"Evolutionary biology"

Evolutionary theory predicts that accumulation of deleterious mutations in asexually reproducing organisms should lead to genomic decay. Clonally reproducing cell lines, i.e., transmissible cancers, when cells are transmitted as allografts/xenografts, break these rules, and survive for centuries and millennia. The currently known 11 transmissible cancer lineages occur in dogs (Canine Venereal Tumour Disease, CTVT), in Tasmanian devils (Devil Facial Tumour Diseases, DFT 1 and DFT2) and in bivalves (bivalve transmissible neoplasia, BTN)...

Quantitative genetic theory on multivariate character evolution predicts that a population's response to directional selection is biased toward the major axis of the genetic covariance matrix G-the so-called genetic line of least resistance. Inferences on the genetic constraints in this sense have traditionally been made by measuring the angle of deviation of evolutionary trajectories from the major axis, or more recently by calculating the amount of genetic variance-the Hansen-Houle evolvability-available along the trajectories...

Archosauria originated around the Earth's largest biotic crisis that severely affected all ecosystems globally, the Permotriassic Mass extinction event, and comprises two crown-group lineages: the bird-lineage and the crocodylian lineage. The bird lineage includes the iconic pterosaurs, as well as dinosaurs and birds, whereas the crocodylian lineage includes clades such as aetosaurs, poposaurs, "rauisuchians," as well as Crocodylomorpha; the latter being represented today only by less than 30 extant species of Crocodylia...

Cave-adapted animals evolve a suite of regressive and constructive traits that allow survival in the dark. Most studies aiming at understanding cave animal evolution have focused on the genetics and environmental underpinnings of regressive traits, with special emphasis on vision loss. Possibly as a result of vision loss, other non-visual sensory systems have expanded and compensated in cave species. For instance, in many cave-dwelling fish species, including the blind cavefish of the Mexican tetra, Astyanax mexicanus , a major non-visual mechanosensory system called the lateral line, compensated for vision loss through morphological expansions...

Dispersal is an important facet of the life history of many organisms and is therefore subject to selective pressure, but does not evolve in isolation. Across nature there are examples of dispersal syndromes, life history strategies in which suites of traits coevolve and covary with dispersal in combinations that serve to maximise fitness in a given ecological context. The red rust flour beetle, Tribolium castaneum, is a model organism and globally significant post-harvest pest which relies on dispersal to reach new patches of ephemeral habitat...

The machairodontine felid Homotherium achieved a global geographic distribution throughout much of the Pleistocene. Accordingly, that large carnivore is important for understanding patterns of community composition. We report on a new record of Homotherium based on a fragmentary premaxilla-maxilla discovered on McFaddin Beach, Texas, along the Gulf of Mexico. Skeletal remains of extinct, Pleistocene vertebrates accumulate on McFaddin Beach. Those fossils appear to originate from submerged deposits on the continental shelf in the Gulf of Mexico, an area that was subaerially exposed in the Late Pleistocene during glacial intervals...

Instances of convergent or parallel evolution provide a potent model system for exploring contingency and determinism in evolutionary biology. Likewise, the multiple, independent habitat transitions from saltwater to freshwater biomes offer opportunity for studying convergent evolution within and among different vertebrate lineages. For example, stingrays have invaded freshwater habitats multiple times across different continents, sometimes even several times within the same clade (e.g., Dasyatidae). We evaluated the frequency of saltwater-freshwater invasions in stingrays, compared ecological and phenotypic diversification among freshwater and saltwater lineages, and assessed the degree of convergence among freshwater species...

Reassortment is an evolutionary process common in viruses with segmented genomes. These viruses can swap whole genomic segments during cellular co-infection, giving rise to novel progeny formed from the mixture of parental segments. Because large-scale genome rearrangements have the potential to generate new phenotypes, reassortment is important to both evolutionary biology and public health research. However, statistical inference of the pattern of reassortment events from phylogenetic data is exceptionally difficult, potentially involving inference of general graphs in which individual segment trees are embedded...

The mitochondrial (mt) genome can provide data for phylogenetic analyses and evolutionary biology. Herein, we sequenced and annotated the complete mt genome of Ergasilus anchoratus. This mt genome was 13852 bp long and comprised 13 protein-coding genes (PCGs), 22 tRNAs and 2 rRNAs. All PCGs used the standard ATN start codons and complete TAA/TAG termination codons. A majority of tRNA genes exhibited standard cloverleaf secondary structures, with the exception of one tRNA that lacked the TψC arm (trnC), and three tRNAs that lacked the DHU arm (trnR, trnS1 and trnS2)...

Elongated upper canine teeth, commonly known as saber-teeth, have evolved three times within the sub-order Feliformia. The species that wielded them flourished throughout the Cenozoic and have historically been separated into two morphological groups: the dirk-tooths with longer, flatter canines, and the scimitar-tooths with shorter, serrated teeth. However, quantitative morphological analysis has not been conducted on these teeth to determine the true amount of diversity within the group, and how the upper canine morphology of extant feliforms compared to their extinct relatives has also not been explored...

Over the past quarter-century, the field of evolutionary biology has been transformed by the emergence of complete genome sequences and the conceptual framework known as the 'Net of Life.' This paradigm shift challenges traditional notions of evolution as a tree-like process, emphasizing the complex, interconnected network of gene flow that may blur the boundaries between distinct lineages. In this context, gene loss, rather than horizontal gene transfer, is the primary driver of gene content, with vertical inheritance playing a principal role...

CD4+ T cell activation is driven by five-module receptor complexes. The T cell receptor (TCR) is the receptor module that binds composite surfaces of peptide antigens embedded within MHCII molecules (pMHCII). It associates with three signaling modules (CD3γε, CD3δε, and CD3ζζ) to form TCR-CD3 complexes. CD4 is the coreceptor module. It reciprocally associates with TCR-CD3-pMHCII assemblies on the outside of a CD4+ T cells and with the Src kinase, LCK, on the inside. Previously, we reported that the CD4 transmembrane GGXXG and cytoplasmic juxtamembrane (C/F)CV+C motifs found in eutherian (placental mammal) CD4 have constituent residues that evolved under purifying selection (Lee et al...

Despite rapid evolution across eutherian mammals, the X-linked MIR-506 family miRNAs are located in a region flanked by two highly conserved protein-coding genes ( SLITRK2 and FMR1 ) on the X chromosome. Intriguingly, these miRNAs are predominantly expressed in the testis, suggesting a potential role in spermatogenesis and male fertility. Here, we report that the X-linked MIR-506 family miRNAs were derived from the MER91C DNA transposons. Selective inactivation of individual miRNAs or clusters caused no discernible defects, but simultaneous ablation of five clusters containing 19 members of the MIR-506 family led to reduced male fertility in mice...

Spatially-resolved datasets are revolutionizing knowledge in molecular biology, yet are under-utilized for questions in evolutionary biology. To gain insight from these large-scale datasets of spatial organization, we need mathematical representations and modeling techniques that can both capture their complexity, but also allow for mathematical tractability. Evolutionary graph theory utilizes the mathematical representation of networks as a proxy for heterogeneous population structure and has started to reshape our understanding of how spatial structure can direct evolutionary dynamics...

The clade Pseudosuchia appeared 250 million years ago. The exclusively semi-aquatic Crocodylia, which includes crocodiles, alligators, caimans, and gharials is the only surviving subgroup. Investigating Crocodylia biology is pivotal for inferring traits of extinct pseudosuchians. Alligator femur length is widely used for modeling pseudosuchian body mass, but the regression is influenced by sex and captivity status, leading to potential accuracy problems. An alternative model results from the correlation between alligator femur volume and body mass, which is unaffected by those covariates...

A quarter of marine mammals are at risk of extinction, with disease and poor habitat quality contributing to population decline. Investigation of the Major Histocompatibility Complex (MHC) provides insight into species' capacity to respond to immune and environmental challenges. The eighteen available cetacean chromosome level genomes were used to annotate MHC Class I loci, and to reconstruct the phylogenetic relationship of the described loci. The highest number of loci was observed in the striped dolphin ( Stenella coeruleoalba ), while the least was observed in the pygmy sperm whale ( Kogia breviceps ) and rough toothed dolphin ( Steno bredanensis )...

Domains as functional protein units and their rearrangements along the phylogeny can shed light on the functional changes of proteomes associated with the evolution of complex traits like eusociality. This complex trait is associated with sterile soldiers and workers, and long-lived, highly fecund reproductives. Unlike in Hymenotpera (ants, bees, and wasps), the evolution of eusociality within Blattodea, where termites evolved from within cockroaches, was accompanied by a reduction in proteome size, raising the question of whether functional novelty was achieved with existing rather than novel proteins...

Glycans, present across all domains of life, comprise a wide range of monosaccharides assembled into complex, branching structures. Here, we present an in silico protocol to construct biosynthetic networks from a list of observed glycans using the Python package glycowork. We describe steps for data preparation, network construction, feature analysis, and data export. This protocol is implemented in Python using example data and can be adapted for use with customized datasets. For complete details on the use and execution of this protocol, please refer to Thomès et al...

The impact of climate change on populations will be contingent upon their contemporary adaptive evolution. In this study, we investigated the contemporary evolution of four populations of the cold-water kelp Laminaria digitata by analysing their spatial and temporal genomic variation using ddRAD-sequencing. These populations were sampled from the center to the southern margin of its north-eastern Atlantic distribution at two-time points, spanning at least two generations. Through genome scans for local adaptation at a single time point, we identified candidate loci that showed clinal variation correlated with changes in sea surface temperature (SST) along latitudinal gradients...

Python for Population Genomics (PyPop) is a software package that processes genotype and allele data and performs large-scale population genetic analyses on highly polymorphic multi-locus genotype data. In particular, PyPop tests data conformity to Hardy-Weinberg equilibrium expectations, performs Ewens-Watterson tests for selection, estimates haplotype frequencies, measures linkage disequilibrium, and tests significance. Standardized means of performing these tests is key for contemporary studies of evolutionary biology and population genetics, and these tests are central to genetic studies of disease association as well...