling across its distribution, as well as the use of multiple genetic markers, may be useful in determining the genetic diversity and population structure of this endemic species. The present study also recommends that more molecular data on the Soricomorphs lineages, and estimates of their divergence times, will shed light on the evolution of these small mammals on Earth. [ABSTRACT FROM AUTHOR]

The genetic bases underlying the evolution of morphological and functional innovations of the mammalian inner ear are poorly understood. Gene regulatory regions are thought to play an important role in the evolution of form and function. To uncover crucial hearing genes whose regulatory machinery evolved specifically in mammalian lineages, we mapped accelerated noncoding elements (ANCEs) in inner ear transcription factor (TF) genes and found that PKNOX2 harbors the largest number of ANCEs within its transcriptional unit. Using reporter gene expression assays in transgenic zebrafish, we determined that four PKNOX2 -ANCEs drive differential expression patterns when compared with ortholog sequences from close outgroup species. Because the functional role of PKNOX2 in cochlear hair cells has not been previously investigated, we decided to study Pknox2 null mice generated by CRISPR/Cas9 technology. We found that Pknox2−/− mice exhibit reduced distortion product otoacoustic emissions (DPOAEs) and auditory brainstem response (ABR) thresholds at high frequencies together with an increase in peak 1 amplitude, consistent with a higher number of inner hair cells (IHCs)-auditory nerve synapsis observed at the cochlear basal region. A comparative cochlear transcriptomic analysis of Pknox2−/− and Pknox2+/+ mice revealed that key auditory genes are under Pknox2 control. Hence, we report that PKNOX2 plays a critical role in cochlear sensitivity at higher frequencies and that its transcriptional regulation underwent lineage-specific evolution in mammals. Our results provide novel insights about the contribution of PKNOX2 to normal auditory function and to the evolution of high-frequency hearing in mammals. [ABSTRACT FROM AUTHOR]

In recent years, highly pathogenic avian influenza H5 subtype (HPAI H5) viruses have been prevalent around the world in both avian and mammalian species, causing serious economic losses to farmers. HPAI H5 infections of zoonotic origin also pose a threat to human health. Upon evaluating the global distribution of HPAI H5 viruses from 2019 to 2022, we found that the dominant strain of HPAI H5 rapidly changed from H5N8 to H5N1. A comparison of HA sequences from human- and avian-derived HPAI H5 viruses indicated high homology within the same subtype of viruses. Moreover, amino acid residues 137A, 192I, and 193R in the receptor-binding domain of HA1 were the key mutation sites for human infection in the current HPAI H5 subtype viruses. The recent rapid transmission of H5N1 HPAI in minks may result in the further evolution of the virus in mammals, thereby causing cross-species transmission to humans in the near future. This potential cross-species transmission calls for the development of an H5-specific influenza vaccine, as well as a universal influenza vaccine able to provide protection against a broad range of influenza strains. [ABSTRACT FROM AUTHOR]

At the very deepest molecular level, the mechanisms of life depend on the operation of proteins, the so-called "workhorses" of the cell. Proteins are nanoscale machines that transform energy into useful cellular work, such as ion or nutrient transport, information processing, or energy transformation. Behind every biological task, there is a nanometer-sized molecule whose shape and intrinsic motions, binding, and sensing properties have been evolutionarily polished for billions of years. With the emergence of structural biology, the most crucial property of biomolecules was thought to be their 3D shape, but how this relates to function was unclear. During the past years, Elastic Network Models have revealed that protein shape, motion and function are deeply intertwined, so that each structure displays robustly shape-encoded functional movements that can be extraordinarily conserved across the tree of life. Here, we briefly review the growing literature exploring the interplay between sequence evolution, protein shape, intrinsic motions and function, and highlight examples from our research in which fundamental movements are conserved from bacteria to mammals or selected by cancer cells to modulate function. [ABSTRACT FROM AUTHOR]

Positive selection refers to the process by which certain genetic variations are more likely to be passed on to future generations because they confer some advantage in terms of survival or reproduction. Zinc finger proteins are a type of transcription factor that plays a role in regulating gene expression, particularly in undifferentiated stem cells. Suppose it has been found that certain zinc finger proteins show genetic signatures of positive selection in mammals. In that case, it suggests that these proteins may have played a role in adaptive evolution in undifferentiated stem cells. This could mean that the specific genetic changes in these zinc finger proteins gave an advantage to the organisms that possessed them, helping them survive and reproduce more effectively. These genetic changes may have allowed the organisms to adapt to changing environments or to develop new abilities, such as increased resistance to disease or faster growth. Undifferentiated stem cells that underwent adaptive evolution during the evolution of mammals can be identified genetically by the outcomes of positive selection on zinc finger proteins. Because of selection pressures like environmental shifts or the introduction of novel pathogens, it is plausible that some zinc finger proteins have experienced fast evolution. The emergence of novel activities or higher expression levels of these proteins as a result of this quick evolution may have given the creatures that possessed them a survival edge. Another possible outcome of positive selection in zinc finger proteins is the emergence of new genetic variations that allow for increased diversity and plasticity in stem cells. This increased diversity and plasticity could have allowed for more efficient adaptation to changing environments and could have played a role in the evolution of new organisms or new characteristics in existing organisms. Overall, the results of positive selection in zinc finger proteins can provide insight into how adaptive evolution occurred in undifferentiated stem cells during the evolution of mammals and how this evolution may have contributed to the development of new organisms and new characteristics and adaptations to changing environments. [ABSTRACT FROM AUTHOR]

Mammals have developed different kinds of renal structures during evolution, yet the origin of the renal structural phenotypes and the molecular mechanisms underlying their adaptive evolution remains unclear. Here, we reconstructed the ancestral state of the renal structures across mammals and found that the unilobar kidney was the ancestral character in mammals. The subsequent correlation analyses between renal phenotypes and life history traits revealed that species with a larger body or in aquatic habitats tend to have evolved discrete multirenculate kidneys (DMKs). To explore the molecular convergent mechanisms among mammals with this most distinct renal structure, the DMK, we used 45 genes related to duplex/multiplex kidney diseases to compare the evolutions of species with DMKs and with other renal phenotypes. Twelve rapidly evolving genes that were functionally enriched in cilium assembly and centrosome were identified in species with DMKs, suggesting that these genes played key roles in the evolution of DMKs. In addition, positive selection was detected in six crucial genes which are mainly involved in epithelial tube morphogenesis and the regulation of neurogenesis. Finally, 12 convergent amino acid substitutions, 6 of which are in crucial domain of proteins, were shared by 2 or more lineages with DMKs. These findings could provide some novel insights into the origin and evolution of renal structures across mammals and the pathogenesis of renal diseases in humans. [ABSTRACT FROM AUTHOR]

The origin of embryo implantation in mammals ~148 million years ago was a dramatic shift in reproductive strategy, yet the molecular changes that established mammal implantation are largely unknown. Although progesterone receptor signalling predates the origin of mammals and is highly conserved in, and critical for, successful mammal pregnancy, it alone cannot explain the origin and subsequent diversity of implantation strategies throughout the placental mammal radiation. MiRNAs are known to be flexible and dynamic regulators with a well-established role in the pathophysiology of mammal placenta. We propose that a dynamic core microRNA (miRNA) network originated early in placental mammal evolution, responds to conserved mammal pregnancy cues (e.g. progesterone), and facilitates species-specific responses. Here we identify 13 miRNA gene families that arose at the origin of placental mammals and were subsequently retained in all descendent lineages. The expression of these miRNAs in response to early pregnancy molecules is regulated in a species-specific manner in endometrial epithelia of species with extreme implantation strategies (i.e. bovine and human). Furthermore, this set of miRNAs preferentially target proteins under positive selective pressure on the ancestral eutherian lineage. Discovery of this core embryo implantation toolkit and specifically adapted proteins helps explain the origin and evolution of implantation in mammals. Here 13 conserved miRNAs are identified that arose at the origin of placental mammals. Their expression is triggered by early pregnancy cues in a species-specific way, providing insights into the origin and evolution of implantation in mammals [ABSTRACT FROM AUTHOR]

Seventy‐five percent of Madagascar is treeless C4‐grassland adapted to human‐lit fire, which likely succeeded pre‐human mosaics of forest, ericoids, grassy‐woodlands and some smaller treeless‐grasslands. In support of pre‐settlement Malagasy grasslands having evolved with many grassland specialist faunal elements, Bond et al. (2022) cite "considerable overlap" in African and Malagasy hippo diets, and suggest time‐scale hampered mammal radiation into treeless‐grasslands. We find, however, that faunal elements referenced are predominantly habitat generalists (not grassland specialists), that African and Malagasy hippos occupy significantly different feeding‐niches, and that despite shared Miocene timeframes, Malagasy non‐arboreal mammals remained forest‐adapted whilst species that share ancestry with them on the African mainland radiated into open habitats. [ABSTRACT FROM AUTHOR]

The pattern of dental replacement in marsupial mammals has received much attention for its derived nature and potential relationship to the life history of the group. However, few species have been studied thoroughly, and little is known about the embryonic structures and their use in addressing issues of homology and dental evolution in general. We studied a developmental series of ten individuals of pouch young Caluromys philander to thoroughly document dental development with histological sections and 3D models of dental series. We report that the successor P3 arises from a lingual successional lamina from its predecessor dP3. The germs of vestigial, unerupted deciduous incisors and canines are present alongside their respective permanent successors. These discoveries demonstrate significant differences from the developmental patterns reported for Didelphis and Monodelphis and illustrate that an unsuspected diversity of dental ontogeny is not reflected in the adult pattern of mineralised, erupted or almost erupted teeth. [ABSTRACT FROM AUTHOR]

Island ecosystems represent outstanding natural laboratories for studying the interplay between ecology and evolution. Lavery et al. (2024) use genomic approaches to identify a remarkable example of repeated evolution in Hipposideros bats across the Solomon Islands archipelago. They show that larger-bodied bats have independently evolved on different islands, highlighting an exciting new system for exploring the ecological and evolutionary drivers of repeated evolution in mammals. [ABSTRACT FROM AUTHOR]

The article focuses on the evolutionary history of the capacity for heat generation in mammals, particularly through nonshivering thermogenesis (NST) in brown adipose tissue (BAT), facilitated by the expression of uncoupling protein 1 (UCP1). Keipert et al. explore the origins of UCP1's role in thermogenesis, shedding light on how this mechanism evolved in mammals. It discusses various pathways for temperature regulation in different animals, including basal metabolic rate (BMR).

This study contains an analysis of basal metabolic rate (BMR) in 1817 endothermic species. The aim was to establish how metabolic scaling varies between the main groups of endotherms during evolution. The data for all the considered groups were combined and the common exponent in the allometric relationship between the BMR and body weight was established as b = 0.7248. Reduced to the common slope, the relative metabolic rate forms the following series: Neognathae - Passeriformes - 1.00, Neognathae - Non-Passeriformes - 0.75, Palaeognathae - 0.53, Eutheria - 0.57, Marsupialia - 0.44, and Monotremata - 0.26. The main finding is that the metabolic rate in the six main groups of mammals and birds consistently increases as the geological time of the group's divergence approaches the present. In parallel, the average body temperature in the group rises, the duration of sleep decreases and the duration of activity increases. BMR in a taxon correlates with its evolutionary age: the later a clade diverged, the higher is its metabolic rate and the longer is its activity period; group exponents decrease as group divergence nears present times while with increase metabolic rate during activity, they not only do not decrease but can increase. Sleep duration in mammals was on average 40% longer than in birds while BMR, in contrast, was 40% higher in birds. The evolution of metabolic scaling, body temperature, sleep duration, and activity during the development of endothermic life forms is demonstrated, allowing for a better understanding of the underlying principles of endothermy formation. [ABSTRACT FROM AUTHOR]

The amygdala is a complex brain structure in the vertebrate telencephalon, essential for regulating social behaviors, emotions, and (social) cognition. In contrast to the vast majority of neuron types described in the many nuclei of the mammalian amygdala, little is known about the neuronal diversity in non-mammals, making reconstruction of its evolution particularly difficult. Here, we characterize glutamatergic neuron types in the amygdala of the urodele amphibian Pleurodeles waltl. Our single-cell RNA sequencing data indicate the existence of at least ten distinct types and subtypes of glutamatergic neurons in the salamander amygdala. These neuron types are molecularly distinct from neurons in the ventral pallium (VP), suggesting that the pallial amygdala and the VP are two separate areas in the telencephalon. In situ hybridization for marker genes indicates that amygdalar glutamatergic neuron types are located in three major subdivisions: the lateral amygdala, the medial amygdala, and a newly defined area demarcated by high expression of the transcription factor Sim1. The gene expression profiles of these neuron types suggest similarities with specific neurons in the sauropsid and mammalian amygdala. In particular, we identify Sim1+ and Sim1+ Otp+ expressing neuron types, potentially homologous to the mammalian nucleus of the lateral olfactory tract (NLOT) and to hypothalamic-derived neurons of the medial amygdala, respectively. Taken together, our results reveal a surprising diversity of glutamatergic neuron types in the amygdala of salamanders, despite the anatomical simplicity of their brain. These results offer new insights on the cellular and anatomical complexity of the amygdala in tetrapod ancestors. [ABSTRACT FROM AUTHOR]

Constitutive heterochromatin, consisting of repetitive sequences, diverges very rapidly; therefore, its nucleotide sequences and chromosomal distributions are often largely different, even between closely related species. The chromosome C-banding patterns of two Gerbillinae species, Meriones unguiculatus and Gerbillus perpallidus, vary greatly, even though they belong to the same subfamily. To understand the evolution of C-positive heterochromatin in these species, we isolated highly repetitive sequences, determined their nucleotide sequences, and characterized them using chromosomal and filter hybridization. We obtained a centromeric repeat (MUN-HaeIII) and a chromosome 13-specific repeat (MUN-EcoRI) from M. unguiculatus. We also isolated a centromeric/pericentromeric repeat (GPE-MBD) and an interspersed-type repeat that was predominantly amplified in the X and Y chromosomes (GPE-EcoRI) from G. perpallidus. GPE-MBD was found to contain a 17-bp motif that is essential for binding to the centromere-associated protein CENP-B. This indicates that it may play a role in the formation of a specified structure and/or function of centromeres. The nucleotide sequences of the three sequence families, except GPE-EcoRI, were conserved only in Gerbillinae. GPE-EcoRI was derived from the long interspersed nuclear elements 1 retrotransposon and showed sequence homology throughout Muridae and Cricetidae species, indicating that the repeat sequence occurred at least in the common ancestor of Muridae and Cricetidae. Due to a lack of assembly data of highly repetitive sequences constituting heterochromatin in whole-genome sequences of vertebrate species published to date, the knowledge obtained in this study provides useful information for a deep understanding of the evolution of repetitive sequences in not only rodents but also in mammals. [ABSTRACT FROM AUTHOR]